Starting phenix.real_space_refine
on Thu May  1 05:44:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uo5_42428/05_2025/8uo5_42428_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uo5_42428/05_2025/8uo5_42428.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.27
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uo5_42428/05_2025/8uo5_42428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uo5_42428/05_2025/8uo5_42428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uo5_42428/05_2025/8uo5_42428_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uo5_42428/05_2025/8uo5_42428_neut.cif"
  }
  resolution = 3.27
  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=  -0.001 sd=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      1      7.16       5
     Zn      1      6.06       5
     S      57      5.16       5
     C    6470      2.51       5
     N    1752      2.21       5
     O    1935      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 10216
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4478
          Classifications: {'peptide': 575}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 25, 'TRANS': 549}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3004
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3004
          Classifications: {'peptide': 385}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 11, 'TRANS': 373}
          Chain breaks: 4
          Unresolved chain link angles: 4
          Unresolved non-hydrogen bonds: 169
          Unresolved non-hydrogen angles: 214
          Unresolved non-hydrogen dihedrals: 138
          Unresolved non-hydrogen chiralities: 11
          Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6}
          Unresolved non-hydrogen planarities: 104
    Chain: "C"
      Number of atoms: 2404
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 300, 2404
          Classifications: {'peptide': 300}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 286}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 26
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 21
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "D"
      Number of atoms: 328
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 43, 328
          Classifications: {'peptide': 43}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'TRANS': 42}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 20
          Unresolved non-hydrogen dihedrals: 14
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 9
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' FE': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 7.16, per 1000 atoms: 0.70
  Number of scatterers: 10216
  At special positions: 0
  Unit cell: (109.725, 112.2, 103.125, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     Fe      1     26.01
     S      57     16.00
     O    1935      8.00
     N    1752      7.00
     C    6470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.87
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2494

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 10 sheets defined
      53.7% alpha, 11.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 12 through 20
      removed outlier: 4.128A  pdb=" N   ILE A  17 " --> pdb=" O   ILE A  13 " (cutoff:3.500A)
      removed outlier: 6.313A  pdb=" N   ASP A  18 " --> pdb=" O   ALA A  14 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   GLU A  19 " --> pdb=" O   VAL A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 33
    Processing helix  chain 'A' and resid 35 through 42
      removed outlier: 4.245A  pdb=" N   LEU A  40 " --> pdb=" O   SER A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 74
    Processing helix  chain 'A' and resid 75 through 80
      removed outlier: 4.219A  pdb=" N   LEU A  79 " --> pdb=" O   THR A  75 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 86
    Processing helix  chain 'A' and resid 89 through 98
    Processing helix  chain 'A' and resid 101 through 117
      removed outlier: 3.841A  pdb=" N   HIS A 117 " --> pdb=" O   ARG A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 127
    Processing helix  chain 'A' and resid 127 through 138
    Processing helix  chain 'A' and resid 140 through 148
      removed outlier: 3.712A  pdb=" N   ARG A 144 " --> pdb=" O   TRP A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 3.738A  pdb=" N   CYS A 154 " --> pdb=" O   LEU A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 158
      No H-bonds generated for 'chain 'A' and resid 156 through 158'
    Processing helix  chain 'A' and resid 159 through 175
      removed outlier: 3.924A  pdb=" N   ARG A 167 " --> pdb=" O   LYS A 163 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   GLN A 168 " --> pdb=" O   ALA A 164 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 196
      removed outlier: 4.085A  pdb=" N   GLY A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 5.115A  pdb=" N   GLU A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
      removed outlier: 3.626A  pdb=" N   LYS A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
      removed outlier: 3.989A  pdb=" N   VAL A 195 " --> pdb=" O   GLU A 191 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 213
      removed outlier: 4.071A  pdb=" N   ILE A 206 " --> pdb=" O   LYS A 202 " (cutoff:3.500A)
      Proline residue:  A 207  - end of helix
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 223 through 235
      removed outlier: 3.733A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 244
      removed outlier: 4.264A  pdb=" N   GLU A 241 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 5.500A  pdb=" N   ALA A 242 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 253
      removed outlier: 3.638A  pdb=" N   GLN A 250 " --> pdb=" O   PRO A 246 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 256 through 266
    Processing helix  chain 'A' and resid 266 through 292
      Proline residue:  A 276  - end of helix
      removed outlier: 4.888A  pdb=" N   VAL A 284 " --> pdb=" O   LYS A 280 " (cutoff:3.500A)
      Proline residue:  A 285  - end of helix
    Processing helix  chain 'A' and resid 295 through 305
    Processing helix  chain 'A' and resid 305 through 313
    Processing helix  chain 'A' and resid 314 through 326
      removed outlier: 4.502A  pdb=" N   GLU A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
      removed outlier: 5.135A  pdb=" N   ASN A 320 " --> pdb=" O   ASP A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 326 through 335
      removed outlier: 3.882A  pdb=" N   GLU A 332 " --> pdb=" O   PRO A 328 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   SER A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 350
      removed outlier: 3.646A  pdb=" N   VAL A 348 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   MET A 350 " --> pdb=" O   ALA A 346 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 352 through 357
    Processing helix  chain 'A' and resid 359 through 364
    Processing helix  chain 'A' and resid 364 through 373
    Processing helix  chain 'A' and resid 377 through 386
      removed outlier: 4.095A  pdb=" N   ARG A 381 " --> pdb=" O   CYS A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
    Processing helix  chain 'A' and resid 397 through 412
      removed outlier: 4.297A  pdb=" N   GLN A 402 " --> pdb=" O   ARG A 398 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   SER A 403 " --> pdb=" O   GLN A 399 " (cutoff:3.500A)
