Starting phenix.real_space_refine
on Wed Sep 17 19:37:44 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9c6b_45243/09_2025/9c6b_45243.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9c6b_45243/09_2025/9c6b_45243.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9c6b_45243/09_2025/9c6b_45243.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9c6b_45243/09_2025/9c6b_45243.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9c6b_45243/09_2025/9c6b_45243.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9c6b_45243/09_2025/9c6b_45243.cif"
  }
  resolution = 2.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.010
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      61      5.16       5
     C    6783      2.51       5
     N    1841      2.21       5
     O    2050      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10737
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4527
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 581, 4527
          Classifications: {'peptide': 581}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 26, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 3553
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 434, 3553
          Classifications: {'peptide': 434}
          Link IDs: {'PTRANS': 15, 'TRANS': 418}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 2498
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 2498
          Classifications: {'peptide': 308}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 294}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Planarities with less than four sites: {'MLL%COO:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "D"
      Number of atoms: 157
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 21, 157
          Classifications: {'peptide': 21}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 2, 'TRANS': 18}
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 14
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 1, 'FE2': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.83, per 1000 atoms: 0.26
  Number of scatterers: 10737
  At special positions: 0
  Unit cell: (102.498, 103.325, 123.163, 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      61     16.00
     O    2050      8.00
     N    1841      7.00
     C    6783      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: 1.12
  Conformation dependent library (CDL) restraints added in 444.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C 402 "
        pdb="ZN    ZN C 402 " - pdb=" NE2 HIS C  59 "


