Starting phenix.real_space_refine
on Sat Nov 16 13:33:20 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/11_2024/8c80_16467.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/11_2024/8c80_16467.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/11_2024/8c80_16467.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/11_2024/8c80_16467.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/11_2024/8c80_16467.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c80_16467/11_2024/8c80_16467.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.019
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: 5
    Type Number    sf(0)   Gaussians
     P       1      5.49       5
     S      55      5.16       5
     C    7088      2.51       5
     N    1795      2.21       5
     O    2029      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 10968
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1502
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 184, 1502
          Classifications: {'peptide': 184}
          Link IDs: {'PTRANS': 10, 'TRANS': 173}
    Chain: "B"
      Number of atoms: 4214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 537, 4214
          Classifications: {'peptide': 537}
          Link IDs: {'PTRANS': 26, 'TRANS': 510}
    Chain: "C"
      Number of atoms: 4394
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 555, 4394
          Classifications: {'peptide': 555}
          Link IDs: {'PTRANS': 29, 'TRANS': 525}
    Chain: "D"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 74, 626
          Classifications: {'peptide': 74}
          Link IDs: {'PTRANS': 2, 'TRANS': 71}
    Chain: "A"
      Number of atoms: 107
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 107
          Unusual residues: {'ERG': 2, 'Z8A': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 29
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 29
          Unusual residues: {'ERG': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 96
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 96
          Unusual residues: {'PLP': 1, 'Q7G': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
  Time building chain proxies: 8.13, per 1000 atoms: 0.74
  Number of scatterers: 10968
  At special positions: 0
  Unit cell: (90.552, 108.108, 126.588, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      55     16.00
     P       1     15.00
     O    2029      8.00
     N    1795      7.00
     C    7088      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.83
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2542

