Starting phenix.real_space_refine
on Tue Mar  3 22:22:29 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m4o_30080/03_2026/6m4o_30080.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m4o_30080/03_2026/6m4o_30080.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m4o_30080/03_2026/6m4o_30080.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m4o_30080/03_2026/6m4o_30080.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m4o_30080/03_2026/6m4o_30080.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m4o_30080/03_2026/6m4o_30080.map"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 15 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      50      5.16       5
     C    5746      2.51       5
     N    1507      2.21       5
     O    1614      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8918
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "S"
      Number of atoms: 3258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 420, 3258
          Classifications: {'peptide': 420}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 21, 'TRANS': 398}
          Unresolved non-hydrogen bonds: 13
          Unresolved non-hydrogen angles: 16
          Unresolved non-hydrogen dihedrals: 12
          Planarities with less than four sites: {'ASP:plan': 1, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 8
    Chain: "T"
      Number of atoms: 3887
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 491, 3887
          Classifications: {'peptide': 491}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 17, 'TRANS': 473}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 1128
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 139, 1128
          Classifications: {'peptide': 139}
          Link IDs: {'PTRANS': 7, 'TRANS': 131}
    Chain: "E"
      Number of atoms: 390
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 49, 390
          Classifications: {'peptide': 49}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 1, 'TRANS': 47}
          Unresolved non-hydrogen bonds: 33
          Unresolved non-hydrogen angles: 45
          Unresolved non-hydrogen dihedrals: 34
          Planarities with less than four sites: {'ARG:plan': 1, 'TRP:plan': 1, 'TYR:plan': 2}
          Unresolved non-hydrogen planarities: 28
    Chain: "B"
      Number of atoms: 240
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 28, 240
          Classifications: {'peptide': 28}
          Link IDs: {'PTRANS': 1, 'TRANS': 26}
    Chain: "T"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'PLP': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" C2  PLP T 601 " occ=0.80
      ... (13 atoms not shown)
      pdb=" P   PLP T 601 " occ=0.80
  Time building chain proxies: 1.79, per 1000 atoms: 0.20
  Number of scatterers: 8918
  At special positions: 0
  Unit cell: (90.234, 83.55, 119.198, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      50     16.00
     P       1     15.00
     O    1614      8.00
     N    1507      7.00
     C    5746      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.47
  Conformation dependent library (CDL) restraints added in 321.5 milliseconds
  

