Starting phenix.real_space_refine
on Sat Aug 23 06:28:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uo5_42428/08_2025/8uo5_42428_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uo5_42428/08_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_42428/08_2025/8uo5_42428.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uo5_42428/08_2025/8uo5_42428.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uo5_42428/08_2025/8uo5_42428_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uo5_42428/08_2025/8uo5_42428_neut.cif"
  }
  resolution = 3.27
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: {'ASP:plan': 6, 'GLN:plan1': 1, 'PHE:plan': 2, 'GLU:plan': 5, 'ARG:plan': 6, 'TYR:plan': 2, 'ASN:plan1': 2}
          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: {'ARG:plan': 1, 'GLN:plan1': 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: 2.61, per 1000 atoms: 0.26
  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: 1.07
  Conformation dependent library (CDL) restraints added in 380.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.37
  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: 1.63

  Time building geometry restraints manager: 1.38 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:             3.140
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.290
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.960
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  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
 ARG   0.030   0.002   ARG A 105 
 TYR   0.070   0.007   TYR B 337 
 PHE   0.116   0.006   PHE D   3 
 TRP   0.046   0.007   TRP B 311 
 HIS   0.016   0.003   HIS B 425 

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

*********************** 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  : 0.414 
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: 0.4134 (p90)
REVERT: C  229 ASN cc_start: 0.7987 (m-40) cc_final: 0.7521 (m-40)
REVERT: C  255 ASN cc_start: 0.8347 (m-40) cc_final: 0.7578 (t0)
  outliers start: 9
  outliers final: 3
  residues processed: 154
  average time/residue: 0.1180
  time to fit residues: 25.0352
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  : 0.386 
-------------------------------------------------------------------------------
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 98 optimal weight:    0.2980
   chunk 107 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    7.9990
   chunk 77 optimal weight:    0.1980
   chunk 122 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 55 optimal weight:    0.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
A 339 GLN
A 360 ASN
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  59 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.102257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.088734 restraints weight = 39706.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3816 rms_B_bonded: 4.28
r_work (final): 0.3816
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7046
moved from start:          0.1668

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= 0.138
  Angle     :  0.653  10.839  14111  Z= 0.346
  Chirality :  0.044   0.178   1616
  Planarity :  0.005   0.045   1816
  Dihedral  :  5.731  43.434   1408
  Min Nonbonded Distance : 2.102

Molprobity Statistics.
  All-atom Clashscore : 8.42
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.12 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 12.03 %
    Favored  : 86.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.26 (0.23), residues: 1283
  helix: -0.42 (0.20), residues: 601
  sheet: -1.05 (0.36), residues: 196
  loop : -1.07 (0.29), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 113 
 TYR   0.016   0.002   TYR A  11 
 PHE   0.026   0.002   PHE A 538 
 TRP   0.024   0.002   TRP B 311 
 HIS   0.005   0.001   HIS B 421 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10409)
  covalent geometry    : angle       0.65253 (14111)
  hydrogen bonds       : bond        0.04564 (  459)
  hydrogen bonds       : angle       5.95447 ( 1329)

*********************** 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  : 0.411 
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: 0.6662 (OUTLIER) cc_final: 0.6423 (mm)
REVERT: A   24 ASP cc_start: 0.9286 (t0) cc_final: 0.9077 (t0)
REVERT: A  124 LEU cc_start: 0.8895 (tp) cc_final: 0.8549 (mt)
REVERT: A  353 SER cc_start: 0.8613 (m) cc_final: 0.8251 (p)
REVERT: A  473 PHE cc_start: 0.7215 (m-80) cc_final: 0.6500 (t80)
REVERT: A  521 MET cc_start: 0.7297 (tmm) cc_final: 0.6906 (tmm)
REVERT: A  569 GLN cc_start: 0.7691 (mm-40) cc_final: 0.7303 (tp-100)
REVERT: B  114 THR cc_start: 0.7972 (m) cc_final: 0.7636 (t)
REVERT: B  301 MET cc_start: 0.6616 (ttp) cc_final: 0.6225 (ttp)
REVERT: B  368 MET cc_start: 0.7639 (tmm) cc_final: 0.6131 (tmm)
REVERT: B  370 ASP cc_start: 0.6851 (t0) cc_final: 0.6055 (m-30)
REVERT: C   10 LEU cc_start: 0.8471 (tp) cc_final: 0.8257 (tp)
REVERT: C   83 MET cc_start: 0.7306 (mpp) cc_final: 0.6047 (mpp)
REVERT: C  229 ASN cc_start: 0.7037 (m-40) cc_final: 0.6590 (m-40)
REVERT: C  255 ASN cc_start: 0.7190 (m-40) cc_final: 0.6513 (t0)
REVERT: C  276 MET cc_start: 0.7599 (ptt) cc_final: 0.7304 (ptt)
  outliers start: 16
  outliers final: 11
  residues processed: 147
  average time/residue: 0.1070
  time to fit residues: 22.3291
Evaluate side-chains
  115 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 103
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
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 110 optimal weight:    5.9990
   chunk 16 optimal weight:    3.9990
   chunk 107 optimal weight:    7.9990
   chunk 120 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 4 optimal weight:    6.9990
   chunk 106 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 114 optimal weight:    2.9990
   chunk 123 optimal weight:    1.9990
   overall best weight:    2.3788