  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2576

  Finding SS restraints...
    Secondary structure from input PDB file:
      72 helices and 12 sheets defined
      53.5% alpha, 14.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 20
      removed outlier: 3.537A  pdb=" N   LEU A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 24 through 34
    Processing helix  chain 'A' and resid 34 through 43
    Processing helix  chain 'A' and resid 44 through 50
    Processing helix  chain 'A' and resid 50 through 57
      removed outlier: 4.546A  pdb=" N   ASP A  57 " --> pdb=" O   PRO A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 74
      removed outlier: 3.722A  pdb=" N   GLY A  74 " --> pdb=" O   ALA A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 88
      removed outlier: 4.953A  pdb=" N   HIS A  87 " --> pdb=" O   GLU A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 89 through 97
    Processing helix  chain 'A' and resid 101 through 117
      removed outlier: 3.892A  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 137
    Processing helix  chain 'A' and resid 140 through 148
    Processing helix  chain 'A' and resid 150 through 155
      removed outlier: 3.936A  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: 3.585A  pdb=" N   SER A 175 " --> pdb=" O   ARG A 171 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 178 through 194
      removed outlier: 4.659A  pdb=" N   GLY A 190 " --> pdb=" O   ALA A 186 " (cutoff:3.500A)
      removed outlier: 5.042A  pdb=" N   GLU A 191 " --> pdb=" O   SER A 187 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 197 through 204
    Processing helix  chain 'A' and resid 204 through 214
    Processing helix  chain 'A' and resid 217 through 222
    Processing helix  chain 'A' and resid 223 through 233
      removed outlier: 3.712A  pdb=" N   ALA A 227 " --> pdb=" O   LEU A 223 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 244
      removed outlier: 4.509A  pdb=" N   GLU A 241 " --> pdb=" O   GLN A 237 " (cutoff:3.500A)
      removed outlier: 4.958A  pdb=" N   ALA A 242 " --> pdb=" O   GLU A 238 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 253
    Processing helix  chain 'A' and resid 256 through 266
    Processing helix  chain 'A' and resid 266 through 275
    Processing helix  chain 'A' and resid 275 through 282
    Processing helix  chain 'A' and resid 282 through 292
    Processing helix  chain 'A' and resid 295 through 305
      removed outlier: 3.796A  pdb=" N   LYS A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 312
    Processing helix  chain 'A' and resid 317 through 325
    Processing helix  chain 'A' and resid 326 through 335
      removed outlier: 3.888A  pdb=" N   SER A 335 " --> pdb=" O   LYS A 331 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 350
      removed outlier: 3.560A  pdb=" N   SER A 347 " --> pdb=" O   SER A 343 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   VAL A 348 " --> pdb=" O   ALA A 344 " (cutoff:3.500A)
      removed outlier: 4.102A  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 357 through 364
    Processing helix  chain 'A' and resid 364 through 374
      removed outlier: 3.908A  pdb=" N   LEU A 368 " --> pdb=" O   HIS A 364 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 377 through 387
      removed outlier: 3.721A  pdb=" N   ASN A 387 " --> pdb=" O   ASN A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 388 through 393
      removed outlier: 4.212A  pdb=" N   GLU A 393 " --> pdb=" O   ASP A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 413
      removed outlier: 4.497A  pdb=" N   GLN A 402 " --> pdb=" O   ARG A 398 " (cutoff:3.500A)
      removed outlier: 5.490A  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 426
      removed outlier: 3.509A  pdb=" N   ARG A 420 " --> pdb=" O   LYS A 416 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   TYR A 426 " --> pdb=" O   ALA A 422 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 435
    Processing helix  chain 'A' and resid 435 through 442
    Processing helix  chain 'A' and resid 442 through 451
      removed outlier: 4.543A  pdb=" N   LEU A 446 " --> pdb=" O   LYS A 442 " (cutoff:3.500A)
      removed outlier: 3.843A  pdb=" N   LEU A 451 " --> pdb=" O   CYS A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 474
    Processing helix  chain 'A' and resid 474 through 482
      removed outlier: 3.648A  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 521
      removed outlier: 3.569A  pdb=" N   ARG A 498 " --> pdb=" O   ASN A 494 " (cutoff:3.500A)
      removed outlier: 4.481A  pdb=" N   GLU A 510 " --> pdb=" O   ASN A 506 " (cutoff:3.500A)
      removed outlier: 4.573A  pdb=" N   VAL A 511 " --> pdb=" O   VAL A 507 " (cutoff:3.500A)
      removed outlier: 3.922A  pdb=" N   GLY A 513 " --> pdb=" O   SER A 509 " (cutoff:3.500A)
      removed outlier: 7.237A  pdb=" N   GLN A 514 " --> pdb=" O   GLU A 510 " (cutoff:3.500A)
      removed outlier: 8.438A  pdb=" N   ASP A 515 " --> pdb=" O   VAL A 511 " (cutoff:3.500A)
      removed outlier: 4.251A  pdb=" N   ILE A 516 " --> pdb=" O   CYS A 512 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 521 through 528
    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 547
    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 587
    Processing helix  chain 'B' and resid 145 through 149
      removed outlier: 4.024A  pdb=" N   VAL B 149 " --> pdb=" O   PRO B 146 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 221 through 225
      removed outlier: 4.001A  pdb=" N   GLU B 224 " --> pdb=" O   ASN B 221 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 278
    Processing helix  chain 'B' and resid 326 through 330
      removed outlier: 3.754A  pdb=" N   LEU B 329 " --> pdb=" O   HIS B 326 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 339
      removed outlier: 3.753A  pdb=" N   ASN B 339 " --> pdb=" O   SER B 335 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 344
      removed outlier: 3.628A  pdb=" N   PHE B 343 " --> pdb=" O   ASP B 340 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ASP B 344 " --> pdb=" O   CYS B 341 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 340 through 344'
    Processing helix  chain 'B' and resid 382 through 386
      removed outlier: 4.126A  pdb=" N   ASN B 385 " --> pdb=" O   SER B 382 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 413
      No H-bonds generated for 'chain 'B' and resid 411 through 413'
    Processing helix  chain 'C' and resid 3 through 19
      removed outlier: 3.886A  pdb=" N   GLU C  19 " --> pdb=" O   GLU C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 24 through 41
      removed outlier: 4.416A  pdb=" N   LYS C  41 " --> pdb=" O   GLU C  37 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 61 through 73
    Processing helix  chain 'C' and resid 92 through 107
    Processing helix  chain 'C' and resid 120 through 127
      removed outlier: 3.746A  pdb=" N   VAL C 126 " --> pdb=" O   GLN C 122 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 128 through 138
    Processing helix  chain 'C' and resid 140 through 151
      removed outlier: 3.618A  pdb=" N   ASP C 151 " --> pdb=" O   THR C 147 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 176 through 183
      removed outlier: 3.669A  pdb=" N   ILE C 180 " --> pdb=" O   THR C 176 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 199
      removed outlier: 4.003A  pdb=" N   CYS C 196 " --> pdb=" O   GLU C 192 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   LEU C 199 " --> pdb=" O   MET C 195 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 221 through 233
    Processing helix  chain 'C' and resid 264 through 268
    Processing helix  chain 'D' and resid 619 through 631
    Processing sheet with id=AA1, first strand: chain 'B' and resid 390 through 391
      removed outlier: 4.166A  pdb=" N   THR B 390 " --> pdb=" O   PHE B  14 " (cutoff:3.500A)
      removed outlier: 6.784A  pdb=" N   ILE B 441 " --> pdb=" O   SER B  15 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   VAL B  17 " --> pdb=" O   LEU B 439 " (cutoff:3.500A)
      removed outlier: 6.426A  pdb=" N   LEU B 439 " --> pdb=" O   VAL B  17 " (cutoff:3.500A)
      removed outlier: 4.487A  pdb=" N   HIS B 421 " --> pdb=" O   ALA B 434 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 31 through 36
      removed outlier: 6.403A  pdb=" N   GLY B  46 " --> pdb=" O   SER B  32 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   VAL B  34 " --> pdb=" O   ALA B  44 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ALA B  44 " --> pdb=" O   VAL B  34 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   PHE B  36 " --> pdb=" O   LEU B  42 " (cutoff:3.500A)
      removed outlier: 7.099A  pdb=" N   LEU B  42 " --> pdb=" O   PHE B  36 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ASP B  47 " --> pdb=" O   ARG B  51 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   ARG B  51 " --> pdb=" O   ASP B  47 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   VAL B  52 " --> pdb=" O   THR B  76 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   THR B  76 " --> pdb=" O   VAL B  52 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ILE B  54 " --> pdb=" O   TYR B  74 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 83 through 85
    Processing sheet with id=AA4, first strand: chain 'B' and resid 98 through 101
      removed outlier: 3.699A  pdb=" N   LYS B  98 " --> pdb=" O   THR B 114 " (cutoff:3.500A)
      removed outlier: 6.827A  pdb=" N   ILE B 119 " --> pdb=" O   ILE B 171 " (cutoff:3.500A)
      removed outlier: 4.737A  pdb=" N   ILE B 171 " --> pdb=" O   ILE B 119 " (cutoff:3.500A)
      removed outlier: 6.722A  pdb=" N   LEU B 121 " --> pdb=" O   ARG B 169 " (cutoff:3.500A)
      removed outlier: 6.029A  pdb=" N   LYS B 129 " --> pdb=" O   ASP B 161 " (cutoff:3.500A)
      removed outlier: 7.905A  pdb=" N   ASP B 161 " --> pdb=" O   LYS B 129 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 182 through 185
      removed outlier: 6.769A  pdb=" N   ILE B 200 " --> pdb=" O   ILE B 214 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   HIS B 204 " --> pdb=" O   ARG B 210 " (cutoff:3.500A)
      removed outlier: 7.876A  pdb=" N   ARG B 210 " --> pdb=" O   HIS B 204 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234
      removed outlier: 3.818A  pdb=" N   ALA B 231 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 290 through 293
      removed outlier: 3.564A  pdb=" N   ASP B 290 " --> pdb=" O   ARG B 303 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   GLU B 321 " --> pdb=" O   ILE B 310 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 348 through 350
    Processing sheet with id=AA9, first strand: chain 'B' and resid 396 through 398
      removed outlier: 6.867A  pdb=" N   LYS B 396 " --> pdb=" O   ILE B 408 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'C' and resid 45 through 48
      removed outlier: 6.315A  pdb=" N   PHE C 164 " --> pdb=" O   SER C 238 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   VAL C 237 " --> pdb=" O   VAL C 257 " (cutoff:3.500A)
      removed outlier: 7.829A  pdb=" N   ILE C 259 " --> pdb=" O   VAL C 237 " (cutoff:3.500A)
      removed outlier: 6.486A  pdb=" N   ARG C 239 " --> pdb=" O   ILE C 259 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 111 through 113
      removed outlier: 3.516A  pdb=" N   VAL C  52 " --> pdb=" O   LEU C 278 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 202 through 203
      removed outlier: 6.728A  pdb=" N   ASP C 202 " --> pdb=" O   PHE C 220 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3