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      43.2% alpha, 6.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'S' and resid 56 through 61
    Processing helix  chain 'S' and resid 114 through 123
    Processing helix  chain 'S' and resid 124 through 129
    Processing helix  chain 'S' and resid 143 through 156
      removed outlier: 3.999A  pdb=" N   GLU S 149 " --> pdb=" O   HIS S 145 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LYS S 154 " --> pdb=" O   ASP S 150 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 167 through 171
      removed outlier: 4.014A  pdb=" N   THR S 170 " --> pdb=" O   GLY S 167 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ILE S 171 " --> pdb=" O   PHE S 168 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 167 through 171'
    Processing helix  chain 'S' and resid 197 through 202
    Processing helix  chain 'S' and resid 217 through 229
      removed outlier: 3.591A  pdb=" N   GLN S 224 " --> pdb=" O   LEU S 220 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   GLU S 227 " --> pdb=" O   GLU S 223 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 233 through 237
    Processing helix  chain 'S' and resid 257 through 268
      removed outlier: 3.567A  pdb=" N   LYS S 262 " --> pdb=" O   PRO S 258 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   LEU S 263 " --> pdb=" O   GLU S 259 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   TYR S 265 " --> pdb=" O   VAL S 261 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   LYS S 266 " --> pdb=" O   LYS S 262 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   TYR S 267 " --> pdb=" O   LEU S 263 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 288 through 293
    Processing helix  chain 'S' and resid 296 through 300
    Processing helix  chain 'S' and resid 321 through 326
      removed outlier: 3.935A  pdb=" N   ASP S 326 " --> pdb=" O   SER S 322 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 327 through 330
      removed outlier: 3.549A  pdb=" N   LEU S 330 " --> pdb=" O   HIS S 327 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 327 through 330'
    Processing helix  chain 'S' and resid 342 through 359
    Processing helix  chain 'S' and resid 361 through 374
      removed outlier: 3.598A  pdb=" N   VAL S 365 " --> pdb=" O   GLY S 361 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   LYS S 367 " --> pdb=" O   PHE S 363 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LYS S 369 " --> pdb=" O   VAL S 365 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   GLN S 372 " --> pdb=" O   GLU S 368 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 404 through 420
      removed outlier: 3.588A  pdb=" N   GLU S 414 " --> pdb=" O   ARG S 410 " (cutoff:3.500A)
      removed outlier: 4.059A  pdb=" N   ILE S 415 " --> pdb=" O   LEU S 411 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   VAL S 416 " --> pdb=" O   LEU S 412 " (cutoff:3.500A)
    Processing helix  chain 'S' and resid 421 through 423
      No H-bonds generated for 'chain 'S' and resid 421 through 423'
    Processing helix  chain 'S' and resid 453 through 456
    Processing helix  chain 'S' and resid 457 through 470
      removed outlier: 3.505A  pdb=" N   ILE S 464 " --> pdb=" O   ALA S 460 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL S 467 " --> pdb=" O   THR S 463 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ALA S 468 " --> pdb=" O   ILE S 464 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   GLN S 469 " --> pdb=" O   LYS S 465 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ALA S 470 " --> pdb=" O   GLU S 466 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 69 through 91
      removed outlier: 3.615A  pdb=" N   LEU T  73 " --> pdb=" O   LEU T  69 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   TYR T  75 " --> pdb=" O   ALA T  71 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL T  76 " --> pdb=" O   VAL T  72 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 117 through 120
    Processing helix  chain 'T' and resid 121 through 126
    Processing helix  chain 'T' and resid 189 through 197
      removed outlier: 3.767A  pdb=" N   ALA T 193 " --> pdb=" O   GLN T 189 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   LYS T 194 " --> pdb=" O   GLU T 190 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL T 195 " --> pdb=" O   ALA T 191 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 213 through 228
      removed outlier: 3.685A  pdb=" N   GLU T 217 " --> pdb=" O   LEU T 213 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ALA T 224 " --> pdb=" O   GLU T 220 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 238 through 243
      removed outlier: 3.742A  pdb=" N   ASN T 242 " --> pdb=" O   GLY T 238 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 245 through 250
    Processing helix  chain 'T' and resid 263 through 273
      removed outlier: 3.597A  pdb=" N   VAL T 267 " --> pdb=" O   HIS T 263 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ALA T 270 " --> pdb=" O   LEU T 266 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   SER T 273 " --> pdb=" O   GLY T 269 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 284 through 297
      removed outlier: 3.580A  pdb=" N   LEU T 291 " --> pdb=" O   SER T 287 " (cutoff:3.500A)
      removed outlier: 3.728A  pdb=" N   ILE T 296 " --> pdb=" O   LEU T 292 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 327 through 335
      removed outlier: 4.450A  pdb=" N   LEU T 333 " --> pdb=" O   GLU T 329 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 358 through 363
      removed outlier: 3.642A  pdb=" N   TYR T 362 " --> pdb=" O   GLY T 358 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 366 through 370
      removed outlier: 3.635A  pdb=" N   ASP T 369 " --> pdb=" O   ASP T 366 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL T 370 " --> pdb=" O   PRO T 367 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'T' and resid 366 through 370'
    Processing helix  chain 'T' and resid 391 through 396
    Processing helix  chain 'T' and resid 412 through 428
      removed outlier: 3.698A  pdb=" N   GLU T 417 " --> pdb=" O   PRO T 413 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ILE T 419 " --> pdb=" O   VAL T 415 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   CYS T 425 " --> pdb=" O   THR T 421 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   ILE T 426 " --> pdb=" O   SER T 422 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   MET T 427 " --> pdb=" O   MET T 423 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 438 through 455
      removed outlier: 3.676A  pdb=" N   ARG T 447 " --> pdb=" O   ALA T 443 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   ARG T 450 " --> pdb=" O   THR T 446 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   ARG T 451 " --> pdb=" O   ARG T 447 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 478 through 489
      removed outlier: 3.790A  pdb=" N   ARG T 484 " --> pdb=" O   GLY T 480 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   LEU T 487 " --> pdb=" O   GLY T 483 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   LYS T 488 " --> pdb=" O   ARG T 484 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG T 489 " --> pdb=" O   GLU T 485 " (cutoff:3.500A)
    Processing helix  chain 'T' and resid 517 through 535
      removed outlier: 3.619A  pdb=" N   ALA T 524 " --> pdb=" O   ILE T 520 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   VAL T 531 " --> pdb=" O   GLU T 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 39
      removed outlier: 3.514A  pdb=" N   LEU A  28 " --> pdb=" O   LEU A  24 " (cutoff:3.500A)
      removed outlier: 4.035A  pdb=" N   ALA A  29 " --> pdb=" O   SER A  25 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   ILE A  30 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   VAL A  36 " --> pdb=" O   LEU A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 45 through 50
      removed outlier: 3.698A  pdb=" N   TRP A  49 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 63
      removed outlier: 3.563A  pdb=" N   LEU A  54 " --> pdb=" O   THR A  50 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   HIS A  56 " --> pdb=" O   THR A  52 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   TYR A  61 " --> pdb=" O   ASN A  57 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 116
      Proline residue:  A 106  - end of helix
      removed outlier: 3.533A  pdb=" N   LEU A 112 " --> pdb=" O   VAL A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 117 through 119
      No H-bonds generated for 'chain 'A' and resid 117 through 119'
    Processing helix  chain 'A' and resid 121 through 129
      removed outlier: 3.676A  pdb=" N   VAL A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 131 through 136
      removed outlier: 3.551A  pdb=" N   LEU A 135 " --> pdb=" O   LEU A 131 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 8 through 23
      removed outlier: 3.583A  pdb=" N   MET E  13 " --> pdb=" O   ALA E   9 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   PHE E  16 " --> pdb=" O   GLN E  12 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 24 through 26
      No H-bonds generated for 'chain 'E' and resid 24 through 26'
    Processing helix  chain 'E' and resid 33 through 46
      removed outlier: 3.756A  pdb=" N   PHE E  37 " --> pdb=" O   GLU E  33 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ILE E  44 " --> pdb=" O   MET E  40 " (cutoff:3.500A)
      removed outlier: 3.816A  pdb=" N   VAL E  45 " --> pdb=" O   LEU E  41 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 55
      removed outlier: 3.587A  pdb=" N   TYR E  50 " --> pdb=" O   GLY E  46 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLY E  52 " --> pdb=" O   ALA E  48 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL E  54 " --> pdb=" O   TYR E  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 40
      removed outlier: 3.597A  pdb=" N   LEU B  33 " --> pdb=" O   GLY B  29 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ILE B  36 " --> pdb=" O   ILE B  32 " (cutoff:3.500A)
      removed outlier: 3.705A  pdb=" N   ARG B  37 " --> pdb=" O   LEU B  33 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE B  40 " --> pdb=" O   ILE B  36 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'S' and resid 92 through 94
    Processing sheet with id=AA2, first strand: chain 'S' and resid 160 through 164
      removed outlier: 3.512A  pdb=" N   ILE S 162 " --> pdb=" O   CYS S 318 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   CYS S 318 " --> pdb=" O   ILE S 162 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'S' and resid 205 through 208
      removed outlier: 6.302A  pdb=" N   VAL S 185 " --> pdb=" O   LYS S 207 " (cutoff:3.500A)
      removed outlier: 6.183A  pdb=" N   ILE S 184 " --> pdb=" O   PHE S 241 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   VAL S 243 " --> pdb=" O   ILE S 184 " (cutoff:3.500A)
      removed outlier: 5.994A  pdb=" N   PHE S 186 " --> pdb=" O   VAL S 243 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   ILE S 242 " --> pdb=" O   PHE S 272 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'T' and resid 145 through 152
      removed outlier: 5.705A  pdb=" N   VAL T 146 " --> pdb=" O   GLY T 169 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   GLY T 169 " --> pdb=" O   VAL T 146 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   GLU T 150 " --> pdb=" O   ASN T 165 " (cutoff:3.500A)
      removed outlier: 4.802A  pdb=" N   ASN T 165 " --> pdb=" O   GLU T 150 " (cutoff:3.500A)
      removed outlier: 8.762A  pdb=" N   GLN T 152 " --> pdb=" O   THR T 163 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   THR T 163 " --> pdb=" O   GLN T 152 " (cutoff:3.500A)
      removed outlier: 8.019A  pdb=" N   GLY T 492 " --> pdb=" O   GLY T 169 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ILE T 171 " --> pdb=" O   GLY T 492 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'T' and resid 231 through 235
      removed outlier: 3.588A  pdb=" N   GLY T 386 " --> pdb=" O   TYR T 235 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY T 389 " --> pdb=" O   MET T 373 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL T 372 " --> pdb=" O   LEU T 341 " (cutoff:3.500A)
      removed outlier: 7.048A  pdb=" N   ILE T 310 " --> pdb=" O   TYR T 340 " (cutoff:3.500A)
      removed outlier: 8.000A  pdb=" N   TYR T 342 " --> pdb=" O   ILE T 310 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   ILE T 312 " --> pdb=" O   TYR T 342 " (cutoff:3.500A)
      removed outlier: 7.360A  pdb=" N   ASP T 344 " --> pdb=" O   ILE T 312 " (cutoff:3.500A)
      removed outlier: 7.498A  pdb=" N   VAL T 314 " --> pdb=" O   ASP T 344 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'T' and resid 468 through 471
      removed outlier: 3.837A  pdb=" N   VAL T 494 " --> pdb=" O   ARG T 509 " (cutoff:3.500A)

    254 hydrogen bonds defined for protein.
    729 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.30

