Starting phenix.real_space_refine
on Wed Sep 17 18:57:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jbg_61313/09_2025/9jbg_61313.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jbg_61313/09_2025/9jbg_61313.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jbg_61313/09_2025/9jbg_61313.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jbg_61313/09_2025/9jbg_61313.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jbg_61313/09_2025/9jbg_61313.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jbg_61313/09_2025/9jbg_61313.cif"
  }
  resolution = 3.76
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.026
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       5      5.49       5
     S      65      5.16       5
     C    6812      2.51       5
     N    1564      2.21       5
     O    1741      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 27 residue(s): 0.01s

  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: 10187
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 5452
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 691, 5452
          Classifications: {'peptide': 691}
          Link IDs: {'PTRANS': 21, 'TRANS': 669}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 4454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 568, 4454
          Classifications: {'peptide': 568}
          Link IDs: {'PTRANS': 21, 'TRANS': 546}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 156
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 156
          Unusual residues: {'3PE': 2}
          Classifications: {'peptide': 1, 'undetermined': 2}
          Link IDs: {None: 2}
    Chain: "B"
      Number of atoms: 125
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 125
          Unusual residues: {'3PE': 1, 'OLA': 1, 'PC1': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
  Time building chain proxies: 2.56, per 1000 atoms: 0.25
  Number of scatterers: 10187
  At special positions: 0
  Unit cell: (95.344, 99.384, 130.088, 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      65     16.00
     P       5     15.00
     O    1741      8.00
     N    1564      7.00
     C    6812      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: 1.14
  Conformation dependent library (CDL) restraints added in 312.6 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2354

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 1 sheets defined
      79.1% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 40
      No H-bonds generated for 'chain 'A' and resid 38 through 40'
    Processing helix  chain 'A' and resid 41 through 62
    Processing helix  chain 'A' and resid 66 through 80
      removed outlier: 3.779A  pdb=" N   GLY A  72 " --> pdb=" O   THR A  68 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   LEU A  73 " --> pdb=" O   GLN A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 80 through 92
      removed outlier: 3.925A  pdb=" N   VAL A  92 " --> pdb=" O   LYS A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 99 through 124
    Processing helix  chain 'A' and resid 129 through 143
      Proline residue:  A 138  - end of helix
    Processing helix  chain 'A' and resid 149 through 159
      removed outlier: 3.675A  pdb=" N   ILE A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 177
      removed outlier: 3.586A  pdb=" N   TYR A 170 " --> pdb=" O   LEU A 166 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ALA A 173 " --> pdb=" O   ILE A 169 " (cutoff:3.500A)
      Proline residue:  A 174  - end of helix
    Processing helix  chain 'A' and resid 179 through 196
      removed outlier: 3.750A  pdb=" N   ILE A 183 " --> pdb=" O   MET A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 207 through 216
      removed outlier: 3.886A  pdb=" N   VAL A 214 " --> pdb=" O   GLY A 210 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 220 through 233
    Processing helix  chain 'A' and resid 238 through 250
      removed outlier: 3.790A  pdb=" N   ASN A 243 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
      removed outlier: 5.256A  pdb=" N   PHE A 244 " --> pdb=" O   TYR A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 252 through 263
    Processing helix  chain 'A' and resid 272 through 288
    Processing helix  chain 'A' and resid 288 through 302
    Processing helix  chain 'A' and resid 306 through 320
    Processing helix  chain 'A' and resid 326 through 337
      removed outlier: 4.021A  pdb=" N   ALA A 330 " --> pdb=" O   ALA A 326 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 340 through 367
      Proline residue:  A 356  - end of helix
    Processing helix  chain 'A' and resid 371 through 405