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

Flipped N/Q/H residues before XYZ refinement:
A 360 ASN
B 204 HIS
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 241 HIS
** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.098674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.085153 restraints weight = 40398.093|
|-----------------------------------------------------------------------------|
r_work (start): 0.3736 rms_B_bonded: 4.19
r_work: 0.3619 rms_B_bonded: 4.85 restraints_weight: 0.5000
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7288
moved from start:          0.1980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044  10409  Z= 0.231
  Angle     :  0.681   9.262  14111  Z= 0.361
  Chirality :  0.045   0.170   1616
  Planarity :  0.005   0.044   1816
  Dihedral  :  5.799  45.410   1405
  Min Nonbonded Distance : 1.928

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.68 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 12.93 %
    Favored  : 83.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.23), residues: 1283
  helix: -0.44 (0.21), residues: 597
  sheet: -1.13 (0.36), residues: 187
  loop : -1.18 (0.28), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  25 
 TYR   0.019   0.002   TYR A  11 
 PHE   0.035   0.003   PHE C 150 
 TRP   0.024   0.002   TRP B 311 
 HIS   0.015   0.002   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00510 (10409)
  covalent geometry    : angle       0.68109 (14111)
  hydrogen bonds       : bond        0.04675 (  459)
  hydrogen bonds       : angle       5.83842 ( 1329)

*********************** 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
  142 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 101
  time to evaluate  : 0.419 
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: 0.6756 (OUTLIER) cc_final: 0.6542 (mm)
REVERT: A  212 LEU cc_start: 0.9459 (OUTLIER) cc_final: 0.9251 (mp)
REVERT: A  350 MET cc_start: 0.8751 (pmm) cc_final: 0.7902 (pmm)
REVERT: A  353 SER cc_start: 0.8856 (m) cc_final: 0.8599 (p)
REVERT: A  473 PHE cc_start: 0.7547 (m-80) cc_final: 0.6851 (t80)
REVERT: A  521 MET cc_start: 0.7528 (tmm) cc_final: 0.7246 (tmm)
REVERT: A  569 GLN cc_start: 0.7888 (mm-40) cc_final: 0.7377 (tp-100)
REVERT: B  301 MET cc_start: 0.7521 (ttp) cc_final: 0.7216 (ttp)
REVERT: B  368 MET cc_start: 0.8226 (tmm) cc_final: 0.7129 (tmm)
REVERT: B  370 ASP cc_start: 0.7067 (t0) cc_final: 0.6364 (m-30)
REVERT: C   10 LEU cc_start: 0.8546 (tp) cc_final: 0.8300 (tp)
REVERT: C   83 MET cc_start: 0.7454 (mpp) cc_final: 0.6183 (mpp)
REVERT: C  229 ASN cc_start: 0.7351 (m-40) cc_final: 0.6947 (m-40)
REVERT: C  255 ASN cc_start: 0.7510 (m-40) cc_final: 0.6569 (t0)
REVERT: C  290 ASP cc_start: 0.8391 (OUTLIER) cc_final: 0.7609 (p0)
REVERT: D   41 ARG cc_start: 0.7077 (OUTLIER) cc_final: 0.6521 (mtp-110)
  outliers start: 41
  outliers final: 25
  residues processed: 130
  average time/residue: 0.0962
  time to fit residues: 18.5325
Evaluate side-chains
  119 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
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  128 PHE
Chi-restraints excluded: chain A residue  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
Chi-restraints excluded: chain A residue  212 LEU
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   94 GLU
Chi-restraints excluded: chain B residue  215 VAL
Chi-restraints excluded: chain B residue  221 ASN
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   53 THR
Chi-restraints excluded: chain C residue   63 HIS
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  290 ASP
Chi-restraints excluded: chain D residue   39 VAL
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 51 optimal weight:    0.0870
   chunk 75 optimal weight:    0.6980
   chunk 40 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 64 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 115 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 18 optimal weight:    4.9990
   chunk 110 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.8960

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.101040 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.087293 restraints weight = 40530.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3785 rms_B_bonded: 4.28
r_work: 0.3666 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7216
moved from start:          0.2247