    501 hydrogen bonds defined for protein.
    1434 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: 2.00

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 3582
        1.34 -     1.46: 2100
        1.46 -     1.58: 5178
        1.58 -     1.69: 0
        1.69 -     1.81: 89
  Bond restraints: 10949
  Sorted by residual:
  bond pdb=" C   MLL C 309 "
       pdb=" OXT MLL C 309 "
    ideal  model  delta    sigma   weight residual
    1.231  1.364 -0.133 2.00e-02 2.50e+03 4.44e+01
  bond pdb=" CA  VAL B 149 "
       pdb=" CB  VAL B 149 "
    ideal  model  delta    sigma   weight residual
    1.530  1.547 -0.017 1.05e-02 9.07e+03 2.49e+00
  bond pdb=" CD  GLU C  15 "
       pdb=" OE1 GLU C  15 "
    ideal  model  delta    sigma   weight residual
    1.249  1.233  0.016 1.90e-02 2.77e+03 7.33e-01
  bond pdb=" C   ASP C 290 "
       pdb=" N   PRO C 291 "
    ideal  model  delta    sigma   weight residual
    1.332  1.343 -0.011 1.30e-02 5.92e+03 7.30e-01
  bond pdb=" CG  GLU C  15 "
       pdb=" CD  GLU C  15 "
    ideal  model  delta    sigma   weight residual
    1.516  1.495  0.021 2.50e-02 1.60e+03 7.13e-01
  ... (remaining 10944 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.47: 14614
        1.47 -     2.94: 169
        2.94 -     4.41: 33
        4.41 -     5.88: 19
        5.88 -     7.36: 3
  Bond angle restraints: 14838
  Sorted by residual:
  angle pdb=" N   VAL C  58 "
        pdb=" CA  VAL C  58 "
        pdb=" C   VAL C  58 "
      ideal   model   delta    sigma   weight residual
     111.90  108.87    3.03 8.10e-01 1.52e+00 1.40e+01
  angle pdb=" C   ARG A 537 "
        pdb=" N   PHE A 538 "
        pdb=" CA  PHE A 538 "
      ideal   model   delta    sigma   weight residual
     121.14  115.85    5.29 1.75e+00 3.27e-01 9.13e+00
  angle pdb=" N   GLU C  15 "
        pdb=" CA  GLU C  15 "
        pdb=" CB  GLU C  15 "
      ideal   model   delta    sigma   weight residual
     110.28  114.73   -4.45 1.55e+00 4.16e-01 8.26e+00
  angle pdb=" CA  GLY B 401 "
        pdb=" C   GLY B 401 "
        pdb=" O   GLY B 401 "
      ideal   model   delta    sigma   weight residual
     122.57  120.10    2.47 9.20e-01 1.18e+00 7.19e+00
  angle pdb=" N   GLY C 296 "
        pdb=" CA  GLY C 296 "
        pdb=" C   GLY C 296 "
      ideal   model   delta    sigma   weight residual
     112.29  115.15   -2.86 1.12e+00 7.97e-01 6.51e+00
  ... (remaining 14833 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.94: 6207
       17.94 -    35.88: 393
       35.88 -    53.82: 58
       53.82 -    71.76: 3
       71.76 -    89.71: 8
  Dihedral angle restraints: 6669
    sinusoidal: 2712
      harmonic: 3957
  Sorted by residual:
  dihedral pdb=" CA  GLU C 297 "
           pdb=" C   GLU C 297 "
           pdb=" N   PRO C 298 "
           pdb=" CA  PRO C 298 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -138.08  -41.92     0      5.00e+00 4.00e-02 7.03e+01
  dihedral pdb=" CA  TYR C 127 "
           pdb=" C   TYR C 127 "
           pdb=" N   GLY C 128 "
           pdb=" CA  GLY C 128 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.82   17.18     0      5.00e+00 4.00e-02 1.18e+01
  dihedral pdb=" CB  GLU A 110 "
           pdb=" CG  GLU A 110 "
           pdb=" CD  GLU A 110 "
           pdb=" OE1 GLU A 110 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -89.71   89.71     1      3.00e+01 1.11e-03 1.06e+01
  ... (remaining 6666 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.027: 972
       0.027 -    0.055: 424
       0.055 -    0.082: 161
       0.082 -    0.109: 96
       0.109 -    0.136: 22
  Chirality restraints: 1675
  Sorted by residual:
  chirality pdb=" CA  PHE A 538 "
            pdb=" N   PHE A 538 "
            pdb=" C   PHE A 538 "
            pdb=" CB  PHE A 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.65e-01
  chirality pdb=" CA  GLU C  15 "
            pdb=" N   GLU C  15 "
            pdb=" C   GLU C  15 "
            pdb=" CB  GLU C  15 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.46e-01
  chirality pdb=" CA  VAL B 154 "
            pdb=" N   VAL B 154 "
            pdb=" C   VAL B 154 "
            pdb=" CB  VAL B 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.24e-01
  ... (remaining 1672 not shown)