    Processing helix  chain 'A' and resid 411 through 435
    Processing helix  chain 'A' and resid 440 through 449
    Processing helix  chain 'A' and resid 449 through 473
      removed outlier: 3.634A  pdb=" N   SER A 453 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 481 through 490
    Processing helix  chain 'A' and resid 492 through 503
    Processing helix  chain 'A' and resid 518 through 544
    Processing helix  chain 'A' and resid 639 through 653
      removed outlier: 4.289A  pdb=" N   GLU A 643 " --> pdb=" O   ILE A 639 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 654 through 682
      removed outlier: 3.629A  pdb=" N   HIS A 658 " --> pdb=" O   GLN A 654 " (cutoff:3.500A)
      removed outlier: 4.797A  pdb=" N   ILE A 667 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   GLY A 668 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 711
      removed outlier: 3.592A  pdb=" N   GLU A 691 " --> pdb=" O   ARG A 687 " (cutoff:3.500A)
      removed outlier: 5.923A  pdb=" N   GLY A 704 " --> pdb=" O   ASN A 700 " (cutoff:3.500A)
      removed outlier: 6.072A  pdb=" N   PHE A 705 " --> pdb=" O   PHE A 701 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 758
    Processing helix  chain 'A' and resid 762 through 767
    Processing helix  chain 'A' and resid 783 through 793
      removed outlier: 3.590A  pdb=" N   VAL A 793 " --> pdb=" O   TRP A 789 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 798 through 812
    Processing helix  chain 'B' and resid 38 through 40
      No H-bonds generated for 'chain 'B' and resid 38 through 40'
    Processing helix  chain 'B' and resid 41 through 62
      removed outlier: 3.718A  pdb=" N   VAL B  53 " --> pdb=" O   CYS B  49 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 80
      removed outlier: 3.864A  pdb=" N   LYS B  71 " --> pdb=" O   SER B  67 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   GLY B  72 " --> pdb=" O   THR B  68 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LEU B  73 " --> pdb=" O   GLN B  69 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   PHE B  76 " --> pdb=" O   GLY B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 80 through 93
      removed outlier: 3.588A  pdb=" N   ASN B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 99 through 125
      removed outlier: 3.774A  pdb=" N   LEU B 103 " --> pdb=" O   ASP B  99 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   CYS B 118 " --> pdb=" O   PHE B 114 " (cutoff:3.500A)
      removed outlier: 3.999A  pdb=" N   VAL B 119 " --> pdb=" O   PHE B 115 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 126 through 128
      No H-bonds generated for 'chain 'B' and resid 126 through 128'
    Processing helix  chain 'B' and resid 129 through 134
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'B' and resid 150 through 159
    Processing helix  chain 'B' and resid 164 through 196
      removed outlier: 3.796A  pdb=" N   TYR B 168 " --> pdb=" O   GLU B 164 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   ILE B 169 " --> pdb=" O   TYR B 165 " (cutoff:3.500A)
      removed outlier: 4.590A  pdb=" N   TYR B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   ALA B 173 " --> pdb=" O   ILE B 169 " (cutoff:3.500A)
      Proline residue:  B 174  - end of helix
      removed outlier: 5.088A  pdb=" N   ASN B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      Proline residue:  B 182  - end of helix
      removed outlier: 3.591A  pdb=" N   GLU B 189 " --> pdb=" O   PHE B 185 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   ILE B 190 " --> pdb=" O   ILE B 186 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLN B 191 " --> pdb=" O   PHE B 187 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 216
    Processing helix  chain 'B' and resid 217 through 233
      removed outlier: 3.516A  pdb=" N   PHE B 221 " --> pdb=" O   ASN B 217 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   PHE B 224 " --> pdb=" O   VAL B 220 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 238 through 250
      removed outlier: 4.096A  pdb=" N   ASN B 243 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 5.096A  pdb=" N   PHE B 244 " --> pdb=" O   TYR B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 263
      removed outlier: 3.731A  pdb=" N   GLY B 261 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 3.864A  pdb=" N   LEU B 262 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 275 through 288
      removed outlier: 3.609A  pdb=" N   LEU B 281 " --> pdb=" O   VAL B 277 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 302
      removed outlier: 3.543A  pdb=" N   GLU B 299 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 320