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= 0.133
  Angle     :  0.606  10.504  14111  Z= 0.318
  Chirality :  0.042   0.161   1616
  Planarity :  0.005   0.044   1816
  Dihedral  :  5.588  47.689   1405
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.36 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 13.83 %
    Favored  : 82.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.13 (0.23), residues: 1283
  helix: -0.23 (0.21), residues: 602
  sheet: -1.03 (0.37), residues: 188
  loop : -1.11 (0.29), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 113 
 TYR   0.027   0.001   TYR A  11 
 PHE   0.038   0.002   PHE C 150 
 TRP   0.014   0.002   TRP B 311 
 HIS   0.012   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 (10409)
  covalent geometry    : angle       0.60620 (14111)
  hydrogen bonds       : bond        0.03920 (  459)
  hydrogen bonds       : angle       5.49690 ( 1329)

*********************** 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: 38
    poor density    : 108
  time to evaluate  : 0.307 
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: 0.6897 (OUTLIER) cc_final: 0.6562 (mm)
REVERT: A  110 GLU cc_start: 0.8722 (pp20) cc_final: 0.8254 (pp20)
REVERT: A  124 LEU cc_start: 0.8923 (tp) cc_final: 0.8666 (mt)
REVERT: A  350 MET cc_start: 0.8710 (pmm) cc_final: 0.8012 (pmm)
REVERT: A  353 SER cc_start: 0.8798 (m) cc_final: 0.8467 (p)
REVERT: A  569 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7361 (tp-100)
REVERT: B  114 THR cc_start: 0.7915 (m) cc_final: 0.7649 (t)
REVERT: B  190 GLU cc_start: 0.8047 (OUTLIER) cc_final: 0.7345 (mp0)
REVERT: B  233 GLU cc_start: 0.7291 (OUTLIER) cc_final: 0.7004 (tt0)
REVERT: B  256 MET cc_start: 0.8583 (mpp) cc_final: 0.8295 (mpp)
REVERT: B  301 MET cc_start: 0.7483 (ttp) cc_final: 0.7190 (ttp)
REVERT: B  368 MET cc_start: 0.8256 (tmm) cc_final: 0.7507 (tmm)
REVERT: B  370 ASP cc_start: 0.6932 (t0) cc_final: 0.6304 (m-30)
REVERT: C   10 LEU cc_start: 0.8524 (tp) cc_final: 0.8314 (tp)
REVERT: C   83 MET cc_start: 0.7511 (mpp) cc_final: 0.6071 (mpp)
REVERT: C  111 ILE cc_start: 0.6087 (OUTLIER) cc_final: 0.5765 (mp)
REVERT: C  229 ASN cc_start: 0.7203 (m-40) cc_final: 0.6738 (m-40)
REVERT: C  255 ASN cc_start: 0.7347 (m-40) cc_final: 0.6526 (t0)
REVERT: D   41 ARG cc_start: 0.6904 (OUTLIER) cc_final: 0.6456 (mtp-110)
  outliers start: 38
  outliers final: 24
  residues processed: 136
  average time/residue: 0.1000
  time to fit residues: 19.4722
Evaluate side-chains
  126 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 97
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
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  128 PHE
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 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  190 GLU
Chi-restraints excluded: chain B residue  233 GLU
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   63 HIS
Chi-restraints excluded: chain C residue   75 SER
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 18 optimal weight:    5.9990
   chunk 34 optimal weight:    7.9990
   chunk 120 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 42 optimal weight:    3.9990
   chunk 124 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 109 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 30 optimal weight:    7.9990
   chunk 62 optimal weight:    0.3980
   overall best weight:    1.1784

-------------------------------------------------------------------------------
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 = 0.4067 r_free = 0.4067 target = 0.100520 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.087114 restraints weight = 39933.849|
|-----------------------------------------------------------------------------|
r_work (start): 0.3777 rms_B_bonded: 4.19
r_work: 0.3662 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7225
moved from start:          0.2429

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10409  Z= 0.145
  Angle     :  0.606   9.092  14111  Z= 0.316
  Chirality :  0.043   0.185   1616
  Planarity :  0.005   0.048   1816
  Dihedral  :  5.507  48.032   1405
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.14 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 14.47 %
    Favored  : 81.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.98 (0.24), residues: 1283
  helix: -0.10 (0.21), residues: 599
  sheet: -0.84 (0.38), residues: 193
  loop : -1.09 (0.29), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 113 
 TYR   0.026   0.001   TYR A  11 
 PHE   0.037   0.002   PHE C 150 
 TRP   0.018   0.002   TRP B 311 
 HIS   0.007   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10409)
  covalent geometry    : angle       0.60607 (14111)
  hydrogen bonds       : bond        0.03799 (  459)
  hydrogen bonds       : angle       5.34287 ( 1329)