  Time building geometry restraints manager: 0.64 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 2619
        1.33 -     1.45: 1432
        1.45 -     1.57: 4977
        1.57 -     1.69: 2
        1.69 -     1.81: 82
  Bond restraints: 9112
  Sorted by residual:
  bond pdb=" CA  LEU T 261 "
       pdb=" CB  LEU T 261 "
    ideal  model  delta    sigma   weight residual
    1.527  1.589 -0.062 1.75e-02 3.27e+03 1.27e+01
  bond pdb=" CG1 ILE S 162 "
       pdb=" CD1 ILE S 162 "
    ideal  model  delta    sigma   weight residual
    1.513  1.443  0.070 3.90e-02 6.57e+02 3.26e+00
  bond pdb=" N   SER T 540 "
       pdb=" CA  SER T 540 "
    ideal  model  delta    sigma   weight residual
    1.453  1.475 -0.022 1.31e-02 5.83e+03 2.70e+00
  bond pdb=" C   GLU E  30 "
       pdb=" N   PRO E  31 "
    ideal  model  delta    sigma   weight residual
    1.334  1.372 -0.038 2.34e-02 1.83e+03 2.65e+00
  bond pdb=" CA  ILE T 246 "
       pdb=" C   ILE T 246 "
    ideal  model  delta    sigma   weight residual
    1.520  1.533 -0.013 8.80e-03 1.29e+04 2.33e+00
  ... (remaining 9107 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 11852
        2.55 -     5.10: 392
        5.10 -     7.64: 60
        7.64 -    10.19: 20
       10.19 -    12.74: 4
  Bond angle restraints: 12328
  Sorted by residual:
  angle pdb=" C   TYR A 116 "
        pdb=" N   THR A 117 "
        pdb=" CA  THR A 117 "
      ideal   model   delta    sigma   weight residual
     121.54  130.39   -8.85 1.91e+00 2.74e-01 2.15e+01
  angle pdb=" C   THR S 453 "
        pdb=" N   GLU S 454 "
        pdb=" CA  GLU S 454 "
      ideal   model   delta    sigma   weight residual
     121.54  129.88   -8.34 1.91e+00 2.74e-01 1.91e+01
  angle pdb=" N   VAL S  73 "
        pdb=" CA  VAL S  73 "
        pdb=" C   VAL S  73 "
      ideal   model   delta    sigma   weight residual
     108.88  118.22   -9.34 2.16e+00 2.14e-01 1.87e+01
  angle pdb=" C   LYS T 109 "
        pdb=" N   ASP T 110 "
        pdb=" CA  ASP T 110 "
      ideal   model   delta    sigma   weight residual
     121.54  129.59   -8.05 1.91e+00 2.74e-01 1.78e+01
  angle pdb=" CA  ARG S 239 "
        pdb=" CB  ARG S 239 "
        pdb=" CG  ARG S 239 "
      ideal   model   delta    sigma   weight residual
     114.10  122.32   -8.22 2.00e+00 2.50e-01 1.69e+01
  ... (remaining 12323 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.46: 5039
       15.46 -    30.92: 309
       30.92 -    46.38: 85
       46.38 -    61.85: 6
       61.85 -    77.31: 8
  Dihedral angle restraints: 5447
    sinusoidal: 2189
      harmonic: 3258
  Sorted by residual:
  dihedral pdb=" CA  VAL T  48 "
           pdb=" C   VAL T  48 "
           pdb=" N   THR T  49 "
           pdb=" CA  THR T  49 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -144.44  -35.56     0      5.00e+00 4.00e-02 5.06e+01
  dihedral pdb=" CA  VAL S 281 "
           pdb=" C   VAL S 281 "
           pdb=" N   LEU S 282 "
           pdb=" CA  LEU S 282 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.93   31.07     0      5.00e+00 4.00e-02 3.86e+01
  dihedral pdb=" CA  PHE S 394 "
           pdb=" C   PHE S 394 "
           pdb=" N   HIS S 395 "
           pdb=" CA  HIS S 395 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.38   29.62     0      5.00e+00 4.00e-02 3.51e+01
  ... (remaining 5444 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.057: 930
       0.057 -    0.113: 355
       0.113 -    0.170: 81
       0.170 -    0.226: 10
       0.226 -    0.283: 4
  Chirality restraints: 1380
  Sorted by residual:
  chirality pdb=" CB  ILE T 459 "
            pdb=" CA  ILE T 459 "
            pdb=" CG1 ILE T 459 "
            pdb=" CG2 ILE T 459 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.36    0.28 2.00e-01 2.50e+01 2.00e+00
  chirality pdb=" CB  ILE T 171 "
            pdb=" CA  ILE T 171 "
            pdb=" CG1 ILE T 171 "
            pdb=" CG2 ILE T 171 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.69e+00
  chirality pdb=" CB  VAL S 237 "
            pdb=" CA  VAL S 237 "
            pdb=" CG1 VAL S 237 "
            pdb=" CG2 VAL S 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.68e+00
  ... (remaining 1377 not shown)

  Planarity restraints: 1562
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR T 501 "   -0.051 5.00e-02 4.00e+02   7.68e-02 9.43e+00
        pdb=" N   PRO T 502 "    0.133 5.00e-02 4.00e+02
        pdb=" CA  PRO T 502 "   -0.039 5.00e-02 4.00e+02
        pdb=" CD  PRO T 502 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER T 402 "   -0.013 2.00e-02 2.50e+03   2.53e-02 6.42e+00
        pdb=" C   SER T 402 "    0.044 2.00e-02 2.50e+03
        pdb=" O   SER T 402 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   HIS T 403 "   -0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR T 103 "    0.012 2.00e-02 2.50e+03   2.37e-02 5.60e+00
        pdb=" C   THR T 103 "   -0.041 2.00e-02 2.50e+03
        pdb=" O   THR T 103 "    0.015 2.00e-02 2.50e+03
        pdb=" N   GLU T 104 "    0.014 2.00e-02 2.50e+03
  ... (remaining 1559 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1010
        2.74 -     3.28: 8210
        3.28 -     3.82: 14181
        3.82 -     4.36: 17142
        4.36 -     4.90: 29531
  Nonbonded interactions: 70074
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP S 188 "
            pdb=" OH  TYR S 248 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" OH  TYR S 178 "
            pdb=" O   VAL S 324 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" OG1 THR S 427 "
            pdb=" OE1 GLU T 209 "
     model   vdw
     2.250 3.040
  nonbonded pdb=" OH  TYR A 110 "
            pdb=" OG1 THR A 128 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OH  TYR T 448 "
            pdb=" OD1 ASP T 522 "
     model   vdw
     2.323 3.040
  ... (remaining 70069 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=0.80 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.510
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.770
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7897
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      :  0.007   0.073   9113  Z= 0.326
  Angle     :  1.144  12.740  12328  Z= 0.613
  Chirality :  0.062   0.283   1380
  Planarity :  0.008   0.077   1562
  Dihedral  : 11.527  77.308   3361
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 4.58
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  : 11.41 %
    Favored  : 88.41 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  :  7.23 %
    Favored  : 91.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.19 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.81 (0.17), residues: 1113
  helix: -4.55 (0.10), residues: 459
  sheet: -3.66 (0.42), residues: 101
  loop : -3.22 (0.22), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG S 405 
 TYR   0.034   0.003   TYR S 166 
 PHE   0.030   0.003   PHE S 209 
 TRP   0.028   0.003   TRP T 134 
 HIS   0.010   0.002   HIS T 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00746 ( 9112)
  covalent geometry    : angle       1.14366 (12328)
  hydrogen bonds       : bond        0.31671 (  254)
  hydrogen bonds       : angle       9.79548 (  729)
  Misc. bond           : bond        0.00082 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  279 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 268
  time to evaluate  : 0.398 
Fit side-chains
   revert: symmetry clash
REVERT: S   95 VAL cc_start: 0.9104 (t) cc_final: 0.8815 (p)
REVERT: S  107 ASN cc_start: 0.8117 (p0) cc_final: 0.7889 (p0)
REVERT: S  146 LEU cc_start: 0.8843 (mm) cc_final: 0.8335 (mm)
REVERT: S  345 LEU cc_start: 0.8823 (mm) cc_final: 0.8432 (mt)
REVERT: T   82 THR cc_start: 0.9049 (t) cc_final: 0.8629 (p)
REVERT: T   86 TYR cc_start: 0.8506 (m-80) cc_final: 0.7582 (m-80)
REVERT: T  155 ASP cc_start: 0.7079 (t0) cc_final: 0.6841 (t70)
REVERT: T  177 ASN cc_start: 0.8167 (t0) cc_final: 0.7582 (t0)
REVERT: T  304 ARG cc_start: 0.7976 (mmt90) cc_final: 0.7012 (ttp-170)
REVERT: T  537 LEU cc_start: 0.8750 (OUTLIER) cc_final: 0.8514 (pp)
REVERT: A  116 TYR cc_start: 0.7117 (m-80) cc_final: 0.6867 (m-80)
REVERT: E   13 MET cc_start: 0.8130 (tpt) cc_final: 0.7665 (tpt)
  outliers start: 11
  outliers final: 2
  residues processed: 275
  average time/residue: 0.0996
  time to fit residues: 36.4980
Evaluate side-chains
  142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 139
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  537 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.5980
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    0.8980
   chunk 106 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
S  81 ASN
S 114 ASN
S 211 HIS
S 231 ASN
S 428 GLN
T  47 HIS
T  50 GLN
T 116 GLN
T 212 ASN
T 216 HIS
T 242 ASN
T 284 ASN
T 490 ASN
T 516 HIS
B  24 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126861 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.110285 restraints weight = 15584.997|
|-----------------------------------------------------------------------------|
r_work (start): 0.3454 rms_B_bonded: 2.35
r_work: 0.3354 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3358
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3358 r_free = 0.3358    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3358
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2554