  Planarity restraints: 1922
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU C 297 "    0.059 5.00e-02 4.00e+02   8.96e-02 1.28e+01
        pdb=" N   PRO C 298 "   -0.155 5.00e-02 4.00e+02
        pdb=" CA  PRO C 298 "    0.047 5.00e-02 4.00e+02
        pdb=" CD  PRO C 298 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  90 "   -0.026 5.00e-02 4.00e+02   3.95e-02 2.50e+00
        pdb=" N   PRO A  91 "    0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A  91 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A  91 "   -0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 548 "   -0.026 5.00e-02 4.00e+02   3.86e-02 2.39e+00
        pdb=" N   PRO A 549 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO A 549 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 549 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1919 not shown)

  Histogram of nonbonded interaction distances:
        1.43 -     2.12: 5
        2.12 -     2.82: 3095
        2.82 -     3.51: 14736
        3.51 -     4.21: 25399
        4.21 -     4.90: 46496
  Nonbonded interactions: 89731
  Sorted by model distance:
  nonbonded pdb=" OXT MLL C 309 "
            pdb=" C10 MLL C 309 "
     model   vdw
     1.427 3.460
  nonbonded pdb=" OD2 ASP C  85 "
            pdb="FE   FE2 C 401 "
     model   vdw
     1.940 3.000
  nonbonded pdb=" ND1 HIS C 241 "
            pdb="FE   FE2 C 401 "
     model   vdw
     1.998 3.080
  nonbonded pdb=" NE2 HIS C 167 "
            pdb="FE   FE2 C 401 "
     model   vdw
     2.015 3.080
  nonbonded pdb=" OD2 ASP C  85 "
            pdb="ZN    ZN C 402 "
     model   vdw
     2.066 2.230
  ... (remaining 89726 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:             3.940
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     13.920
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:8.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   26.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8470
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      :  0.003   0.133  10950  Z= 0.141
  Angle     :  0.474   7.356  14838  Z= 0.253
  Chirality :  0.041   0.136   1675
  Planarity :  0.004   0.090   1922
  Dihedral  : 11.993  89.706   4093
  Min Nonbonded Distance : 1.427

Molprobity Statistics.
  All-atom Clashscore : 4.87
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.40 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.17 %
    Favored  : 99.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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:  0.89 (0.24), residues: 1333
  helix:  1.32 (0.22), residues: 604
  sheet:  0.24 (0.36), residues: 227
  loop :  0.01 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 158 
 TYR   0.009   0.001   TYR B 244 
 PHE   0.019   0.001   PHE A 538 
 TRP   0.023   0.001   TRP B 424 
 HIS   0.003   0.001   HIS C 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (10949)
  covalent geometry    : angle       0.47450 (14838)
  hydrogen bonds       : bond        0.19646 (  501)
  hydrogen bonds       : angle       6.10739 ( 1434)
  metal coordination   : bond        0.00099 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.418 
Fit side-chains
REVERT: B  396 LYS cc_start: 0.8931 (tppp) cc_final: 0.8662 (ttmm)
REVERT: C   15 GLU cc_start: 0.8397 (mp0) cc_final: 0.8170 (mp0)
REVERT: C  131 ASP cc_start: 0.8449 (t70) cc_final: 0.8173 (t0)
REVERT: C  179 HIS cc_start: 0.9231 (m90) cc_final: 0.8774 (m170)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.8419
  time to fit residues: 64.5237
Evaluate side-chains
  54 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 54
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 98 optimal weight:    3.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    0.5980
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    8.9990
   chunk 77 optimal weight:    0.0870
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    2.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.7364

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

Flipped N/Q/H residues before XYZ refinement:
B   8 ASN
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 191 HIS
D 619 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.085286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2899 r_free = 0.2899 target = 0.056428 restraints weight = 22040.009|
|-----------------------------------------------------------------------------|
r_work (start): 0.2869 rms_B_bonded: 3.08
r_work: 0.2715 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.0986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  10950  Z= 0.206
  Angle     :  0.543   6.677  14838  Z= 0.288
  Chirality :  0.043   0.145   1675
  Planarity :  0.004   0.065   1922
  Dihedral  :  4.213  40.435   1461
  Min Nonbonded Distance : 1.941