*********************** 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
  141 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 100
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6794 (OUTLIER) cc_final: 0.6417 (mm)
REVERT: A  110 GLU cc_start: 0.8846 (pp20) cc_final: 0.8393 (pp20)
REVERT: A  124 LEU cc_start: 0.8912 (OUTLIER) cc_final: 0.8657 (mt)
REVERT: A  353 SER cc_start: 0.8753 (m) cc_final: 0.8425 (p)
REVERT: A  521 MET cc_start: 0.7343 (tmm) cc_final: 0.6894 (tmm)
REVERT: A  569 GLN cc_start: 0.7761 (mm-40) cc_final: 0.7318 (tp-100)
REVERT: B  114 THR cc_start: 0.8015 (m) cc_final: 0.7757 (t)
REVERT: B  190 GLU cc_start: 0.8132 (OUTLIER) cc_final: 0.7404 (mp0)
REVERT: B  233 GLU cc_start: 0.7323 (OUTLIER) cc_final: 0.7007 (tt0)
REVERT: B  301 MET cc_start: 0.7473 (ttp) cc_final: 0.7188 (ttp)
REVERT: B  368 MET cc_start: 0.8227 (tmm) cc_final: 0.7550 (tmm)
REVERT: B  370 ASP cc_start: 0.7029 (t0) cc_final: 0.6367 (m-30)
REVERT: C   10 LEU cc_start: 0.8532 (tp) cc_final: 0.8315 (tp)
REVERT: C   83 MET cc_start: 0.7510 (mpp) cc_final: 0.5984 (mpp)
REVERT: C  185 ARG cc_start: 0.7782 (OUTLIER) cc_final: 0.7279 (ptp90)
REVERT: C  229 ASN cc_start: 0.7183 (m-40) cc_final: 0.6264 (m-40)
REVERT: C  255 ASN cc_start: 0.7374 (m-40) cc_final: 0.7025 (t0)
REVERT: D   41 ARG cc_start: 0.6848 (OUTLIER) cc_final: 0.6392 (mtp-110)
  outliers start: 41
  outliers final: 29
  residues processed: 130
  average time/residue: 0.0963
  time to fit residues: 18.2263
Evaluate side-chains
  126 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 91
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
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  124 LEU
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  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  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  190 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 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  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=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 96 optimal weight:    0.5980
   chunk 17 optimal weight:    2.9990
   chunk 63 optimal weight:    8.9990
   chunk 61 optimal weight:    0.5980
   chunk 78 optimal weight:    0.9980
   chunk 113 optimal weight:    0.0970
   chunk 1 optimal weight:    0.7980
   chunk 102 optimal weight:    0.9990
   chunk 81 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.6178

-------------------------------------------------------------------------------
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 = 0.4089 r_free = 0.4089 target = 0.101694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.088163 restraints weight = 40069.152|
|-----------------------------------------------------------------------------|
r_work (start): 0.3803 rms_B_bonded: 4.27
r_work: 0.3688 rms_B_bonded: 4.92 restraints_weight: 0.5000
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7180
moved from start:          0.2647

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10409  Z= 0.117
  Angle     :  0.585  10.145  14111  Z= 0.305
  Chirality :  0.042   0.170   1616
  Planarity :  0.004   0.041   1816
  Dihedral  :  5.337  48.864   1405
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 10.60
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.60 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.83 %
    Favored  : 81.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.24), residues: 1283
  helix:  0.17 (0.22), residues: 594
  sheet: -0.69 (0.39), residues: 193
  loop : -1.06 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 113 
 TYR   0.023   0.001   TYR A  11 
 PHE   0.032   0.002   PHE C 150 
 TRP   0.016   0.001   TRP B 311 
 HIS   0.006   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00256 (10409)
  covalent geometry    : angle       0.58527 (14111)
  hydrogen bonds       : bond        0.03465 (  459)
  hydrogen bonds       : angle       5.15528 ( 1329)

*********************** 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
  146 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 110
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6492 (mm)
REVERT: A  110 GLU cc_start: 0.8934 (pp20) cc_final: 0.8500 (pp20)
REVERT: A  350 MET cc_start: 0.8276 (pmm) cc_final: 0.7316 (pmm)
REVERT: A  353 SER cc_start: 0.8724 (m) cc_final: 0.8368 (p)
REVERT: A  521 MET cc_start: 0.7401 (tmm) cc_final: 0.6873 (tmm)
REVERT: B  114 THR cc_start: 0.7906 (m) cc_final: 0.7662 (t)
REVERT: B  190 GLU cc_start: 0.8120 (OUTLIER) cc_final: 0.7337 (mp0)
REVERT: B  301 MET cc_start: 0.7416 (ttp) cc_final: 0.7132 (ttp)
REVERT: B  368 MET cc_start: 0.8246 (tmm) cc_final: 0.7646 (tmm)
REVERT: B  370 ASP cc_start: 0.6966 (t0) cc_final: 0.6327 (m-30)
REVERT: C   10 LEU cc_start: 0.8537 (tp) cc_final: 0.8319 (tp)
REVERT: C  185 ARG cc_start: 0.7745 (OUTLIER) cc_final: 0.7245 (ptp90)
REVERT: C  220 PHE cc_start: 0.4260 (p90) cc_final: 0.1835 (p90)
REVERT: C  229 ASN cc_start: 0.7139 (m-40) cc_final: 0.6211 (m-40)
REVERT: C  245 MET cc_start: 0.8399 (mmt) cc_final: 0.7896 (mmt)
REVERT: C  255 ASN cc_start: 0.7285 (m-40) cc_final: 0.6958 (t0)
REVERT: D   41 ARG cc_start: 0.6762 (OUTLIER) cc_final: 0.6504 (mtp-110)
  outliers start: 36
  outliers final: 26
  residues processed: 134
  average time/residue: 0.0977
  time to fit residues: 19.1477
Evaluate side-chains
  125 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 95
  time to evaluate  : 0.440 
-------------------------------------------------------------------------------
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  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  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  190 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 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  149 LEU
Chi-restraints excluded: chain C residue  156 THR
Chi-restraints excluded: chain C residue  185 ARG
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 2 optimal weight:    0.2980
   chunk 9 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9990
   chunk 114 optimal weight:    0.0770
   chunk 85 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    4.9990
   chunk 25 optimal weight:    6.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.6140