    Processing helix  chain 'B' and resid 326 through 337
      removed outlier: 3.909A  pdb=" N   ALA B 330 " --> pdb=" O   ALA B 326 " (cutoff:3.500A)
      removed outlier: 4.015A  pdb=" N   THR B 334 " --> pdb=" O   ALA B 330 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 340 through 367
      removed outlier: 3.745A  pdb=" N   ALA B 355 " --> pdb=" O   THR B 351 " (cutoff:3.500A)
      Proline residue:  B 356  - end of helix
      removed outlier: 3.519A  pdb=" N   TYR B 359 " --> pdb=" O   ALA B 355 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ALA B 362 " --> pdb=" O   MET B 358 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR B 366 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 404
      removed outlier: 3.900A  pdb=" N   ILE B 388 " --> pdb=" O   PHE B 384 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   VAL B 389 " --> pdb=" O   ASP B 385 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   ILE B 392 " --> pdb=" O   ILE B 388 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   SER B 393 " --> pdb=" O   VAL B 389 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   LEU B 402 " --> pdb=" O   LEU B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 435
      removed outlier: 3.576A  pdb=" N   ASN B 417 " --> pdb=" O   MET B 413 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ILE B 424 " --> pdb=" O   ILE B 420 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   MET B 429 " --> pdb=" O   VAL B 425 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   MET B 430 " --> pdb=" O   CYS B 426 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE B 431 " --> pdb=" O   ALA B 427 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ASN B 433 " --> pdb=" O   MET B 429 " (cutoff:3.500A)
      removed outlier: 3.794A  pdb=" N   PHE B 434 " --> pdb=" O   MET B 430 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 440 through 446
    Processing helix  chain 'B' and resid 446 through 472
      removed outlier: 4.337A  pdb=" N   LEU B 450 " --> pdb=" O   VAL B 446 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   TYR B 458 " --> pdb=" O   LEU B 454 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLY B 462 " --> pdb=" O   TYR B 458 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ILE B 466 " --> pdb=" O   GLY B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 481 through 489
      removed outlier: 3.718A  pdb=" N   TRP B 489 " --> pdb=" O   ILE B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 491 through 493
      No H-bonds generated for 'chain 'B' and resid 491 through 493'
    Processing helix  chain 'B' and resid 494 through 502
      removed outlier: 3.703A  pdb=" N   VAL B 498 " --> pdb=" O   LEU B 494 " (cutoff:3.500A)
      removed outlier: 3.896A  pdb=" N   LEU B 499 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 518 through 544
      removed outlier: 3.947A  pdb=" N   LEU B 528 " --> pdb=" O   THR B 524 " (cutoff:3.500A)
      removed outlier: 4.044A  pdb=" N   PHE B 529 " --> pdb=" O   ALA B 525 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   CYS B 530 " --> pdb=" O   VAL B 526 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   SER B 531 " --> pdb=" O   THR B 527 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   ILE B 537 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU B 539 " --> pdb=" O   ALA B 535 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   MET B 540 " --> pdb=" O   GLY B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 682
      removed outlier: 3.988A  pdb=" N   VAL B 659 " --> pdb=" O   LEU B 655 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   LEU B 660 " --> pdb=" O   THR B 656 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   ILE B 667 " --> pdb=" O   LEU B 663 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   GLY B 668 " --> pdb=" O   LEU B 664 " (cutoff:3.500A)
      removed outlier: 4.671A  pdb=" N   TRP B 679 " --> pdb=" O   SER B 675 " (cutoff:3.500A)
      removed outlier: 4.939A  pdb=" N   LEU B 680 " --> pdb=" O   CYS B 676 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 688 through 701
    Processing helix  chain 'B' and resid 703 through 712
      removed outlier: 3.692A  pdb=" N   SER B 707 " --> pdb=" O   GLN B 703 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   GLY B 709 " --> pdb=" O   PHE B 705 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ILE B 710 " --> pdb=" O   ILE B 706 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   PHE B 711 " --> pdb=" O   SER B 707 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 780 through 782

    649 hydrogen bonds defined for protein.
