Starting phenix.real_space_refine
on Wed Apr 30 01:23:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6nd1_0440/04_2025/6nd1_0440.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6nd1_0440/04_2025/6nd1_0440.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6nd1_0440/04_2025/6nd1_0440.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6nd1_0440/04_2025/6nd1_0440.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6nd1_0440/04_2025/6nd1_0440.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6nd1_0440/04_2025/6nd1_0440.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    5990      2.51       5
     N    1514      2.21       5
     O    1646      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9186
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 390, 3031
          Classifications: {'peptide': 390}
          Link IDs: {'PTRANS': 17, 'TRANS': 372}
          Chain breaks: 5
    Chain: "A"
      Number of atoms: 3565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 461, 3565
          Classifications: {'peptide': 461}
          Incomplete info: {'truncation_to_alanine': 46}
          Link IDs: {'PTRANS': 27, 'TRANS': 433}
          Chain breaks: 5
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 179
          Unresolved non-hydrogen angles: 236
          Unresolved non-hydrogen dihedrals: 152
          Unresolved non-hydrogen chiralities: 21
          Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 3, 'ARG:plan': 3}
          Unresolved non-hydrogen planarities: 95
    Chain: "C"
      Number of atoms: 443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 443
          Classifications: {'peptide': 56}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 53}
    Chain: "D"
      Number of atoms: 270
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 41, 270
          Classifications: {'peptide': 41}
          Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 39}
          Unresolved non-hydrogen bonds: 45
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 35
          Unresolved non-hydrogen chiralities: 6
          Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 22
    Chain: "E"
      Number of atoms: 1143
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1143
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 4, 'TRANS': 134}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 734
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 734
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 3, 'TRANS': 88}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   LEU A 284 " occ=0.88
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 284 " occ=0.75
    residue:
      pdb=" N   GLY A 316 " occ=0.88
      ... (2 atoms not shown)
      pdb=" O   GLY A 316 " occ=0.88
    residue:
      pdb=" N   LEU A 398 " occ=0.88
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 398 " occ=0.75
    residue:
      pdb=" N   ALA A 413 " occ=0.88
      ... (3 atoms not shown)
      pdb=" CB  ALA A 413 " occ=0.88
  Time building chain proxies: 5.56, per 1000 atoms: 0.61
  Number of scatterers: 9186
  At special positions: 0
  Unit cell: (108, 106.65, 121.5, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      36     16.00
     O    1646      8.00
     N    1514      7.00
     C    5990      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.45
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2228