Molprobity Statistics.
  All-atom Clashscore : 3.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  4.59 %
    Favored  : 94.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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:  0.77 (0.23), residues: 1333
  helix:  1.22 (0.22), residues: 627
  sheet:  0.36 (0.37), residues: 216
  loop : -0.24 (0.26), residues: 490

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 398 
 TYR   0.012   0.001   TYR B  74 
 PHE   0.033   0.002   PHE A 538 
 TRP   0.015   0.002   TRP B 424 
 HIS   0.015   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (10949)
  covalent geometry    : angle       0.54313 (14838)
  hydrogen bonds       : bond        0.04857 (  501)
  hydrogen bonds       : angle       4.83916 ( 1434)
  metal coordination   : bond        0.00208 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 55
  time to evaluate  : 0.538 
Fit side-chains
REVERT: A  323 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8312 (mpp)
REVERT: C  131 ASP cc_start: 0.8896 (t70) cc_final: 0.8648 (t0)
REVERT: C  179 HIS cc_start: 0.9320 (m90) cc_final: 0.9081 (m-70)
REVERT: C  230 HIS cc_start: 0.8647 (m-70) cc_final: 0.8393 (m-70)
  outliers start: 7
  outliers final: 1
  residues processed: 55
  average time/residue: 0.7776
  time to fit residues: 46.0240
Evaluate side-chains
  49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.460 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain A residue  323 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 7 optimal weight:    3.9990
   chunk 56 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 45 optimal weight:    0.5980
   chunk 60 optimal weight:    1.9990
   chunk 88 optimal weight:    1.9990
   chunk 13 optimal weight:    0.3980
   chunk 15 optimal weight:    1.9990
   chunk 115 optimal weight:    3.9990
   chunk 81 optimal weight:    2.9990
   chunk 96 optimal weight:    0.0670
   overall best weight:    0.8122

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

Flipped N/Q/H residues before XYZ refinement:
** B 326 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.086713 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2956 r_free = 0.2956 target = 0.058500 restraints weight = 21878.187|
|-----------------------------------------------------------------------------|
r_work (start): 0.2917 rms_B_bonded: 3.01
r_work: 0.2764 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2764
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8242
moved from start:          0.1196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10950  Z= 0.121
  Angle     :  0.481   6.597  14838  Z= 0.254
  Chirality :  0.040   0.137   1675
  Planarity :  0.004   0.066   1922
  Dihedral  :  4.090  37.430   1461
  Min Nonbonded Distance : 2.045

Molprobity Statistics.
  All-atom Clashscore : 3.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  6.42 %
    Favored  : 93.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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:  0.88 (0.23), residues: 1333
  helix:  1.38 (0.22), residues: 631
  sheet:  0.33 (0.37), residues: 216
  loop : -0.24 (0.26), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 398 
 TYR   0.012   0.001   TYR B 244 
 PHE   0.027   0.001   PHE A 538 
 TRP   0.014   0.001   TRP B 203 
 HIS   0.010   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10949)
  covalent geometry    : angle       0.48068 (14838)
  hydrogen bonds       : bond        0.03882 (  501)
  hydrogen bonds       : angle       4.43403 ( 1434)
  metal coordination   : bond        0.00135 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 51
  time to evaluate  : 0.430 
Fit side-chains
REVERT: B  358 MET cc_start: 0.9594 (ttp) cc_final: 0.9386 (ttp)
REVERT: C  131 ASP cc_start: 0.8835 (t70) cc_final: 0.8546 (t0)
REVERT: C  179 HIS cc_start: 0.9311 (m90) cc_final: 0.9057 (m-70)
REVERT: C  230 HIS cc_start: 0.8643 (m-70) cc_final: 0.8363 (m-70)
  outliers start: 6
  outliers final: 1
  residues processed: 53
  average time/residue: 0.7252
  time to fit residues: 41.5312
Evaluate side-chains
  48 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 47
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  281 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 99 optimal weight:    0.7980
   chunk 37 optimal weight:    0.7980
   chunk 52 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 21 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   chunk 31 optimal weight:    0.2980
   chunk 46 optimal weight:    4.9990
   chunk 25 optimal weight:    0.1980
   chunk 108 optimal weight:    2.9990
   chunk 71 optimal weight:    0.0770
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
B 326 HIS
C 191 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.088583 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3002 r_free = 0.3002 target = 0.060436 restraints weight = 21827.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.2959 rms_B_bonded: 3.02
r_work: 0.2808 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8212
moved from start:          0.1469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10950  Z= 0.090
  Angle     :  0.470  11.072  14838  Z= 0.241
  Chirality :  0.040   0.135   1675
  Planarity :  0.003   0.040   1922
  Dihedral  :  3.876  32.692   1461
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 3.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.75 %
    Allowed  :  7.26 %
    Favored  : 91.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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:  1.04 (0.24), residues: 1333
  helix:  1.55 (0.22), residues: 631
  sheet:  0.31 (0.37), residues: 231
  loop : -0.19 (0.27), residues: 471