  Finding SS restraints...
    Secondary structure from input PDB file:
      55 helices and 7 sheets defined
      51.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 62 through 72
      removed outlier: 4.072A  pdb=" N   LEU A  72 " --> pdb=" O   ASP A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 86 through 101
      removed outlier: 4.224A  pdb=" N   VAL A  90 " --> pdb=" O   TRP A  86 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 107 through 129
      removed outlier: 3.632A  pdb=" N   LEU A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 137 through 141
      removed outlier: 3.547A  pdb=" N   ALA A 141 " --> pdb=" O   ASN A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 158 through 179
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 182 through 198
      removed outlier: 4.539A  pdb=" N   PHE A 195 " --> pdb=" O   PHE A 191 " (cutoff:3.500A)
      removed outlier: 3.504A  pdb=" N   VAL A 198 " --> pdb=" O   THR A 194 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 36
      removed outlier: 4.178A  pdb=" N   LEU B  25 " --> pdb=" O   THR B  21 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   TRP B  26 " --> pdb=" O   SER B  22 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   TYR B  27 " --> pdb=" O   SER B  23 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU B  33 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 39 through 50
    Processing helix  chain 'B' and resid 53 through 73
      removed outlier: 3.907A  pdb=" N   THR B  57 " --> pdb=" O   ASP B  53 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   LEU B  63 " --> pdb=" O   VAL B  59 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU B  65 " --> pdb=" O   ILE B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 89 through 100
      removed outlier: 3.521A  pdb=" N   TRP B 100 " --> pdb=" O   LEU B  96 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 120
    Processing helix  chain 'B' and resid 161 through 176
    Processing helix  chain 'B' and resid 189 through 204
      removed outlier: 3.536A  pdb=" N   TYR B 193 " --> pdb=" O   GLN B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 213 through 216
    Processing helix  chain 'B' and resid 217 through 226
      Proline residue:  B 223  - end of helix
    Processing helix  chain 'B' and resid 239 through 250
      removed outlier: 4.067A  pdb=" N   ARG B 250 " --> pdb=" O   LEU B 246 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 279
      removed outlier: 3.817A  pdb=" N   LYS B 279 " --> pdb=" O   GLU B 275 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 314
      removed outlier: 4.015A  pdb=" N   LEU B 306 " --> pdb=" O   PRO B 302 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 339
      removed outlier: 3.511A  pdb=" N   HIS B 338 " --> pdb=" O   GLY B 334 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 347
      removed outlier: 3.868A  pdb=" N   ILE B 347 " --> pdb=" O   ARG B 343 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 379
      removed outlier: 3.576A  pdb=" N   CYS B 372 " --> pdb=" O   ASP B 368 " (cutoff:3.500A)
      removed outlier: 4.046A  pdb=" N   ILE B 377 " --> pdb=" O   LEU B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 384
    Processing helix  chain 'B' and resid 389 through 406
      removed outlier: 3.726A  pdb=" N   VAL B 393 " --> pdb=" O   PRO B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 408 through 426
    Processing helix  chain 'B' and resid 450 through 459
      removed outlier: 3.725A  pdb=" N   SER B 455 " --> pdb=" O   PRO B 451 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS B 457 " --> pdb=" O   TYR B 453 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 461 through 476
    Processing helix  chain 'B' and resid 482 through 503
    Processing helix  chain 'B' and resid 513 through 517
    Processing helix  chain 'B' and resid 534 through 555
      removed outlier: 3.537A  pdb=" N   CYS B 552 " --> pdb=" O   SER B 548 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   GLU B 555 " --> pdb=" O   ALA B 551 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 21 through 26
    Processing helix  chain 'C' and resid 57 through 86
      removed outlier: 3.930A  pdb=" N   SER C  61 " --> pdb=" O   PRO C  57 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   VAL C  77 " --> pdb=" O   ILE C  73 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASP C  79 " --> pdb=" O   GLY C  75 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 94
      removed outlier: 3.914A  pdb=" N   LEU C  94 " --> pdb=" O   LEU C  91 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 105 through 109
    Processing helix  chain 'C' and resid 115 through 117
      No H-bonds generated for 'chain 'C' and resid 115 through 117'
    Processing helix  chain 'C' and resid 118 through 123
      removed outlier: 4.289A  pdb=" N   PHE C 122 " --> pdb=" O   ILE C 118 " (cutoff:3.500A)
      removed outlier: 4.263A  pdb=" N   SER C 123 " --> pdb=" O   ASP C 119 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 118 through 123'
    Processing helix  chain 'C' and resid 173 through 186
      removed outlier: 3.593A  pdb=" N   VAL C 183 " --> pdb=" O   ALA C 179 " (cutoff:3.500A)
      removed outlier: 4.097A  pdb=" N   ASP C 184 " --> pdb=" O   LEU C 180 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LYS C 185 " --> pdb=" O   GLU C 181 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 200 through 215
      removed outlier: 3.522A  pdb=" N   ILE C 204 " --> pdb=" O   THR C 200 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 224 through 231
    Processing helix  chain 'C' and resid 232 through 236
      removed outlier: 3.596A  pdb=" N   PHE C 236 " --> pdb=" O   PHE C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 250 through 261
      removed outlier: 3.509A  pdb=" N   ARG C 254 " --> pdb=" O   HIS C 250 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   GLY C 256 " --> pdb=" O   SER C 252 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 273 through 286
      removed outlier: 3.734A  pdb=" N   VAL C 284 " --> pdb=" O   ARG C 280 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 313 through 324
      removed outlier: 3.570A  pdb=" N   GLU C 319 " --> pdb=" O   PRO C 315 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   LYS C 322 " --> pdb=" O   VAL C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 345 through 350
    Processing helix  chain 'C' and resid 378 through 389
      removed outlier: 3.857A  pdb=" N   LEU C 387 " --> pdb=" O   ASP C 383 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 390 through 395
    Processing helix  chain 'C' and resid 399 through 410
      removed outlier: 3.733A  pdb=" N   LEU C 403 " --> pdb=" O   PRO C 399 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 422 through 427
    Processing helix  chain 'C' and resid 427 through 444
    Processing helix  chain 'C' and resid 464 through 476
      removed outlier: 3.688A  pdb=" N   ALA C 468 " --> pdb=" O   SER C 464 " (cutoff:3.500A)
      removed outlier: 3.923A  pdb=" N   MET C 473 " --> pdb=" O   PHE C 469 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU C 474 " --> pdb=" O   SER C 470 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   GLN C 475 " --> pdb=" O   ARG C 471 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ARG C 476 " --> pdb=" O   MET C 472 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 484 through 488
    Processing helix  chain 'C' and resid 504 through 523
    Processing helix  chain 'C' and resid 541 through 553
      Proline residue:  C 550  - end of helix
    Processing helix  chain 'D' and resid 13 through 22
      removed outlier: 3.993A  pdb=" N   LYS D  18 " --> pdb=" O   THR D  14 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 28 through 46
      removed outlier: 4.151A  pdb=" N   GLU D  33 " --> pdb=" O   ASN D  29 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   VAL D  34 " --> pdb=" O   THR D  30 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   THR D  41 " --> pdb=" O   LYS D  37 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   TYR D  42 " --> pdb=" O   LEU D  38 " (cutoff:3.500A)
      removed outlier: 5.019A  pdb=" N   TYR D  43 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
      removed outlier: 3.809A  pdb=" N   HIS D  45 " --> pdb=" O   THR D  41 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   LEU D  46 " --> pdb=" O   TYR D  42 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 52 through 76
      removed outlier: 3.612A  pdb=" N   LEU D  75 " --> pdb=" O   PHE D  71 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 55 through 57
    Processing sheet with id=AA2, first strand: chain 'B' and resid 123 through 124
      removed outlier: 6.406A  pdb=" N   ILE B 133 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   GLU B 142 " --> pdb=" O   ARG B 137 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   LEU B 506 " --> pdb=" O   ASN B 146 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   PHE B 148 " --> pdb=" O   LEU B 506 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 207 through 211
      removed outlier: 3.587A  pdb=" N   GLY B 367 " --> pdb=" O   GLY B 207 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ARG B 316 " --> pdb=" O   LYS B 286 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   VAL B 231 " --> pdb=" O   PHE B 287 " (cutoff:3.500A)
      removed outlier: 7.983A  pdb=" N   VAL B 289 " --> pdb=" O   VAL B 231 " (cutoff:3.500A)
      removed outlier: 6.461A  pdb=" N   VAL B 233 " --> pdb=" O   VAL B 289 " (cutoff:3.500A)
      removed outlier: 8.789A  pdb=" N   GLU B 291 " --> pdb=" O   VAL B 233 " (cutoff:3.500A)
      removed outlier: 9.014A  pdb=" N   ASP B 235 " --> pdb=" O   GLU B 291 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ILE B 232 " --> pdb=" O   TYR B 254 " (cutoff:3.500A)
      removed outlier: 7.979A  pdb=" N   PHE B 256 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   ALA B 234 " --> pdb=" O   PHE B 256 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 434 through 436
      removed outlier: 3.558A  pdb=" N   ILE B 435 " --> pdb=" O   GLN B 448 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 133 through 142
      removed outlier: 3.523A  pdb=" N   CYS C 136 " --> pdb=" O   TYR C 155 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   TYR C 155 " --> pdb=" O   CYS C 136 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ASP C 138 " --> pdb=" O   ALA C 153 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   ALA C 153 " --> pdb=" O   ASP C 138 " (cutoff:3.500A)
      removed outlier: 9.256A  pdb=" N   ILE C 140 " --> pdb=" O   SER C 151 " (cutoff:3.500A)
      removed outlier: 7.907A  pdb=" N   SER C 151 " --> pdb=" O   ILE C 140 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   HIS C 142 " --> pdb=" O   THR C 149 " (cutoff:3.500A)
      removed outlier: 7.514A  pdb=" N   THR C 149 " --> pdb=" O   HIS C 142 " (cutoff:3.500A)
      removed outlier: 8.106A  pdb=" N   ALA C 479 " --> pdb=" O   PRO C 156 " (cutoff:3.500A)
      removed outlier: 7.128A  pdb=" N   MET C 158 " --> pdb=" O   ALA C 479 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 218 through 222
      removed outlier: 3.536A  pdb=" N   ASP C 218 " --> pdb=" O   ALA C 377 " (cutoff:3.500A)
      removed outlier: 3.764A  pdb=" N   GLY C 373 " --> pdb=" O   PHE C 222 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   ILE C 359 " --> pdb=" O   LEU C 328 " (cutoff:3.500A)
      removed outlier: 6.952A  pdb=" N   ILE C 297 " --> pdb=" O   TYR C 327 " (cutoff:3.500A)
      removed outlier: 8.233A  pdb=" N   PHE C 329 " --> pdb=" O   ILE C 297 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ILE C 299 " --> pdb=" O   PHE C 329 " (cutoff:3.500A)
      removed outlier: 8.136A  pdb=" N   ASP C 331 " --> pdb=" O   ILE C 299 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASP C 246 " --> pdb=" O   CYS C 300 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   PHE C 267 " --> pdb=" O   SER C 245 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 455 through 460
      removed outlier: 3.587A  pdb=" N   SER C 493 " --> pdb=" O   LEU C 460 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   VAL C 481 " --> pdb=" O   ARG C 496 " (cutoff:3.500A)