-------------------------------------------------------------------------------
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 = 0.4091 r_free = 0.4091 target = 0.101900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.088484 restraints weight = 39599.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.3812 rms_B_bonded: 4.24
r_work: 0.3692 rms_B_bonded: 4.97 restraints_weight: 0.5000
r_work (final): 0.3692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.2836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  10409  Z= 0.121
  Angle     :  0.602  10.492  14111  Z= 0.311
  Chirality :  0.042   0.214   1616
  Planarity :  0.004   0.042   1816
  Dihedral  :  5.228  48.549   1405
  Min Nonbonded Distance : 2.086

Molprobity Statistics.
  All-atom Clashscore : 10.30
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.68 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 15.64 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.72 (0.24), residues: 1283
  helix:  0.17 (0.22), residues: 595
  sheet: -0.52 (0.40), residues: 188
  loop : -1.12 (0.29), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 113 
 TYR   0.022   0.001   TYR A  11 
 PHE   0.030   0.002   PHE C 150 
 TRP   0.016   0.001   TRP B 311 
 HIS   0.005   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (10409)
  covalent geometry    : angle       0.60246 (14111)
  hydrogen bonds       : bond        0.03488 (  459)
  hydrogen bonds       : angle       5.13627 ( 1329)

*********************** 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
  145 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 107
  time to evaluate  : 0.427 
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: 0.6846 (OUTLIER) cc_final: 0.6471 (mm)
REVERT: A  110 GLU cc_start: 0.9002 (pp20) cc_final: 0.8582 (pp20)
REVERT: A  160 SER cc_start: 0.8617 (m) cc_final: 0.8260 (t)
REVERT: A  350 MET cc_start: 0.8201 (pmm) cc_final: 0.7266 (pmm)
REVERT: A  353 SER cc_start: 0.8736 (m) cc_final: 0.8381 (p)
REVERT: A  473 PHE cc_start: 0.7460 (m-80) cc_final: 0.6966 (t80)
REVERT: A  521 MET cc_start: 0.7435 (tmm) cc_final: 0.6949 (tmm)
REVERT: B  114 THR cc_start: 0.7882 (m) cc_final: 0.7651 (t)
REVERT: B  233 GLU cc_start: 0.7289 (OUTLIER) cc_final: 0.6977 (tt0)
REVERT: B  301 MET cc_start: 0.7416 (ttp) cc_final: 0.7137 (ttp)
REVERT: B  368 MET cc_start: 0.8294 (tmm) cc_final: 0.7757 (tmm)
REVERT: B  370 ASP cc_start: 0.6931 (t0) cc_final: 0.6342 (m-30)
REVERT: C    9 GLU cc_start: 0.8828 (OUTLIER) cc_final: 0.8420 (mp0)
REVERT: C   83 MET cc_start: 0.7393 (mpp) cc_final: 0.6096 (mpp)
REVERT: C  185 ARG cc_start: 0.7720 (OUTLIER) cc_final: 0.7220 (ptp90)
REVERT: C  220 PHE cc_start: 0.4380 (p90) cc_final: 0.1923 (p90)
REVERT: C  229 ASN cc_start: 0.7131 (m-40) cc_final: 0.6748 (m-40)
REVERT: C  245 MET cc_start: 0.8423 (mmt) cc_final: 0.7937 (mmt)
REVERT: C  255 ASN cc_start: 0.7266 (m-40) cc_final: 0.6510 (t0)
REVERT: D   41 ARG cc_start: 0.6749 (OUTLIER) cc_final: 0.6480 (mtp-110)
  outliers start: 38
  outliers final: 29
  residues processed: 131
  average time/residue: 0.1033
  time to fit residues: 19.4751
Evaluate side-chains
  133 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 99
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
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  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  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 C residue    9 GLU
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  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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    0.0030
   chunk 71 optimal weight:    0.9980
   chunk 40 optimal weight:    0.3980
   chunk 34 optimal weight:    5.9990
   chunk 54 optimal weight:    0.5980
   chunk 52 optimal weight:    0.9980
   chunk 7 optimal weight:    6.9990
   chunk 94 optimal weight:    1.9990
   chunk 32 optimal weight:    0.5980
   chunk 27 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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
** 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 = 0.4098 r_free = 0.4098 target = 0.102217 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.088888 restraints weight = 40039.678|
|-----------------------------------------------------------------------------|
r_work (start): 0.3819 rms_B_bonded: 4.26
r_work: 0.3702 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3702
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7159
moved from start:          0.2975