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   9113  Z= 0.152
  Angle     :  0.714   8.531  12328  Z= 0.367
  Chirality :  0.047   0.223   1380
  Planarity :  0.006   0.082   1562
  Dihedral  :  6.622  51.517   1238
  Min Nonbonded Distance : 2.441

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.07 %
    Favored  : 90.93 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 13.30 %
    Favored  : 83.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -4.34 (0.20), residues: 1113
  helix: -2.84 (0.18), residues: 463
  sheet: -3.26 (0.42), residues: 106
  loop : -2.79 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG T  57 
 TYR   0.015   0.002   TYR S 166 
 PHE   0.019   0.002   PHE T 449 
 TRP   0.022   0.002   TRP T 134 
 HIS   0.003   0.001   HIS S 395 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 9112)
  covalent geometry    : angle       0.71406 (12328)
  hydrogen bonds       : bond        0.05054 (  254)
  hydrogen bonds       : angle       5.29941 (  729)
  Misc. bond           : bond        0.00014 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 162
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
REVERT: S  107 ASN cc_start: 0.8275 (p0) cc_final: 0.8066 (p0)
REVERT: T   68 MET cc_start: 0.8902 (tpt) cc_final: 0.8643 (tpt)
REVERT: T   86 TYR cc_start: 0.8736 (m-80) cc_final: 0.7693 (m-80)
REVERT: T  126 LEU cc_start: 0.9040 (OUTLIER) cc_final: 0.8695 (tt)
REVERT: T  155 ASP cc_start: 0.7691 (t0) cc_final: 0.7164 (t0)
REVERT: T  177 ASN cc_start: 0.8492 (t0) cc_final: 0.7868 (t0)
REVERT: T  304 ARG cc_start: 0.8239 (mmt90) cc_final: 0.7247 (ttp-110)
REVERT: T  418 GLN cc_start: 0.9052 (tp40) cc_final: 0.8699 (tp40)
REVERT: E   13 MET cc_start: 0.8275 (tpt) cc_final: 0.7593 (tpt)
  outliers start: 35
  outliers final: 21
  residues processed: 186
  average time/residue: 0.0970
  time to fit residues: 24.4725
Evaluate side-chains
  158 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 136
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  170 THR
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  330 LEU
Chi-restraints excluded: chain S residue  368 GLU
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  378 THR
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  533 ASP
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain E residue   12 GLN
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain B residue   30 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 29 optimal weight:    0.7980
   chunk 42 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 39 optimal weight:    3.9990
   chunk 53 optimal weight:    2.9990
   chunk 101 optimal weight:    0.0870
   chunk 95 optimal weight:    3.9990
   overall best weight:    0.9362

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

Flipped N/Q/H residues before XYZ refinement:
** S 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 282 HIS
T 445 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.126199 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.109620 restraints weight = 15642.698|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.35
r_work: 0.3347 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3351
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3351 r_free = 0.3351    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3351
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8065
moved from start:          0.3070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   9113  Z= 0.144
  Angle     :  0.672   7.913  12328  Z= 0.338
  Chirality :  0.046   0.182   1380
  Planarity :  0.005   0.070   1562
  Dihedral  :  5.964  35.702   1236
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 14.03 %
    Favored  : 81.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.39 (0.22), residues: 1113
  helix: -1.78 (0.22), residues: 457
  sheet: -2.97 (0.44), residues: 104
  loop : -2.49 (0.24), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG T 541 
 TYR   0.012   0.001   TYR S 166 
 PHE   0.017   0.002   PHE B  40 
 TRP   0.019   0.001   TRP T 134 
 HIS   0.003   0.001   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 9112)
  covalent geometry    : angle       0.67192 (12328)
  hydrogen bonds       : bond        0.04051 (  254)
  hydrogen bonds       : angle       4.74909 (  729)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 147
  time to evaluate  : 0.342 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8292 (mm) cc_final: 0.8016 (mt)
REVERT: S  274 GLU cc_start: 0.8584 (tm-30) cc_final: 0.8380 (tm-30)
REVERT: S  465 LYS cc_start: 0.8464 (tmtt) cc_final: 0.7960 (tttm)
REVERT: T   86 TYR cc_start: 0.8704 (m-80) cc_final: 0.7686 (m-80)
REVERT: T   87 LEU cc_start: 0.9011 (OUTLIER) cc_final: 0.8770 (tt)
REVERT: T  126 LEU cc_start: 0.9045 (OUTLIER) cc_final: 0.8751 (tt)
REVERT: T  155 ASP cc_start: 0.7629 (t0) cc_final: 0.7143 (t0)
REVERT: T  177 ASN cc_start: 0.8507 (t0) cc_final: 0.7831 (t0)
REVERT: T  218 GLU cc_start: 0.7883 (tt0) cc_final: 0.7516 (tp30)
REVERT: T  304 ARG cc_start: 0.8314 (mmt90) cc_final: 0.7150 (ttp-170)
REVERT: T  317 ILE cc_start: 0.8710 (mp) cc_final: 0.8441 (mt)
REVERT: A  110 TYR cc_start: 0.7041 (t80) cc_final: 0.6828 (t80)
REVERT: E   13 MET cc_start: 0.8275 (tpt) cc_final: 0.7613 (tpt)
  outliers start: 40
  outliers final: 24
  residues processed: 172
  average time/residue: 0.0809
  time to fit residues: 19.5216
Evaluate side-chains
  157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 131
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  170 THR
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  307 MET
Chi-restraints excluded: chain S residue  419 CYS
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue   87 LEU
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  520 ILE
Chi-restraints excluded: chain T residue  533 ASP
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain E residue   12 GLN
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   31 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 52 optimal weight:    0.8980
   chunk 64 optimal weight:    3.9990
   chunk 69 optimal weight:    0.6980
   chunk 27 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 76 optimal weight:    0.6980
   chunk 22 optimal weight:    4.9990
   chunk 108 optimal weight:    4.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
S 397 GLN
** S 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 154 HIS
T 242 ASN
A 127 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.127236 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.110201 restraints weight = 15964.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.3448 rms_B_bonded: 2.44
r_work: 0.3346 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8047
moved from start:          0.3353