      Proline residue:  A 406  - end of helix
    Processing helix  chain 'A' and resid 416 through 443
      removed outlier: 3.770A  pdb=" N   ARG A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   TYR A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A 427 " --> pdb=" O   ILE A 423 " (cutoff:3.500A)
      Proline residue:  A 428  - end of helix
      removed outlier: 6.244A  pdb=" N   VAL A 436 " --> pdb=" O   GLY A 432 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   GLU A 437 " --> pdb=" O   GLN A 433 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   PHE A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 452
    Processing helix  chain 'A' and resid 455 through 474
    Processing helix  chain 'A' and resid 474 through 482
      removed outlier: 4.052A  pdb=" N   ALA A 478 " --> pdb=" O   GLY A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 487
    Processing helix  chain 'A' and resid 488 through 492
    Processing helix  chain 'A' and resid 494 through 520
      removed outlier: 3.505A  pdb=" N   ARG A 498 " --> pdb=" O   ASN A 494 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLU A 510 " --> pdb=" O   ASN A 506 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL A 511 " --> pdb=" O   VAL A 507 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   GLN A 514 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
      removed outlier: 8.508A  pdb=" N   ASP A 515 " --> pdb=" O   VAL A 511 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ILE A 516 " --> pdb=" O   CYS A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 522 through 528
      removed outlier: 3.825A  pdb=" N   LEU A 526 " --> pdb=" O   LEU A 522 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   MET A 528 " --> pdb=" O   THR A 524 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 531
      No H-bonds generated for 'chain 'A' and resid 529 through 531'
    Processing helix  chain 'A' and resid 533 through 548
    Processing helix  chain 'A' and resid 549 through 551
      No H-bonds generated for 'chain 'A' and resid 549 through 551'
    Processing helix  chain 'A' and resid 552 through 559
    Processing helix  chain 'A' and resid 559 through 568
    Processing helix  chain 'A' and resid 572 through 586
    Processing helix  chain 'B' and resid 129 through 136
      removed outlier: 3.553A  pdb=" N   TYR B 134 " --> pdb=" O   ARG B 130 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 149 through 157
      removed outlier: 3.560A  pdb=" N   ARG B 153 " --> pdb=" O   VAL B 149 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL B 154 " --> pdb=" O   THR B 150 " (cutoff:3.500A)
      Proline residue:  B 155  - end of helix
      No H-bonds generated for 'chain 'B' and resid 149 through 157'
    Processing helix  chain 'B' and resid 221 through 225
    Processing helix  chain 'B' and resid 281 through 286
    Processing helix  chain 'B' and resid 334 through 339
    Processing helix  chain 'B' and resid 340 through 344
    Processing helix  chain 'C' and resid 5 through 19
      removed outlier: 3.849A  pdb=" N   GLU C  15 " --> pdb=" O   ASP C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 34
      removed outlier: 3.663A  pdb=" N   LYS C  34 " --> pdb=" O   SER C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 73
    Processing helix  chain 'C' and resid 92 through 107
      removed outlier: 3.659A  pdb=" N   LEU C  99 " --> pdb=" O   GLU C  95 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 121 through 127
    Processing helix  chain 'C' and resid 128 through 137
    Processing helix  chain 'C' and resid 139 through 149
      removed outlier: 4.173A  pdb=" N   TRP C 143 " --> pdb=" O   ASN C 139 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   LEU C 149 " --> pdb=" O   TYR C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 183
    Processing helix  chain 'C' and resid 193 through 201
      removed outlier: 3.645A  pdb=" N   ASP C 197 " --> pdb=" O   GLY C 193 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   LEU C 199 " --> pdb=" O   MET C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 231
    Processing helix  chain 'D' and resid 7 through 22
      removed outlier: 3.970A  pdb=" N   VAL D  11 " --> pdb=" O   ALA D   7 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   SER D  12 " --> pdb=" O   HIS D   8 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   ARG D  22 " --> pdb=" O   ILE D  18 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 29 through 39
      removed outlier: 3.532A  pdb=" N   VAL D  39 " --> pdb=" O   LEU D  35 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 34 through 36
      removed outlier: 6.669A  pdb=" N   VAL B  52 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
      removed outlier: 4.665A  pdb=" N   THR B  76 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   ILE B  54 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 98 through 101
      removed outlier: 3.608A  pdb=" N   LYS B  98 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 7.446A  pdb=" N   ILE B 119 " --> pdb=" O   ILE B 171 " (cutoff:3.500A)
      removed outlier: 5.393A  pdb=" N   ILE B 171 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 6.799A  pdb=" N   LEU B 121 " --> pdb=" O   ARG B 169 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 180 through 185
      removed outlier: 6.591A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 232 through 234
    Processing sheet with id=AA5, first strand: chain 'B' and resid 288 through 293
      removed outlier: 3.546A  pdb=" N   ASP B 290 " --> pdb=" O   ARG B 303 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   SER B 307 " --> pdb=" O   ASP B 304 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 348 through 350
      removed outlier: 3.587A  pdb=" N   PHE B 365 " --> pdb=" O   SER B 361 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 421 through 424
      removed outlier: 4.060A  pdb=" N   HIS B 421 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 111 through 116
      removed outlier: 6.322A  pdb=" N   TYR C  80 " --> pdb=" O   THR C 112 " (cutoff:3.500A)
      removed outlier: 7.991A  pdb=" N   LEU C 114 " --> pdb=" O   TYR C  80 " (cutoff:3.500A)
      removed outlier: 6.749A  pdb=" N   PHE C  82 " --> pdb=" O   LEU C 114 " (cutoff:3.500A)
      removed outlier: 6.790A  pdb=" N   GLY C 116 " --> pdb=" O   PHE C  82 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   GLY C  84 " --> pdb=" O   GLY C 116 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   THR C  53 " --> pdb=" O   LEU C  81 " (cutoff:3.500A)
      removed outlier: 7.673A  pdb=" N   MET C  83 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   CYS C  55 " --> pdb=" O   MET C  83 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA C 273 " --> pdb=" O   PHE C 289 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 164 through 165
      removed outlier: 7.341A  pdb=" N   PHE C 164 " --> pdb=" O   SER C 238 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   VAL C 237 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
      removed outlier: 7.563A  pdb=" N   ILE C 259 " --> pdb=" O   VAL C 237 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   ARG C 239 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'C' and resid 202 through 203
      removed outlier: 6.457A  pdb=" N   ASP C 202 " --> pdb=" O   PHE C 220 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1

