Starting phenix.real_space_refine
on Thu Feb 13 12:56:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6m4o_30080/02_2025/6m4o_30080.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6m4o_30080/02_2025/6m4o_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6m4o_30080/02_2025/6m4o_30080.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6m4o_30080/02_2025/6m4o_30080.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6m4o_30080/02_2025/6m4o_30080.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6m4o_30080/02_2025/6m4o_30080.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: {'HIS:plan': 1, 'ASP: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: {'TYR:plan': 2, 'ARG:plan': 1, 'TRP:plan': 1}
          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: 5.79, per 1000 atoms: 0.65
  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: 2.31
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.86
  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: 1.90

  Time building geometry restraints manager: 2.58 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:                  0.010
  Normalize map: mean=0, sd=1:             1.460
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     22.510
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.430
-------------------------------------------------------------------------------
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   9112  Z= 0.466
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.028   0.003   TRP T 134 
 HIS   0.010   0.002   HIS T 347 
 PHE   0.030   0.003   PHE S 209 
 TYR   0.034   0.003   TYR S 166 
 ARG   0.011   0.002   ARG S 405 

*********************** 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  : 1.123 
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: 0.7890 (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: 0.8433 (mt)
REVERT: T   82 THR cc_start: 0.9049 (t) cc_final: 0.8631 (p)
REVERT: T   86 TYR cc_start: 0.8506 (m-80) cc_final: 0.7581 (m-80)
REVERT: T  155 ASP cc_start: 0.7079 (t0) cc_final: 0.6842 (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: 0.2621
  time to fit residues: 94.4484
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  : 1.073 
-------------------------------------------------------------------------------
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 92 optimal weight:    2.9990
   chunk 83 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 44 optimal weight:    0.4980
   chunk 86 optimal weight:    2.9990
   chunk 33 optimal weight:    0.9980
   chunk 52 optimal weight:    5.9990
   chunk 64 optimal weight:    0.7980
   chunk 99 optimal weight:    4.9990
   overall best weight:    1.2582

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**
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: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.125973 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.109171 restraints weight = 15690.128|
|-----------------------------------------------------------------------------|
r_work (start): 0.3425 rms_B_bonded: 2.35
r_work: 0.3324 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.3204 rms_B_bonded: 4.99 restraints_weight: 0.2500
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3211
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3211 r_free = 0.3211    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.80   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3210 r_free = 0.3210    target_work(ls_wunit_k1) = 0.094         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3210
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.2527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9112  Z= 0.257
  Angle     :  0.734   9.137  12328  Z= 0.378
  Chirality :  0.048   0.229   1380
  Planarity :  0.006   0.084   1562
  Dihedral  :  6.731  52.047   1238
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.43 %
    Favored  : 90.57 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 13.30 %
    Favored  : 82.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.32 (0.20), residues: 1113
  helix: -2.78 (0.19), residues: 463
  sheet: -3.30 (0.42), residues: 106
  loop : -2.81 (0.23), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP T 134 
 HIS   0.004   0.001   HIS S 395 
 PHE   0.020   0.002   PHE T 449 
 TYR   0.016   0.002   TYR S 166 
 ARG   0.009   0.001   ARG T  57 

*********************** 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
  194 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 157
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
REVERT: S  428 GLN cc_start: 0.8927 (OUTLIER) cc_final: 0.8236 (tm130)
REVERT: T   86 TYR cc_start: 0.8859 (m-80) cc_final: 0.7779 (m-80)
REVERT: T  126 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8775 (tt)
REVERT: T  155 ASP cc_start: 0.7575 (t0) cc_final: 0.7067 (t0)
REVERT: T  177 ASN cc_start: 0.8658 (t0) cc_final: 0.8025 (t0)
REVERT: T  183 ARG cc_start: 0.8344 (pmm-80) cc_final: 0.7406 (ptp90)
REVERT: T  304 ARG cc_start: 0.8483 (mmt90) cc_final: 0.7362 (ttp-110)
  outliers start: 37
  outliers final: 23
  residues processed: 183
  average time/residue: 0.2593
  time to fit residues: 64.3632
Evaluate side-chains
  159 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 134
  time to evaluate  : 0.956 
-------------------------------------------------------------------------------
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  419 CYS
Chi-restraints excluded: chain S residue  428 GLN
Chi-restraints excluded: chain S residue  434 LYS
Chi-restraints excluded: chain T residue   48 VAL
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 2 optimal weight:    0.0020
   chunk 52 optimal weight:    5.9990
   chunk 85 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 64 optimal weight:    3.9990
   chunk 100 optimal weight:    2.9990
   chunk 45 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 93 optimal weight:    7.9990
   chunk 3 optimal weight:    4.9990
   chunk 44 optimal weight:    0.8980
   overall best weight:    0.8590