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 5 sheets defined
      65.8% alpha, 5.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'B' and resid 28 through 48
      removed outlier: 3.743A  pdb=" N   ILE B  34 " --> pdb=" O   ASN B  30 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   THR B  36 " --> pdb=" O   LYS B  32 " (cutoff:3.500A)
      removed outlier: 4.065A  pdb=" N   LEU B  41 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ILE B  45 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 71
      removed outlier: 4.073A  pdb=" N   MET B  69 " --> pdb=" O   TRP B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.731A  pdb=" N   ILE B  86 " --> pdb=" O   VAL B  82 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   SER B  88 " --> pdb=" O   PRO B  84 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER B  89 " --> pdb=" O   ILE B  85 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   PHE B  92 " --> pdb=" O   SER B  88 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 137
    Processing helix  chain 'B' and resid 146 through 174
      removed outlier: 4.015A  pdb=" N   CYS B 150 " --> pdb=" O   GLY B 146 " (cutoff:3.500A)
      removed outlier: 4.078A  pdb=" N   GLY B 174 " --> pdb=" O   LEU B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 197
      removed outlier: 3.878A  pdb=" N   LEU B 183 " --> pdb=" O   SER B 179 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   PHE B 184 " --> pdb=" O   GLY B 180 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ILE B 189 " --> pdb=" O   THR B 185 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 215 through 223
      removed outlier: 3.998A  pdb=" N   LEU B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU B 222 " --> pdb=" O   PHE B 218 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   ALA B 223 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 229 through 238
      removed outlier: 4.208A  pdb=" N   VAL B 233 " --> pdb=" O   LYS B 229 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ARG B 238 " --> pdb=" O   GLU B 234 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 262
      removed outlier: 4.016A  pdb=" N   ALA B 252 " --> pdb=" O   LEU B 248 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU B 258 " --> pdb=" O   PHE B 254 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLY B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 286 through 289
      removed outlier: 3.722A  pdb=" N   SER B 289 " --> pdb=" O   PHE B 286 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 286 through 289'
    Processing helix  chain 'B' and resid 290 through 314
      removed outlier: 3.707A  pdb=" N   MET B 294 " --> pdb=" O   ASN B 290 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   LEU B 295 " --> pdb=" O   THR B 291 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   PHE B 304 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   LEU B 305 " --> pdb=" O   SER B 301 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   ILE B 306 " --> pdb=" O   ASN B 302 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   SER B 307 " --> pdb=" O   ILE B 303 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   GLN B 308 " --> pdb=" O   PHE B 304 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 384
      removed outlier: 4.000A  pdb=" N   THR B 362 " --> pdb=" O   ASP B 358 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE B 363 " --> pdb=" O   PRO B 359 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLU B 382 " --> pdb=" O   LYS B 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 387 through 399
      removed outlier: 4.170A  pdb=" N   LYS B 393 " --> pdb=" O   ARG B 389 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN B 398 " --> pdb=" O   GLN B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 440
      removed outlier: 3.870A  pdb=" N   LYS B 416 " --> pdb=" O   ARG B 412 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   ILE B 417 " --> pdb=" O   GLU B 413 " (cutoff:3.500A)
      Proline residue:  B 419  - end of helix
      removed outlier: 3.628A  pdb=" N   ASP B 437 " --> pdb=" O   SER B 433 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 464
      removed outlier: 3.595A  pdb=" N   ILE B 448 " --> pdb=" O   SER B 444 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR B 454 " --> pdb=" O   MET B 450 " (cutoff:3.500A)
      removed outlier: 4.323A  pdb=" N   LYS B 464 " --> pdb=" O   GLU B 460 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 15 through 21
      removed outlier: 4.027A  pdb=" N   THR A  20 " --> pdb=" O   SER A  16 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   GLY A  21 " --> pdb=" O   PHE A  17 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 30 through 36
    Processing helix  chain 'A' and resid 59 through 64
      removed outlier: 4.385A  pdb=" N   GLU A  64 " --> pdb=" O   LYS A  60 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 68 through 78
      removed outlier: 3.590A  pdb=" N   PHE A  78 " --> pdb=" O   PHE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 110
    Processing helix  chain 'A' and resid 221 through 232
      removed outlier: 3.541A  pdb=" N   VAL A 225 " --> pdb=" O   PRO A 221 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS A 226 " --> pdb=" O   LEU A 222 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   TYR A 227 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 246
      removed outlier: 3.678A  pdb=" N   VAL A 239 " --> pdb=" O   LEU A 235 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   SER A 240 " --> pdb=" O   PRO A 236 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ALA A 244 " --> pdb=" O   SER A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 268
      removed outlier: 3.861A  pdb=" N   ASN A 268 " --> pdb=" O   SER A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 276 through 286
      removed outlier: 3.828A  pdb=" N   ILE A 280 " --> pdb=" O   THR A 276 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   SER A 285 " --> pdb=" O   LEU A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 311
      removed outlier: 3.794A  pdb=" N   GLU A 303 " --> pdb=" O   PRO A 299 " (cutoff:3.500A)
      removed outlier: 4.774A  pdb=" N   LYS A 304 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   LEU A 305 " --> pdb=" O   ASP A 301 " (cutoff:3.500A)
      removed outlier: 4.383A  pdb=" N   HIS A 309 " --> pdb=" O   LEU A 305 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   ILE A 310 " --> pdb=" O   LEU A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 318 through 328
    Processing helix  chain 'A' and resid 328 through 341
      removed outlier: 3.893A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 328 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 360
      removed outlier: 3.855A  pdb=" N   PHE A 356 " --> pdb=" O   ALA A 352 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   VAL A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 373
      removed outlier: 4.100A  pdb=" N   LEU A 372 " --> pdb=" O   ASN A 368 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   GLN A 373 " --> pdb=" O   CYS A 369 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 368 through 373'
    Processing helix  chain 'A' and resid 378 through 386
    Processing helix  chain 'A' and resid 391 through 397
      removed outlier: 3.616A  pdb=" N   LEU A 395 " --> pdb=" O   THR A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 399 through 407
    Processing helix  chain 'A' and resid 411 through 424
    Processing helix  chain 'A' and resid 480 through 484
    Processing helix  chain 'A' and resid 486 through 494
      removed outlier: 3.986A  pdb=" N   ALA A 489 " --> pdb=" O   ASP A 486 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 537 through 541
    Processing helix  chain 'C' and resid 26 through 36
    Processing helix  chain 'C' and resid 43 through 80
      removed outlier: 3.523A  pdb=" N   TYR C  47 " --> pdb=" O   ASP C  43 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   THR C  48 " --> pdb=" O   LEU C  44 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   LYS C  52 " --> pdb=" O   THR C  48 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ALA C  53 " --> pdb=" O   LYS C  49 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   LYS C  69 " --> pdb=" O   GLY C  65 " (cutoff:3.500A)
      Proline residue:  C  74  - end of helix
      removed outlier: 3.682A  pdb=" N   TYR C  77 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 38 through 47
      removed outlier: 3.767A  pdb=" N   ALA D  47 " --> pdb=" O   TYR D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 75
      removed outlier: 3.818A  pdb=" N   PHE D  59 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   VAL D  73 " --> pdb=" O   VAL D  69 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   ILE D  74 " --> pdb=" O   ALA D  70 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   SER D  75 " --> pdb=" O   LEU D  71 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 60
      removed outlier: 4.378A  pdb=" N   LEU E  34 " --> pdb=" O   VAL E  30 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   ILE E  59 " --> pdb=" O   GLN E  55 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 70 through 81
      removed outlier: 4.198A  pdb=" N   PHE E  76 " --> pdb=" O   HIS E  72 " (cutoff:3.500A)
      removed outlier: 4.379A  pdb=" N   GLN E  77 " --> pdb=" O   ASP E  73 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   ILE E  78 " --> pdb=" O   LEU E  74 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   MET E  81 " --> pdb=" O   GLN E  77 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 124
      Proline residue:  E 115  - end of helix
      removed outlier: 3.862A  pdb=" N   GLY E 124 " --> pdb=" O   LEU E 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 127 through 153
      removed outlier: 3.680A  pdb=" N   TRP E 131 " --> pdb=" O   GLY E 127 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   LYS E 139 " --> pdb=" O   GLU E 135 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU E 142 " --> pdb=" O   VAL E 138 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU E 149 " --> pdb=" O   PHE E 145 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 159 through 176
      removed outlier: 4.282A  pdb=" N   VAL E 164 " --> pdb=" O   VAL E 160 " (cutoff:3.500A)
      removed outlier: 6.650A  pdb=" N   MET E 165 " --> pdb=" O   GLN E 161 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   VAL E 166 " --> pdb=" O   LEU E 162 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   CYS E 167 " --> pdb=" O   PHE E 163 " (cutoff:3.500A)
      removed outlier: 4.221A  pdb=" N   LYS E 168 " --> pdb=" O   VAL E 164 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   GLU E 169 " --> pdb=" O   MET E 165 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN E 174 " --> pdb=" O   ILE E 170 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 102 through 120
    Processing helix  chain 'F' and resid 122 through 136
      removed outlier: 3.792A  pdb=" N   LEU F 126 " --> pdb=" O   HIS F 122 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLN F 127 " --> pdb=" O   LEU F 123 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   ASP F 128 " --> pdb=" O   GLU F 124 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   PHE F 131 " --> pdb=" O   GLN F 127 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   GLY F 136 " --> pdb=" O   LEU F 132 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 139 through 152
      removed outlier: 4.120A  pdb=" N   PHE F 143 " --> pdb=" O   GLN F 139 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   VAL F 144 " --> pdb=" O   PRO F 140 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 156 through 170
    Processing helix  chain 'F' and resid 175 through 192
      removed outlier: 3.629A  pdb=" N   LEU F 179 " --> pdb=" O   LYS F 175 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 198 through 203
      removed outlier: 5.832A  pdb=" N   THR B 201 " --> pdb=" O   GLU B 212 " (cutoff:3.500A)
      removed outlier: 3.851A  pdb=" N   GLU B 212 " --> pdb=" O   THR B 201 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLU B 210 " --> pdb=" O   VAL B 203 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 264 through 269
    Processing sheet with id=AA3, first strand: chain 'A' and resid 430 through 436
      removed outlier: 3.969A  pdb=" N   LYS A 432 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 524 through 525
      removed outlier: 3.575A  pdb=" N   LYS A 524 " --> pdb=" O   SER A 519 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 524 through 525
      removed outlier: 3.575A  pdb=" N   LYS A 524 " --> pdb=" O   SER A 519 " (cutoff:3.500A)

    506 hydrogen bonds defined for protein.
    1473 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: 2.32