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= 0.118
  Angle     :  0.618  10.544  14111  Z= 0.316
  Chirality :  0.042   0.196   1616
  Planarity :  0.004   0.042   1816
  Dihedral  :  5.165  48.751   1405
  Min Nonbonded Distance : 2.095

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.83 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 16.18 %
    Favored  : 80.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.67 (0.24), residues: 1283
  helix:  0.21 (0.22), residues: 597
  sheet: -0.51 (0.39), residues: 190
  loop : -1.09 (0.29), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 113 
 TYR   0.021   0.001   TYR A  11 
 PHE   0.028   0.001   PHE C 150 
 TRP   0.042   0.002   TRP A 450 
 HIS   0.005   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10409)
  covalent geometry    : angle       0.61798 (14111)
  hydrogen bonds       : bond        0.03403 (  459)
  hydrogen bonds       : angle       5.07096 ( 1329)

*********************** 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
  147 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 111
  time to evaluate  : 0.416 
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: 0.6846 (OUTLIER) cc_final: 0.6465 (mm)
REVERT: A  110 GLU cc_start: 0.9036 (pp20) cc_final: 0.8639 (pp20)
REVERT: A  160 SER cc_start: 0.8616 (m) cc_final: 0.8268 (t)
REVERT: A  180 MET cc_start: 0.8397 (tpp) cc_final: 0.8127 (mmm)
REVERT: A  350 MET cc_start: 0.8181 (pmm) cc_final: 0.7277 (pmm)
REVERT: A  353 SER cc_start: 0.8729 (m) cc_final: 0.8368 (p)
REVERT: A  473 PHE cc_start: 0.7482 (m-80) cc_final: 0.6977 (t80)
REVERT: A  521 MET cc_start: 0.7554 (tmm) cc_final: 0.7121 (tmm)
REVERT: B  114 THR cc_start: 0.7882 (m) cc_final: 0.7653 (t)
REVERT: B  190 GLU cc_start: 0.7999 (OUTLIER) cc_final: 0.7688 (pp20)
REVERT: B  233 GLU cc_start: 0.7217 (OUTLIER) cc_final: 0.6865 (tt0)
REVERT: B  301 MET cc_start: 0.7471 (ttp) cc_final: 0.7198 (ttp)
REVERT: B  368 MET cc_start: 0.8285 (tmm) cc_final: 0.7779 (tmm)
REVERT: B  370 ASP cc_start: 0.6911 (t0) cc_final: 0.6348 (m-30)
REVERT: C    9 GLU cc_start: 0.8762 (OUTLIER) cc_final: 0.8301 (mp0)
REVERT: C   83 MET cc_start: 0.7339 (mpp) cc_final: 0.6049 (mpp)
REVERT: C  185 ARG cc_start: 0.7705 (OUTLIER) cc_final: 0.7239 (ptp90)
REVERT: C  229 ASN cc_start: 0.7156 (m-40) cc_final: 0.6781 (m-40)
REVERT: C  245 MET cc_start: 0.8422 (mmt) cc_final: 0.7954 (mmt)
REVERT: C  255 ASN cc_start: 0.7301 (m-40) cc_final: 0.6561 (t0)
REVERT: D   41 ARG cc_start: 0.6673 (OUTLIER) cc_final: 0.6420 (mtp-110)
  outliers start: 36
  outliers final: 30
  residues processed: 135
  average time/residue: 0.1029
  time to fit residues: 20.0643
Evaluate side-chains
  138 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 102
  time to evaluate  : 0.517 
-------------------------------------------------------------------------------
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  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  190 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 C residue    9 GLU
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   93 SER
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  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 22 optimal weight:    0.4980
   chunk 5 optimal weight:    8.9990
   chunk 7 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 56 optimal weight:    2.9990
   chunk 112 optimal weight:    7.9990
   chunk 116 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 120 optimal weight:    0.0670
   chunk 114 optimal weight:    0.2980
   overall best weight:    0.9720

-------------------------------------------------------------------------------
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 = 0.4086 r_free = 0.4086 target = 0.101690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.088081 restraints weight = 40911.762|
|-----------------------------------------------------------------------------|
r_work (start): 0.3798 rms_B_bonded: 4.33
r_work: 0.3684 rms_B_bonded: 4.98 restraints_weight: 0.5000
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.3018