    466 hydrogen bonds defined for protein.
    1350 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.95

  Time building geometry restraints manager: 3.19 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2964
        1.33 -     1.45: 2008
        1.45 -     1.57: 6179
        1.57 -     1.69: 4
        1.69 -     1.81: 83
  Bond restraints: 11238
  Sorted by residual:
  bond pdb=" N   ILE D  27 "
       pdb=" CA  ILE D  27 "
    ideal  model  delta    sigma   weight residual
    1.459  1.503 -0.044 1.25e-02 6.40e+03 1.23e+01
  bond pdb=" N   ASN B 188 "
       pdb=" CA  ASN B 188 "
    ideal  model  delta    sigma   weight residual
    1.455  1.498 -0.044 1.27e-02 6.20e+03 1.18e+01
  bond pdb=" N   ASN A 144 "
       pdb=" CA  ASN A 144 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.031 9.00e-03 1.23e+04 1.16e+01
  bond pdb=" N   GLN C  23 "
       pdb=" CA  GLN C  23 "
    ideal  model  delta    sigma   weight residual
    1.457  1.501 -0.044 1.32e-02 5.74e+03 1.13e+01
  bond pdb=" N   HIS B  51 "
       pdb=" CA  HIS B  51 "
    ideal  model  delta    sigma   weight residual
    1.456  1.497 -0.041 1.31e-02 5.83e+03 9.76e+00
  ... (remaining 11233 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 14943
        2.55 -     5.10: 284
        5.10 -     7.65: 38
        7.65 -    10.20: 6
       10.20 -    12.76: 2
  Bond angle restraints: 15273
  Sorted by residual:
  angle pdb=" N   LEU D  28 "
        pdb=" CA  LEU D  28 "
        pdb=" C   LEU D  28 "
      ideal   model   delta    sigma   weight residual
     113.16  100.40   12.76 1.24e+00 6.50e-01 1.06e+02
  angle pdb=" N   THR A 194 "
        pdb=" CA  THR A 194 "
        pdb=" C   THR A 194 "
      ideal   model   delta    sigma   weight residual
     110.97  120.01   -9.04 1.09e+00 8.42e-01 6.88e+01
  angle pdb=" C   ILE D  31 "
        pdb=" N   GLU D  32 "
        pdb=" CA  GLU D  32 "
      ideal   model   delta    sigma   weight residual
     120.38  111.58    8.80 1.37e+00 5.33e-01 4.12e+01
  angle pdb=" C   THR D  30 "
        pdb=" N   ILE D  31 "
        pdb=" CA  ILE D  31 "
      ideal   model   delta    sigma   weight residual
     122.66  116.60    6.06 9.70e-01 1.06e+00 3.90e+01
  angle pdb=" N   ILE D  31 "
        pdb=" CA  ILE D  31 "
        pdb=" C   ILE D  31 "
      ideal   model   delta    sigma   weight residual
     111.90  107.04    4.86 8.10e-01 1.52e+00 3.60e+01
  ... (remaining 15268 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.51: 6746
       27.51 -    55.01: 231
       55.01 -    82.52: 35
       82.52 -   110.03: 16
      110.03 -   137.53: 12
  Dihedral angle restraints: 7040
    sinusoidal: 3090
      harmonic: 3950
  Sorted by residual:
  dihedral pdb=" C5A PLP C 601 "
           pdb=" O4P PLP C 601 "
           pdb=" P   PLP C 601 "
           pdb=" O1P PLP C 601 "
      ideal   model   delta sinusoidal    sigma   weight residual
      76.43  174.49  -98.06     1      2.00e+01 2.50e-03 2.74e+01
  dihedral pdb=" C2B Q7G C 602 "
           pdb=" C1B Q7G C 602 "
           pdb=" O5B Q7G C 602 "
           pdb=" C5B Q7G C 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -63.14   74.39 -137.53     1      3.00e+01 1.11e-03 1.85e+01
  dihedral pdb=" C5B Q7G C 602 "
           pdb=" C1B Q7G C 602 "
           pdb=" O5B Q7G C 602 "
           pdb=" O1B Q7G C 602 "
      ideal   model   delta sinusoidal    sigma   weight residual
     301.16  167.13  134.03     1      3.00e+01 1.11e-03 1.81e+01
  ... (remaining 7037 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1508
       0.072 -    0.143: 202
       0.143 -    0.215: 14
       0.215 -    0.286: 14
       0.286 -    0.358: 2
  Chirality restraints: 1740
  Sorted by residual:
  chirality pdb=" CA  LEU D  28 "
            pdb=" N   LEU D  28 "
            pdb=" C   LEU D  28 "
            pdb=" CB  LEU D  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.87   -0.36 2.00e-01 2.50e+01 3.20e+00
  chirality pdb=" C4  Z8A A 302 "
            pdb=" C3  Z8A A 302 "
            pdb=" C5  Z8A A 302 "
            pdb=" O2  Z8A A 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.29   -2.63    0.34 2.00e-01 2.50e+01 2.89e+00
  chirality pdb=" C51 Q7G C 602 "
            pdb=" C41 Q7G C 602 "
            pdb=" C61 Q7G C 602 "
            pdb=" O51 Q7G C 602 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.21   -2.49    0.28 2.00e-01 2.50e+01 2.01e+00
  ... (remaining 1737 not shown)