-------------------------------------------------------------------------------
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**
T 445 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.126764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.109941 restraints weight = 15919.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.3446 rms_B_bonded: 2.37
r_work: 0.3345 rms_B_bonded: 2.95 restraints_weight: 0.5000
r_work (final): 0.3345
-------------------------------------------------------------------------------
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: 0.8072
moved from start:          0.3053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9112  Z= 0.202
  Angle     :  0.669   8.113  12328  Z= 0.336
  Chirality :  0.046   0.192   1380
  Planarity :  0.005   0.070   1562
  Dihedral  :  5.992  36.037   1236
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 14.14 %
    Favored  : 81.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.37 (0.23), residues: 1113
  helix: -1.69 (0.22), residues: 457
  sheet: -3.42 (0.46), residues: 92
  loop : -2.48 (0.24), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP T 134 
 HIS   0.003   0.001   HIS T 263 
 PHE   0.015   0.001   PHE A 124 
 TYR   0.018   0.001   TYR E  18 
 ARG   0.008   0.001   ARG T 541 

*********************** 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
  195 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 153
  time to evaluate  : 1.057 
Fit side-chains
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8283 (mm) cc_final: 0.7993 (mt)
REVERT: S  274 GLU cc_start: 0.8587 (tm-30) cc_final: 0.8366 (tm-30)
REVERT: S  428 GLN cc_start: 0.8935 (OUTLIER) cc_final: 0.8572 (tm-30)
REVERT: S  465 LYS cc_start: 0.8448 (tmtt) cc_final: 0.7964 (tttm)
REVERT: T   86 TYR cc_start: 0.8693 (m-80) cc_final: 0.7670 (m-80)
REVERT: T   87 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8740 (tt)
REVERT: T  126 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8758 (tt)
REVERT: T  155 ASP cc_start: 0.7651 (t0) cc_final: 0.7147 (t0)
REVERT: T  177 ASN cc_start: 0.8501 (t0) cc_final: 0.7821 (t0)
REVERT: T  218 GLU cc_start: 0.7890 (tt0) cc_final: 0.7524 (tp30)
REVERT: T  304 ARG cc_start: 0.8315 (mmt90) cc_final: 0.7131 (ttp-170)
REVERT: T  317 ILE cc_start: 0.8753 (mp) cc_final: 0.8494 (mt)
REVERT: T  505 GLU cc_start: 0.7989 (mp0) cc_final: 0.7770 (mm-30)
REVERT: A  110 TYR cc_start: 0.7034 (t80) cc_final: 0.6822 (t80)
REVERT: E   13 MET cc_start: 0.8359 (tpt) cc_final: 0.7737 (tpt)
  outliers start: 42
  outliers final: 21
  residues processed: 179
  average time/residue: 0.2195
  time to fit residues: 54.1066
Evaluate side-chains
  158 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 134
  time to evaluate  : 1.116 
-------------------------------------------------------------------------------
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  428 GLN
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  533 ASP
Chi-restraints excluded: chain A residue   67 VAL
Chi-restraints excluded: chain A residue  103 THR
Chi-restraints excluded: chain A residue  125 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   42 VAL
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 47 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 79 optimal weight:    1.9990
   chunk 88 optimal weight:    4.9990
   chunk 65 optimal weight:    2.9990
   chunk 98 optimal weight:    0.0370
   chunk 40 optimal weight:    6.9990
   chunk 107 optimal weight:    0.4980
   chunk 106 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 75 optimal weight:    4.9990
   overall best weight:    1.1064