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9113  Z= 0.127
  Angle     :  0.652   7.905  12328  Z= 0.325
  Chirality :  0.046   0.244   1380
  Planarity :  0.005   0.063   1562
  Dihedral  :  5.662  37.439   1236
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  4.19 %
    Allowed  : 15.39 %
    Favored  : 80.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.82 (0.24), residues: 1113
  helix: -1.10 (0.24), residues: 459
  sheet: -3.19 (0.46), residues: 92
  loop : -2.29 (0.24), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG T 541 
 TYR   0.017   0.001   TYR E  18 
 PHE   0.013   0.001   PHE B  40 
 TRP   0.015   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 9112)
  covalent geometry    : angle       0.65227 (12328)
  hydrogen bonds       : bond        0.03461 (  254)
  hydrogen bonds       : angle       4.47169 (  729)
  Misc. bond           : bond        0.00004 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  189 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 149
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8308 (mm) cc_final: 0.8035 (mt)
REVERT: S  274 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8319 (tm-30)
REVERT: S  395 HIS cc_start: 0.8416 (m-70) cc_final: 0.7973 (m-70)
REVERT: S  465 LYS cc_start: 0.8454 (tmtt) cc_final: 0.8019 (tttm)
REVERT: T   86 TYR cc_start: 0.8656 (m-80) cc_final: 0.7677 (m-80)
REVERT: T   87 LEU cc_start: 0.8980 (OUTLIER) cc_final: 0.8741 (tt)
REVERT: T  126 LEU cc_start: 0.9014 (OUTLIER) cc_final: 0.8720 (tt)
REVERT: T  128 MET cc_start: 0.8866 (tpp) cc_final: 0.8534 (ttm)
REVERT: T  155 ASP cc_start: 0.7677 (t0) cc_final: 0.7137 (t0)
REVERT: T  177 ASN cc_start: 0.8453 (t0) cc_final: 0.8031 (t0)
REVERT: T  183 ARG cc_start: 0.8221 (pmm-80) cc_final: 0.7663 (ptt180)
REVERT: T  218 GLU cc_start: 0.7937 (tt0) cc_final: 0.7537 (tp30)
REVERT: T  304 ARG cc_start: 0.8314 (mmt90) cc_final: 0.7106 (ttp-170)
REVERT: T  317 ILE cc_start: 0.8760 (mp) cc_final: 0.8487 (mt)
REVERT: A  121 GLN cc_start: 0.7285 (tt0) cc_final: 0.6942 (tt0)
REVERT: E   13 MET cc_start: 0.8253 (tpt) cc_final: 0.7607 (tpt)
REVERT: B   45 LYS cc_start: 0.8334 (pptt) cc_final: 0.7911 (pptt)
  outliers start: 40
  outliers final: 26
  residues processed: 176
  average time/residue: 0.0855
  time to fit residues: 20.8509
Evaluate side-chains
  157 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 129
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  170 THR
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  307 MET
Chi-restraints excluded: chain S residue  368 GLU
Chi-restraints excluded: chain S residue  419 CYS
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue   87 LEU
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  378 THR
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  388 ILE
Chi-restraints excluded: chain T residue  520 ILE
Chi-restraints excluded: chain T residue  533 ASP
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  145 VAL
Chi-restraints excluded: chain E residue   12 GLN
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain B residue   31 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 48 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 82 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 13 optimal weight:    3.9990
   chunk 24 optimal weight:    0.1980
   chunk 95 optimal weight:    6.9990
   chunk 109 optimal weight:    0.5980
   chunk 32 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.125840 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.109204 restraints weight = 15923.893|
|-----------------------------------------------------------------------------|
r_work (start): 0.3437 rms_B_bonded: 2.37
r_work: 0.3334 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3334
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3338
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3338 r_free = 0.3338    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3338
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3568

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   9113  Z= 0.136
  Angle     :  0.647   7.566  12328  Z= 0.323
  Chirality :  0.046   0.215   1380
  Planarity :  0.005   0.063   1562
  Dihedral  :  5.539  39.737   1236
  Min Nonbonded Distance : 2.398