    1947 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.54

  Time building geometry restraints manager: 1.37 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1515
        1.31 -     1.43: 2783
        1.43 -     1.56: 6005
        1.56 -     1.69: 11
        1.69 -     1.82: 100
  Bond restraints: 10414
  Sorted by residual:
  bond pdb=" C10 OLA B 902 "
       pdb=" C9  OLA B 902 "
    ideal  model  delta    sigma   weight residual
    1.332  1.469 -0.137 2.00e-02 2.50e+03 4.72e+01
  bond pdb=" C   MET B  90 "
       pdb=" O   MET B  90 "
    ideal  model  delta    sigma   weight residual
    1.236  1.179  0.057 1.15e-02 7.56e+03 2.49e+01
  bond pdb=" C   ASN B 181 "
       pdb=" O   ASN B 181 "
    ideal  model  delta    sigma   weight residual
    1.243  1.213  0.030 9.50e-03 1.11e+04 1.02e+01
  bond pdb=" N   ILE A 169 "
       pdb=" CA  ILE A 169 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.037 1.21e-02 6.83e+03 9.27e+00
  bond pdb=" N   ILE A 357 "
       pdb=" CA  ILE A 357 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.21e-02 6.83e+03 9.00e+00
  ... (remaining 10409 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.89: 13155
        1.89 -     3.79: 727
        3.79 -     5.68: 152
        5.68 -     7.58: 27
        7.58 -     9.47: 7
  Bond angle restraints: 14068
  Sorted by residual:
  angle pdb=" N   THR A 461 "
        pdb=" CA  THR A 461 "
        pdb=" C   THR A 461 "
      ideal   model   delta    sigma   weight residual
     111.36  104.92    6.44 1.09e+00 8.42e-01 3.50e+01
  angle pdb=" N   ILE B 522 "
        pdb=" CA  ILE B 522 "
        pdb=" C   ILE B 522 "
      ideal   model   delta    sigma   weight residual
     110.53  105.42    5.11 9.40e-01 1.13e+00 2.95e+01
  angle pdb=" CA  PRO A 327 "
        pdb=" N   PRO A 327 "
        pdb=" CD  PRO A 327 "
      ideal   model   delta    sigma   weight residual
     112.00  104.66    7.34 1.40e+00 5.10e-01 2.75e+01
  angle pdb=" N   VAL A 448 "
        pdb=" CA  VAL A 448 "
        pdb=" C   VAL A 448 "
      ideal   model   delta    sigma   weight residual
     113.07  105.95    7.12 1.37e+00 5.33e-01 2.70e+01
  angle pdb=" C   ASN B 439 "
        pdb=" CA  ASN B 439 "
        pdb=" CB  ASN B 439 "
      ideal   model   delta    sigma   weight residual
     117.23  110.21    7.02 1.36e+00 5.41e-01 2.67e+01
  ... (remaining 14063 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.95: 5841
       30.95 -    61.90: 331
       61.90 -    92.86: 23
       92.86 -   123.81: 8
      123.81 -   154.76: 3
  Dihedral angle restraints: 6206
    sinusoidal: 2553
      harmonic: 3653
  Sorted by residual:
  dihedral pdb=" CA  THR A 369 "
           pdb=" C   THR A 369 "
           pdb=" N   MET A 370 "
           pdb=" CA  MET A 370 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.24   27.76     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" C21 P5S A 903 "
           pdb=" C22 P5S A 903 "
           pdb=" C23 P5S A 903 "
           pdb=" C24 P5S A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -64.63   90.13 -154.76     1      3.00e+01 1.11e-03 2.03e+01
  dihedral pdb=" C38 P5S A 903 "
           pdb=" C39 P5S A 903 "
           pdb=" C40 P5S A 903 "
           pdb=" C41 P5S A 903 "
      ideal   model   delta sinusoidal    sigma   weight residual
      64.51  -73.40  137.91     1      3.00e+01 1.11e-03 1.86e+01
  ... (remaining 6203 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1143
       0.050 -    0.101: 348
       0.101 -    0.151: 97
       0.151 -    0.202: 45
       0.202 -    0.252: 6
  Chirality restraints: 1639
  Sorted by residual:
  chirality pdb=" CG  LEU A 215 "
            pdb=" CB  LEU A 215 "
            pdb=" CD1 LEU A 215 "
            pdb=" CD2 LEU A 215 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.34   -0.25 2.00e-01 2.50e+01 1.59e+00
  chirality pdb=" CA  ILE B 190 "
            pdb=" N   ILE B 190 "
            pdb=" C   ILE B 190 "
            pdb=" CB  ILE B 190 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.21e+00
  chirality pdb=" CA  ILE B 710 "
            pdb=" N   ILE B 710 "
            pdb=" C   ILE B 710 "
            pdb=" CB  ILE B 710 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.20e+00
  ... (remaining 1636 not shown)

  Planarity restraints: 1687