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

Flipped N/Q/H residues before XYZ refinement:
T  47 HIS
T 154 HIS
T 242 ASN
T 282 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.125651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.108710 restraints weight = 15880.290|
|-----------------------------------------------------------------------------|
r_work (start): 0.3423 rms_B_bonded: 2.41
r_work: 0.3322 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3335
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3335 r_free = 0.3335    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 = 0.3335 r_free = 0.3335    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3335
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8080
moved from start:          0.3333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9112  Z= 0.224
  Angle     :  0.667   8.132  12328  Z= 0.333
  Chirality :  0.046   0.245   1380
  Planarity :  0.005   0.063   1562
  Dihedral  :  5.771  39.640   1236
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 15.08 %
    Favored  : 80.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.24), residues: 1113
  helix: -1.10 (0.24), residues: 461
  sheet: -2.99 (0.44), residues: 106
  loop : -2.27 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 
 PHE   0.018   0.001   PHE B  40 
 TYR   0.012   0.001   TYR B  23 
 ARG   0.008   0.001   ARG T 541 

*********************** 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
  191 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 145
  time to evaluate  : 1.111 
Fit side-chains
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8283 (mm) cc_final: 0.8008 (mt)
REVERT: S  274 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8342 (tm-30)
REVERT: S  395 HIS cc_start: 0.8545 (m-70) cc_final: 0.8115 (m-70)
REVERT: T   86 TYR cc_start: 0.8677 (m-80) cc_final: 0.7619 (m-80)
REVERT: T   87 LEU cc_start: 0.8963 (OUTLIER) cc_final: 0.8742 (tt)
REVERT: T  126 LEU cc_start: 0.9038 (OUTLIER) cc_final: 0.8731 (tt)
REVERT: T  155 ASP cc_start: 0.7480 (t0) cc_final: 0.6992 (t0)
REVERT: T  177 ASN cc_start: 0.8467 (t0) cc_final: 0.8002 (t0)
REVERT: T  183 ARG cc_start: 0.8253 (pmm-80) cc_final: 0.7699 (ptt180)
REVERT: T  218 GLU cc_start: 0.7924 (tt0) cc_final: 0.7546 (tp30)
REVERT: T  304 ARG cc_start: 0.8334 (mmt90) cc_final: 0.7152 (ttp-110)
REVERT: T  317 ILE cc_start: 0.8837 (mp) cc_final: 0.8568 (mt)
REVERT: A  110 TYR cc_start: 0.6979 (t80) cc_final: 0.6733 (t80)
REVERT: A  113 THR cc_start: 0.7311 (p) cc_final: 0.7091 (t)
REVERT: A  121 GLN cc_start: 0.7288 (tt0) cc_final: 0.6876 (tt0)
REVERT: A  150 ILE cc_start: 0.7003 (OUTLIER) cc_final: 0.6595 (tt)
REVERT: E   13 MET cc_start: 0.8215 (tpt) cc_final: 0.7602 (tpt)
REVERT: E   26 LEU cc_start: 0.9006 (OUTLIER) cc_final: 0.8653 (mm)
REVERT: B   45 LYS cc_start: 0.8305 (pptt) cc_final: 0.7972 (pptt)
  outliers start: 46
  outliers final: 24
  residues processed: 174
  average time/residue: 0.2145
  time to fit residues: 51.9791
Evaluate side-chains
  161 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 133
  time to evaluate  : 1.182 
-------------------------------------------------------------------------------
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  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  491 ILE
Chi-restraints excluded: chain T residue  520 ILE
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  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   42 VAL
Chi-restraints excluded: chain B residue   30 ILE
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 25 optimal weight:    0.9980
   chunk 35 optimal weight:    4.9990
   chunk 103 optimal weight:    1.9990
   chunk 102 optimal weight:    0.8980
   chunk 98 optimal weight:    1.9990
   chunk 6 optimal weight:    0.2980
   chunk 71 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 9 optimal weight:    2.9990
   chunk 58 optimal weight:    4.9990
   overall best weight:    1.0382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.125351 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.108478 restraints weight = 15836.875|
|-----------------------------------------------------------------------------|
r_work (start): 0.3421 rms_B_bonded: 2.40
r_work: 0.3319 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work (final): 0.3319
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3325
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3325 r_free = 0.3325    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 = 0.3325 r_free = 0.3325    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3325
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.3531