  Time building geometry restraints manager: 2.87 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: 2687
        1.34 -     1.46: 1685
        1.46 -     1.58: 4938
        1.58 -     1.69: 0
        1.69 -     1.81: 56
  Bond restraints: 9366
  Sorted by residual:
  bond pdb=" C   THR B 379 "
       pdb=" N   TRP B 380 "
    ideal  model  delta    sigma   weight residual
    1.335  1.226  0.110 1.38e-02 5.25e+03 6.30e+01
  bond pdb=" C   TRP A 566 "
       pdb=" N   GLU A 567 "
    ideal  model  delta    sigma   weight residual
    1.331  1.238  0.093 1.37e-02 5.33e+03 4.61e+01
  bond pdb=" C   GLY A 576 "
       pdb=" N   GLN A 577 "
    ideal  model  delta    sigma   weight residual
    1.331  1.221  0.110 2.07e-02 2.33e+03 2.83e+01
  bond pdb=" C   GLN B 398 "
       pdb=" N   GLY B 399 "
    ideal  model  delta    sigma   weight residual
    1.330  1.258  0.072 1.42e-02 4.96e+03 2.56e+01
  bond pdb=" N   ILE C  79 "
       pdb=" CA  ILE C  79 "
    ideal  model  delta    sigma   weight residual
    1.461  1.494 -0.034 1.19e-02 7.06e+03 8.10e+00
  ... (remaining 9361 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.03: 12522
        4.03 -     8.06: 127
        8.06 -    12.09: 30
       12.09 -    16.11: 3
       16.11 -    20.14: 3
  Bond angle restraints: 12685
  Sorted by residual:
  angle pdb=" C   ILE C  75 "
        pdb=" CA  ILE C  75 "
        pdb=" CB  ILE C  75 "
      ideal   model   delta    sigma   weight residual
     112.14  129.12  -16.98 1.35e+00 5.49e-01 1.58e+02
  angle pdb=" C   GLU F 124 "
        pdb=" CA  GLU F 124 "
        pdb=" CB  GLU F 124 "
      ideal   model   delta    sigma   weight residual
     110.85  130.99  -20.14 1.70e+00 3.46e-01 1.40e+02
  angle pdb=" C   ALA B 463 "
        pdb=" CA  ALA B 463 "
        pdb=" CB  ALA B 463 "
      ideal   model   delta    sigma   weight residual
     110.68  125.60  -14.92 1.70e+00 3.46e-01 7.70e+01
  angle pdb=" C   GLU A 440 "
        pdb=" CA  GLU A 440 "
        pdb=" CB  GLU A 440 "
      ideal   model   delta    sigma   weight residual
     110.45   91.69   18.76 2.15e+00 2.16e-01 7.61e+01
  angle pdb=" C   PHE B 218 "
        pdb=" CA  PHE B 218 "
        pdb=" CB  PHE B 218 "
      ideal   model   delta    sigma   weight residual
     109.56  123.30  -13.74 1.65e+00 3.67e-01 6.94e+01
  ... (remaining 12680 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.48: 4902
       17.48 -    34.95: 569
       34.95 -    52.43: 124
       52.43 -    69.91: 28
       69.91 -    87.39: 14
  Dihedral angle restraints: 5637
    sinusoidal: 2211
      harmonic: 3426
  Sorted by residual:
  dihedral pdb=" C   GLU A 440 "
           pdb=" N   GLU A 440 "
           pdb=" CA  GLU A 440 "
           pdb=" CB  GLU A 440 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -100.10  -22.50     0      2.50e+00 1.60e-01 8.10e+01
  dihedral pdb=" C   GLU F 124 "
           pdb=" N   GLU F 124 "
           pdb=" CA  GLU F 124 "
           pdb=" CB  GLU F 124 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -143.24   20.64     0      2.50e+00 1.60e-01 6.82e+01
  dihedral pdb=" CA  PRO B  62 "
           pdb=" C   PRO B  62 "
           pdb=" N   LEU B  63 "
           pdb=" CA  LEU B  63 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.65   39.35     0      5.00e+00 4.00e-02 6.19e+01
  ... (remaining 5634 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1385
       0.131 -    0.261: 89
       0.261 -    0.392: 11
       0.392 -    0.523: 6
       0.523 -    0.654: 2
  Chirality restraints: 1493
  Sorted by residual:
  chirality pdb=" CA  GLU F 124 "
            pdb=" N   GLU F 124 "
            pdb=" C   GLU F 124 "
            pdb=" CB  GLU F 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.86    0.65 2.00e-01 2.50e+01 1.07e+01
  chirality pdb=" CA  PHE B 236 "
            pdb=" N   PHE B 236 "
            pdb=" C   PHE B 236 "
            pdb=" CB  PHE B 236 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.20e+00
  chirality pdb=" CA  ALA B 462 "
            pdb=" N   ALA B 462 "
            pdb=" C   ALA B 462 "
            pdb=" CB  ALA B 462 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.96    0.52 2.00e-01 2.50e+01 6.80e+00
  ... (remaining 1490 not shown)

  Planarity restraints: 1586
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 444 "   -0.059 5.00e-02 4.00e+02   9.00e-02 1.30e+01
        pdb=" N   PRO A 445 "    0.156 5.00e-02 4.00e+02
        pdb=" CA  PRO A 445 "   -0.048 5.00e-02 4.00e+02
        pdb=" CD  PRO A 445 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 265 "   -0.015 2.00e-02 2.50e+03   3.07e-02 9.43e+00
        pdb=" C   TYR B 265 "    0.053 2.00e-02 2.50e+03
        pdb=" O   TYR B 265 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLU B 266 "   -0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL E 160 "   -0.015 2.00e-02 2.50e+03   3.06e-02 9.38e+00
        pdb=" C   VAL E 160 "    0.053 2.00e-02 2.50e+03
        pdb=" O   VAL E 160 "   -0.020 2.00e-02 2.50e+03
        pdb=" N   GLN E 161 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 1583 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2168
        2.78 -     3.31: 8588
        3.31 -     3.84: 14120
        3.84 -     4.37: 15051
        4.37 -     4.90: 26046
  Nonbonded interactions: 65973
  Sorted by model distance:
  nonbonded pdb=" OG1 THR A 599 "
            pdb=" N   THR A 600 "
     model   vdw
     2.249 3.120
  nonbonded pdb=" OG1 THR A 444 "
            pdb=" OG  SER A 447 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   HIS A 390 "
            pdb=" OH  TYR F 190 "
     model   vdw
     2.295 3.040
  nonbonded pdb=" O   SER A 483 "
            pdb=" OG  SER A 483 "
     model   vdw
     2.301 3.040
  nonbonded pdb=" O   ASN B 290 "
            pdb=" OD1 ASN B 290 "
     model   vdw
     2.302 3.040
  ... (remaining 65968 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=0.75 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     23.480
  Find NCS groups from input model:        0.080
  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:2.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8164
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      :  0.009   0.110   9366  Z= 0.441
  Angle     :  1.231  20.144  12685  Z= 0.718
  Chirality :  0.079   0.654   1493
  Planarity :  0.009   0.090   1586
  Dihedral  : 16.242  87.386   3409
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  3.67 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  : 15.61 %
    Favored  : 84.29 %
  Cbeta Deviations :  1.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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: -3.89 (0.20), residues: 1145
  helix: -2.28 (0.15), residues: 689
  sheet: -2.93 (0.45), residues: 80
  loop : -2.70 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.003   TRP A 242 
 HIS   0.011   0.002   HIS A 334 
 PHE   0.041   0.003   PHE E  66 
 TYR   0.030   0.002   TYR B 287 
 ARG   0.009   0.001   ARG A 509 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.15592 (  505)
  hydrogen bonds       : angle       6.72425 ( 1473)
  covalent geometry    : bond        0.00919 ( 9366)
  covalent geometry    : angle       1.23096 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  252 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 251
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  119 LYS cc_start: 0.5483 (tttt) cc_final: 0.4969 (tttt)
REVERT: B  237 TYR cc_start: 0.7040 (m-80) cc_final: 0.6619 (m-80)
REVERT: B  238 ARG cc_start: 0.7011 (mmm160) cc_final: 0.5533 (mmm160)
REVERT: B  400 MET cc_start: 0.8025 (mtt) cc_final: 0.7735 (mtm)
REVERT: B  406 ARG cc_start: 0.7122 (mpt-90) cc_final: 0.6734 (mpt-90)
REVERT: A  359 ILE cc_start: 0.9160 (mm) cc_final: 0.8940 (mp)
REVERT: A  431 ILE cc_start: 0.8864 (mt) cc_final: 0.8610 (mm)
REVERT: A  473 GLU cc_start: 0.7963 (tp30) cc_final: 0.7537 (tp30)
REVERT: A  491 MET cc_start: 0.8933 (mtp) cc_final: 0.8639 (mtp)
REVERT: A  521 LYS cc_start: 0.9150 (tptm) cc_final: 0.8519 (ttmt)
REVERT: A  562 ASP cc_start: 0.6913 (p0) cc_final: 0.6705 (p0)
REVERT: C   49 LYS cc_start: 0.8446 (tttp) cc_final: 0.8129 (tttt)
REVERT: E   46 MET cc_start: 0.6966 (ttm) cc_final: 0.6523 (tmm)
REVERT: E   54 LYS cc_start: 0.7560 (tttt) cc_final: 0.7030 (tmtt)
REVERT: E   99 ARG cc_start: 0.6868 (ttp-170) cc_final: 0.6605 (mmm-85)
REVERT: E  165 MET cc_start: 0.6274 (mmm) cc_final: 0.6073 (mmp)
REVERT: F  152 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8334 (mmmt)
REVERT: F  158 GLU cc_start: 0.8521 (mt-10) cc_final: 0.7866 (mt-10)
REVERT: F  182 GLU cc_start: 0.7656 (tp30) cc_final: 0.7260 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 252
  average time/residue: 0.2402
  time to fit residues: 80.7681
Evaluate side-chains
  192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.069 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 87 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 30 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9980
   chunk 46 optimal weight:   20.0000
   chunk 90 optimal weight:    9.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 67 optimal weight:    0.0030
   chunk 105 optimal weight:   10.0000
   overall best weight:    0.9192