  Planarity restraints: 1904
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C20 ERG A 301 "   -0.097 2.00e-02 2.50e+03   9.78e-02 9.56e+01
        pdb=" C22 ERG A 301 "    0.096 2.00e-02 2.50e+03
        pdb=" C23 ERG A 301 "    0.099 2.00e-02 2.50e+03
        pdb=" C24 ERG A 301 "   -0.098 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C11 Q7G C 602 "    0.018 2.00e-02 2.50e+03   6.86e-02 5.88e+01
        pdb=" C13 Q7G C 602 "    0.011 2.00e-02 2.50e+03
        pdb=" C14 Q7G C 602 "    0.113 2.00e-02 2.50e+03
        pdb=" C15 Q7G C 602 "   -0.083 2.00e-02 2.50e+03
        pdb=" C16 Q7G C 602 "   -0.059 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C20 ERG A 303 "   -0.052 2.00e-02 2.50e+03   5.20e-02 2.71e+01
        pdb=" C22 ERG A 303 "    0.052 2.00e-02 2.50e+03
        pdb=" C23 ERG A 303 "    0.052 2.00e-02 2.50e+03
        pdb=" C24 ERG A 303 "   -0.052 2.00e-02 2.50e+03
  ... (remaining 1901 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 46
        2.56 -     3.15: 8566
        3.15 -     3.73: 14955
        3.73 -     4.32: 20247
        4.32 -     4.90: 35209
  Nonbonded interactions: 79023
  Sorted by model distance:
  nonbonded pdb=" CD1 PHE B 185 "
            pdb=" CD1 TYR B 186 "
     model   vdw
     1.975 3.640
  nonbonded pdb=" CD1 PHE B 185 "
            pdb=" N   TYR B 186 "
     model   vdw
     2.182 3.420
  nonbonded pdb=" OH  TYR B 460 "
            pdb=" OE1 GLU B 488 "
     model   vdw
     2.215 3.040
  nonbonded pdb=" O   ALA B 183 "
            pdb=" ND2 ASN B 188 "
     model   vdw
     2.262 3.120
  nonbonded pdb=" O   ASN A  74 "
            pdb=" OG1 THR A  78 "
     model   vdw
     2.273 3.040
  ... (remaining 79018 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:             5.690
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     27.920
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   37.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
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      :  0.006   0.055  11238  Z= 0.362
  Angle     :  0.848  12.756  15273  Z= 0.489
  Chirality :  0.054   0.358   1740
  Planarity :  0.006   0.098   1904
  Dihedral  : 15.812 137.534   4498
  Min Nonbonded Distance : 1.975

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  5.02 %
    Favored  : 94.23 %
  Cbeta Deviations :  0.08 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.48 (0.20), residues: 1342
  helix: -0.34 (0.19), residues: 595
  sheet:  0.32 (0.51), residues: 113
  loop : -1.86 (0.21), residues: 634

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 102 
 HIS   0.010   0.001   HIS A 206 
 PHE   0.013   0.001   PHE C 109 
 TYR   0.028   0.002   TYR B 186 
 ARG   0.004   0.001   ARG B 454 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 233
  time to evaluate  : 1.180 
Fit side-chains
REVERT: A   82 GLN cc_start: 0.8846 (mm110) cc_final: 0.8629 (mm-40)
REVERT: B  274 GLN cc_start: 0.8092 (tp-100) cc_final: 0.7826 (tp-100)
REVERT: B  373 LEU cc_start: 0.9189 (tp) cc_final: 0.8924 (tt)
REVERT: B  547 GLN cc_start: 0.7334 (tp40) cc_final: 0.7081 (tm-30)
REVERT: C   23 GLN cc_start: 0.8608 (tp40) cc_final: 0.8380 (tp40)
REVERT: D    7 SER cc_start: 0.8750 (t) cc_final: 0.8382 (p)
  outliers start: 9
  outliers final: 2
  residues processed: 240
  average time/residue: 0.2608
  time to fit residues: 86.2098
Evaluate side-chains
  114 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 112
  time to evaluate  : 1.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   42 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 112 optimal weight:    3.9990
   chunk 100 optimal weight:    0.6980
   chunk 55 optimal weight:    0.7980
   chunk 34 optimal weight:    5.9990
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    0.9980
   chunk 104 optimal weight:    0.7980
   chunk 40 optimal weight:    0.7980
   chunk 63 optimal weight:    2.9990
   chunk 77 optimal weight:    0.6980
   chunk 120 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 116 ASN
A 180 HIS
B  50 HIS
C  90 HIS
C 142 HIS
C 145 ASN
C 170 GLN
C 229 ASN
C 291 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7670
moved from start:          0.2860

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  11238  Z= 0.218
  Angle     :  0.646  11.443  15273  Z= 0.323
  Chirality :  0.044   0.242   1740
  Planarity :  0.005   0.043   1904
  Dihedral  : 12.840 124.847   1923
  Min Nonbonded Distance : 2.440

Molprobity Statistics.
  All-atom Clashscore : 4.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  1.76 %
    Allowed  : 12.05 %
    Favored  : 86.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.17 (0.22), residues: 1342
  helix:  1.20 (0.21), residues: 612
  sheet:  0.84 (0.49), residues: 116
  loop : -1.74 (0.22), residues: 614