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9112  Z= 0.211
  Angle     :  0.650   7.616  12328  Z= 0.325
  Chirality :  0.046   0.211   1380
  Planarity :  0.005   0.061   1562
  Dihedral  :  5.626  41.242   1236
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 7.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.70 %
    Favored  : 90.30 %
  Rotamer:
    Outliers :  4.82 %
    Allowed  : 15.92 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.48 (0.24), residues: 1113
  helix: -0.71 (0.25), residues: 452
  sheet: -3.23 (0.46), residues: 94
  loop : -2.15 (0.25), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 
 PHE   0.014   0.001   PHE B  40 
 TYR   0.017   0.001   TYR T 461 
 ARG   0.010   0.000   ARG T 541 

*********************** 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
  182 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 136
  time to evaluate  : 1.122 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   60 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7635 (tp)
REVERT: S   61 ILE cc_start: 0.8277 (mm) cc_final: 0.8007 (mt)
REVERT: S  274 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8287 (tm-30)
REVERT: S  359 ASN cc_start: 0.8520 (t0) cc_final: 0.7349 (m-40)
REVERT: S  395 HIS cc_start: 0.8584 (m-70) cc_final: 0.8136 (m-70)
REVERT: T   86 TYR cc_start: 0.8640 (m-80) cc_final: 0.7657 (m-80)
REVERT: T   87 LEU cc_start: 0.8956 (OUTLIER) cc_final: 0.8755 (tt)
REVERT: T  126 LEU cc_start: 0.9018 (OUTLIER) cc_final: 0.8702 (tt)
REVERT: T  155 ASP cc_start: 0.7723 (t0) cc_final: 0.7220 (t0)
REVERT: T  177 ASN cc_start: 0.8462 (t0) cc_final: 0.8010 (t0)
REVERT: T  183 ARG cc_start: 0.8290 (pmm-80) cc_final: 0.7753 (ptt180)
REVERT: T  218 GLU cc_start: 0.7895 (tt0) cc_final: 0.7554 (tp30)
REVERT: T  317 ILE cc_start: 0.8852 (mp) cc_final: 0.8585 (mt)
REVERT: T  537 LEU cc_start: 0.8615 (OUTLIER) cc_final: 0.8399 (pp)
REVERT: A  121 GLN cc_start: 0.7333 (tt0) cc_final: 0.7004 (tt0)
REVERT: E   13 MET cc_start: 0.8227 (tpt) cc_final: 0.7663 (tpt)
REVERT: E   26 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8627 (mm)
  outliers start: 46
  outliers final: 28
  residues processed: 167
  average time/residue: 0.2176
  time to fit residues: 50.1732
Evaluate side-chains
  158 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 1.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue   60 LEU
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   66 THR
Chi-restraints excluded: chain T residue   87 LEU
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  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 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   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 107 optimal weight:    0.8980
   chunk 71 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9980
   chunk 39 optimal weight:    0.6980
   chunk 15 optimal weight:    4.9990
   chunk 76 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0870
   chunk 5 optimal weight:    0.7980
   chunk 20 optimal weight:    0.2980
   chunk 62 optimal weight:    0.9980
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
S 428 GLN
S 452 GLN
** 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 = 0.3686 r_free = 0.3686 target = 0.127445 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.110647 restraints weight = 15812.537|
|-----------------------------------------------------------------------------|
r_work (start): 0.3442 rms_B_bonded: 2.39
r_work: 0.3341 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work (final): 0.3341
-------------------------------------------------------------------------------
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: 0.8055
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9112  Z= 0.160
  Angle     :  0.631   8.809  12328  Z= 0.313
  Chirality :  0.044   0.161   1380
  Planarity :  0.005   0.062   1562
  Dihedral  :  5.366  40.234   1236
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.98 %
    Favored  : 91.02 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 17.59 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.25), residues: 1113
  helix: -0.46 (0.25), residues: 464
  sheet: -3.13 (0.47), residues: 94
  loop : -2.02 (0.25), residues: 555