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

Flipped N/Q/H residues before XYZ refinement:
** B 129 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 ASN
B 220 HIS
B 261 GLN
B 347 GLN
B 403 ASN
A  55 ASN
A 255 HIS
A 261 ASN
A 334 HIS
A 376 ASN
A 427 ASN
A 494 GLN
F 106 HIS

Total number of N/Q/H flips: 13

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.145984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.115087 restraints weight = 17162.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.117047 restraints weight = 12045.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.118242 restraints weight = 9568.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3321
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3321
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3321 r_free = 0.3321    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.75   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3320 r_free = 0.3320    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3320
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9366  Z= 0.132
  Angle     :  0.638   9.115  12685  Z= 0.324
  Chirality :  0.043   0.154   1493
  Planarity :  0.005   0.066   1586
  Dihedral  :  5.409  71.694   1242
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  0.41 %
    Allowed  :  3.88 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.82 (0.23), residues: 1145
  helix: -0.49 (0.18), residues: 720
  sheet: -2.27 (0.50), residues: 77
  loop : -2.25 (0.32), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B  65 
 HIS   0.007   0.001   HIS A 255 
 PHE   0.023   0.001   PHE E  66 
 TYR   0.016   0.001   TYR B 344 
 ARG   0.004   0.000   ARG E 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04275 (  505)
  hydrogen bonds       : angle       4.28163 ( 1473)
  covalent geometry    : bond        0.00290 ( 9366)
  covalent geometry    : angle       0.63753 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 252
  time to evaluate  : 1.119 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  119 LYS cc_start: 0.5339 (tttt) cc_final: 0.4905 (tttt)
REVERT: B  131 LEU cc_start: 0.8772 (tp) cc_final: 0.8526 (tp)
REVERT: B  261 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.8275 (mm-40)
REVERT: B  400 MET cc_start: 0.7844 (mtt) cc_final: 0.7556 (mtm)
REVERT: B  406 ARG cc_start: 0.7177 (mpt-90) cc_final: 0.6712 (mpt-90)
REVERT: B  439 LEU cc_start: 0.9273 (tt) cc_final: 0.8662 (mt)
REVERT: A  336 LEU cc_start: 0.8892 (tp) cc_final: 0.8437 (tt)
REVERT: A  376 ASN cc_start: 0.8799 (OUTLIER) cc_final: 0.8241 (m110)
REVERT: A  431 ILE cc_start: 0.8777 (mt) cc_final: 0.8482 (mm)
REVERT: A  521 LYS cc_start: 0.9043 (tptm) cc_final: 0.8330 (ttmt)
REVERT: A  562 ASP cc_start: 0.6299 (p0) cc_final: 0.5808 (p0)
REVERT: A  601 ASP cc_start: 0.7925 (m-30) cc_final: 0.7644 (m-30)
REVERT: E   46 MET cc_start: 0.6927 (ttm) cc_final: 0.6475 (tmm)
REVERT: E   54 LYS cc_start: 0.7743 (tttt) cc_final: 0.7244 (tmtt)
REVERT: E   99 ARG cc_start: 0.6833 (ttp-170) cc_final: 0.6376 (mmm-85)
REVERT: E  103 SER cc_start: 0.8825 (p) cc_final: 0.8471 (p)
REVERT: E  165 MET cc_start: 0.6338 (mmm) cc_final: 0.5518 (mpp)
REVERT: F  110 ARG cc_start: 0.6417 (tmm-80) cc_final: 0.6201 (tmm-80)
REVERT: F  152 LYS cc_start: 0.8549 (mmtt) cc_final: 0.8310 (mmmt)
REVERT: F  182 GLU cc_start: 0.7720 (tp30) cc_final: 0.7342 (tp30)
  outliers start: 4
  outliers final: 1
  residues processed: 255
  average time/residue: 0.2117
  time to fit residues: 75.4347
Evaluate side-chains
  199 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 196
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 31 optimal weight:    6.9990
   chunk 83 optimal weight:    7.9990
   chunk 4 optimal weight:    8.9990
   chunk 2 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 79 optimal weight:    9.9990
   chunk 112 optimal weight:    2.9990
   chunk 25 optimal weight:    7.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.9586