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.34 %
    Favored  : 90.66 %
  Rotamer:
    Outliers :  5.03 %
    Allowed  : 15.71 %
    Favored  : 79.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.53 (0.24), residues: 1113
  helix: -0.80 (0.24), residues: 465
  sheet: -3.23 (0.45), residues: 94
  loop : -2.15 (0.25), residues: 554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG T 541 
 TYR   0.017   0.001   TYR T 461 
 PHE   0.013   0.001   PHE B  40 
 TRP   0.014   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 ( 9112)
  covalent geometry    : angle       0.64654 (12328)
  hydrogen bonds       : bond        0.03392 (  254)
  hydrogen bonds       : angle       4.38852 (  729)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 135
  time to evaluate  : 0.310 
Fit side-chains
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8304 (mm) cc_final: 0.8041 (mt)
REVERT: S  274 GLU cc_start: 0.8534 (tm-30) cc_final: 0.8265 (tm-30)
REVERT: S  359 ASN cc_start: 0.8516 (t0) cc_final: 0.7333 (m-40)
REVERT: S  395 HIS cc_start: 0.8504 (m-70) cc_final: 0.8156 (m-70)
REVERT: T   86 TYR cc_start: 0.8636 (m-80) cc_final: 0.7668 (m-80)
REVERT: T   87 LEU cc_start: 0.8951 (OUTLIER) cc_final: 0.8750 (tt)
REVERT: T  126 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8668 (tt)
REVERT: T  155 ASP cc_start: 0.7692 (t0) cc_final: 0.7215 (t0)
REVERT: T  177 ASN cc_start: 0.8460 (t0) cc_final: 0.8017 (t0)
REVERT: T  183 ARG cc_start: 0.8256 (pmm-80) cc_final: 0.7727 (ptt180)
REVERT: T  218 GLU cc_start: 0.7871 (tt0) cc_final: 0.7537 (tp30)
REVERT: T  304 ARG cc_start: 0.8305 (mmt90) cc_final: 0.7109 (ttp-170)
REVERT: T  317 ILE cc_start: 0.8790 (mp) cc_final: 0.8519 (mt)
REVERT: T  537 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8384 (pp)
REVERT: A  121 GLN cc_start: 0.7299 (tt0) cc_final: 0.6966 (tt0)
REVERT: A  150 ILE cc_start: 0.7036 (OUTLIER) cc_final: 0.6616 (tt)
REVERT: E   13 MET cc_start: 0.8273 (tpt) cc_final: 0.7620 (tpt)
REVERT: E   26 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8643 (mm)
REVERT: B   45 LYS cc_start: 0.8382 (pptt) cc_final: 0.8051 (pptt)
  outliers start: 48
  outliers final: 27
  residues processed: 167
  average time/residue: 0.0944
  time to fit residues: 21.9270
Evaluate side-chains
  159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 127
  time to evaluate  : 0.248 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  170 THR
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  344 LEU
Chi-restraints excluded: chain S residue  419 CYS
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue   48 VAL
Chi-restraints excluded: chain T residue   87 LEU
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  378 THR
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  388 ILE
Chi-restraints excluded: chain T residue  491 ILE
Chi-restraints excluded: chain T residue  520 ILE
Chi-restraints excluded: chain T residue  537 LEU
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  125 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain E residue   12 GLN
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain E residue   41 LEU
Chi-restraints excluded: chain E residue   42 VAL
Chi-restraints excluded: chain E residue   47 MET
Chi-restraints excluded: chain B residue   30 ILE
Chi-restraints excluded: chain B residue   31 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 33 optimal weight:    0.0670
   chunk 47 optimal weight:    9.9990
   chunk 6 optimal weight:    0.1980
   chunk 71 optimal weight:    2.9990
   chunk 98 optimal weight:    6.9990
   chunk 23 optimal weight:    0.0870
   chunk 0 optimal weight:    4.9990
   chunk 41 optimal weight:    2.9990
   chunk 64 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9990
   overall best weight:    0.3898

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

Flipped N/Q/H residues before XYZ refinement:
** S 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S 452 GLN
T 263 HIS
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.127966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.111508 restraints weight = 15634.360|
|-----------------------------------------------------------------------------|
r_work (start): 0.3463 rms_B_bonded: 2.35
r_work: 0.3364 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3380
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3380 r_free = 0.3380    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3380
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9113  Z= 0.104
  Angle     :  0.618   8.863  12328  Z= 0.306
  Chirality :  0.044   0.159   1380
  Planarity :  0.004   0.060   1562
  Dihedral  :  5.281  38.910   1236
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.45 %
    Favored  : 91.55 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 17.38 %
    Favored  : 79.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.20 (0.25), residues: 1113
  helix: -0.49 (0.25), residues: 462
  sheet: -2.86 (0.46), residues: 100
  loop : -2.04 (0.25), residues: 551

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG T 541 
 TYR   0.013   0.001   TYR T 461 
 PHE   0.011   0.001   PHE B  40 
 TRP   0.012   0.001   TRP T 134 
 HIS   0.003   0.000   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 9112)
  covalent geometry    : angle       0.61789 (12328)
  hydrogen bonds       : bond        0.02938 (  254)
  hydrogen bonds       : angle       4.20469 (  729)
  Misc. bond           : bond        0.00000 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 147
  time to evaluate  : 0.338 
Fit side-chains
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8283 (mm) cc_final: 0.8016 (mt)
REVERT: S  107 ASN cc_start: 0.8108 (p0) cc_final: 0.7900 (p0)
REVERT: S  274 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: S  359 ASN cc_start: 0.8473 (t0) cc_final: 0.7366 (m-40)
REVERT: S  395 HIS cc_start: 0.8423 (m-70) cc_final: 0.8103 (m-70)
REVERT: T   86 TYR cc_start: 0.8560 (m-80) cc_final: 0.7664 (m-80)
REVERT: T  126 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8650 (tt)
REVERT: T  128 MET cc_start: 0.8782 (ttm) cc_final: 0.8456 (ttm)
REVERT: T  177 ASN cc_start: 0.8475 (t0) cc_final: 0.8037 (t0)
REVERT: T  183 ARG cc_start: 0.8240 (pmm-80) cc_final: 0.7718 (ptt180)
REVERT: T  218 GLU cc_start: 0.7825 (tt0) cc_final: 0.7519 (tp30)
REVERT: T  317 ILE cc_start: 0.8693 (mp) cc_final: 0.8436 (mt)
REVERT: T  533 ASP cc_start: 0.8418 (OUTLIER) cc_final: 0.8086 (t0)
REVERT: A  121 GLN cc_start: 0.7329 (tt0) cc_final: 0.7103 (tt0)
REVERT: A  150 ILE cc_start: 0.7108 (OUTLIER) cc_final: 0.6783 (tt)
REVERT: E   13 MET cc_start: 0.8262 (tpt) cc_final: 0.7579 (tpt)
  outliers start: 34
  outliers final: 19
  residues processed: 168
  average time/residue: 0.0848
  time to fit residues: 20.2169
Evaluate side-chains
  149 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 127
  time to evaluate  : 0.333 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  330 LEU
Chi-restraints excluded: chain S residue  419 CYS
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  378 THR
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  388 ILE
Chi-restraints excluded: chain T residue  533 ASP
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain E residue   12 GLN
Chi-restraints excluded: chain E residue   22 LEU
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain E residue   41 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 96 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   chunk 22 optimal weight:    3.9990
   chunk 20 optimal weight:    0.5980
   chunk 106 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0670
   chunk 51 optimal weight:    0.9990
   chunk 89 optimal weight:    3.9990
   chunk 6 optimal weight:    0.5980
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6120