    459 hydrogen bonds defined for protein.
    1329 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: 3.43

  Time building geometry restraints manager: 3.34 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 3141
        1.33 -     1.46: 1334
        1.46 -     1.59: 5852
        1.59 -     1.71: 0
        1.71 -     1.84: 82
  Bond restraints: 10409
  Sorted by residual:
  bond pdb=" CG  HIS C 118 "
       pdb=" ND1 HIS C 118 "
    ideal  model  delta    sigma   weight residual
    1.378  1.422 -0.044 1.10e-02 8.26e+03 1.62e+01
  bond pdb=" CA  SER C 238 "
       pdb=" CB  SER C 238 "
    ideal  model  delta    sigma   weight residual
    1.529  1.469  0.060 1.53e-02 4.27e+03 1.52e+01
  bond pdb=" N   ILE A  59 "
       pdb=" CA  ILE A  59 "
    ideal  model  delta    sigma   weight residual
    1.455  1.494 -0.038 1.04e-02 9.25e+03 1.36e+01
  bond pdb=" CA  SER B 289 "
       pdb=" CB  SER B 289 "
    ideal  model  delta    sigma   weight residual
    1.529  1.471  0.058 1.74e-02 3.30e+03 1.11e+01
  bond pdb=" CD  GLU D   6 "
       pdb=" OE2 GLU D   6 "
    ideal  model  delta    sigma   weight residual
    1.249  1.312 -0.063 1.90e-02 2.77e+03 1.10e+01
  ... (remaining 10404 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.76: 12187
        1.76 -     3.52: 1695
        3.52 -     5.28: 181
        5.28 -     7.05: 43
        7.05 -     8.81: 5
  Bond angle restraints: 14111
  Sorted by residual:
  angle pdb=" CA  PHE D   3 "
        pdb=" CB  PHE D   3 "
        pdb=" CG  PHE D   3 "
      ideal   model   delta    sigma   weight residual
     113.80  120.98   -7.18 1.00e+00 1.00e+00 5.15e+01
  angle pdb=" N   PRO B 155 "
        pdb=" CA  PRO B 155 "
        pdb=" CB  PRO B 155 "
      ideal   model   delta    sigma   weight residual
     103.25  110.74   -7.49 1.05e+00 9.07e-01 5.08e+01
  angle pdb=" N   PRO B 159 "
        pdb=" CA  PRO B 159 "
        pdb=" CB  PRO B 159 "
      ideal   model   delta    sigma   weight residual
     103.25  109.95   -6.70 1.05e+00 9.07e-01 4.07e+01
  angle pdb=" N   PRO B 131 "
        pdb=" CA  PRO B 131 "
        pdb=" CB  PRO B 131 "
      ideal   model   delta    sigma   weight residual
     103.44  110.26   -6.82 1.12e+00 7.97e-01 3.71e+01
  angle pdb=" N   PRO B 146 "
        pdb=" CA  PRO B 146 "
        pdb=" CB  PRO B 146 "
      ideal   model   delta    sigma   weight residual
     103.25  109.12   -5.87 1.05e+00 9.07e-01 3.13e+01
  ... (remaining 14106 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.53: 5706
       17.53 -    35.05: 448
       35.05 -    52.58: 103
       52.58 -    70.11: 22
       70.11 -    87.64: 15
  Dihedral angle restraints: 6294
    sinusoidal: 2466
      harmonic: 3828
  Sorted by residual:
  dihedral pdb=" CA  LYS D   4 "
           pdb=" C   LYS D   4 "
           pdb=" N   LEU D   5 "
           pdb=" CA  LEU D   5 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.35  -22.65     0      5.00e+00 4.00e-02 2.05e+01
  dihedral pdb=" CA  VAL C  87 "
           pdb=" C   VAL C  87 "
           pdb=" N   ASP C  88 "
           pdb=" CA  ASP C  88 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.18  -20.82     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  GLY C  84 "
           pdb=" C   GLY C  84 "
           pdb=" N   ASP C  85 "
           pdb=" CA  ASP C  85 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.04   18.96     0      5.00e+00 4.00e-02 1.44e+01
  ... (remaining 6291 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 1081
       0.067 -    0.134: 459
       0.134 -    0.202: 59
       0.202 -    0.269: 13
       0.269 -    0.336: 4
  Chirality restraints: 1616
  Sorted by residual:
  chirality pdb=" CB  ILE A 505 "
            pdb=" CA  ILE A 505 "
            pdb=" CG1 ILE A 505 "
            pdb=" CG2 ILE A 505 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.31    0.34 2.00e-01 2.50e+01 2.82e+00
  chirality pdb=" CB  VAL B 243 "
            pdb=" CA  VAL B 243 "
            pdb=" CG1 VAL B 243 "
            pdb=" CG2 VAL B 243 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.33   -0.30 2.00e-01 2.50e+01 2.21e+00
  chirality pdb=" CA  VAL C 189 "
            pdb=" N   VAL C 189 "
            pdb=" C   VAL C 189 "
            pdb=" CB  VAL C 189 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.72   -0.28 2.00e-01 2.50e+01 1.94e+00
  ... (remaining 1613 not shown)

  Planarity restraints: 1816
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE D   3 "   -0.051 2.00e-02 2.50e+03   5.87e-02 6.03e+01
        pdb=" CG  PHE D   3 "    0.116 2.00e-02 2.50e+03
        pdb=" CD1 PHE D   3 "   -0.067 2.00e-02 2.50e+03
        pdb=" CD2 PHE D   3 "    0.017 2.00e-02 2.50e+03
        pdb=" CE1 PHE D   3 "    0.039 2.00e-02 2.50e+03
        pdb=" CE2 PHE D   3 "   -0.040 2.00e-02 2.50e+03
        pdb=" CZ  PHE D   3 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 337 "    0.070 2.00e-02 2.50e+03   3.73e-02 2.78e+01
        pdb=" CG  TYR B 337 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 337 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 337 "   -0.046 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 337 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 337 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 337 "    0.033 2.00e-02 2.50e+03
        pdb=" OH  TYR B 337 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 305 "    0.039 2.00e-02 2.50e+03   2.21e-02 9.81e+00
        pdb=" CG  TYR B 305 "   -0.030 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 305 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 305 "   -0.027 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 305 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 305 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 305 "    0.021 2.00e-02 2.50e+03
        pdb=" OH  TYR B 305 "    0.006 2.00e-02 2.50e+03
  ... (remaining 1813 not shown)

  Histogram of nonbonded interaction distances:
        2.05 -     2.62: 168
        2.62 -     3.19: 10013
        3.19 -     3.76: 16553
        3.76 -     4.33: 23228
        4.33 -     4.90: 37284
  Nonbonded interactions: 87246
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN C 117 "
            pdb="ZN    ZN C 402 "
     model   vdw
     2.047 2.230
  nonbonded pdb=" O   HIS C 241 "
            pdb="FE    FE C 401 "
     model   vdw
     2.206 2.260
  nonbonded pdb=" OD2 ASP C  85 "
            pdb="FE    FE C 401 "
     model   vdw
     2.237 2.260
  nonbonded pdb=" OE1 GLU B 321 "
            pdb=" OH  TYR B 323 "
     model   vdw
     2.238 3.040
  nonbonded pdb="FE    FE C 401 "
            pdb="ZN    ZN C 402 "
     model   vdw
     2.283 1.450
  ... (remaining 87241 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.450
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.480
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     27.870
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7596
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      :  0.011   0.063  10409  Z= 0.791
  Angle     :  1.267   8.808  14111  Z= 0.839
  Chirality :  0.070   0.336   1616
  Planarity :  0.008   0.074   1816
  Dihedral  : 14.356  87.635   3800
  Min Nonbonded Distance : 2.047

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  4.05 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  0.81 %
    Allowed  :  6.87 %
    Favored  : 92.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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: -2.58 (0.21), residues: 1283
  helix: -1.67 (0.19), residues: 577
  sheet: -0.94 (0.36), residues: 186
  loop : -1.88 (0.27), residues: 520

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.007   TRP B 311 
 HIS   0.016   0.003   HIS B 425 
 PHE   0.116   0.006   PHE D   3 
 TYR   0.070   0.007   TYR B 337 
 ARG   0.030   0.002   ARG A 105 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18493 (  459)
  hydrogen bonds       : angle       7.97380 ( 1329)
  covalent geometry    : bond        0.01131 (10409)
  covalent geometry    : angle       1.26735 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 145
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   24 ASP cc_start: 0.9270 (t0) cc_final: 0.9040 (t0)
REVERT: A  128 PHE cc_start: 0.8755 (t80) cc_final: 0.8351 (t80)
REVERT: A  353 SER cc_start: 0.9218 (m) cc_final: 0.8993 (p)
REVERT: A  569 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8230 (tp-100)
REVERT: B  262 CYS cc_start: 0.8302 (m) cc_final: 0.7905 (p)
REVERT: B  301 MET cc_start: 0.7701 (ttp) cc_final: 0.7422 (ttp)
REVERT: B  368 MET cc_start: 0.7803 (tmm) cc_final: 0.6563 (tmm)
REVERT: B  370 ASP cc_start: 0.8239 (t0) cc_final: 0.7532 (m-30)
REVERT: C   16 GLN cc_start: 0.8952 (tm-30) cc_final: 0.8727 (tm-30)
REVERT: C   47 GLU cc_start: 0.9336 (mt-10) cc_final: 0.8906 (tp30)
REVERT: C   77 ASP cc_start: 0.8742 (OUTLIER) cc_final: 0.8424 (m-30)
REVERT: C  220 PHE cc_start: 0.5977 (p90) cc_final: 0.4124 (p90)
REVERT: C  229 ASN cc_start: 0.7987 (m-40) cc_final: 0.7695 (m-40)
  outliers start: 9
  outliers final: 3
  residues processed: 154
  average time/residue: 0.2481
  time to fit residues: 52.6699
Evaluate side-chains
  113 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 109
  time to evaluate  : 1.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain C residue   77 ASP
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain D residue   39 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.8980
   chunk 52 optimal weight:    0.6980
   chunk 101 optimal weight:    0.0870
   chunk 39 optimal weight:    0.9980
   chunk 61 optimal weight:    2.9990
   chunk 75 optimal weight:    0.7980
   chunk 117 optimal weight:    0.8980
   overall best weight:    0.6558