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 ASN
A 307 GLN
** A 330 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 361 GLN
A 427 ASN
E  69 ASN
E  72 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.144987 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113363 restraints weight = 17617.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.115480 restraints weight = 11962.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.116796 restraints weight = 9352.909|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3290
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3290 r_free = 0.3290    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3289 r_free = 0.3289    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3289
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9366  Z= 0.150
  Angle     :  0.617   8.192  12685  Z= 0.312
  Chirality :  0.043   0.183   1493
  Planarity :  0.005   0.058   1586
  Dihedral  :  4.980  61.523   1242
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 6.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  4.90 %
    Favored  : 95.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -1.04 (0.24), residues: 1145
  helix:  0.17 (0.19), residues: 720
  sheet: -1.92 (0.53), residues: 77
  loop : -2.08 (0.33), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  65 
 HIS   0.003   0.001   HIS A 288 
 PHE   0.016   0.001   PHE E  66 
 TYR   0.017   0.001   TYR B 344 
 ARG   0.004   0.000   ARG E 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03956 (  505)
  hydrogen bonds       : angle       4.12816 ( 1473)
  covalent geometry    : bond        0.00348 ( 9366)
  covalent geometry    : angle       0.61672 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 238
  time to evaluate  : 1.030 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   73 ASN cc_start: 0.8853 (t0) cc_final: 0.8466 (t0)
REVERT: B  238 ARG cc_start: 0.6758 (mmm160) cc_final: 0.5399 (mmm160)
REVERT: B  347 GLN cc_start: 0.7246 (tm-30) cc_final: 0.7028 (tm-30)
REVERT: B  400 MET cc_start: 0.7873 (mtt) cc_final: 0.7556 (mtm)
REVERT: B  406 ARG cc_start: 0.7345 (mpt-90) cc_final: 0.6749 (mpt-90)
REVERT: A  248 SER cc_start: 0.9231 (p) cc_final: 0.8977 (t)
REVERT: A  431 ILE cc_start: 0.8772 (mt) cc_final: 0.8452 (mm)
REVERT: A  521 LYS cc_start: 0.8972 (tptm) cc_final: 0.8311 (ttmt)
REVERT: A  562 ASP cc_start: 0.6386 (p0) cc_final: 0.6041 (p0)
REVERT: A  601 ASP cc_start: 0.7993 (m-30) cc_final: 0.7709 (m-30)
REVERT: E   46 MET cc_start: 0.7064 (ttm) cc_final: 0.6458 (tmm)
REVERT: E   54 LYS cc_start: 0.7960 (tttt) cc_final: 0.7354 (tmtt)
REVERT: E   99 ARG cc_start: 0.6716 (ttp-170) cc_final: 0.6332 (mmm-85)
REVERT: E  165 MET cc_start: 0.6341 (mmm) cc_final: 0.5538 (mpp)
REVERT: F  152 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8352 (mmmt)
REVERT: F  154 ARG cc_start: 0.7300 (mtp180) cc_final: 0.6218 (ttp80)
REVERT: F  158 GLU cc_start: 0.8632 (mt-10) cc_final: 0.8420 (mt-10)
REVERT: F  182 GLU cc_start: 0.7777 (tp30) cc_final: 0.7364 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 239
  average time/residue: 0.2051
  time to fit residues: 67.3816
Evaluate side-chains
  195 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 19 optimal weight:   10.0000
   chunk 24 optimal weight:    3.9990
   chunk 35 optimal weight:    9.9990
   chunk 50 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0980
   chunk 39 optimal weight:    0.0980
   chunk 105 optimal weight:    8.9990
   chunk 74 optimal weight:    5.9990
   chunk 115 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 112 optimal weight:    9.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 261 ASN
A 330 HIS
E  69 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.145355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.113395 restraints weight = 17296.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.115398 restraints weight = 11948.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.116647 restraints weight = 9456.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3318
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3318 r_free = 0.3318    target_work(ls_wunit_k1) = 0.116         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3318
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9366  Z= 0.142
  Angle     :  0.608   9.897  12685  Z= 0.306
  Chirality :  0.043   0.205   1493
  Planarity :  0.004   0.060   1586
  Dihedral  :  4.770  58.330   1242
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.23 %
    Favored  : 96.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.96 %
    Favored  : 96.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.25), residues: 1145
  helix:  0.44 (0.19), residues: 729
  sheet: -1.64 (0.55), residues: 77
  loop : -2.05 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B  35 
 HIS   0.004   0.001   HIS D  72 
 PHE   0.015   0.001   PHE E  66 
 TYR   0.024   0.001   TYR B 287 
 ARG   0.003   0.000   ARG B 406 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03779 (  505)
  hydrogen bonds       : angle       3.99600 ( 1473)
  covalent geometry    : bond        0.00329 ( 9366)
  covalent geometry    : angle       0.60845 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 234
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6298 (p0) cc_final: 0.5994 (p0)
REVERT: B  131 LEU cc_start: 0.9000 (tp) cc_final: 0.8780 (tp)
REVERT: B  238 ARG cc_start: 0.6722 (mmm160) cc_final: 0.5429 (mmm160)
REVERT: B  249 MET cc_start: 0.8492 (mmm) cc_final: 0.8028 (mmm)
REVERT: B  347 GLN cc_start: 0.7432 (tm-30) cc_final: 0.7180 (tm-30)
REVERT: B  400 MET cc_start: 0.7874 (mtt) cc_final: 0.7568 (mtm)
REVERT: B  406 ARG cc_start: 0.7199 (mpt-90) cc_final: 0.6700 (mpt-90)
REVERT: A  248 SER cc_start: 0.9212 (p) cc_final: 0.8992 (t)
REVERT: A  431 ILE cc_start: 0.8790 (mt) cc_final: 0.8444 (mm)
REVERT: A  521 LYS cc_start: 0.8986 (tptm) cc_final: 0.8381 (ttmt)
REVERT: A  562 ASP cc_start: 0.6445 (p0) cc_final: 0.6210 (p0)
REVERT: A  601 ASP cc_start: 0.8005 (m-30) cc_final: 0.7734 (m-30)
REVERT: A  606 MET cc_start: 0.8977 (mtm) cc_final: 0.8632 (mtp)
REVERT: E   46 MET cc_start: 0.7011 (ttm) cc_final: 0.6463 (tmm)
REVERT: E   54 LYS cc_start: 0.7922 (tttt) cc_final: 0.7360 (tmtt)
REVERT: E   69 ASN cc_start: 0.6844 (OUTLIER) cc_final: 0.6604 (p0)
REVERT: E   97 LEU cc_start: 0.7848 (mt) cc_final: 0.7577 (mt)
REVERT: E  103 SER cc_start: 0.8757 (p) cc_final: 0.8509 (p)
REVERT: E  159 TRP cc_start: 0.7062 (t-100) cc_final: 0.6771 (t-100)
REVERT: E  165 MET cc_start: 0.6250 (mmm) cc_final: 0.5400 (mpp)
REVERT: F  152 LYS cc_start: 0.8512 (mmtt) cc_final: 0.8308 (mmmt)
REVERT: F  154 ARG cc_start: 0.7240 (mtp180) cc_final: 0.6193 (ttp80)
REVERT: F  158 GLU cc_start: 0.8645 (mt-10) cc_final: 0.8010 (mt-10)
REVERT: F  182 GLU cc_start: 0.7683 (tp30) cc_final: 0.7461 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2162
  time to fit residues: 70.3744
Evaluate side-chains
  194 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 1.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 111 optimal weight:    9.9990
   chunk 71 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 65 optimal weight:    7.9990
   chunk 32 optimal weight:    0.8980
   chunk 97 optimal weight:    5.9990
   chunk 42 optimal weight:    7.9990
   chunk 75 optimal weight:    0.6980
   chunk 16 optimal weight:    9.9990
   chunk 74 optimal weight:    0.9990
   chunk 64 optimal weight:    2.9990
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 HIS
E  69 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.146406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.114643 restraints weight = 17306.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.116665 restraints weight = 12021.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.118021 restraints weight = 9498.240|
|-----------------------------------------------------------------------------|
r_work (final): 0.3316
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3326
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3326 r_free = 0.3326    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3326
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.3078