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 
 PHE   0.012   0.001   PHE B  40 
 TYR   0.018   0.001   TYR E  18 
 ARG   0.007   0.000   ARG T 541 

*********************** 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
  178 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 139
  time to evaluate  : 0.991 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8309 (mm) cc_final: 0.8035 (mt)
REVERT: S  107 ASN cc_start: 0.8287 (p0) cc_final: 0.8073 (p0)
REVERT: S  274 GLU cc_start: 0.8567 (tm-30) cc_final: 0.8294 (tm-30)
REVERT: S  359 ASN cc_start: 0.8525 (t0) cc_final: 0.7368 (m-40)
REVERT: S  395 HIS cc_start: 0.8517 (m-70) cc_final: 0.8150 (m-70)
REVERT: T   86 TYR cc_start: 0.8584 (m-80) cc_final: 0.7603 (m-80)
REVERT: T  126 LEU cc_start: 0.8995 (OUTLIER) cc_final: 0.8643 (tt)
REVERT: T  177 ASN cc_start: 0.8467 (t0) cc_final: 0.8021 (t0)
REVERT: T  183 ARG cc_start: 0.8270 (pmm-80) cc_final: 0.7752 (ptt180)
REVERT: T  218 GLU cc_start: 0.7883 (tt0) cc_final: 0.7564 (tp30)
REVERT: T  317 ILE cc_start: 0.8774 (mp) cc_final: 0.8514 (mt)
REVERT: A  121 GLN cc_start: 0.7355 (tt0) cc_final: 0.7138 (tt0)
REVERT: E   13 MET cc_start: 0.8221 (tpt) cc_final: 0.7597 (tpt)
  outliers start: 39
  outliers final: 25
  residues processed: 168
  average time/residue: 0.2138
  time to fit residues: 50.1799
Evaluate side-chains
  148 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 122
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
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  344 LEU
Chi-restraints excluded: chain S residue  428 GLN
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  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  533 ASP
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   22 LEU
Chi-restraints excluded: chain E residue   26 LEU
Chi-restraints excluded: chain E residue   32 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 108 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 105 optimal weight:    4.9990
   chunk 64 optimal weight:    4.9990
   chunk 46 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 95 optimal weight:    0.9990
   chunk 65 optimal weight:    0.9990
   chunk 55 optimal weight:    0.0050
   overall best weight:    0.7396

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.126981 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.110021 restraints weight = 15993.927|
|-----------------------------------------------------------------------------|
r_work (start): 0.3445 rms_B_bonded: 2.41
r_work: 0.3342 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3345
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3345 r_free = 0.3345    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 = 0.3345 r_free = 0.3345    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3345
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.3859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9112  Z= 0.177
  Angle     :  0.650  13.080  12328  Z= 0.317
  Chirality :  0.045   0.160   1380
  Planarity :  0.005   0.061   1562
  Dihedral  :  5.279  40.814   1236
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.12 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.25), residues: 1113
  helix: -0.29 (0.25), residues: 461
  sheet: -3.10 (0.47), residues: 94
  loop : -1.92 (0.26), residues: 558

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 
 PHE   0.013   0.001   PHE B  40 
 TYR   0.012   0.001   TYR T 461 
 ARG   0.006   0.000   ARG T  57 