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 188 
 HIS   0.006   0.001   HIS C  96 
 PHE   0.025   0.001   PHE C 106 
 TYR   0.022   0.001   TYR B  66 
 ARG   0.004   0.000   ARG D  19 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 131
  time to evaluate  : 1.215 
Fit side-chains
REVERT: A   82 GLN cc_start: 0.8783 (mm110) cc_final: 0.8558 (mm-40)
REVERT: A  143 ASP cc_start: 0.8420 (t0) cc_final: 0.8207 (t0)
REVERT: A  207 ARG cc_start: 0.8735 (mtp85) cc_final: 0.8277 (mtt-85)
REVERT: B   91 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7642 (mp10)
REVERT: B  274 GLN cc_start: 0.7923 (tp-100) cc_final: 0.7717 (tp-100)
REVERT: C  292 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7095 (mtp85)
REVERT: D    7 SER cc_start: 0.8776 (t) cc_final: 0.8396 (p)
REVERT: D   37 LYS cc_start: 0.7365 (tttm) cc_final: 0.6968 (tppt)
  outliers start: 21
  outliers final: 11
  residues processed: 144
  average time/residue: 0.2645
  time to fit residues: 53.2888
Evaluate side-chains
  113 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 102
  time to evaluate  : 1.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain D residue   53 SER
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   75 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 100 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 33 optimal weight:    0.4980
   chunk 120 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 119 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 97 optimal weight:    0.9980
   overall best weight:    0.9982

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

Flipped N/Q/H residues before XYZ refinement:
A 138 ASN
C  90 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.4235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  11238  Z= 0.238
  Angle     :  0.626   8.798  15273  Z= 0.313
  Chirality :  0.045   0.313   1740
  Planarity :  0.004   0.043   1904
  Dihedral  : 10.650 112.463   1920
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 12.55 %
    Favored  : 84.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.16 (0.23), residues: 1342
  helix:  1.60 (0.22), residues: 607
  sheet:  0.82 (0.46), residues: 128
  loop : -1.69 (0.23), residues: 607

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 188 
 HIS   0.007   0.001   HIS C  90 
 PHE   0.021   0.002   PHE D  62 
 TYR   0.018   0.001   TYR B  66 
 ARG   0.005   0.000   ARG D  19 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 121
  time to evaluate  : 1.264 
Fit side-chains
   revert: symmetry clash
REVERT: A  143 ASP cc_start: 0.8529 (t0) cc_final: 0.8304 (t0)
REVERT: A  178 TYR cc_start: 0.5486 (t80) cc_final: 0.5279 (t80)
REVERT: B   91 GLN cc_start: 0.8265 (mm-40) cc_final: 0.7783 (pm20)
REVERT: B  337 GLU cc_start: 0.8516 (OUTLIER) cc_final: 0.8308 (tt0)
REVERT: C  272 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7954 (mmt)
REVERT: C  292 ARG cc_start: 0.7746 (mtp85) cc_final: 0.7283 (mtp85)
REVERT: C  405 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7935 (tt0)
REVERT: C  424 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.7870 (tm-30)
REVERT: D    7 SER cc_start: 0.8830 (t) cc_final: 0.8412 (p)
REVERT: D   37 LYS cc_start: 0.7591 (tttm) cc_final: 0.7156 (tppt)
  outliers start: 32
  outliers final: 20
  residues processed: 145
  average time/residue: 0.2505
  time to fit residues: 51.5178
Evaluate side-chains
  128 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 104
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  552 CYS
Chi-restraints excluded: chain C residue   22 ILE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   86 GLN
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  199 THR
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain C residue  405 GLN
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  424 GLU
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   56 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 119 optimal weight:    2.9990
   chunk 90 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 57 optimal weight:    3.9990
   chunk 81 optimal weight:    0.8980
   chunk 121 optimal weight:    1.9990
   chunk 128 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 115 optimal weight:    2.9990
   chunk 34 optimal weight:    2.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 138 ASN
B 258 HIS
B 502 ASN
C 143 ASN
D  60 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.5082