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9366  Z= 0.123
  Angle     :  0.596  10.135  12685  Z= 0.297
  Chirality :  0.043   0.198   1493
  Planarity :  0.004   0.060   1586
  Dihedral  :  4.578  56.650   1242
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 7.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.84 %
    Favored  : 98.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.25), residues: 1145
  helix:  0.72 (0.19), residues: 716
  sheet: -1.50 (0.56), residues: 77
  loop : -1.57 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP B  35 
 HIS   0.004   0.001   HIS D  72 
 PHE   0.011   0.001   PHE E  66 
 TYR   0.014   0.001   TYR B 344 
 ARG   0.006   0.000   ARG E 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03495 (  505)
  hydrogen bonds       : angle       3.78195 ( 1473)
  covalent geometry    : bond        0.00281 ( 9366)
  covalent geometry    : angle       0.59569 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 1.128 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6076 (p0) cc_final: 0.5821 (p0)
REVERT: B  131 LEU cc_start: 0.8990 (tp) cc_final: 0.8741 (tp)
REVERT: B  238 ARG cc_start: 0.6631 (mmm160) cc_final: 0.5386 (mmm160)
REVERT: B  347 GLN cc_start: 0.7259 (tm-30) cc_final: 0.7033 (tm-30)
REVERT: B  377 SER cc_start: 0.8566 (m) cc_final: 0.8227 (t)
REVERT: B  400 MET cc_start: 0.7898 (mtt) cc_final: 0.7681 (mtt)
REVERT: B  406 ARG cc_start: 0.7318 (mpt-90) cc_final: 0.6748 (mpt-90)
REVERT: A  248 SER cc_start: 0.9170 (p) cc_final: 0.8925 (t)
REVERT: A  336 LEU cc_start: 0.8748 (tp) cc_final: 0.8397 (tt)
REVERT: A  431 ILE cc_start: 0.8844 (mt) cc_final: 0.8493 (mm)
REVERT: A  521 LYS cc_start: 0.8846 (tptm) cc_final: 0.8266 (ttpt)
REVERT: A  562 ASP cc_start: 0.6535 (p0) cc_final: 0.6310 (p0)
REVERT: A  601 ASP cc_start: 0.7747 (m-30) cc_final: 0.7471 (m-30)
REVERT: A  606 MET cc_start: 0.8989 (mtm) cc_final: 0.8675 (mtp)
REVERT: E   46 MET cc_start: 0.7019 (ttm) cc_final: 0.6414 (tmm)
REVERT: E   54 LYS cc_start: 0.7873 (tttt) cc_final: 0.7333 (tmtt)
REVERT: E  165 MET cc_start: 0.6106 (mmm) cc_final: 0.5340 (mpp)
REVERT: F  154 ARG cc_start: 0.7208 (mtp180) cc_final: 0.6322 (ttp80)
REVERT: F  158 GLU cc_start: 0.8651 (mt-10) cc_final: 0.8243 (mt-10)
REVERT: F  182 GLU cc_start: 0.7797 (tp30) cc_final: 0.7442 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 232
  average time/residue: 0.2051
  time to fit residues: 66.5660
Evaluate side-chains
  195 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.174 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 18 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 13 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 91 optimal weight:    1.9990
   chunk 102 optimal weight:    4.9990
   chunk 105 optimal weight:    9.9990
   chunk 29 optimal weight:    8.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 ASN
B 220 HIS
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 ASN
E  69 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.110292 restraints weight = 16733.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.112181 restraints weight = 11528.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.113663 restraints weight = 9054.418|
|-----------------------------------------------------------------------------|
r_work (final): 0.3242
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3238
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3238 r_free = 0.3238    target_work(ls_wunit_k1) = 0.111         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3238
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9366  Z= 0.159
  Angle     :  0.626  10.579  12685  Z= 0.312
  Chirality :  0.044   0.186   1493
  Planarity :  0.004   0.062   1586
  Dihedral  :  4.594  53.790   1242
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.24 %
    Favored  : 97.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.25), residues: 1145
  helix:  0.86 (0.19), residues: 719
  sheet: -1.41 (0.58), residues: 75
  loop : -1.70 (0.34), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B  35 
 HIS   0.003   0.001   HIS E  72 
 PHE   0.016   0.001   PHE E  66 
 TYR   0.014   0.001   TYR B 344 
 ARG   0.004   0.000   ARG E 106 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03783 (  505)
  hydrogen bonds       : angle       3.96142 ( 1473)
  covalent geometry    : bond        0.00376 ( 9366)
  covalent geometry    : angle       0.62570 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  235 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 234
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  125 LEU cc_start: 0.8682 (mm) cc_final: 0.8436 (mm)
REVERT: B  131 LEU cc_start: 0.9031 (tp) cc_final: 0.8721 (tp)
REVERT: B  193 ILE cc_start: 0.9109 (pt) cc_final: 0.8908 (pt)
REVERT: B  238 ARG cc_start: 0.6723 (mmm160) cc_final: 0.5468 (mmm160)
REVERT: B  249 MET cc_start: 0.8551 (mmm) cc_final: 0.7990 (mmm)
REVERT: B  347 GLN cc_start: 0.7335 (tm-30) cc_final: 0.7053 (tm-30)
REVERT: B  400 MET cc_start: 0.7918 (mtt) cc_final: 0.7704 (mtt)
REVERT: B  406 ARG cc_start: 0.7295 (mpt-90) cc_final: 0.6738 (mpt-90)
REVERT: A  248 SER cc_start: 0.9210 (p) cc_final: 0.8971 (t)
REVERT: A  431 ILE cc_start: 0.8974 (mt) cc_final: 0.8658 (mm)
REVERT: A  521 LYS cc_start: 0.8881 (tptm) cc_final: 0.8322 (ttpt)
REVERT: A  538 LYS cc_start: 0.9061 (tttt) cc_final: 0.8844 (tttt)
REVERT: A  562 ASP cc_start: 0.6511 (p0) cc_final: 0.6281 (p0)
REVERT: A  601 ASP cc_start: 0.8051 (m-30) cc_final: 0.7790 (m-30)
REVERT: A  606 MET cc_start: 0.9028 (mtm) cc_final: 0.8692 (mtp)
REVERT: E   46 MET cc_start: 0.7042 (ttm) cc_final: 0.6381 (tmm)
REVERT: E   54 LYS cc_start: 0.7972 (tttt) cc_final: 0.7371 (tmtt)
REVERT: E  165 MET cc_start: 0.5909 (mmm) cc_final: 0.5273 (mpp)
REVERT: F  154 ARG cc_start: 0.7419 (mtp180) cc_final: 0.6411 (ttp80)
REVERT: F  158 GLU cc_start: 0.8596 (mt-10) cc_final: 0.7931 (mt-10)
REVERT: F  182 GLU cc_start: 0.7811 (tp30) cc_final: 0.7454 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 235
  average time/residue: 0.2209
  time to fit residues: 72.0417
Evaluate side-chains
  192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.023 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 30 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 45 optimal weight:   30.0000
   chunk 90 optimal weight:   20.0000
   chunk 74 optimal weight:    0.0970
   chunk 49 optimal weight:    2.9990
   chunk 28 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9990
   chunk 114 optimal weight:    6.9990
   chunk 101 optimal weight:    4.9990
   chunk 0 optimal weight:    8.9990
   overall best weight:    2.6186

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 ASN
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.140095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.108242 restraints weight = 17113.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.110432 restraints weight = 11689.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.111701 restraints weight = 9030.034|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3230
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3230 r_free = 0.3230    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3230
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.3214