*********************** 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
  160 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 124
  time to evaluate  : 1.019 
Fit side-chains
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8305 (mm) cc_final: 0.8055 (mt)
REVERT: S  274 GLU cc_start: 0.8572 (tm-30) cc_final: 0.8299 (tm-30)
REVERT: S  359 ASN cc_start: 0.8523 (t0) cc_final: 0.7361 (m-40)
REVERT: S  395 HIS cc_start: 0.8535 (m-70) cc_final: 0.8188 (m-70)
REVERT: S  428 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.8572 (tt0)
REVERT: T   86 TYR cc_start: 0.8646 (m-80) cc_final: 0.7565 (m-80)
REVERT: T  126 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8694 (tt)
REVERT: T  177 ASN cc_start: 0.8474 (t0) cc_final: 0.8026 (t0)
REVERT: T  183 ARG cc_start: 0.8275 (pmm-80) cc_final: 0.7738 (ptt180)
REVERT: T  218 GLU cc_start: 0.7883 (tt0) cc_final: 0.7601 (tp30)
REVERT: T  317 ILE cc_start: 0.8775 (mp) cc_final: 0.8509 (mt)
REVERT: E   12 GLN cc_start: 0.6831 (OUTLIER) cc_final: 0.6522 (mp10)
REVERT: E   13 MET cc_start: 0.8232 (tpt) cc_final: 0.7609 (tpt)
  outliers start: 36
  outliers final: 28
  residues processed: 151
  average time/residue: 0.2096
  time to fit residues: 44.4959
Evaluate side-chains
  151 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 120
  time to evaluate  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  210 LYS
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  428 GLN
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  250 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   47 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   47 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 102 optimal weight:    0.0670
   chunk 14 optimal weight:    2.9990
   chunk 96 optimal weight:    6.9990
   chunk 84 optimal weight:    0.8980
   chunk 83 optimal weight:    1.9990
   chunk 28 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   chunk 104 optimal weight:    2.9990
   chunk 61 optimal weight:    0.4980
   chunk 99 optimal weight:    6.9990
   chunk 86 optimal weight:    0.7980
   overall best weight:    0.8520

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.126524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.109540 restraints weight = 16129.590|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 2.46
r_work: 0.3327 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.3327
-------------------------------------------------------------------------------
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: 0.8068
moved from start:          0.3919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9112  Z= 0.189
  Angle     :  0.657  12.936  12328  Z= 0.320
  Chirality :  0.045   0.160   1380
  Planarity :  0.004   0.059   1562
  Dihedral  :  5.258  41.068   1236
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.52 %
    Favored  : 90.48 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.43 %
    Favored  : 77.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.92 (0.25), residues: 1113
  helix: -0.18 (0.25), residues: 462
  sheet: -3.10 (0.47), residues: 94
  loop : -1.89 (0.26), residues: 557

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 
 PHE   0.012   0.001   PHE B  40 
 TYR   0.011   0.001   TYR T 461 
 ARG   0.006   0.000   ARG T  57 

*********************** 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
  162 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 126
  time to evaluate  : 1.169 
Fit side-chains
   revert: symmetry clash
REVERT: S   61 ILE cc_start: 0.8257 (mm) cc_final: 0.8057 (mt)
REVERT: S  274 GLU cc_start: 0.8580 (tm-30) cc_final: 0.8305 (tm-30)
REVERT: S  359 ASN cc_start: 0.8498 (t0) cc_final: 0.7340 (m-40)
REVERT: S  395 HIS cc_start: 0.8544 (m-70) cc_final: 0.8176 (m-70)
REVERT: S  465 LYS cc_start: 0.8142 (tmtt) cc_final: 0.7811 (tttm)
REVERT: T   86 TYR cc_start: 0.8647 (m-80) cc_final: 0.7629 (m-80)
REVERT: T  126 LEU cc_start: 0.9029 (OUTLIER) cc_final: 0.8722 (tt)
REVERT: T  177 ASN cc_start: 0.8496 (t0) cc_final: 0.8025 (t0)
REVERT: T  183 ARG cc_start: 0.8278 (pmm-80) cc_final: 0.7773 (ptt180)
REVERT: T  218 GLU cc_start: 0.7879 (tt0) cc_final: 0.7589 (tp30)
REVERT: T  317 ILE cc_start: 0.8780 (mp) cc_final: 0.8525 (mt)
REVERT: E   12 GLN cc_start: 0.6826 (OUTLIER) cc_final: 0.6532 (mp10)
REVERT: E   13 MET cc_start: 0.8195 (tpt) cc_final: 0.7573 (tpt)
  outliers start: 36
  outliers final: 29
  residues processed: 151
  average time/residue: 0.2041
  time to fit residues: 43.7433
Evaluate side-chains
  152 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 1.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  210 LYS
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  386 VAL
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   22 ILE
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  125 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   47 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0010
   chunk 58 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 34 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 70 optimal weight:    2.9990
   chunk 8 optimal weight:    0.2980
   chunk 109 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 42 optimal weight:    0.0980
   overall best weight:    0.3586