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

Flipped N/Q/H residues before XYZ refinement:
A 339 GLN
A 360 ASN
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 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 = 0.4095 r_free = 0.4095 target = 0.102218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.088569 restraints weight = 39825.677|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 4.27
r_work: 0.3691 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3691
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7150
moved from start:          0.1662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10409  Z= 0.139
  Angle     :  0.652  10.871  14111  Z= 0.345
  Chirality :  0.044   0.178   1616
  Planarity :  0.005   0.045   1816
  Dihedral  :  5.742  43.618   1408
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 8.57
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.20 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.39 %
    Favored  : 86.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    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: -1.27 (0.23), residues: 1283
  helix: -0.41 (0.21), residues: 595
  sheet: -1.05 (0.36), residues: 196
  loop : -1.08 (0.29), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 311 
 HIS   0.005   0.001   HIS B 421 
 PHE   0.026   0.002   PHE A 538 
 TYR   0.016   0.002   TYR A  11 
 ARG   0.005   0.001   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04558 (  459)
  hydrogen bonds       : angle       5.95556 ( 1329)
  covalent geometry    : bond        0.00295 (10409)
  covalent geometry    : angle       0.65181 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 137
  time to evaluate  : 1.172 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6672 (OUTLIER) cc_final: 0.6426 (mm)
REVERT: A  124 LEU cc_start: 0.8964 (tp) cc_final: 0.8614 (mt)
REVERT: A  353 SER cc_start: 0.8751 (m) cc_final: 0.8397 (p)
REVERT: A  521 MET cc_start: 0.7382 (tmm) cc_final: 0.6962 (tmm)
REVERT: A  569 GLN cc_start: 0.7833 (mm-40) cc_final: 0.7384 (tp-100)
REVERT: B  114 THR cc_start: 0.7949 (m) cc_final: 0.7588 (t)
REVERT: B  252 ARG cc_start: 0.8081 (mtt90) cc_final: 0.7791 (mtt90)
REVERT: B  301 MET cc_start: 0.7222 (ttp) cc_final: 0.6865 (ttp)
REVERT: B  368 MET cc_start: 0.8220 (tmm) cc_final: 0.6896 (tmm)
REVERT: B  370 ASP cc_start: 0.6821 (t0) cc_final: 0.6051 (m-30)
REVERT: C   10 LEU cc_start: 0.8531 (tp) cc_final: 0.8307 (tp)
REVERT: C   21 LYS cc_start: 0.8484 (mtmm) cc_final: 0.8271 (ptpp)
REVERT: C   83 MET cc_start: 0.7432 (mpp) cc_final: 0.6105 (mpp)
REVERT: C  229 ASN cc_start: 0.7105 (m-40) cc_final: 0.6762 (m-40)
REVERT: C  255 ASN cc_start: 0.7448 (m-40) cc_final: 0.6538 (t0)
REVERT: C  276 MET cc_start: 0.8443 (ptt) cc_final: 0.8142 (ptt)
  outliers start: 16
  outliers final: 11
  residues processed: 147
  average time/residue: 0.2295
  time to fit residues: 47.9245
Evaluate side-chains
  117 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 105
  time to evaluate  : 1.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  279 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 52 optimal weight:    0.1980
   chunk 82 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 39 optimal weight:    4.9990
   chunk 28 optimal weight:    8.9990
   chunk 59 optimal weight:    0.5980
   chunk 62 optimal weight:    1.9990
   chunk 86 optimal weight:    0.0370
   chunk 51 optimal weight:    0.9980
   chunk 12 optimal weight:    8.9990
   overall best weight:    0.5058

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 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 = 0.4098 r_free = 0.4098 target = 0.102422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.088962 restraints weight = 39714.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 4.29
r_work: 0.3699 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.2103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10409  Z= 0.121
  Angle     :  0.599  10.298  14111  Z= 0.316
  Chirality :  0.042   0.190   1616
  Planarity :  0.004   0.046   1816
  Dihedral  :  5.433  44.702   1405
  Min Nonbonded Distance : 2.101

Molprobity Statistics.
  All-atom Clashscore : 8.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.27 %
    Favored  : 96.65 %
  Rotamer:
    Outliers :  2.62 %
    Allowed  : 13.11 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.24), residues: 1283
  helix: -0.12 (0.21), residues: 599
  sheet: -0.93 (0.37), residues: 188
  loop : -0.91 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 311 
 HIS   0.011   0.001   HIS B 176 
 PHE   0.035   0.002   PHE C 150 
 TYR   0.018   0.001   TYR A  11 
 ARG   0.004   0.000   ARG D  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04037 (  459)
  hydrogen bonds       : angle       5.54126 ( 1329)
  covalent geometry    : bond        0.00256 (10409)
  covalent geometry    : angle       0.59880 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 117
  time to evaluate  : 1.149 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6702 (OUTLIER) cc_final: 0.6469 (mm)
REVERT: A  124 LEU cc_start: 0.8909 (tp) cc_final: 0.8633 (mt)
REVERT: A  350 MET cc_start: 0.8758 (pmm) cc_final: 0.8017 (pmm)
REVERT: A  353 SER cc_start: 0.8767 (m) cc_final: 0.8411 (p)
REVERT: A  473 PHE cc_start: 0.7167 (m-80) cc_final: 0.6485 (t80)
REVERT: A  521 MET cc_start: 0.7442 (tmm) cc_final: 0.7188 (tmm)
REVERT: A  569 GLN cc_start: 0.7736 (mm-40) cc_final: 0.7301 (tp-100)
REVERT: B  114 THR cc_start: 0.7879 (m) cc_final: 0.7567 (t)
REVERT: B  252 ARG cc_start: 0.8025 (mtt90) cc_final: 0.7640 (mtt90)
REVERT: B  301 MET cc_start: 0.7298 (ttp) cc_final: 0.6934 (ttp)
REVERT: B  368 MET cc_start: 0.8180 (tmm) cc_final: 0.7091 (tmm)
REVERT: B  370 ASP cc_start: 0.6958 (t0) cc_final: 0.6348 (m-30)
REVERT: C   10 LEU cc_start: 0.8529 (tp) cc_final: 0.8312 (tp)
REVERT: C   21 LYS cc_start: 0.8447 (mtmm) cc_final: 0.8064 (ptpp)
REVERT: C   83 MET cc_start: 0.7454 (mpp) cc_final: 0.6114 (mpp)
REVERT: C  229 ASN cc_start: 0.7096 (m-40) cc_final: 0.6807 (m-40)
REVERT: C  255 ASN cc_start: 0.7357 (m-40) cc_final: 0.6478 (t0)
REVERT: D   41 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6458 (mtp-110)
  outliers start: 29
  outliers final: 18
  residues processed: 135
  average time/residue: 0.2081
  time to fit residues: 41.0015
Evaluate side-chains
  121 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 101
  time to evaluate  : 1.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   63 HIS
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain D residue   41 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 24 optimal weight:    3.9990
   chunk 91 optimal weight:    0.7980
   chunk 122 optimal weight:    2.9990
   chunk 105 optimal weight:    6.9990
   chunk 52 optimal weight:    3.9990
   chunk 61 optimal weight:    0.3980
   chunk 79 optimal weight:    0.7980
   chunk 121 optimal weight:    5.9990
   chunk 19 optimal weight:    0.4980
   chunk 7 optimal weight:    9.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
B 179 HIS
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  59 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 = 0.4089 r_free = 0.4089 target = 0.101901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.088153 restraints weight = 40351.782|
|-----------------------------------------------------------------------------|
r_work (start): 0.3799 rms_B_bonded: 4.32
r_work: 0.3683 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7182
moved from start:          0.2252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10409  Z= 0.139
  Angle     :  0.592   9.706  14111  Z= 0.311
  Chirality :  0.042   0.157   1616
  Planarity :  0.004   0.048   1816
  Dihedral  :  5.349  43.907   1405
  Min Nonbonded Distance : 2.024