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.048  11238  Z= 0.446
  Angle     :  0.731  10.873  15273  Z= 0.378
  Chirality :  0.049   0.222   1740
  Planarity :  0.005   0.045   1904
  Dihedral  : 10.298 122.747   1920
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 13.22 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.23), residues: 1342
  helix:  1.39 (0.22), residues: 601
  sheet:  0.55 (0.47), residues: 121
  loop : -1.84 (0.22), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 188 
 HIS   0.005   0.001   HIS C  76 
 PHE   0.023   0.002   PHE B 318 
 TYR   0.023   0.002   TYR C 510 
 ARG   0.005   0.001   ARG C 132 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 105
  time to evaluate  : 1.259 
Fit side-chains
REVERT: A  143 ASP cc_start: 0.8544 (t0) cc_final: 0.8324 (t0)
REVERT: A  178 TYR cc_start: 0.5952 (t80) cc_final: 0.5656 (t80)
REVERT: B   91 GLN cc_start: 0.8328 (mm-40) cc_final: 0.8078 (mm-40)
REVERT: B  337 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8410 (tt0)
REVERT: B  533 MET cc_start: 0.8676 (mtt) cc_final: 0.8325 (mtt)
REVERT: C  117 ARG cc_start: 0.8230 (mpt180) cc_final: 0.7359 (mmm-85)
REVERT: C  239 LYS cc_start: 0.8496 (ttmt) cc_final: 0.8027 (ttpp)
REVERT: C  247 GLU cc_start: 0.7592 (pt0) cc_final: 0.7305 (pt0)
REVERT: C  272 MET cc_start: 0.8344 (OUTLIER) cc_final: 0.7936 (mmt)
REVERT: C  292 ARG cc_start: 0.7818 (mtp85) cc_final: 0.7349 (mtp85)
REVERT: C  405 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8083 (tt0)
REVERT: D   37 LYS cc_start: 0.7989 (tttm) cc_final: 0.7604 (tppt)
  outliers start: 45
  outliers final: 30
  residues processed: 137
  average time/residue: 0.2373
  time to fit residues: 47.1354
Evaluate side-chains
  129 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 96
  time to evaluate  : 1.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  138 ASN
Chi-restraints excluded: chain A residue  153 ASP
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  436 VAL
Chi-restraints excluded: chain B residue  519 LEU
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain C residue  357 VAL
Chi-restraints excluded: chain C residue  405 GLN
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  460 LEU
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain D residue   14 THR
Chi-restraints excluded: chain D residue   18 LYS
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   56 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 107 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 53 optimal weight:    0.7980
   chunk 109 optimal weight:    2.9990
   chunk 88 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 115 optimal weight:    0.8980
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A  76 ASN
B 502 ASN
C  78 HIS
D  60 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7869
moved from start:          0.5228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  11238  Z= 0.201
  Angle     :  0.566   9.990  15273  Z= 0.287
  Chirality :  0.043   0.226   1740
  Planarity :  0.004   0.041   1904
  Dihedral  :  9.860 123.767   1920
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.91 %
    Favored  : 97.09 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 13.97 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.13 (0.23), residues: 1342
  helix:  1.71 (0.22), residues: 602
  sheet:  0.44 (0.49), residues: 116
  loop : -1.71 (0.23), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 110 
 HIS   0.005   0.001   HIS D  60 
 PHE   0.015   0.001   PHE C 329 
 TYR   0.017   0.001   TYR B  66 
 ARG   0.002   0.000   ARG C 132 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 112
  time to evaluate  : 1.258 
Fit side-chains
REVERT: B  280 LEU cc_start: 0.8887 (OUTLIER) cc_final: 0.8614 (tt)
REVERT: B  337 GLU cc_start: 0.8578 (OUTLIER) cc_final: 0.8296 (tt0)
REVERT: B  533 MET cc_start: 0.8558 (mtt) cc_final: 0.8272 (mtt)
REVERT: C   23 GLN cc_start: 0.8951 (tp40) cc_final: 0.8737 (tp-100)
REVERT: C  117 ARG cc_start: 0.8148 (mpt180) cc_final: 0.7373 (mmm-85)
REVERT: C  146 GLU cc_start: 0.8436 (mm-30) cc_final: 0.8236 (mt-10)
REVERT: C  239 LYS cc_start: 0.8447 (ttmt) cc_final: 0.8032 (ttpp)
REVERT: C  272 MET cc_start: 0.8240 (OUTLIER) cc_final: 0.7980 (mmt)
REVERT: C  292 ARG cc_start: 0.7763 (mtp85) cc_final: 0.7305 (mtp85)
REVERT: C  405 GLN cc_start: 0.8303 (OUTLIER) cc_final: 0.8080 (tp40)
REVERT: D   37 LYS cc_start: 0.7993 (tttm) cc_final: 0.7604 (tppt)
  outliers start: 35
  outliers final: 24
  residues processed: 140
  average time/residue: 0.2422
  time to fit residues: 49.0361
Evaluate side-chains
  134 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 106
  time to evaluate  : 1.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue   86 GLN
Chi-restraints excluded: chain C residue   91 LEU
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  248 LEU
Chi-restraints excluded: chain C residue  260 SER
Chi-restraints excluded: chain C residue  272 MET
Chi-restraints excluded: chain C residue  357 VAL
Chi-restraints excluded: chain C residue  405 GLN
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   69 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 43 optimal weight:    2.9990
   chunk 115 optimal weight:    0.3980
   chunk 25 optimal weight:    1.9990
   chunk 75 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9990
   chunk 128 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9990
   chunk 10 optimal weight:    0.7980
   chunk 42 optimal weight:    0.9980
   chunk 67 optimal weight:    0.0870
   overall best weight:    0.6560

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

Flipped N/Q/H residues before XYZ refinement:
A 138 ASN
D  29 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.5341

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11238  Z= 0.175
  Angle     :  0.536   9.082  15273  Z= 0.272
  Chirality :  0.042   0.230   1740
  Planarity :  0.004   0.039   1904
  Dihedral  :  9.624 122.673   1920
  Min Nonbonded Distance : 2.323

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  3.01 %
    Allowed  : 14.98 %
    Favored  : 82.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.27 (0.23), residues: 1342
  helix:  1.82 (0.22), residues: 608
  sheet:  0.48 (0.50), residues: 118
  loop : -1.66 (0.23), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 110 
 HIS   0.005   0.001   HIS D  60 
 PHE   0.014   0.001   PHE C 329 
 TYR   0.016   0.001   TYR B  66 
 ARG   0.002   0.000   ARG C 132 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 109
  time to evaluate  : 1.290 
Fit side-chains
REVERT: B  280 LEU cc_start: 0.8857 (OUTLIER) cc_final: 0.8563 (tt)
REVERT: B  337 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8271 (tt0)
REVERT: B  533 MET cc_start: 0.8549 (mtt) cc_final: 0.8247 (mtt)
REVERT: C   17 GLU cc_start: 0.8374 (pm20) cc_final: 0.7549 (tm-30)
REVERT: C   23 GLN cc_start: 0.8962 (tp40) cc_final: 0.8737 (tp-100)
REVERT: C  117 ARG cc_start: 0.8097 (mpt180) cc_final: 0.7394 (mmm-85)
REVERT: C  146 GLU cc_start: 0.8490 (mm-30) cc_final: 0.8283 (mt-10)
REVERT: C  239 LYS cc_start: 0.8320 (ttmt) cc_final: 0.7901 (ttpp)
REVERT: C  292 ARG cc_start: 0.7712 (mtp85) cc_final: 0.7187 (mtp85)
REVERT: C  405 GLN cc_start: 0.8295 (OUTLIER) cc_final: 0.8083 (tp40)
REVERT: C  521 LYS cc_start: 0.7627 (ttmt) cc_final: 0.7374 (ttmm)
REVERT: D   37 LYS cc_start: 0.7944 (tttm) cc_final: 0.7554 (tppt)
  outliers start: 36
  outliers final: 24
  residues processed: 135
  average time/residue: 0.2403
  time to fit residues: 46.5450
Evaluate side-chains
  133 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 106
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  138 ASN
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue   78 HIS
Chi-restraints excluded: chain C residue   84 THR
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  162 SER
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  357 VAL
Chi-restraints excluded: chain C residue  405 GLN
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   56 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0970
   chunk 93 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 108 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9990
   chunk 128 optimal weight:    9.9990
   chunk 80 optimal weight:    6.9990
   chunk 78 optimal weight:    2.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.6778