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

Flipped N/Q/H residues before XYZ refinement:
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.128188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.111392 restraints weight = 15915.159|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.43
r_work: 0.3359 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3366
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3366 r_free = 0.3366    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3366
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8037
moved from start:          0.3924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9113  Z= 0.115
  Angle     :  0.644  13.152  12328  Z= 0.313
  Chirality :  0.044   0.158   1380
  Planarity :  0.004   0.057   1562
  Dihedral  :  5.172  39.922   1236
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 17.17 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.25), residues: 1113
  helix: -0.34 (0.25), residues: 468
  sheet: -2.79 (0.46), residues: 100
  loop : -1.94 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG T  57 
 TYR   0.019   0.001   TYR E  18 
 PHE   0.012   0.001   PHE B  40 
 TRP   0.012   0.001   TRP T 134 
 HIS   0.003   0.001   HIS T 403 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9112)
  covalent geometry    : angle       0.64418 (12328)
  hydrogen bonds       : bond        0.03036 (  254)
  hydrogen bonds       : angle       4.16232 (  729)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 132
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8303 (mm) cc_final: 0.8050 (mt)
REVERT: S  274 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8295 (tm-30)
REVERT: S  359 ASN cc_start: 0.8470 (t0) cc_final: 0.7339 (m-40)
REVERT: S  395 HIS cc_start: 0.8526 (m-70) cc_final: 0.8178 (m-70)
REVERT: S  465 LYS cc_start: 0.8237 (tmtt) cc_final: 0.7871 (tttm)
REVERT: T   86 TYR cc_start: 0.8647 (m-80) cc_final: 0.7688 (m-80)
REVERT: T  126 LEU cc_start: 0.9013 (OUTLIER) cc_final: 0.8697 (tt)
REVERT: T  177 ASN cc_start: 0.8391 (t0) cc_final: 0.7977 (t0)
REVERT: T  183 ARG cc_start: 0.8270 (pmm-80) cc_final: 0.7728 (ptt180)
REVERT: T  218 GLU cc_start: 0.7823 (tt0) cc_final: 0.7545 (tp30)
REVERT: T  304 ARG cc_start: 0.8258 (mmt90) cc_final: 0.7084 (ttp-170)
REVERT: T  317 ILE cc_start: 0.8720 (mp) cc_final: 0.8454 (mt)
REVERT: T  533 ASP cc_start: 0.8413 (OUTLIER) cc_final: 0.8092 (t0)
REVERT: A  121 GLN cc_start: 0.7348 (tt0) cc_final: 0.7141 (tt0)
REVERT: E   13 MET cc_start: 0.8271 (tpt) cc_final: 0.7524 (tpt)
  outliers start: 38
  outliers final: 25
  residues processed: 161
  average time/residue: 0.0785
  time to fit residues: 18.3701
Evaluate side-chains
  152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 125
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  330 LEU
Chi-restraints excluded: chain S residue  344 LEU
Chi-restraints excluded: chain S residue  419 CYS
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue   66 THR
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  130 ILE
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  203 VAL
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  378 THR
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  388 ILE
Chi-restraints excluded: chain T residue  491 ILE
Chi-restraints excluded: chain T residue  533 ASP
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain E residue   12 GLN
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain E residue   41 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 18 optimal weight:    0.5980
   chunk 88 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 74 optimal weight:    2.9990
   chunk 39 optimal weight:    0.0070
   chunk 6 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0870
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    0.1980
   overall best weight:    0.3576

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

Flipped N/Q/H residues before XYZ refinement:
** S 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3713 r_free = 0.3713 target = 0.129573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.112741 restraints weight = 15884.257|
|-----------------------------------------------------------------------------|
r_work (start): 0.3488 rms_B_bonded: 2.45
r_work: 0.3387 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3387
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.4091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9113  Z= 0.103
  Angle     :  0.643  12.943  12328  Z= 0.309
  Chirality :  0.044   0.161   1380
  Planarity :  0.004   0.055   1562
  Dihedral  :  4.967  38.774   1236
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.00 %
    Favored  : 92.00 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.12 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.84 (0.25), residues: 1113
  helix: -0.15 (0.25), residues: 469
  sheet: -2.76 (0.47), residues: 99
  loop : -1.87 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG T  57 
 TYR   0.009   0.001   TYR T 461 
 PHE   0.009   0.001   PHE B  40 
 TRP   0.011   0.001   TRP T 134 
 HIS   0.002   0.000   HIS A 123 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 9112)
  covalent geometry    : angle       0.64255 (12328)
  hydrogen bonds       : bond        0.02856 (  254)
  hydrogen bonds       : angle       4.12658 (  729)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 0.262 
Fit side-chains
REVERT: S   61 ILE cc_start: 0.8289 (mm) cc_final: 0.8035 (mt)
REVERT: S  274 GLU cc_start: 0.8538 (tm-30) cc_final: 0.8254 (tm-30)
REVERT: S  359 ASN cc_start: 0.8391 (t0) cc_final: 0.7276 (m-40)
REVERT: S  395 HIS cc_start: 0.8435 (m-70) cc_final: 0.8124 (m-70)
REVERT: S  465 LYS cc_start: 0.8103 (tmtt) cc_final: 0.7896 (tttm)
REVERT: T   86 TYR cc_start: 0.8602 (m-80) cc_final: 0.7629 (m-80)
REVERT: T   91 LEU cc_start: 0.8868 (mp) cc_final: 0.8389 (pp)
REVERT: T  126 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8733 (tt)
REVERT: T  177 ASN cc_start: 0.8387 (t0) cc_final: 0.8020 (t0)
REVERT: T  183 ARG cc_start: 0.8254 (pmm-80) cc_final: 0.7755 (ptt180)
REVERT: T  218 GLU cc_start: 0.7895 (tt0) cc_final: 0.7525 (tp30)
REVERT: T  317 ILE cc_start: 0.8648 (mp) cc_final: 0.8401 (mt)
REVERT: A   49 TRP cc_start: 0.7596 (m100) cc_final: 0.7351 (m100)
REVERT: A  121 GLN cc_start: 0.7341 (tt0) cc_final: 0.7120 (tt0)
REVERT: E   13 MET cc_start: 0.8321 (tpt) cc_final: 0.8118 (tpt)
REVERT: E   49 LEU cc_start: 0.5736 (OUTLIER) cc_final: 0.5240 (pp)
  outliers start: 32
  outliers final: 22
  residues processed: 161
  average time/residue: 0.0801
  time to fit residues: 18.5142
Evaluate side-chains
  150 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 126
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  330 LEU
Chi-restraints excluded: chain S residue  344 LEU
Chi-restraints excluded: chain S residue  419 CYS
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue   66 THR
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  130 ILE
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  203 VAL
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  378 THR
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  388 ILE
Chi-restraints excluded: chain T residue  491 ILE
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain E residue   49 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 78 optimal weight:    3.9990
   chunk 12 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 96 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 104 optimal weight:    4.9990
   chunk 56 optimal weight:    3.9990
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126806 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.110375 restraints weight = 15779.651|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.36
r_work: 0.3355 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3355
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3355 r_free = 0.3355    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3355
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8060
moved from start:          0.4102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9113  Z= 0.130
  Angle     :  0.664  12.335  12328  Z= 0.321
  Chirality :  0.046   0.160   1380
  Planarity :  0.004   0.056   1562
  Dihedral  :  5.058  40.508   1236
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.72 %
    Favored  : 91.28 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 18.43 %
    Favored  : 78.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.77 (0.25), residues: 1113
  helix: -0.04 (0.25), residues: 469
  sheet: -2.76 (0.46), residues: 100
  loop : -1.88 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG T  57 
 TYR   0.016   0.001   TYR A  26 
 PHE   0.014   0.001   PHE B  40 
 TRP   0.014   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 9112)
  covalent geometry    : angle       0.66356 (12328)
  hydrogen bonds       : bond        0.03009 (  254)
  hydrogen bonds       : angle       4.24031 (  729)
  Misc. bond           : bond        0.00011 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 124
  time to evaluate  : 0.328 
Fit side-chains
REVERT: S   61 ILE cc_start: 0.8291 (mm) cc_final: 0.8050 (mt)
REVERT: S  274 GLU cc_start: 0.8554 (tm-30) cc_final: 0.8310 (tm-30)
REVERT: S  359 ASN cc_start: 0.8465 (t0) cc_final: 0.7329 (m-40)
REVERT: S  465 LYS cc_start: 0.8196 (tmtt) cc_final: 0.7932 (tttm)
REVERT: T   86 TYR cc_start: 0.8667 (m-80) cc_final: 0.7610 (m-80)
REVERT: T  126 LEU cc_start: 0.9067 (OUTLIER) cc_final: 0.8757 (tt)
REVERT: T  177 ASN cc_start: 0.8411 (t0) cc_final: 0.7989 (t0)
REVERT: T  183 ARG cc_start: 0.8263 (pmm-80) cc_final: 0.7750 (ptt180)
REVERT: T  218 GLU cc_start: 0.7846 (tt0) cc_final: 0.7567 (tp30)
REVERT: T  317 ILE cc_start: 0.8709 (mp) cc_final: 0.8449 (mt)
REVERT: T  533 ASP cc_start: 0.8392 (OUTLIER) cc_final: 0.8056 (t0)
REVERT: T  537 LEU cc_start: 0.8554 (pp) cc_final: 0.8331 (pp)
REVERT: A   49 TRP cc_start: 0.7690 (m100) cc_final: 0.7490 (m100)
REVERT: A  121 GLN cc_start: 0.7383 (tt0) cc_final: 0.7158 (tt0)
REVERT: E   49 LEU cc_start: 0.5875 (OUTLIER) cc_final: 0.5313 (pp)
  outliers start: 29
  outliers final: 23
  residues processed: 148
  average time/residue: 0.0757
  time to fit residues: 16.3551
Evaluate side-chains
  146 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  330 LEU
Chi-restraints excluded: chain S residue  344 LEU
Chi-restraints excluded: chain S residue  419 CYS
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue   48 VAL
Chi-restraints excluded: chain T residue   66 THR
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  130 ILE
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  203 VAL
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  378 THR
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  388 ILE
Chi-restraints excluded: chain T residue  491 ILE
Chi-restraints excluded: chain T residue  533 ASP
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain E residue   49 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 99 optimal weight:    5.9990
   chunk 20 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 96 optimal weight:    7.9990
   chunk 14 optimal weight:    0.4980
   chunk 45 optimal weight:    0.5980
   chunk 81 optimal weight:    0.7980
   chunk 75 optimal weight:    0.4980
   chunk 76 optimal weight:    0.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** S 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.128816 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.111944 restraints weight = 15834.494|
|-----------------------------------------------------------------------------|
r_work (start): 0.3473 rms_B_bonded: 2.44
r_work: 0.3372 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3374
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3374 r_free = 0.3374    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3374
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.4176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9113  Z= 0.108
  Angle     :  0.643   8.697  12328  Z= 0.312
  Chirality :  0.044   0.161   1380
  Planarity :  0.004   0.056   1562
  Dihedral  :  4.959  39.610   1236
  Min Nonbonded Distance : 2.375