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.36 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 14.01 %
    Favored  : 82.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.84 (0.24), residues: 1283
  helix: -0.02 (0.21), residues: 599
  sheet: -0.79 (0.37), residues: 193
  loop : -0.96 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 311 
 HIS   0.009   0.001   HIS B 176 
 PHE   0.038   0.002   PHE C 150 
 TYR   0.017   0.001   TYR A  11 
 ARG   0.003   0.000   ARG D  25 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03839 (  459)
  hydrogen bonds       : angle       5.34705 ( 1329)
  covalent geometry    : bond        0.00307 (10409)
  covalent geometry    : angle       0.59219 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 111
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6801 (OUTLIER) cc_final: 0.6466 (mm)
REVERT: A  110 GLU cc_start: 0.8684 (pp20) cc_final: 0.8202 (pp20)
REVERT: A  124 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8614 (mt)
REVERT: A  350 MET cc_start: 0.8661 (pmm) cc_final: 0.8071 (pmm)
REVERT: A  353 SER cc_start: 0.8755 (m) cc_final: 0.8422 (p)
REVERT: A  398 ARG cc_start: 0.9097 (ptp90) cc_final: 0.8885 (ptp90)
REVERT: A  569 GLN cc_start: 0.7697 (mm-40) cc_final: 0.7264 (tp-100)
REVERT: B  114 THR cc_start: 0.7890 (m) cc_final: 0.7652 (t)
REVERT: B  301 MET cc_start: 0.7425 (ttp) cc_final: 0.7131 (ttp)
REVERT: B  368 MET cc_start: 0.8271 (tmm) cc_final: 0.7633 (tmm)
REVERT: B  370 ASP cc_start: 0.7003 (t0) cc_final: 0.6386 (m-30)
REVERT: C   10 LEU cc_start: 0.8486 (tp) cc_final: 0.8261 (tp)
REVERT: C   21 LYS cc_start: 0.8381 (mtmm) cc_final: 0.8136 (ptpp)
REVERT: C   83 MET cc_start: 0.7442 (mpp) cc_final: 0.6063 (mpp)
REVERT: C  111 ILE cc_start: 0.6021 (OUTLIER) cc_final: 0.5688 (mp)
REVERT: C  229 ASN cc_start: 0.7195 (m-40) cc_final: 0.6911 (m-40)
REVERT: C  255 ASN cc_start: 0.7538 (m-40) cc_final: 0.6643 (t0)
REVERT: D   41 ARG cc_start: 0.6786 (OUTLIER) cc_final: 0.6493 (mtp-110)
  outliers start: 35
  outliers final: 22
  residues processed: 134
  average time/residue: 0.2321
  time to fit residues: 44.5524
Evaluate side-chains
  130 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 1.249 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  124 LEU
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  334 VAL
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   63 HIS
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain C residue  111 ILE
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 69 optimal weight:    9.9990
   chunk 48 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 101 optimal weight:    2.9990
   chunk 59 optimal weight:    0.5980
   chunk 105 optimal weight:    0.9980
   chunk 93 optimal weight:    0.6980
   chunk 95 optimal weight:    3.9990
   chunk 4 optimal weight:    8.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
A  26 GLN
A 360 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.4087 r_free = 0.4087 target = 0.101787 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.087986 restraints weight = 40536.904|
|-----------------------------------------------------------------------------|
r_work (start): 0.3797 rms_B_bonded: 4.34
r_work (final): 0.3797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.2444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10409  Z= 0.135
  Angle     :  0.595   9.183  14111  Z= 0.310
  Chirality :  0.042   0.184   1616
  Planarity :  0.004   0.041   1816
  Dihedral  :  5.325  46.638   1405
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.52 %
    Favored  : 95.40 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.38 %
    Favored  : 82.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.24), residues: 1283
  helix:  0.11 (0.21), residues: 594
  sheet: -0.72 (0.38), residues: 193
  loop : -1.03 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 311 
 HIS   0.006   0.001   HIS B 176 
 PHE   0.035   0.002   PHE C 150 
 TYR   0.028   0.001   TYR A  11 
 ARG   0.004   0.000   ARG C  49 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03655 (  459)
  hydrogen bonds       : angle       5.21831 ( 1329)
  covalent geometry    : bond        0.00298 (10409)
  covalent geometry    : angle       0.59538 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 108
  time to evaluate  : 1.243 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6738 (OUTLIER) cc_final: 0.6412 (mm)
REVERT: A  110 GLU cc_start: 0.8654 (pp20) cc_final: 0.8177 (pp20)
REVERT: A  353 SER cc_start: 0.8604 (m) cc_final: 0.8260 (p)
REVERT: A  398 ARG cc_start: 0.9039 (ptp90) cc_final: 0.8816 (ptp90)
REVERT: A  521 MET cc_start: 0.7345 (tmm) cc_final: 0.6904 (tmm)
REVERT: A  569 GLN cc_start: 0.7637 (mm-40) cc_final: 0.7263 (tp-100)
REVERT: B  114 THR cc_start: 0.7887 (m) cc_final: 0.7629 (t)
REVERT: B  301 MET cc_start: 0.6918 (ttp) cc_final: 0.6619 (ttp)
REVERT: B  368 MET cc_start: 0.7615 (tmm) cc_final: 0.7016 (tmm)
REVERT: B  370 ASP cc_start: 0.6894 (t0) cc_final: 0.6305 (m-30)
REVERT: C   10 LEU cc_start: 0.8509 (tp) cc_final: 0.8298 (tp)
REVERT: C   21 LYS cc_start: 0.8355 (mtmm) cc_final: 0.8086 (ptpp)
REVERT: C   83 MET cc_start: 0.7363 (mpp) cc_final: 0.5937 (mpp)
REVERT: C  229 ASN cc_start: 0.7054 (m-40) cc_final: 0.6706 (m-40)
REVERT: C  255 ASN cc_start: 0.7387 (m-40) cc_final: 0.6537 (t0)
REVERT: D   41 ARG cc_start: 0.6668 (OUTLIER) cc_final: 0.6402 (mtp-110)
  outliers start: 36
  outliers final: 26
  residues processed: 133
  average time/residue: 0.2228
  time to fit residues: 43.9063
Evaluate side-chains
  124 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 1.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  311 TRP
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   63 HIS
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 86 optimal weight:    1.9990
   chunk 6 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 97 optimal weight:    8.9990
   chunk 68 optimal weight:   30.0000
   chunk 109 optimal weight:    0.9990
   chunk 45 optimal weight:    6.9990
   chunk 103 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.099888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.086211 restraints weight = 40757.286|
|-----------------------------------------------------------------------------|
r_work (start): 0.3761 rms_B_bonded: 4.29
r_work: 0.3645 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7257
moved from start:          0.2509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  10409  Z= 0.182
  Angle     :  0.626   9.539  14111  Z= 0.327
  Chirality :  0.043   0.166   1616
  Planarity :  0.005   0.052   1816
  Dihedral  :  5.462  47.757   1405
  Min Nonbonded Distance : 1.980