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9366  Z= 0.172
  Angle     :  0.656  11.207  12685  Z= 0.329
  Chirality :  0.045   0.200   1493
  Planarity :  0.005   0.094   1586
  Dihedral  :  4.645  51.921   1242
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.14 %
    Favored  : 97.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.25), residues: 1145
  helix:  0.82 (0.19), residues: 718
  sheet: -1.32 (0.58), residues: 75
  loop : -1.71 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B  35 
 HIS   0.004   0.001   HIS E  72 
 PHE   0.019   0.001   PHE A 238 
 TYR   0.028   0.001   TYR B 287 
 ARG   0.003   0.000   ARG A  76 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03927 (  505)
  hydrogen bonds       : angle       4.03574 ( 1473)
  covalent geometry    : bond        0.00405 ( 9366)
  covalent geometry    : angle       0.65572 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 231
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6504 (p0) cc_final: 0.6218 (p0)
REVERT: B  238 ARG cc_start: 0.6784 (mmm160) cc_final: 0.5618 (mmm160)
REVERT: B  249 MET cc_start: 0.8642 (mmm) cc_final: 0.8139 (mmm)
REVERT: B  296 GLN cc_start: 0.7554 (tm-30) cc_final: 0.7348 (tp40)
REVERT: B  347 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6951 (tm-30)
REVERT: B  377 SER cc_start: 0.8589 (m) cc_final: 0.8291 (t)
REVERT: B  400 MET cc_start: 0.7932 (mtt) cc_final: 0.7638 (mtm)
REVERT: B  406 ARG cc_start: 0.7321 (mpt-90) cc_final: 0.6743 (mpt-90)
REVERT: A  248 SER cc_start: 0.9200 (p) cc_final: 0.8950 (t)
REVERT: A  431 ILE cc_start: 0.8810 (mt) cc_final: 0.8509 (mm)
REVERT: A  521 LYS cc_start: 0.8879 (tptm) cc_final: 0.8317 (ttpt)
REVERT: A  562 ASP cc_start: 0.6621 (p0) cc_final: 0.6352 (p0)
REVERT: A  601 ASP cc_start: 0.8015 (m-30) cc_final: 0.7760 (m-30)
REVERT: E   46 MET cc_start: 0.7031 (ttm) cc_final: 0.6371 (tmm)
REVERT: E   54 LYS cc_start: 0.7965 (tttt) cc_final: 0.7382 (tmtt)
REVERT: E   75 TYR cc_start: 0.7614 (t80) cc_final: 0.7283 (t80)
REVERT: E  105 ARG cc_start: 0.8445 (tmm-80) cc_final: 0.7764 (ptm-80)
REVERT: E  165 MET cc_start: 0.6246 (mmm) cc_final: 0.5816 (mpp)
REVERT: F  154 ARG cc_start: 0.7424 (mtp180) cc_final: 0.6370 (ttp80)
REVERT: F  158 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8445 (mt-10)
REVERT: F  175 LYS cc_start: 0.7761 (pttt) cc_final: 0.7403 (pttt)
REVERT: F  182 GLU cc_start: 0.8163 (tp30) cc_final: 0.7889 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 232
  average time/residue: 0.2032
  time to fit residues: 65.1141
Evaluate side-chains
  194 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.014 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 45 optimal weight:    7.9990
   chunk 48 optimal weight:    2.9990
   chunk 109 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 50 optimal weight:    2.9990
   chunk 7 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9980
   chunk 112 optimal weight:    2.9990
   chunk 67 optimal weight:    8.9990
   chunk 58 optimal weight:    0.9990
   chunk 24 optimal weight:    5.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 427 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.141129 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.109470 restraints weight = 17343.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.111608 restraints weight = 11730.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.113025 restraints weight = 9052.965|
|-----------------------------------------------------------------------------|
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3219
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3219 r_free = 0.3219    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3219
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8073
moved from start:          0.3342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9366  Z= 0.155
  Angle     :  0.654  11.410  12685  Z= 0.323
  Chirality :  0.044   0.190   1493
  Planarity :  0.005   0.081   1586
  Dihedral  :  4.633  51.795   1242
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.03 (0.25), residues: 1145
  helix:  0.93 (0.19), residues: 718
  sheet: -1.30 (0.58), residues: 75
  loop : -1.66 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP B  35 
 HIS   0.003   0.001   HIS A 282 
 PHE   0.011   0.001   PHE E  47 
 TYR   0.020   0.001   TYR B 287 
 ARG   0.002   0.000   ARG B 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03784 (  505)
  hydrogen bonds       : angle       3.99630 ( 1473)
  covalent geometry    : bond        0.00365 ( 9366)
  covalent geometry    : angle       0.65360 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 1.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6150 (p0) cc_final: 0.5927 (p0)
REVERT: B  238 ARG cc_start: 0.6785 (mmm160) cc_final: 0.5602 (mmm160)
REVERT: B  249 MET cc_start: 0.8596 (mmm) cc_final: 0.8250 (mmm)
REVERT: B  347 GLN cc_start: 0.7230 (tm-30) cc_final: 0.6934 (tm-30)
REVERT: B  377 SER cc_start: 0.8598 (m) cc_final: 0.8281 (t)
REVERT: B  400 MET cc_start: 0.7946 (mtt) cc_final: 0.7654 (mtm)
REVERT: B  406 ARG cc_start: 0.7335 (mpt-90) cc_final: 0.6739 (mpt-90)
REVERT: A  248 SER cc_start: 0.9174 (p) cc_final: 0.8944 (t)
REVERT: A  521 LYS cc_start: 0.8878 (tptm) cc_final: 0.8269 (ttpt)
REVERT: A  567 GLU cc_start: 0.8554 (mm-30) cc_final: 0.8151 (mm-30)
REVERT: A  601 ASP cc_start: 0.7963 (m-30) cc_final: 0.7704 (m-30)
REVERT: E   46 MET cc_start: 0.7029 (ttm) cc_final: 0.6348 (tmm)
REVERT: E   54 LYS cc_start: 0.7927 (tttt) cc_final: 0.7379 (tmtt)
REVERT: E   75 TYR cc_start: 0.7587 (t80) cc_final: 0.7253 (t80)
REVERT: E   99 ARG cc_start: 0.7974 (mmm-85) cc_final: 0.7738 (mmm-85)
REVERT: E  105 ARG cc_start: 0.8308 (tmm-80) cc_final: 0.7281 (ptt90)
REVERT: E  165 MET cc_start: 0.6260 (mmm) cc_final: 0.6031 (mpp)
REVERT: F  154 ARG cc_start: 0.7400 (mtp180) cc_final: 0.6354 (ttp80)
REVERT: F  158 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8413 (mt-10)
REVERT: F  182 GLU cc_start: 0.7889 (tp30) cc_final: 0.7547 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.2158
  time to fit residues: 67.6790
Evaluate side-chains
  192 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 87 optimal weight:    8.9990
   chunk 72 optimal weight:    6.9990
   chunk 61 optimal weight:    6.9990
   chunk 106 optimal weight:    9.9990
   chunk 25 optimal weight:   10.0000
   chunk 27 optimal weight:    0.7980
   chunk 0 optimal weight:    8.9990
   chunk 5 optimal weight:    0.6980
   chunk 103 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
B  48 GLN
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.142726 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.112286 restraints weight = 16558.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.114383 restraints weight = 11160.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.115645 restraints weight = 8634.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3260
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3261
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3261 r_free = 0.3261    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3261
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.3473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9366  Z= 0.133
  Angle     :  0.658  11.185  12685  Z= 0.322
  Chirality :  0.044   0.175   1493
  Planarity :  0.005   0.076   1586
  Dihedral  :  4.561  52.687   1242
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 7.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.25), residues: 1145
  helix:  1.06 (0.19), residues: 710
  sheet: -1.31 (0.58), residues: 75
  loop : -1.33 (0.35), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP E 159 
 HIS   0.008   0.001   HIS A 334 
 PHE   0.012   0.001   PHE E  66 
 TYR   0.018   0.001   TYR B 287 
 ARG   0.003   0.000   ARG B 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03680 (  505)
  hydrogen bonds       : angle       3.88773 ( 1473)
  covalent geometry    : bond        0.00310 ( 9366)
  covalent geometry    : angle       0.65800 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.074 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6825 (p0) cc_final: 0.6576 (p0)
REVERT: B   73 ASN cc_start: 0.8972 (t0) cc_final: 0.8649 (t0)
REVERT: B   85 ILE cc_start: 0.8932 (pt) cc_final: 0.8589 (tp)
REVERT: B  238 ARG cc_start: 0.6758 (mmm160) cc_final: 0.5616 (mmm160)
REVERT: B  249 MET cc_start: 0.8521 (mmm) cc_final: 0.8196 (mmm)
REVERT: B  377 SER cc_start: 0.8534 (m) cc_final: 0.8238 (t)
REVERT: B  400 MET cc_start: 0.7961 (mtt) cc_final: 0.7669 (mtm)
REVERT: B  406 ARG cc_start: 0.7282 (mpt-90) cc_final: 0.6760 (mpt-90)
REVERT: A  279 LEU cc_start: 0.8804 (tp) cc_final: 0.8579 (tp)
REVERT: A  325 ILE cc_start: 0.8943 (mm) cc_final: 0.8526 (mt)
REVERT: A  521 LYS cc_start: 0.8883 (tptm) cc_final: 0.8309 (ttpt)
REVERT: A  562 ASP cc_start: 0.5610 (p0) cc_final: 0.4670 (p0)
REVERT: A  601 ASP cc_start: 0.7733 (m-30) cc_final: 0.7418 (m-30)
REVERT: E   46 MET cc_start: 0.7271 (ttm) cc_final: 0.6333 (tmm)
REVERT: E   54 LYS cc_start: 0.7885 (tttt) cc_final: 0.7369 (tmtt)
REVERT: E   75 TYR cc_start: 0.7595 (t80) cc_final: 0.7266 (t80)
REVERT: E   99 ARG cc_start: 0.7989 (mmm-85) cc_final: 0.7733 (mmm-85)
REVERT: E  105 ARG cc_start: 0.8241 (tmm-80) cc_final: 0.7345 (ptt90)
REVERT: F  154 ARG cc_start: 0.7373 (mtp180) cc_final: 0.6361 (ttp80)
REVERT: F  158 GLU cc_start: 0.8607 (mt-10) cc_final: 0.8368 (mt-10)
REVERT: F  182 GLU cc_start: 0.7852 (tp30) cc_final: 0.7518 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.2056
  time to fit residues: 67.6299
Evaluate side-chains
  196 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.118 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    6.9990
   chunk 87 optimal weight:    8.9990
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 100 optimal weight:    2.9990
   chunk 110 optimal weight:    0.8980
   chunk 39 optimal weight:    6.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 188 ASN
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.141199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.109803 restraints weight = 16935.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.111830 restraints weight = 11583.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.113039 restraints weight = 9036.738|
|-----------------------------------------------------------------------------|
r_work (final): 0.3246
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3213
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3213 r_free = 0.3213    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3213
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9366  Z= 0.155
  Angle     :  0.687  11.429  12685  Z= 0.336
  Chirality :  0.044   0.169   1493
  Planarity :  0.005   0.075   1586
  Dihedral  :  4.555  52.891   1242
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 7.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.41 %
    Favored  : 99.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.24 (0.26), residues: 1145
  helix:  1.08 (0.19), residues: 710
  sheet: -1.43 (0.58), residues: 77
  loop : -1.27 (0.35), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  35 
 HIS   0.003   0.001   HIS A 330 
 PHE   0.014   0.001   PHE B 236 
 TYR   0.020   0.001   TYR B 344 
 ARG   0.003   0.000   ARG B 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03762 (  505)
  hydrogen bonds       : angle       3.90163 ( 1473)
  covalent geometry    : bond        0.00366 ( 9366)
  covalent geometry    : angle       0.68713 (12685)