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 OLA B 902 "    0.157 2.00e-02 2.50e+03   1.22e-01 1.49e+02
        pdb=" C11 OLA B 902 "   -0.073 2.00e-02 2.50e+03
        pdb=" C8  OLA B 902 "    0.072 2.00e-02 2.50e+03
        pdb=" C9  OLA B 902 "   -0.157 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A 326 "   -0.082 5.00e-02 4.00e+02   1.19e-01 2.28e+01
        pdb=" N   PRO A 327 "    0.206 5.00e-02 4.00e+02
        pdb=" CA  PRO A 327 "   -0.061 5.00e-02 4.00e+02
        pdb=" CD  PRO A 327 "   -0.064 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 181 "   -0.017 2.00e-02 2.50e+03   3.41e-02 1.16e+01
        pdb=" C   ASN B 181 "    0.059 2.00e-02 2.50e+03
        pdb=" O   ASN B 181 "   -0.021 2.00e-02 2.50e+03
        pdb=" N   PRO B 182 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 1684 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1627
        2.76 -     3.29: 11431
        3.29 -     3.83: 17419
        3.83 -     4.36: 21575
        4.36 -     4.90: 33400
  Nonbonded interactions: 85452
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A  99 "
            pdb=" OG  SER A 101 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   LEU A 454 "
            pdb=" OG1 THR A 457 "
     model   vdw
     2.236 3.040
  nonbonded pdb=" OD2 ASP B 146 "
            pdb=" OH  TYR B 320 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   HIS B 412 "
            pdb=" OG1 THR B 415 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" O   SER A 453 "
            pdb=" OG  SER A 456 "
     model   vdw
     2.295 3.040
  ... (remaining 85447 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 group one per residue
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:             4.230
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.710
  Find NCS groups from input model:        0.050
  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:             0.010
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.340
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
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   0.137  10414  Z= 0.385
  Angle     :  0.980   9.473  14068  Z= 0.649
  Chirality :  0.059   0.252   1639
  Planarity :  0.008   0.122   1687
  Dihedral  : 18.836 154.759   3852
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 26.07 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.18 (0.23), residues: 1247
  helix: -0.15 (0.18), residues: 896
  sheet:  None (None), residues: 0
  loop : -2.26 (0.30), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 235 
 TYR   0.020   0.001   TYR A 458 
 PHE   0.034   0.002   PHE B 276 
 TRP   0.030   0.002   TRP B 679 
 HIS   0.006   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 (10414)
  covalent geometry    : angle       0.98007 (14068)
  hydrogen bonds       : bond        0.20402 (  649)
  hydrogen bonds       : angle       7.91297 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 245
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  318 PHE cc_start: 0.8063 (t80) cc_final: 0.7733 (t80)
REVERT: A  413 MET cc_start: 0.6894 (mtm) cc_final: 0.6413 (mpp)
REVERT: A  816 GLN cc_start: 0.8059 (OUTLIER) cc_final: 0.7826 (tt0)
REVERT: B  165 TYR cc_start: 0.7759 (m-10) cc_final: 0.6548 (m-10)
  outliers start: 19
  outliers final: 7
  residues processed: 255
  average time/residue: 0.0868
  time to fit residues: 33.2702
Evaluate side-chains
  226 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 218
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  213 ARG
Chi-restraints excluded: chain A residue  447 PHE
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  816 GLN
Chi-restraints excluded: chain B residue  500 LEU
Chi-restraints excluded: chain B residue  537 ILE
Chi-restraints excluded: chain B residue  662 CYS
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 123 optimal weight:    0.9980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    6.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 191 GLN
A 198 ASN
A 337 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 ASN
A 693 GLN
A 758 HIS
B  63 ASN
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 412 HIS
B 439 ASN