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.77 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 14.56 %
    Favored  : 82.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.24), residues: 1283
  helix:  0.04 (0.21), residues: 592
  sheet: -0.68 (0.39), residues: 188
  loop : -1.14 (0.28), residues: 503

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP B 311 
 HIS   0.006   0.001   HIS B 176 
 PHE   0.034   0.002   PHE C 150 
 TYR   0.028   0.002   TYR A  11 
 ARG   0.004   0.000   ARG B 257 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03839 (  459)
  hydrogen bonds       : angle       5.29029 ( 1329)
  covalent geometry    : bond        0.00405 (10409)
  covalent geometry    : angle       0.62606 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 103
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6752 (OUTLIER) cc_final: 0.6382 (mm)
REVERT: A  110 GLU cc_start: 0.8924 (pp20) cc_final: 0.8523 (pp20)
REVERT: A  350 MET cc_start: 0.8257 (pmm) cc_final: 0.7287 (pmm)
REVERT: A  353 SER cc_start: 0.8738 (m) cc_final: 0.8466 (p)
REVERT: A  521 MET cc_start: 0.7362 (tmm) cc_final: 0.6856 (tmm)
REVERT: A  569 GLN cc_start: 0.7749 (mm-40) cc_final: 0.7332 (tp-100)
REVERT: B  301 MET cc_start: 0.7519 (ttp) cc_final: 0.7257 (ttp)
REVERT: B  368 MET cc_start: 0.8261 (tmm) cc_final: 0.7676 (tmm)
REVERT: B  370 ASP cc_start: 0.7049 (t0) cc_final: 0.6395 (m-30)
REVERT: C   10 LEU cc_start: 0.8603 (tp) cc_final: 0.8385 (tp)
REVERT: C   21 LYS cc_start: 0.8339 (mtmm) cc_final: 0.8052 (ptpp)
REVERT: C   83 MET cc_start: 0.7404 (mpp) cc_final: 0.5917 (mpp)
REVERT: C  255 ASN cc_start: 0.7685 (m-40) cc_final: 0.6640 (t0)
REVERT: C  290 ASP cc_start: 0.8400 (OUTLIER) cc_final: 0.7569 (p0)
REVERT: D   41 ARG cc_start: 0.6920 (OUTLIER) cc_final: 0.6414 (mtp-110)
  outliers start: 37
  outliers final: 29
  residues processed: 129
  average time/residue: 0.2186
  time to fit residues: 40.6824
Evaluate side-chains
  131 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 99
  time to evaluate  : 1.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  143 SER
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  311 TRP
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   63 HIS
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain C residue  290 ASP
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 35 optimal weight:    0.9990
   chunk 4 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   chunk 116 optimal weight:    2.9990
   chunk 95 optimal weight:    5.9990
   chunk 32 optimal weight:    0.9990
   chunk 101 optimal weight:    3.9990
   chunk 28 optimal weight:    1.9990
   chunk 20 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    1.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.4072 r_free = 0.4072 target = 0.100715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.087093 restraints weight = 41228.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 4.33
r_work: 0.3662 rms_B_bonded: 4.93 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7230
moved from start:          0.2654

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10409  Z= 0.144
  Angle     :  0.612  10.445  14111  Z= 0.318
  Chirality :  0.042   0.163   1616
  Planarity :  0.005   0.056   1816
  Dihedral  :  5.389  48.769   1405
  Min Nonbonded Distance : 2.049

Molprobity Statistics.
  All-atom Clashscore : 11.94
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.30 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.37 %
    Favored  : 80.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.79 (0.24), residues: 1283
  helix:  0.11 (0.21), residues: 596
  sheet: -0.60 (0.39), residues: 188
  loop : -1.14 (0.29), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 311 
 HIS   0.004   0.001   HIS B 176 
 PHE   0.032   0.002   PHE C 150 
 TYR   0.024   0.001   TYR A  11 
 ARG   0.013   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03573 (  459)
  hydrogen bonds       : angle       5.21134 ( 1329)
  covalent geometry    : bond        0.00321 (10409)
  covalent geometry    : angle       0.61229 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 108
  time to evaluate  : 1.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6475 (mm)
REVERT: A  110 GLU cc_start: 0.8988 (pp20) cc_final: 0.8566 (pp20)
REVERT: A  160 SER cc_start: 0.8635 (m) cc_final: 0.8281 (t)
REVERT: A  350 MET cc_start: 0.8192 (pmm) cc_final: 0.7265 (pmm)
REVERT: A  353 SER cc_start: 0.8705 (m) cc_final: 0.8365 (p)
REVERT: A  521 MET cc_start: 0.7521 (tmm) cc_final: 0.7236 (tmm)
REVERT: B  114 THR cc_start: 0.7975 (m) cc_final: 0.7685 (t)
REVERT: B  301 MET cc_start: 0.7540 (ttp) cc_final: 0.7271 (ttp)
REVERT: B  309 LYS cc_start: 0.7086 (OUTLIER) cc_final: 0.6825 (mmtm)
REVERT: B  368 MET cc_start: 0.8284 (tmm) cc_final: 0.7747 (tmm)
REVERT: B  370 ASP cc_start: 0.6977 (t0) cc_final: 0.6340 (m-30)
REVERT: C    8 LYS cc_start: 0.8621 (mmmt) cc_final: 0.8157 (mmtt)
REVERT: C   10 LEU cc_start: 0.8607 (tp) cc_final: 0.8394 (tp)
REVERT: C   21 LYS cc_start: 0.8349 (mtmm) cc_final: 0.8039 (ptpp)
REVERT: C   83 MET cc_start: 0.7399 (mpp) cc_final: 0.5877 (mpp)
REVERT: C  185 ARG cc_start: 0.7873 (OUTLIER) cc_final: 0.7339 (ptp90)
REVERT: C  225 SER cc_start: 0.6566 (m) cc_final: 0.6117 (t)
REVERT: C  229 ASN cc_start: 0.7060 (m-40) cc_final: 0.6097 (m-40)
REVERT: C  255 ASN cc_start: 0.7601 (m-40) cc_final: 0.7179 (t0)
REVERT: D   41 ARG cc_start: 0.6854 (OUTLIER) cc_final: 0.6456 (mtp-110)
  outliers start: 41
  outliers final: 33
  residues processed: 133
  average time/residue: 0.2164
  time to fit residues: 41.8916
Evaluate side-chains
  139 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 102
  time to evaluate  : 1.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  228 CYS
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  309 LYS
Chi-restraints excluded: chain B residue  311 TRP
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   63 HIS
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  185 ARG
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 34 optimal weight:    0.5980
   chunk 119 optimal weight:    2.9990
   chunk 83 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 41 optimal weight:    2.9990
   chunk 52 optimal weight:    6.9990
   chunk 84 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    4.9990
   chunk 109 optimal weight:    0.7980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.4083 r_free = 0.4083 target = 0.101341 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.087709 restraints weight = 41001.753|
|-----------------------------------------------------------------------------|
r_work (start): 0.3791 rms_B_bonded: 4.34
r_work: 0.3677 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7207
moved from start:          0.2777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10409  Z= 0.127
  Angle     :  0.606  10.474  14111  Z= 0.313
  Chirality :  0.042   0.160   1616
  Planarity :  0.004   0.044   1816
  Dihedral  :  5.284  48.741   1405
  Min Nonbonded Distance : 2.076