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

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

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2290 Ramachandran restraints generated.
    1145 Oldfield, 0 Emsley, 1145 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 225
  time to evaluate  : 1.007 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   61 ASP cc_start: 0.6616 (p0) cc_final: 0.6358 (p0)
REVERT: B   73 ASN cc_start: 0.9040 (t0) cc_final: 0.8497 (t0)
REVERT: B   85 ILE cc_start: 0.8973 (pt) cc_final: 0.8611 (tp)
REVERT: B  238 ARG cc_start: 0.6740 (mmm160) cc_final: 0.5567 (mmm160)
REVERT: B  249 MET cc_start: 0.8599 (mmm) cc_final: 0.8218 (mmm)
REVERT: B  377 SER cc_start: 0.8563 (m) cc_final: 0.8183 (t)
REVERT: B  400 MET cc_start: 0.7955 (mtt) cc_final: 0.7661 (mtm)
REVERT: B  406 ARG cc_start: 0.7333 (mpt-90) cc_final: 0.6833 (mpt-90)
REVERT: A  325 ILE cc_start: 0.8953 (mm) cc_final: 0.8557 (mt)
REVERT: A  521 LYS cc_start: 0.8903 (tptm) cc_final: 0.8317 (ttpt)
REVERT: A  562 ASP cc_start: 0.6139 (p0) cc_final: 0.5330 (p0)
REVERT: A  567 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7341 (mt-10)
REVERT: A  601 ASP cc_start: 0.7718 (m-30) cc_final: 0.7402 (m-30)
REVERT: E   46 MET cc_start: 0.7145 (ttm) cc_final: 0.6313 (tmm)
REVERT: E   54 LYS cc_start: 0.7934 (tttt) cc_final: 0.7443 (tmtt)
REVERT: E   75 TYR cc_start: 0.7605 (t80) cc_final: 0.7274 (t80)
REVERT: E   99 ARG cc_start: 0.8078 (mmm-85) cc_final: 0.7859 (mmm-85)
REVERT: E  105 ARG cc_start: 0.8259 (tmm-80) cc_final: 0.7361 (ptt90)
REVERT: E  165 MET cc_start: 0.7044 (mpp) cc_final: 0.6758 (mmm)
REVERT: F  154 ARG cc_start: 0.7207 (mtp180) cc_final: 0.6305 (ttp80)
REVERT: F  158 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8055 (mt-10)
REVERT: F  182 GLU cc_start: 0.7893 (tp30) cc_final: 0.7550 (tp30)
  outliers start: 1
  outliers final: 0
  residues processed: 226
  average time/residue: 0.2243
  time to fit residues: 70.5057
Evaluate side-chains
  193 residues out of total 1039 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 2 optimal weight:    0.6980
   chunk 44 optimal weight:    9.9990
   chunk 100 optimal weight:    7.9990
   chunk 34 optimal weight:    0.7980
   chunk 108 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 0 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 94 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 79 optimal weight:   10.0000
   overall best weight:    2.2384

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

Flipped N/Q/H residues before XYZ refinement:
** B 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 HIS
** A  55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 368 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.140677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.109297 restraints weight = 17044.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.111401 restraints weight = 11511.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.112621 restraints weight = 8890.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3221
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3221 r_free = 0.3221    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3220 r_free = 0.3220    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        3 |
|-----------------------------------------------------------------------------|
r_final: 0.3220
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.3514

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9366  Z= 0.156
  Angle     :  0.672  11.511  12685  Z= 0.327
  Chirality :  0.045   0.175   1493
  Planarity :  0.005   0.073   1586
  Dihedral  :  4.568  54.331   1242
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.30 (0.26), residues: 1145
  helix:  1.13 (0.19), residues: 710
  sheet: -1.47 (0.58), residues: 77
  loop : -1.24 (0.36), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP E 159 
 HIS   0.003   0.001   HIS A 334 
 PHE   0.013   0.001   PHE E  66 
 TYR   0.020   0.001   TYR B 344 
 ARG   0.003   0.000   ARG B 412 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03799 (  505)
  hydrogen bonds       : angle       3.91374 ( 1473)
  covalent geometry    : bond        0.00369 ( 9366)
  covalent geometry    : angle       0.67171 (12685)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3228.25 seconds
wall clock time: 56 minutes 46.56 seconds (3406.56 seconds total)