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4119 r_free = 0.4119 target = 0.133029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.108376 restraints weight = 30126.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.111143 restraints weight = 16583.357|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.112867 restraints weight = 11034.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.113982 restraints weight = 8427.512|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.114613 restraints weight = 7070.535|
|-----------------------------------------------------------------------------|
r_work (final): 0.3790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7609
moved from start:          0.1744

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10414  Z= 0.157
  Angle     :  0.701  13.979  14068  Z= 0.352
  Chirality :  0.044   0.194   1639
  Planarity :  0.005   0.065   1687
  Dihedral  : 14.755 178.479   1618
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 13.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  5.20 %
    Allowed  : 20.88 %
    Favored  : 73.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.43 (0.24), residues: 1247
  helix:  0.36 (0.17), residues: 939
  sheet:  None (None), residues: 0
  loop : -2.13 (0.34), residues: 308

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 235 
 TYR   0.045   0.002   TYR A 458 
 PHE   0.037   0.002   PHE A 367 
 TRP   0.016   0.002   TRP B 679 
 HIS   0.005   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10414)
  covalent geometry    : angle       0.70082 (14068)
  hydrogen bonds       : bond        0.05352 (  649)
  hydrogen bonds       : angle       5.52853 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  307 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 250
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  185 PHE cc_start: 0.7108 (m-80) cc_final: 0.6849 (m-80)
REVERT: A  219 ILE cc_start: 0.7360 (OUTLIER) cc_final: 0.7034 (mm)
REVERT: A  318 PHE cc_start: 0.8033 (t80) cc_final: 0.7666 (t80)
REVERT: A  413 MET cc_start: 0.6858 (mtm) cc_final: 0.6484 (mpp)
REVERT: A  429 MET cc_start: 0.8965 (tpt) cc_final: 0.8366 (tpt)
REVERT: A  447 PHE cc_start: 0.7565 (p90) cc_final: 0.7188 (p90)
REVERT: A  797 SER cc_start: 0.4725 (OUTLIER) cc_final: 0.4145 (p)
REVERT: B  674 SER cc_start: 0.9168 (t) cc_final: 0.8867 (p)
REVERT: B  705 PHE cc_start: 0.7972 (OUTLIER) cc_final: 0.7499 (m-80)
  outliers start: 57
  outliers final: 27
  residues processed: 285
  average time/residue: 0.0871
  time to fit residues: 37.7204
Evaluate side-chains
  244 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 214
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   43 PHE
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  466 ILE
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  373 LYS
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 114 optimal weight:    9.9990
   chunk 94 optimal weight:    0.7980
   chunk 99 optimal weight:    5.9990
   chunk 43 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 95 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   chunk 124 optimal weight:    1.9990
   chunk 62 optimal weight:    0.8980
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
A  89 ASN
A 337 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 703 GLN
A 765 ASN
A 816 GLN
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 672 ASN
B 700 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.131767 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.107381 restraints weight = 30502.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.110158 restraints weight = 16858.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.111939 restraints weight = 11217.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.113084 restraints weight = 8506.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.113673 restraints weight = 7084.670|
|-----------------------------------------------------------------------------|
r_work (final): 0.3768
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7633
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10414  Z= 0.153
  Angle     :  0.697  13.135  14068  Z= 0.345
  Chirality :  0.043   0.210   1639
  Planarity :  0.005   0.057   1687
  Dihedral  : 13.929 171.308   1604
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 14.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 22.15 %