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 398 
 TYR   0.012   0.001   TYR B 244 
 PHE   0.023   0.001   PHE A 538 
 TRP   0.013   0.001   TRP B 203 
 HIS   0.008   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00195 (10949)
  covalent geometry    : angle       0.46983 (14838)
  hydrogen bonds       : bond        0.03100 (  501)
  hydrogen bonds       : angle       4.09587 ( 1434)
  metal coordination   : bond        0.00072 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 56
  time to evaluate  : 0.461 
Fit side-chains
REVERT: B  358 MET cc_start: 0.9560 (ttp) cc_final: 0.9295 (ttp)
REVERT: B  389 ARG cc_start: 0.8134 (mmp80) cc_final: 0.7605 (mmp-170)
REVERT: C  131 ASP cc_start: 0.8836 (t70) cc_final: 0.8564 (OUTLIER)
REVERT: C  179 HIS cc_start: 0.9310 (m90) cc_final: 0.9104 (m-70)
REVERT: C  230 HIS cc_start: 0.8677 (m-70) cc_final: 0.8398 (m-70)
REVERT: C  281 THR cc_start: 0.9381 (OUTLIER) cc_final: 0.9101 (p)
REVERT: D  621 ARG cc_start: 0.7999 (mmm160) cc_final: 0.7656 (tpt170)
REVERT: D  624 GLU cc_start: 0.7274 (tm-30) cc_final: 0.6906 (tm-30)
  outliers start: 9
  outliers final: 2
  residues processed: 60
  average time/residue: 0.6941
  time to fit residues: 45.0556
Evaluate side-chains
  51 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 49
  time to evaluate  : 0.470 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  156 VAL
Chi-restraints excluded: chain C residue  281 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 25 optimal weight:    0.7980
   chunk 54 optimal weight:    7.9990
   chunk 76 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 82 optimal weight:    0.0570
   chunk 20 optimal weight:    2.9990
   chunk 81 optimal weight:    0.8980
   chunk 99 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   overall best weight:    0.7098

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

Flipped N/Q/H residues before XYZ refinement:
C 191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.087761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2969 r_free = 0.2969 target = 0.059190 restraints weight = 21818.136|
|-----------------------------------------------------------------------------|
r_work (start): 0.2936 rms_B_bonded: 3.07
r_work: 0.2785 rms_B_bonded: 3.48 restraints_weight: 0.5000
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035  10950  Z= 0.108
  Angle     :  0.473   7.418  14838  Z= 0.244
  Chirality :  0.040   0.147   1675
  Planarity :  0.004   0.069   1922
  Dihedral  :  3.884  34.066   1461
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 3.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.50 %
    Allowed  :  8.59 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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:  1.12 (0.24), residues: 1333
  helix:  1.61 (0.22), residues: 631
  sheet:  0.38 (0.36), residues: 233
  loop : -0.15 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 398 
 TYR   0.011   0.001   TYR B 244 
 PHE   0.022   0.001   PHE A 538 
 TRP   0.010   0.001   TRP B 203 
 HIS   0.006   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 (10949)
  covalent geometry    : angle       0.47282 (14838)
  hydrogen bonds       : bond        0.03238 (  501)
  hydrogen bonds       : angle       4.07839 ( 1434)
  metal coordination   : bond        0.00118 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.418 
Fit side-chains
REVERT: B  389 ARG cc_start: 0.8083 (mmp80) cc_final: 0.7545 (mmp-170)
REVERT: C  131 ASP cc_start: 0.8842 (t70) cc_final: 0.8566 (t0)
REVERT: C  179 HIS cc_start: 0.9314 (m90) cc_final: 0.9082 (m-70)
REVERT: C  230 HIS cc_start: 0.8716 (m-70) cc_final: 0.8428 (m-70)
REVERT: D  621 ARG cc_start: 0.7985 (mmm160) cc_final: 0.7697 (tpt170)
REVERT: D  624 GLU cc_start: 0.7239 (tm-30) cc_final: 0.6936 (tm-30)
  outliers start: 6
  outliers final: 0
  residues processed: 53
  average time/residue: 0.7471
  time to fit residues: 42.6540
Evaluate side-chains
  49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 84 optimal weight:    4.9990
   chunk 121 optimal weight:    6.9990
   chunk 57 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 131 optimal weight:    0.0970
   chunk 53 optimal weight:    0.9980
   chunk 102 optimal weight:    5.9990
   chunk 126 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 23 optimal weight:    0.9990
   chunk 93 optimal weight:    2.9990
   overall best weight:    1.6184

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

Flipped N/Q/H residues before XYZ refinement:
C 191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.085849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.057224 restraints weight = 22145.681|
|-----------------------------------------------------------------------------|
r_work (start): 0.2880 rms_B_bonded: 3.05
r_work: 0.2726 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.1472

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  10950  Z= 0.191
  Angle     :  0.521   8.263  14838  Z= 0.269
  Chirality :  0.042   0.182   1675
  Planarity :  0.004   0.069   1922
  Dihedral  :  4.133  35.452   1461
  Min Nonbonded Distance : 1.967

Molprobity Statistics.
  All-atom Clashscore : 3.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.40 %
    Favored  : 97.60 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  9.09 %
    Favored  : 90.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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:  1.01 (0.23), residues: 1333
  helix:  1.53 (0.22), residues: 631
  sheet:  0.37 (0.37), residues: 216
  loop : -0.24 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 398 
 TYR   0.011   0.001   TYR B  74 
 PHE   0.025   0.001   PHE A 538 
 TRP   0.010   0.001   TRP B 350 
 HIS   0.006   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00458 (10949)
  covalent geometry    : angle       0.52050 (14838)
  hydrogen bonds       : bond        0.03982 (  501)
  hydrogen bonds       : angle       4.32426 ( 1434)
  metal coordination   : bond        0.00219 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 51
  time to evaluate  : 0.502 
Fit side-chains
REVERT: C  131 ASP cc_start: 0.8863 (t70) cc_final: 0.8568 (t0)
REVERT: C  179 HIS cc_start: 0.9285 (m90) cc_final: 0.9046 (m-70)
REVERT: C  230 HIS cc_start: 0.8779 (m-70) cc_final: 0.8578 (m-70)
  outliers start: 3
  outliers final: 2
  residues processed: 53
  average time/residue: 0.7379
  time to fit residues: 42.2201
Evaluate side-chains
  50 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain B residue  156 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9980
   chunk 126 optimal weight:    3.9990
   chunk 67 optimal weight:    1.9990
   chunk 128 optimal weight:    2.9990
   chunk 65 optimal weight:    2.9990
   chunk 30 optimal weight:    0.8980
   chunk 53 optimal weight:    3.9990
   chunk 1 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   overall best weight:    1.1384