-------------------------------------------------------------------------------
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
T 263 HIS
** 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 = 0.3716 r_free = 0.3716 target = 0.129733 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.112775 restraints weight = 15670.310|
|-----------------------------------------------------------------------------|
r_work (start): 0.3481 rms_B_bonded: 2.44
r_work: 0.3380 rms_B_bonded: 3.02 restraints_weight: 0.5000
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3387
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3387 r_free = 0.3387    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 = 0.3387 r_free = 0.3387    target_work(ls_wunit_k1) = 0.106         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3387
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8011
moved from start:          0.4172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9112  Z= 0.144
  Angle     :  0.631  12.085  12328  Z= 0.307
  Chirality :  0.044   0.164   1380
  Planarity :  0.004   0.057   1562
  Dihedral  :  4.948  39.014   1236
  Min Nonbonded Distance : 2.135

Molprobity Statistics.
  All-atom Clashscore : 7.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 19.16 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.25), residues: 1113
  helix:  0.07 (0.25), residues: 456
  sheet: -2.87 (0.46), residues: 101
  loop : -1.88 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP T 134 
 HIS   0.003   0.000   HIS B  24 
 PHE   0.012   0.001   PHE B  40 
 TYR   0.011   0.001   TYR A  26 
 ARG   0.004   0.000   ARG T  57 

*********************** 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
  168 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 1.098 
Fit side-chains
REVERT: S  274 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8289 (tm-30)
REVERT: S  359 ASN cc_start: 0.8421 (t0) cc_final: 0.7276 (m-40)
REVERT: S  395 HIS cc_start: 0.8347 (m-70) cc_final: 0.8017 (m-70)
REVERT: T   86 TYR cc_start: 0.8561 (m-80) cc_final: 0.7663 (m-80)
REVERT: T  126 LEU cc_start: 0.8953 (OUTLIER) cc_final: 0.8648 (tt)
REVERT: T  177 ASN cc_start: 0.8418 (t0) cc_final: 0.7736 (t0)
REVERT: T  183 ARG cc_start: 0.8279 (pmm-80) cc_final: 0.7779 (ptt180)
REVERT: T  218 GLU cc_start: 0.7963 (tt0) cc_final: 0.7560 (tp30)
REVERT: T  533 ASP cc_start: 0.8361 (OUTLIER) cc_final: 0.8046 (t0)
REVERT: A   49 TRP cc_start: 0.7654 (m100) cc_final: 0.7416 (m100)
REVERT: E   13 MET cc_start: 0.8143 (tpt) cc_final: 0.7486 (tpt)
  outliers start: 32
  outliers final: 22
  residues processed: 161
  average time/residue: 0.2139
  time to fit residues: 48.3960
Evaluate side-chains
  146 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 122
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  107 ASN
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  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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 61 optimal weight:    0.0980
   chunk 64 optimal weight:    0.6980
   chunk 67 optimal weight:    1.9990
   chunk 74 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 0 optimal weight:    4.9990
   chunk 18 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 76 optimal weight:    1.9990
   overall best weight:    0.6582