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

Flipped N/Q/H residues before XYZ refinement:
B 192 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.5405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  11238  Z= 0.176
  Angle     :  0.536   9.020  15273  Z= 0.271
  Chirality :  0.042   0.225   1740
  Planarity :  0.004   0.040   1904
  Dihedral  :  9.512 121.179   1920
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 3.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.83 %
    Favored  : 97.17 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 15.73 %
    Favored  : 81.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.38 (0.23), residues: 1342
  helix:  1.92 (0.22), residues: 608
  sheet:  0.52 (0.51), residues: 118
  loop : -1.62 (0.23), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 110 
 HIS   0.004   0.001   HIS D  60 
 PHE   0.013   0.001   PHE C  85 
 TYR   0.016   0.001   TYR B  66 
 ARG   0.002   0.000   ARG C   9 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 106
  time to evaluate  : 1.262 
Fit side-chains
REVERT: A  125 VAL cc_start: 0.8373 (p) cc_final: 0.8167 (p)
REVERT: B  261 MET cc_start: 0.7280 (mmp) cc_final: 0.6541 (mmp)
REVERT: B  280 LEU cc_start: 0.8846 (OUTLIER) cc_final: 0.8571 (tt)
REVERT: B  337 GLU cc_start: 0.8565 (OUTLIER) cc_final: 0.8281 (tt0)
REVERT: B  533 MET cc_start: 0.8545 (mtt) cc_final: 0.8242 (mtt)
REVERT: C   17 GLU cc_start: 0.8363 (pm20) cc_final: 0.7555 (tm-30)
REVERT: C  117 ARG cc_start: 0.8098 (mpt180) cc_final: 0.7426 (mmm-85)
REVERT: C  239 LYS cc_start: 0.8291 (ttmt) cc_final: 0.7875 (ttpp)
REVERT: C  272 MET cc_start: 0.8596 (mmp) cc_final: 0.8175 (mmp)
REVERT: C  405 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8063 (tp40)
REVERT: D   37 LYS cc_start: 0.7930 (tttm) cc_final: 0.7549 (tppt)
  outliers start: 32
  outliers final: 25
  residues processed: 132
  average time/residue: 0.2439
  time to fit residues: 46.7704
Evaluate side-chains
  129 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 101
  time to evaluate  : 1.278 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   78 HIS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  405 GLN
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   56 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 51 optimal weight:    5.9990
   chunk 76 optimal weight:    0.7980
   chunk 38 optimal weight:    0.1980
   chunk 25 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 87 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 11 optimal weight:    0.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    0.9584

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

Flipped N/Q/H residues before XYZ refinement:
A 220 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7873
moved from start:          0.5468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  11238  Z= 0.222
  Angle     :  0.560   9.647  15273  Z= 0.284
  Chirality :  0.043   0.232   1740
  Planarity :  0.004   0.040   1904
  Dihedral  :  9.482 120.224   1920
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  2.51 %
    Allowed  : 16.23 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.39 (0.23), residues: 1342
  helix:  1.92 (0.22), residues: 609
  sheet:  0.65 (0.52), residues: 113
  loop : -1.62 (0.23), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 110 
 HIS   0.003   0.001   HIS C 203 
 PHE   0.013   0.001   PHE B 318 
 TYR   0.017   0.001   TYR C 510 
 ARG   0.002   0.000   ARG C 132 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 103
  time to evaluate  : 1.313 
Fit side-chains
REVERT: B  280 LEU cc_start: 0.8854 (OUTLIER) cc_final: 0.8576 (tt)
REVERT: B  337 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8316 (tt0)
REVERT: B  424 PHE cc_start: 0.7552 (OUTLIER) cc_final: 0.6928 (t80)
REVERT: B  533 MET cc_start: 0.8565 (mtt) cc_final: 0.8240 (mtt)
REVERT: C  117 ARG cc_start: 0.8182 (mpt180) cc_final: 0.7490 (mmm-85)
REVERT: C  239 LYS cc_start: 0.8348 (ttmt) cc_final: 0.7929 (ttpp)
REVERT: C  272 MET cc_start: 0.8554 (mmp) cc_final: 0.8028 (mmp)
REVERT: C  405 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.8098 (tp40)
REVERT: D   37 LYS cc_start: 0.7985 (tttm) cc_final: 0.7576 (tppt)
  outliers start: 30
  outliers final: 25
  residues processed: 126
  average time/residue: 0.2502
  time to fit residues: 45.1670
Evaluate side-chains
  130 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 101
  time to evaluate  : 1.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  176 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue   69 ILE
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  272 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  405 GLN
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   69 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 116 optimal weight:    1.9990
   chunk 122 optimal weight:    0.8980
   chunk 112 optimal weight:    0.5980
   chunk 119 optimal weight:    0.5980
   chunk 71 optimal weight:    0.0030
   chunk 52 optimal weight:    0.5980
   chunk 93 optimal weight:    1.9990
   chunk 36 optimal weight:    0.7980
   chunk 107 optimal weight:    4.9990
   chunk 78 optimal weight:    0.9990
   chunk 126 optimal weight:    4.9990
   overall best weight:    0.5190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.5564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  11238  Z= 0.157
  Angle     :  0.521   9.027  15273  Z= 0.263
  Chirality :  0.041   0.237   1740
  Planarity :  0.004   0.040   1904
  Dihedral  :  9.247 117.998   1920
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.57 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.23), residues: 1342
  helix:  2.03 (0.22), residues: 608
  sheet:  0.60 (0.52), residues: 114
  loop : -1.56 (0.23), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 110 
 HIS   0.003   0.001   HIS C  78 
 PHE   0.012   0.001   PHE C 329 
 TYR   0.015   0.001   TYR B  66 
 ARG   0.002   0.000   ARG C   9 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 1.273 
Fit side-chains
REVERT: B  261 MET cc_start: 0.7143 (mmp) cc_final: 0.6407 (mmp)
REVERT: B  280 LEU cc_start: 0.8832 (OUTLIER) cc_final: 0.8547 (tt)
REVERT: B  337 GLU cc_start: 0.8535 (OUTLIER) cc_final: 0.8244 (tt0)
REVERT: B  424 PHE cc_start: 0.7250 (OUTLIER) cc_final: 0.6739 (t80)
REVERT: B  533 MET cc_start: 0.8525 (mtt) cc_final: 0.8209 (mtt)
REVERT: C   17 GLU cc_start: 0.8326 (pm20) cc_final: 0.7449 (tm-30)
REVERT: C  117 ARG cc_start: 0.8147 (mpt180) cc_final: 0.7467 (mmm-85)
REVERT: C  119 ASP cc_start: 0.9012 (t0) cc_final: 0.8635 (t0)
REVERT: C  239 LYS cc_start: 0.8262 (ttmt) cc_final: 0.7979 (ttpp)
REVERT: C  272 MET cc_start: 0.8533 (mmp) cc_final: 0.8050 (mmp)
  outliers start: 27
  outliers final: 22
  residues processed: 121
  average time/residue: 0.2356
  time to fit residues: 41.1517
Evaluate side-chains
  122 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 97
  time to evaluate  : 1.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain B residue   32 VAL
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  291 GLU
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue   78 HIS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   69 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 77 optimal weight:    3.9990
   chunk 59 optimal weight:    0.9990
   chunk 87 optimal weight:    2.9990
   chunk 132 optimal weight:    0.3980
   chunk 121 optimal weight:    1.9990
   chunk 105 optimal weight:    0.6980
   chunk 10 optimal weight:    4.9990
   chunk 81 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9990
   chunk 83 optimal weight:    0.9990
   chunk 112 optimal weight:    0.1980
   overall best weight:    0.6382