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

Flipped N/Q/H residues before XYZ refinement:
C 191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.086438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2952 r_free = 0.2952 target = 0.058251 restraints weight = 21760.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 2.99
r_work: 0.2766 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.2766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10950  Z= 0.143
  Angle     :  0.509   9.789  14838  Z= 0.261
  Chirality :  0.041   0.166   1675
  Planarity :  0.004   0.057   1922
  Dihedral  :  4.088  36.029   1461
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.58 %
    Allowed  :  9.59 %
    Favored  : 89.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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:  1.06 (0.23), residues: 1333
  helix:  1.57 (0.22), residues: 629
  sheet:  0.59 (0.38), residues: 206
  loop : -0.30 (0.26), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 398 
 TYR   0.012   0.001   TYR B 244 
 PHE   0.023   0.001   PHE A 538 
 TRP   0.012   0.001   TRP B 203 
 HIS   0.005   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (10949)
  covalent geometry    : angle       0.50905 (14838)
  hydrogen bonds       : bond        0.03592 (  501)
  hydrogen bonds       : angle       4.23393 ( 1434)
  metal coordination   : bond        0.00160 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 50
  time to evaluate  : 0.481 
Fit side-chains
REVERT: A  323 MET cc_start: 0.9050 (mpp) cc_final: 0.8812 (mmt)
REVERT: B  389 ARG cc_start: 0.8004 (mmp80) cc_final: 0.7291 (mmp-170)
REVERT: C  131 ASP cc_start: 0.8860 (t70) cc_final: 0.8569 (t0)
REVERT: C  179 HIS cc_start: 0.9282 (m90) cc_final: 0.9047 (m-70)
REVERT: C  230 HIS cc_start: 0.8803 (m-70) cc_final: 0.8581 (m-70)
  outliers start: 7
  outliers final: 2
  residues processed: 53
  average time/residue: 0.7344
  time to fit residues: 42.0937
Evaluate side-chains
  49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.475 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain B residue  156 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 132 optimal weight:    1.9990
   chunk 107 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 37 optimal weight:    0.9980
   chunk 70 optimal weight:    6.9990
   chunk 60 optimal weight:    1.9990
   chunk 31 optimal weight:    0.9990
   chunk 1 optimal weight:    0.5980
   chunk 78 optimal weight:    1.9990
   chunk 92 optimal weight:    1.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
C 191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.086730 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2948 r_free = 0.2948 target = 0.058134 restraints weight = 21768.562|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 3.06
r_work: 0.2752 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2752
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.1586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10950  Z= 0.134
  Angle     :  0.510  11.214  14838  Z= 0.258
  Chirality :  0.041   0.187   1675
  Planarity :  0.004   0.054   1922
  Dihedral  :  4.068  37.712   1461
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 3.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 10.18 %
    Favored  : 89.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.79 %
    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:  1.09 (0.24), residues: 1333
  helix:  1.59 (0.22), residues: 631
  sheet:  0.60 (0.39), residues: 206
  loop : -0.28 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 367 
 TYR   0.011   0.001   TYR B 244 
 PHE   0.022   0.001   PHE A 538 
 TRP   0.012   0.001   TRP B 350 
 HIS   0.005   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 (10949)
  covalent geometry    : angle       0.50987 (14838)
  hydrogen bonds       : bond        0.03459 (  501)
  hydrogen bonds       : angle       4.17991 ( 1434)
  metal coordination   : bond        0.00138 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 52
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
REVERT: B  340 ASP cc_start: 0.8840 (m-30) cc_final: 0.8600 (OUTLIER)
REVERT: B  389 ARG cc_start: 0.8008 (mmp80) cc_final: 0.7288 (mmp-170)
REVERT: C  131 ASP cc_start: 0.8862 (t70) cc_final: 0.8573 (t0)
REVERT: C  179 HIS cc_start: 0.9285 (m90) cc_final: 0.9032 (m-70)
REVERT: C  230 HIS cc_start: 0.8821 (m-70) cc_final: 0.8582 (m-70)
  outliers start: 4
  outliers final: 3
  residues processed: 55
  average time/residue: 0.7310
  time to fit residues: 43.5124
Evaluate side-chains
  50 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 48
  time to evaluate  : 0.458 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain B residue  156 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 122 optimal weight:    8.9990
   chunk 16 optimal weight:    0.9980
   chunk 118 optimal weight:    0.7980
   chunk 70 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 91 optimal weight:    3.9990
   chunk 50 optimal weight:    9.9990
   chunk 120 optimal weight:    3.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
C 191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.085672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.2896 r_free = 0.2896 target = 0.056705 restraints weight = 21557.553|
|-----------------------------------------------------------------------------|
r_work (start): 0.2879 rms_B_bonded: 3.08
r_work: 0.2713 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.2713
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8466
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10950  Z= 0.144
  Angle     :  0.529  12.235  14838  Z= 0.267
  Chirality :  0.041   0.204   1675
  Planarity :  0.004   0.051   1922
  Dihedral  :  4.123  39.520   1461
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 3.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  : 10.34 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.06 (0.24), residues: 1333
  helix:  1.58 (0.22), residues: 631
  sheet:  0.58 (0.39), residues: 206
  loop : -0.30 (0.26), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 367 
 TYR   0.011   0.001   TYR B 244 
 PHE   0.022   0.001   PHE A 538 
 TRP   0.012   0.001   TRP B 350 
 HIS   0.005   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10949)
  covalent geometry    : angle       0.52944 (14838)
  hydrogen bonds       : bond        0.03508 (  501)
  hydrogen bonds       : angle       4.20847 ( 1434)
  metal coordination   : bond        0.00156 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: C  131 ASP cc_start: 0.8805 (t70) cc_final: 0.8530 (t0)
REVERT: C  179 HIS cc_start: 0.9278 (m90) cc_final: 0.9047 (m-70)
REVERT: C  230 HIS cc_start: 0.8774 (m-70) cc_final: 0.8535 (m-70)
  outliers start: 4
  outliers final: 2
  residues processed: 49
  average time/residue: 0.7647
  time to fit residues: 40.4724
Evaluate side-chains
  49 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 47
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  180 MET
Chi-restraints excluded: chain B residue  156 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 91 optimal weight:    3.9990
   chunk 125 optimal weight:    0.3980
   chunk 50 optimal weight:    8.9990
   chunk 54 optimal weight:    0.9990
   chunk 94 optimal weight:    0.9980
   chunk 19 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 106 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9990
   chunk 35 optimal weight:    4.9990
   chunk 53 optimal weight:    0.7980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
C 191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.086154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2907 r_free = 0.2907 target = 0.057262 restraints weight = 21566.413|
|-----------------------------------------------------------------------------|
r_work (start): 0.2893 rms_B_bonded: 3.08
r_work: 0.2727 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8456
moved from start:          0.1658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10950  Z= 0.117
  Angle     :  0.516  13.104  14838  Z= 0.259
  Chirality :  0.040   0.140   1675
  Planarity :  0.004   0.048   1922
  Dihedral  :  4.028  39.365   1461
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.18 %
    Favored  : 97.82 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 10.76 %
    Favored  : 89.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.15 (0.24), residues: 1333
  helix:  1.65 (0.22), residues: 631
  sheet:  0.50 (0.38), residues: 223
  loop : -0.22 (0.27), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 398 
 TYR   0.012   0.001   TYR B 244 
 PHE   0.021   0.001   PHE A 538 
 TRP   0.012   0.001   TRP B 203 
 HIS   0.004   0.001   HIS B 326 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10949)
  covalent geometry    : angle       0.51580 (14838)
  hydrogen bonds       : bond        0.03264 (  501)
  hydrogen bonds       : angle       4.12980 ( 1434)
  metal coordination   : bond        0.00120 (    1)