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.82 %
    Favored  : 92.18 %
  Rotamer:
    Outliers :  2.83 %
    Allowed  : 18.74 %
    Favored  : 78.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.25), residues: 1113
  helix:  0.12 (0.25), residues: 469
  sheet: -2.70 (0.47), residues: 99
  loop : -1.83 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG T  57 
 TYR   0.019   0.001   TYR E  18 
 PHE   0.013   0.001   PHE B  40 
 TRP   0.013   0.001   TRP T 134 
 HIS   0.002   0.000   HIS B  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 9112)
  covalent geometry    : angle       0.64341 (12328)
  hydrogen bonds       : bond        0.02741 (  254)
  hydrogen bonds       : angle       4.09097 (  729)
  Misc. bond           : bond        0.00001 (    1)

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

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

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2226 Ramachandran restraints generated.
    1113 Oldfield, 0 Emsley, 1113 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.339 
Fit side-chains
REVERT: S   61 ILE cc_start: 0.8291 (mm) cc_final: 0.8046 (mt)
REVERT: S  274 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8259 (tm-30)
REVERT: S  359 ASN cc_start: 0.8404 (t0) cc_final: 0.7272 (m-40)
REVERT: S  465 LYS cc_start: 0.8266 (tmtt) cc_final: 0.8048 (tttm)
REVERT: T   86 TYR cc_start: 0.8647 (m-80) cc_final: 0.7635 (m-80)
REVERT: T  126 LEU cc_start: 0.8997 (OUTLIER) cc_final: 0.8686 (tt)
REVERT: T  177 ASN cc_start: 0.8394 (t0) cc_final: 0.7991 (t0)
REVERT: T  183 ARG cc_start: 0.8266 (pmm-80) cc_final: 0.7745 (ptt180)
REVERT: T  218 GLU cc_start: 0.7898 (tt0) cc_final: 0.7486 (tp30)
REVERT: T  317 ILE cc_start: 0.8682 (mp) cc_final: 0.8434 (mt)
REVERT: E   49 LEU cc_start: 0.5745 (OUTLIER) cc_final: 0.5238 (pp)
  outliers start: 27
  outliers final: 24
  residues processed: 148
  average time/residue: 0.0741
  time to fit residues: 15.8944
Evaluate side-chains
  146 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  278 SER
Chi-restraints excluded: chain S residue  282 LEU
Chi-restraints excluded: chain S residue  330 LEU
Chi-restraints excluded: chain S residue  344 LEU
Chi-restraints excluded: chain S residue  419 CYS
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue   48 VAL
Chi-restraints excluded: chain T residue   66 THR
Chi-restraints excluded: chain T residue  126 LEU
Chi-restraints excluded: chain T residue  130 ILE
Chi-restraints excluded: chain T residue  171 ILE
Chi-restraints excluded: chain T residue  203 VAL
Chi-restraints excluded: chain T residue  327 LEU
Chi-restraints excluded: chain T residue  372 VAL
Chi-restraints excluded: chain T residue  378 THR
Chi-restraints excluded: chain T residue  380 SER
Chi-restraints excluded: chain T residue  491 ILE
Chi-restraints excluded: chain T residue  533 ASP
Chi-restraints excluded: chain A residue   43 VAL
Chi-restraints excluded: chain A residue   47 VAL
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Chi-restraints excluded: chain E residue   49 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 97 optimal weight:    0.2980
   chunk 46 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9980
   chunk 41 optimal weight:    1.9990
   chunk 75 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
S  91 HIS
S 107 ASN
** S 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
T 135 ASN
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.127266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.110855 restraints weight = 15668.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3461 rms_B_bonded: 2.34
r_work: 0.3359 rms_B_bonded: 2.97 restraints_weight: 0.5000
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9113  Z= 0.125
  Angle     :  0.661  11.186  12328  Z= 0.321
  Chirality :  0.045   0.201   1380
  Planarity :  0.004   0.055   1562
  Dihedral  :  5.017  40.432   1236
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.89 %
    Favored  : 91.11 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 18.53 %
    Favored  : 78.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.56 (0.26), residues: 1113
  helix:  0.20 (0.25), residues: 469
  sheet: -2.71 (0.47), residues: 100
  loop : -1.81 (0.26), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG T  57 
 TYR   0.020   0.001   TYR T 461 
 PHE   0.014   0.001   PHE B  40 
 TRP   0.014   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9112)
  covalent geometry    : angle       0.66056 (12328)
  hydrogen bonds       : bond        0.02911 (  254)
  hydrogen bonds       : angle       4.16421 (  729)
  Misc. bond           : bond        0.00008 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1727.34 seconds
wall clock time: 30 minutes 24.40 seconds (1824.40 seconds total)