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.5600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11238  Z= 0.173
  Angle     :  0.534   8.612  15273  Z= 0.269
  Chirality :  0.042   0.235   1740
  Planarity :  0.004   0.040   1904
  Dihedral  :  9.159 115.728   1920
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.28 %
    Favored  : 96.72 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 16.57 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.24), residues: 1342
  helix:  2.08 (0.22), residues: 608
  sheet:  0.68 (0.52), residues: 116
  loop : -1.54 (0.23), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 110 
 HIS   0.002   0.001   HIS C  78 
 PHE   0.013   0.001   PHE C 329 
 TYR   0.016   0.001   TYR B  66 
 ARG   0.002   0.000   ARG C 112 

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

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

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2684 Ramachandran restraints generated.
    1342 Oldfield, 0 Emsley, 1342 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 99
  time to evaluate  : 1.298 
Fit side-chains
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8078 (ttmt) cc_final: 0.7680 (ptmt)
REVERT: A  125 VAL cc_start: 0.8274 (p) cc_final: 0.8055 (p)
REVERT: B  280 LEU cc_start: 0.8821 (OUTLIER) cc_final: 0.8536 (tt)
REVERT: B  337 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8257 (tt0)
REVERT: B  424 PHE cc_start: 0.7320 (OUTLIER) cc_final: 0.6808 (t80)
REVERT: B  533 MET cc_start: 0.8521 (mtt) cc_final: 0.8200 (mtt)
REVERT: C   17 GLU cc_start: 0.8328 (pm20) cc_final: 0.7420 (tm-30)
REVERT: C  117 ARG cc_start: 0.8159 (mpt180) cc_final: 0.7531 (mmm-85)
REVERT: C  119 ASP cc_start: 0.9026 (t0) cc_final: 0.8672 (t0)
REVERT: C  239 LYS cc_start: 0.8235 (ttmt) cc_final: 0.7952 (ttpp)
REVERT: C  272 MET cc_start: 0.8537 (mmp) cc_final: 0.8007 (mmp)
  outliers start: 26
  outliers final: 20
  residues processed: 120
  average time/residue: 0.2420
  time to fit residues: 42.1731
Evaluate side-chains
  121 residues out of total 1195 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 98
  time to evaluate  : 1.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   61 GLU
Chi-restraints excluded: chain A residue  107 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  211 SER
Chi-restraints excluded: chain B residue   42 ILE
Chi-restraints excluded: chain B residue  185 PHE
Chi-restraints excluded: chain B residue  205 THR
Chi-restraints excluded: chain B residue  280 LEU
Chi-restraints excluded: chain B residue  337 GLU
Chi-restraints excluded: chain B residue  424 PHE
Chi-restraints excluded: chain C residue   77 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  172 LYS
Chi-restraints excluded: chain C residue  391 THR
Chi-restraints excluded: chain C residue  412 THR
Chi-restraints excluded: chain C residue  466 MET
Chi-restraints excluded: chain C residue  495 VAL
Chi-restraints excluded: chain D residue   34 VAL
Chi-restraints excluded: chain D residue   38 LEU
Chi-restraints excluded: chain D residue   41 THR
Chi-restraints excluded: chain D residue   44 ILE
Chi-restraints excluded: chain D residue   56 SER
Chi-restraints excluded: chain D residue   69 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 97 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 29 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0970
   chunk 44 optimal weight:    0.8980
   chunk 108 optimal weight:    1.9990
   chunk 13 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 92 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
C 143 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.125153 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.102490 restraints weight = 17905.910|
|-----------------------------------------------------------------------------|
r_work (start): 0.3418 rms_B_bonded: 2.60
r_work: 0.3280 rms_B_bonded: 3.26 restraints_weight: 0.5000
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8211
moved from start:          0.5629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  11238  Z= 0.221
  Angle     :  0.566   9.124  15273  Z= 0.287
  Chirality :  0.043   0.225   1740
  Planarity :  0.004   0.039   1904
  Dihedral  :  9.162 114.889   1920
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 3.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  2.26 %
    Allowed  : 16.57 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.53 (0.23), residues: 1342
  helix:  2.03 (0.22), residues: 609
  sheet:  0.88 (0.53), residues: 111
  loop : -1.57 (0.23), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 110 
 HIS   0.003   0.001   HIS C 514 
 PHE   0.013   0.001   PHE C 329 
 TYR   0.017   0.001   TYR B  66 
 ARG   0.002   0.000   ARG C 132 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2415.44 seconds
wall clock time: 45 minutes 10.26 seconds (2710.26 seconds total)