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= 0.133
  Angle     :  0.631  10.154  14111  Z= 0.320
  Chirality :  0.042   0.197   1616
  Planarity :  0.004   0.042   1816
  Dihedral  :  5.162  48.847   1405
  Min Nonbonded Distance : 2.053

Molprobity Statistics.
  All-atom Clashscore : 11.64
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.30 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 16.09 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.69 (0.24), residues: 1283
  helix:  0.21 (0.22), residues: 601
  sheet: -0.56 (0.39), residues: 194
  loop : -1.13 (0.29), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 113 
 TYR   0.021   0.001   TYR A  11 
 PHE   0.025   0.002   PHE C 150 
 TRP   0.033   0.002   TRP A 450 
 HIS   0.004   0.001   HIS B 176 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 (10409)
  covalent geometry    : angle       0.63061 (14111)
  hydrogen bonds       : bond        0.03402 (  459)
  hydrogen bonds       : angle       5.06292 ( 1329)

*********************** 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
  140 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 102
  time to evaluate  : 0.442 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   16 LEU cc_start: 0.6834 (OUTLIER) cc_final: 0.6510 (mm)
REVERT: A  110 GLU cc_start: 0.9064 (pp20) cc_final: 0.8692 (pp20)
REVERT: A  160 SER cc_start: 0.8622 (m) cc_final: 0.8252 (t)
REVERT: A  350 MET cc_start: 0.8136 (pmm) cc_final: 0.7263 (pmm)
REVERT: A  353 SER cc_start: 0.8714 (m) cc_final: 0.8365 (p)
REVERT: A  473 PHE cc_start: 0.7604 (m-80) cc_final: 0.7103 (t80)
REVERT: A  521 MET cc_start: 0.7473 (tmm) cc_final: 0.6992 (tmm)
REVERT: B  114 THR cc_start: 0.7933 (m) cc_final: 0.7705 (t)
REVERT: B  190 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7732 (pp20)
REVERT: B  233 GLU cc_start: 0.7231 (OUTLIER) cc_final: 0.6863 (tt0)
REVERT: B  301 MET cc_start: 0.7532 (ttp) cc_final: 0.7272 (ttp)
REVERT: B  368 MET cc_start: 0.8275 (tmm) cc_final: 0.7806 (tmm)
REVERT: B  370 ASP cc_start: 0.6938 (t0) cc_final: 0.6371 (m-30)
REVERT: C    8 LYS cc_start: 0.8710 (mmmt) cc_final: 0.8311 (mmtt)
REVERT: C    9 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8286 (mp0)
REVERT: C   83 MET cc_start: 0.7393 (mpp) cc_final: 0.6087 (mpp)
REVERT: C  185 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7266 (ptp90)
REVERT: C  229 ASN cc_start: 0.7166 (m-40) cc_final: 0.6810 (m-40)
REVERT: C  245 MET cc_start: 0.8422 (mmt) cc_final: 0.7951 (mmt)
REVERT: C  255 ASN cc_start: 0.7377 (m-40) cc_final: 0.6632 (t0)
REVERT: D   41 ARG cc_start: 0.6744 (OUTLIER) cc_final: 0.6493 (mtp-110)
  outliers start: 38
  outliers final: 29
  residues processed: 126
  average time/residue: 0.0920
  time to fit residues: 17.2815
Evaluate side-chains
  135 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 100
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
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  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  190 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    9 GLU
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   93 SER
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 14 optimal weight:    0.9980
   chunk 59 optimal weight:    5.9990
   chunk 8 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   chunk 82 optimal weight:    0.0270
   chunk 61 optimal weight:    1.9990
   chunk 26 optimal weight:    0.5980
   chunk 43 optimal weight:    4.9990
   chunk 109 optimal weight:    0.4980
   chunk 58 optimal weight:    6.9990
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.5638

-------------------------------------------------------------------------------
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 = 0.4099 r_free = 0.4099 target = 0.102235 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.088992 restraints weight = 39725.428|
|-----------------------------------------------------------------------------|
r_work (start): 0.3820 rms_B_bonded: 4.23
r_work: 0.3704 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3704
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7157
moved from start:          0.3128

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= 0.119
  Angle     :  0.637  10.120  14111  Z= 0.321
  Chirality :  0.042   0.209   1616
  Planarity :  0.004   0.042   1816
  Dihedral  :  5.110  49.274   1405
  Min Nonbonded Distance : 2.090

Molprobity Statistics.
  All-atom Clashscore : 11.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.14 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.16 %
    Allowed  : 16.46 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.65 (0.24), residues: 1283
  helix:  0.26 (0.22), residues: 599
  sheet: -0.45 (0.39), residues: 190
  loop : -1.17 (0.29), residues: 494