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

Flipped N/Q/H residues before XYZ refinement:
S 107 ASN
S 428 GLN
** 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 = 0.3691 r_free = 0.3691 target = 0.127724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.111037 restraints weight = 15643.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3472 rms_B_bonded: 2.36
r_work: 0.3373 rms_B_bonded: 2.94 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3379
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3379 r_free = 0.3379    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 = 0.3379 r_free = 0.3379    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3379
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9112  Z= 0.168
  Angle     :  0.650   9.066  12328  Z= 0.317
  Chirality :  0.045   0.190   1380
  Planarity :  0.005   0.058   1562
  Dihedral  :  4.994  39.718   1236
  Min Nonbonded Distance : 2.172

Molprobity Statistics.
  All-atom Clashscore : 7.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.09 %
    Favored  : 91.91 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 19.58 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.63 (0.25), residues: 1113
  helix:  0.15 (0.25), residues: 465
  sheet: -2.87 (0.46), residues: 101
  loop : -1.83 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP T 134 
 HIS   0.003   0.001   HIS B  24 
 PHE   0.012   0.001   PHE B  40 
 TYR   0.013   0.001   TYR T 362 
 ARG   0.006   0.000   ARG T  57 

********************** 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
  151 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 1.035 
Fit side-chains
REVERT: S  274 GLU cc_start: 0.8588 (tm-30) cc_final: 0.8314 (tm-30)
REVERT: S  359 ASN cc_start: 0.8427 (t0) cc_final: 0.7306 (m-40)
REVERT: S  395 HIS cc_start: 0.8374 (m-70) cc_final: 0.8039 (m-70)
REVERT: T   86 TYR cc_start: 0.8597 (m-80) cc_final: 0.7594 (m-80)
REVERT: T  126 LEU cc_start: 0.8989 (OUTLIER) cc_final: 0.8672 (tt)
REVERT: T  177 ASN cc_start: 0.8438 (t0) cc_final: 0.8009 (t0)
REVERT: T  183 ARG cc_start: 0.8266 (pmm-80) cc_final: 0.7750 (ptt180)
REVERT: T  218 GLU cc_start: 0.7878 (tt0) cc_final: 0.7638 (tp30)
REVERT: T  533 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.7999 (t0)
REVERT: A   49 TRP cc_start: 0.7683 (m100) cc_final: 0.7472 (m100)
  outliers start: 29
  outliers final: 23
  residues processed: 145
  average time/residue: 0.2076
  time to fit residues: 42.3974
Evaluate side-chains
  142 residues out of total 963 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 117
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain S residue  184 ILE
Chi-restraints excluded: chain S residue  210 LYS
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  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   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   47 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 110
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 2 optimal weight:    0.0370
   chunk 56 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 16 optimal weight:    0.5980
   chunk 23 optimal weight:    0.0980
   chunk 52 optimal weight:    1.9990
   chunk 81 optimal weight:    0.7980
   overall best weight:    0.4858

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

Flipped N/Q/H residues before XYZ refinement:
T 242 ASN
** A  65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.129335 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.112914 restraints weight = 15868.223|
|-----------------------------------------------------------------------------|
r_work (start): 0.3476 rms_B_bonded: 2.37
r_work: 0.3373 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3384
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3384 r_free = 0.3384    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 = 0.3384 r_free = 0.3384    target_work(ls_wunit_k1) = 0.105         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3384
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8033
moved from start:          0.4306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9112  Z= 0.158
  Angle     :  0.656  13.004  12328  Z= 0.318
  Chirality :  0.044   0.168   1380
  Planarity :  0.004   0.056   1562
  Dihedral  :  4.958  39.282   1236
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 20.31 %
    Favored  : 77.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.59 (0.25), residues: 1113
  helix:  0.22 (0.25), residues: 465
  sheet: -2.82 (0.46), residues: 101
  loop : -1.84 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP T 134 
 HIS   0.003   0.000   HIS B  24 
 PHE   0.013   0.001   PHE B  40 
 TYR   0.022   0.001   TYR T 461 
 ARG   0.005   0.000   ARG T  57 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3959.77 seconds
wall clock time: 71 minutes 15.48 seconds (4275.48 seconds total)