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.30 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 15.82 %
    Favored  : 80.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.72 (0.24), residues: 1283
  helix:  0.18 (0.22), residues: 599
  sheet: -0.51 (0.40), residues: 188
  loop : -1.17 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 311 
 HIS   0.003   0.001   HIS B 176 
 PHE   0.029   0.002   PHE C 150 
 TYR   0.023   0.001   TYR A  11 
 ARG   0.010   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  459)
  hydrogen bonds       : angle       5.13134 ( 1329)
  covalent geometry    : bond        0.00283 (10409)
  covalent geometry    : angle       0.60582 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 109
  time to evaluate  : 1.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6897 (OUTLIER) cc_final: 0.6493 (mm)
REVERT: A  110 GLU cc_start: 0.9038 (pp20) cc_final: 0.8628 (pp20)
REVERT: A  160 SER cc_start: 0.8610 (m) cc_final: 0.8255 (t)
REVERT: A  350 MET cc_start: 0.8168 (pmm) cc_final: 0.7293 (pmm)
REVERT: A  353 SER cc_start: 0.8699 (m) cc_final: 0.8361 (p)
REVERT: A  521 MET cc_start: 0.7539 (tmm) cc_final: 0.7264 (tmm)
REVERT: B  114 THR cc_start: 0.7899 (m) cc_final: 0.7634 (t)
REVERT: B  301 MET cc_start: 0.7512 (ttp) cc_final: 0.7245 (ttp)
REVERT: B  309 LYS cc_start: 0.7094 (OUTLIER) cc_final: 0.6646 (mmtm)
REVERT: B  368 MET cc_start: 0.8284 (tmm) cc_final: 0.7765 (tmm)
REVERT: B  370 ASP cc_start: 0.6954 (t0) cc_final: 0.6327 (m-30)
REVERT: C    8 LYS cc_start: 0.8713 (mmmt) cc_final: 0.8429 (mmtt)
REVERT: C   10 LEU cc_start: 0.8601 (tp) cc_final: 0.8389 (tp)
REVERT: C  185 ARG cc_start: 0.7861 (OUTLIER) cc_final: 0.7353 (ptp90)
REVERT: C  229 ASN cc_start: 0.7058 (m-40) cc_final: 0.6741 (m-40)
REVERT: C  255 ASN cc_start: 0.7549 (m-40) cc_final: 0.6688 (t0)
REVERT: D   41 ARG cc_start: 0.6755 (OUTLIER) cc_final: 0.6373 (mtp-110)
  outliers start: 41
  outliers final: 34
  residues processed: 138
  average time/residue: 0.2335
  time to fit residues: 46.7479
Evaluate side-chains
  138 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 100
  time to evaluate  : 1.255 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  540 VAL
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  309 LYS
Chi-restraints excluded: chain B residue  311 TRP
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   53 THR
Chi-restraints excluded: chain C residue   63 HIS
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  185 ARG
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue    6 GLU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 9 optimal weight:    0.8980
   chunk 80 optimal weight:   20.0000
   chunk 82 optimal weight:    2.9990
   chunk 83 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 127 optimal weight:    0.7980
   chunk 27 optimal weight:    0.0170
   chunk 45 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 107 optimal weight:    6.9990
   chunk 73 optimal weight:    0.8980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.4088 r_free = 0.4088 target = 0.101632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.088409 restraints weight = 39993.150|
|-----------------------------------------------------------------------------|
r_work (start): 0.3810 rms_B_bonded: 4.24
r_work: 0.3690 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10409  Z= 0.120
  Angle     :  0.618  10.707  14111  Z= 0.318
  Chirality :  0.042   0.216   1616
  Planarity :  0.004   0.042   1816
  Dihedral  :  5.220  48.842   1405
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.22 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 16.64 %
    Favored  : 80.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.61 (0.24), residues: 1283
  helix:  0.29 (0.22), residues: 597
  sheet: -0.45 (0.40), residues: 190
  loop : -1.13 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.044   0.002   TRP A 450 
 HIS   0.003   0.001   HIS B 176 
 PHE   0.027   0.001   PHE C 150 
 TYR   0.022   0.001   TYR A  11 
 ARG   0.009   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03368 (  459)
  hydrogen bonds       : angle       5.09119 ( 1329)
  covalent geometry    : bond        0.00268 (10409)
  covalent geometry    : angle       0.61797 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 108
  time to evaluate  : 1.146 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6890 (OUTLIER) cc_final: 0.6557 (mm)
REVERT: A  110 GLU cc_start: 0.9049 (pp20) cc_final: 0.8656 (pp20)
REVERT: A  160 SER cc_start: 0.8609 (m) cc_final: 0.8266 (t)
REVERT: A  350 MET cc_start: 0.8210 (pmm) cc_final: 0.7350 (pmm)
REVERT: A  353 SER cc_start: 0.8671 (m) cc_final: 0.8328 (p)
REVERT: A  473 PHE cc_start: 0.7686 (m-80) cc_final: 0.7182 (t80)
REVERT: A  521 MET cc_start: 0.7566 (tmm) cc_final: 0.7294 (tmm)
REVERT: B  114 THR cc_start: 0.7907 (m) cc_final: 0.7643 (t)
REVERT: B  301 MET cc_start: 0.7458 (ttp) cc_final: 0.7194 (ttp)
REVERT: B  368 MET cc_start: 0.8255 (tmm) cc_final: 0.7787 (tmm)
REVERT: B  370 ASP cc_start: 0.6918 (t0) cc_final: 0.6303 (m-30)
REVERT: C    8 LYS cc_start: 0.8719 (mmmt) cc_final: 0.8488 (mmtt)
REVERT: C   10 LEU cc_start: 0.8637 (tp) cc_final: 0.8432 (tp)
REVERT: C   83 MET cc_start: 0.7273 (mpp) cc_final: 0.6074 (mpp)
REVERT: C  185 ARG cc_start: 0.7780 (OUTLIER) cc_final: 0.7291 (ptp90)
REVERT: C  229 ASN cc_start: 0.7013 (m-40) cc_final: 0.6712 (m-40)
REVERT: C  255 ASN cc_start: 0.7513 (m-40) cc_final: 0.6588 (t0)
REVERT: D   41 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6400 (mtp-110)
  outliers start: 37
  outliers final: 33
  residues processed: 131
  average time/residue: 0.2125
  time to fit residues: 40.3406
Evaluate side-chains
  140 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 104
  time to evaluate  : 1.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  309 LYS
Chi-restraints excluded: chain B residue  311 TRP
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   63 HIS
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  185 ARG
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 101 optimal weight:    0.6980
   chunk 4 optimal weight:    7.9990
   chunk 23 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    8.9990
   chunk 75 optimal weight:    2.9990
   chunk 16 optimal weight:    0.5980
   chunk 126 optimal weight:    0.7980
   chunk 106 optimal weight:    0.7980
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.4091 r_free = 0.4091 target = 0.101810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.088266 restraints weight = 40941.083|
|-----------------------------------------------------------------------------|
r_work (start): 0.3802 rms_B_bonded: 4.34
r_work: 0.3688 rms_B_bonded: 4.99 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7186
moved from start:          0.3000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  10409  Z= 0.124
  Angle     :  0.626  10.534  14111  Z= 0.318
  Chirality :  0.042   0.178   1616
  Planarity :  0.004   0.042   1816
  Dihedral  :  5.156  48.938   1405
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 11.39
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.38 %
    Favored  : 94.54 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.46 %
    Favored  : 80.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.24), residues: 1283
  helix:  0.39 (0.22), residues: 593
  sheet: -0.41 (0.40), residues: 191
  loop : -1.20 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.002   TRP A 450 
 HIS   0.003   0.001   HIS B 176 
 PHE   0.026   0.001   PHE C 150 
 TYR   0.022   0.001   TYR A  11 
 ARG   0.009   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03319 (  459)
  hydrogen bonds       : angle       5.04334 ( 1329)
  covalent geometry    : bond        0.00281 (10409)
  covalent geometry    : angle       0.62554 (14111)