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 183 
 TYR   0.020   0.001   TYR A  11 
 PHE   0.024   0.001   PHE C 150 
 TRP   0.033   0.002   TRP A 450 
 HIS   0.004   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10409)
  covalent geometry    : angle       0.63723 (14111)
  hydrogen bonds       : bond        0.03314 (  459)
  hydrogen bonds       : angle       5.02438 ( 1329)

********************** 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
  139 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 104
  time to evaluate  : 0.456 
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: 0.6693 (OUTLIER) cc_final: 0.6382 (mm)
REVERT: A  110 GLU cc_start: 0.9087 (pp20) cc_final: 0.8704 (pp20)
REVERT: A  160 SER cc_start: 0.8602 (m) cc_final: 0.8248 (t)
REVERT: A  350 MET cc_start: 0.8171 (pmm) cc_final: 0.7291 (pmm)
REVERT: A  353 SER cc_start: 0.8706 (m) cc_final: 0.8344 (p)
REVERT: A  473 PHE cc_start: 0.7596 (m-80) cc_final: 0.7145 (t80)
REVERT: A  521 MET cc_start: 0.7453 (tmm) cc_final: 0.7063 (tmm)
REVERT: B  114 THR cc_start: 0.7904 (m) cc_final: 0.7669 (t)
REVERT: B  190 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7656 (pp20)
REVERT: B  301 MET cc_start: 0.7491 (ttp) cc_final: 0.7235 (ttp)
REVERT: B  368 MET cc_start: 0.8250 (tmm) cc_final: 0.7768 (tmm)
REVERT: B  370 ASP cc_start: 0.6884 (t0) cc_final: 0.6314 (m-30)
REVERT: C    8 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8449 (mmtt)
REVERT: C    9 GLU cc_start: 0.8750 (OUTLIER) cc_final: 0.8300 (mp0)
REVERT: C  185 ARG cc_start: 0.7756 (OUTLIER) cc_final: 0.7252 (ptp90)
REVERT: C  229 ASN cc_start: 0.7095 (m-40) cc_final: 0.6725 (m-40)
REVERT: C  245 MET cc_start: 0.8442 (mmt) cc_final: 0.7982 (mmt)
REVERT: C  255 ASN cc_start: 0.7187 (m-40) cc_final: 0.6478 (t0)
REVERT: D   41 ARG cc_start: 0.6639 (OUTLIER) cc_final: 0.6394 (mtp-110)
  outliers start: 35
  outliers final: 28
  residues processed: 126
  average time/residue: 0.0981
  time to fit residues: 18.3155
Evaluate side-chains
  131 residues out of total 1160 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 98
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
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  131 LEU
Chi-restraints excluded: chain A residue  204 GLU
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  190 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    9 GLU
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   93 SER
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  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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 40 optimal weight:    2.9990
   chunk 63 optimal weight:    0.0770
   chunk 100 optimal weight:    1.9990
   chunk 99 optimal weight:    0.0980
   chunk 39 optimal weight:    1.9990
   chunk 115 optimal weight:    0.0370
   chunk 119 optimal weight:    1.9990
   chunk 10 optimal weight:    0.0770
   chunk 84 optimal weight:    0.7980
   chunk 48 optimal weight:    4.9990
   overall best weight:    0.2174

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.103205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.089966 restraints weight = 40000.124|
|-----------------------------------------------------------------------------|
r_work (start): 0.3837 rms_B_bonded: 4.31
r_work: 0.3724 rms_B_bonded: 5.00 restraints_weight: 0.5000
r_work (final): 0.3724
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7108
moved from start:          0.3283

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  10409  Z= 0.109
  Angle     :  0.619  10.115  14111  Z= 0.312
  Chirality :  0.042   0.230   1616
  Planarity :  0.004   0.046   1816
  Dihedral  :  5.026  48.759   1405
  Min Nonbonded Distance : 2.129

Molprobity Statistics.
  All-atom Clashscore : 10.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.30 %
    Favored  : 94.62 %
  Rotamer:
    Outliers :  2.89 %
    Allowed  : 16.73 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.04 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.57 (0.24), residues: 1283
  helix:  0.36 (0.22), residues: 603
  sheet: -0.40 (0.39), residues: 193
  loop : -1.21 (0.29), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 183 
 TYR   0.020   0.001   TYR A  11 
 PHE   0.023   0.001   PHE C 150 
 TRP   0.032   0.002   TRP A 450 
 HIS   0.005   0.001   HIS B 179 

Details of bonding type rmsd
  covalent geometry    : bond        0.00238 (10409)
  covalent geometry    : angle       0.61875 (14111)
  hydrogen bonds       : bond        0.03170 (  459)
  hydrogen bonds       : angle       4.95165 ( 1329)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2622.15 seconds
wall clock time: 45 minutes 57.32 seconds (2757.32 seconds total)