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

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

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2666 Ramachandran restraints generated.
    1333 Oldfield, 0 Emsley, 1333 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.458 
Fit side-chains
REVERT: C  131 ASP cc_start: 0.8795 (t70) cc_final: 0.8524 (t0)
REVERT: C  179 HIS cc_start: 0.9279 (m90) cc_final: 0.9053 (m-70)
REVERT: C  230 HIS cc_start: 0.8786 (m-70) cc_final: 0.8538 (m-70)
REVERT: D  624 GLU cc_start: 0.8154 (mt-10) cc_final: 0.7590 (tm-30)
REVERT: D  628 ASP cc_start: 0.8527 (m-30) cc_final: 0.6899 (m-30)
  outliers start: 2
  outliers final: 1
  residues processed: 51
  average time/residue: 0.7578
  time to fit residues: 41.7760
Evaluate side-chains
  50 residues out of total 1201 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  156 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 133
   random chunks:
   chunk 74 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0570
   chunk 3 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0270
   chunk 11 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 129 optimal weight:    1.9990
   chunk 43 optimal weight:    5.9990
   overall best weight:    0.5756

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

Flipped N/Q/H residues before XYZ refinement:
C 191 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.087773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2970 r_free = 0.2970 target = 0.059208 restraints weight = 21931.105|
|-----------------------------------------------------------------------------|
r_work (start): 0.2930 rms_B_bonded: 3.08
r_work: 0.2778 rms_B_bonded: 3.50 restraints_weight: 0.5000
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8217
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  10950  Z= 0.101
  Angle     :  0.518  12.852  14838  Z= 0.258
  Chirality :  0.040   0.205   1675
  Planarity :  0.003   0.045   1922
  Dihedral  :  3.948  38.623   1461
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  : 10.51 %
    Favored  : 89.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.57 %
    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:  1.20 (0.24), residues: 1333
  helix:  1.71 (0.22), residues: 631
  sheet:  0.36 (0.37), residues: 233
  loop : -0.14 (0.27), residues: 469

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 367 
 TYR   0.012   0.001   TYR B 244 
 PHE   0.020   0.001   PHE A 538 
 TRP   0.013   0.001   TRP B 350 
 HIS   0.004   0.001   HIS C 230 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10949)
  covalent geometry    : angle       0.51813 (14838)
  hydrogen bonds       : bond        0.03076 (  501)
  hydrogen bonds       : angle       4.06873 ( 1434)
  metal coordination   : bond        0.00088 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3588.37 seconds
wall clock time: 62 minutes 9.01 seconds (3729.01 seconds total)