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

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

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2566 Ramachandran restraints generated.
    1283 Oldfield, 0 Emsley, 1283 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 107
  time to evaluate  : 1.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6659 (OUTLIER) cc_final: 0.6320 (mm)
REVERT: A  110 GLU cc_start: 0.9075 (pp20) cc_final: 0.8702 (pp20)
REVERT: A  160 SER cc_start: 0.8599 (m) cc_final: 0.8237 (t)
REVERT: A  350 MET cc_start: 0.8151 (pmm) cc_final: 0.7304 (pmm)
REVERT: A  353 SER cc_start: 0.8672 (m) cc_final: 0.8328 (p)
REVERT: A  358 LYS cc_start: 0.8848 (tptt) cc_final: 0.8558 (tppt)
REVERT: A  473 PHE cc_start: 0.7665 (m-80) cc_final: 0.7153 (t80)
REVERT: A  521 MET cc_start: 0.7571 (tmm) cc_final: 0.7324 (tmm)
REVERT: B  114 THR cc_start: 0.7918 (m) cc_final: 0.7662 (t)
REVERT: B  301 MET cc_start: 0.7504 (ttp) cc_final: 0.7255 (ttp)
REVERT: B  368 MET cc_start: 0.8231 (tmm) cc_final: 0.7801 (tmm)
REVERT: B  370 ASP cc_start: 0.6908 (t0) cc_final: 0.6327 (m-30)
REVERT: C    8 LYS cc_start: 0.8705 (mmmt) cc_final: 0.8498 (mmtt)
REVERT: C   10 LEU cc_start: 0.8619 (tp) cc_final: 0.8407 (tp)
REVERT: C   83 MET cc_start: 0.7349 (mpp) cc_final: 0.6139 (mpp)
REVERT: C  185 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7324 (ptp90)
REVERT: C  229 ASN cc_start: 0.7064 (m-40) cc_final: 0.6758 (m-40)
REVERT: C  245 MET cc_start: 0.8371 (mmt) cc_final: 0.7854 (mmt)
REVERT: C  255 ASN cc_start: 0.7585 (m-40) cc_final: 0.6694 (t0)
REVERT: D   41 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.6431 (mtp-110)
  outliers start: 38
  outliers final: 32
  residues processed: 131
  average time/residue: 0.2231
  time to fit residues: 42.1164
Evaluate side-chains
  137 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 102
  time to evaluate  : 1.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   96 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  128 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  210 SER
Chi-restraints excluded: chain A residue  360 ASN
Chi-restraints excluded: chain A residue  362 ILE
Chi-restraints excluded: chain A residue  394 VAL
Chi-restraints excluded: chain A residue  436 VAL
Chi-restraints excluded: chain A residue  469 LEU
Chi-restraints excluded: chain A residue  489 MET
Chi-restraints excluded: chain A residue  525 VAL
Chi-restraints excluded: chain A residue  544 LEU
Chi-restraints excluded: chain B residue   17 VAL
Chi-restraints excluded: chain B residue   43 LEU
Chi-restraints excluded: chain B residue   94 GLU
Chi-restraints excluded: chain B residue  233 GLU
Chi-restraints excluded: chain B residue  311 TRP
Chi-restraints excluded: chain B residue  326 HIS
Chi-restraints excluded: chain B residue  340 ASP
Chi-restraints excluded: chain B residue  417 LYS
Chi-restraints excluded: chain B residue  435 THR
Chi-restraints excluded: chain C residue   32 CYS
Chi-restraints excluded: chain C residue   63 HIS
Chi-restraints excluded: chain C residue   75 SER
Chi-restraints excluded: chain C residue   86 TYR
Chi-restraints excluded: chain C residue  149 LEU
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  185 ARG
Chi-restraints excluded: chain C residue  279 ASP
Chi-restraints excluded: chain C residue  287 LEU
Chi-restraints excluded: chain D residue   39 VAL
Chi-restraints excluded: chain D residue   41 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 89 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 83 optimal weight:    0.6980
   chunk 98 optimal weight:    0.6980
   chunk 28 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 17 optimal weight:    3.9990
   chunk 113 optimal weight:    0.9980
   chunk 118 optimal weight:    6.9990
   chunk 2 optimal weight:    8.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 204 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 326 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 = 0.4094 r_free = 0.4094 target = 0.101898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.088452 restraints weight = 40722.691|
|-----------------------------------------------------------------------------|
r_work (start): 0.3808 rms_B_bonded: 4.33
r_work: 0.3694 rms_B_bonded: 4.96 restraints_weight: 0.5000
r_work (final): 0.3694
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7177
moved from start:          0.3088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10409  Z= 0.124
  Angle     :  0.639  12.604  14111  Z= 0.321
  Chirality :  0.042   0.200   1616
  Planarity :  0.004   0.044   1816
  Dihedral  :  5.134  49.216   1405
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 11.54
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.22 %
    Favored  : 94.70 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 17.00 %
    Favored  : 79.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.24), residues: 1283
  helix:  0.39 (0.22), residues: 598
  sheet: -0.36 (0.39), residues: 191
  loop : -1.20 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 450 
 HIS   0.003   0.001   HIS D  31 
 PHE   0.024   0.002   PHE A 538 
 TYR   0.022   0.001   TYR A  11 
 ARG   0.008   0.000   ARG A 113 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03257 (  459)
  hydrogen bonds       : angle       5.00676 ( 1329)
  covalent geometry    : bond        0.00280 (10409)
  covalent geometry    : angle       0.63888 (14111)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5061.17 seconds
wall clock time: 88 minutes 20.09 seconds (5300.09 seconds total)