    Favored  : 72.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.27 (0.24), residues: 1247
  helix:  0.49 (0.17), residues: 942
  sheet:  None (None), residues: 0
  loop : -2.15 (0.34), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 213 
 TYR   0.054   0.002   TYR A 458 
 PHE   0.030   0.002   PHE B 529 
 TRP   0.020   0.002   TRP B 679 
 HIS   0.004   0.001   HIS A 716 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10414)
  covalent geometry    : angle       0.69724 (14068)
  hydrogen bonds       : bond        0.04983 (  649)
  hydrogen bonds       : angle       5.35567 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 237
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ILE cc_start: 0.7401 (OUTLIER) cc_final: 0.7096 (mm)
REVERT: A  413 MET cc_start: 0.6837 (mtm) cc_final: 0.6472 (mpp)
REVERT: A  440 PHE cc_start: 0.5970 (t80) cc_final: 0.5770 (t80)
REVERT: A  447 PHE cc_start: 0.7504 (p90) cc_final: 0.7223 (p90)
REVERT: A  797 SER cc_start: 0.4443 (OUTLIER) cc_final: 0.3909 (p)
REVERT: B  178 MET cc_start: 0.8196 (mmm) cc_final: 0.7508 (ttt)
REVERT: B  521 MET cc_start: 0.8105 (ttt) cc_final: 0.7532 (tpt)
REVERT: B  674 SER cc_start: 0.9183 (t) cc_final: 0.8877 (p)
REVERT: B  699 PHE cc_start: 0.7004 (t80) cc_final: 0.6218 (t80)
REVERT: B  705 PHE cc_start: 0.7943 (OUTLIER) cc_final: 0.7602 (m-80)
  outliers start: 62
  outliers final: 38
  residues processed: 274
  average time/residue: 0.0894
  time to fit residues: 36.8876
Evaluate side-chains
  260 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 219
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   38 SER
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  287 LEU
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  373 LYS
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  418 LEU
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  432 TRP
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  529 PHE
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 84 optimal weight:    0.9990
   chunk 86 optimal weight:    7.9990
   chunk 117 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 87 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 49 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 337 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 716 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4109 r_free = 0.4109 target = 0.132184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.107757 restraints weight = 30310.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.110530 restraints weight = 16601.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.112280 restraints weight = 10998.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.113394 restraints weight = 8355.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.113899 restraints weight = 6979.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2518

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10414  Z= 0.145
  Angle     :  0.693  14.135  14068  Z= 0.343
  Chirality :  0.043   0.181   1639
  Planarity :  0.005   0.057   1687
  Dihedral  : 13.700 167.916   1604
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 14.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.79 %
    Favored  : 71.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.24), residues: 1247
  helix:  0.55 (0.17), residues: 941
  sheet:  None (None), residues: 0
  loop : -2.05 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 213 
 TYR   0.050   0.001   TYR A 458 
 PHE   0.033   0.002   PHE B 529 
 TRP   0.012   0.001   TRP B 460 
 HIS   0.004   0.001   HIS B 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 (10414)
  covalent geometry    : angle       0.69323 (14068)
  hydrogen bonds       : bond        0.04735 (  649)
  hydrogen bonds       : angle       5.25195 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 226
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  151 TYR cc_start: 0.8303 (t80) cc_final: 0.7933 (t80)
REVERT: A  219 ILE cc_start: 0.7302 (OUTLIER) cc_final: 0.6939 (mm)
REVERT: A  413 MET cc_start: 0.6797 (mtm) cc_final: 0.6434 (mpp)
REVERT: A  447 PHE cc_start: 0.7474 (p90) cc_final: 0.7177 (p90)
REVERT: A  797 SER cc_start: 0.4562 (OUTLIER) cc_final: 0.4023 (p)
REVERT: B  299 GLU cc_start: 0.7036 (mm-30) cc_final: 0.6225 (tm-30)
REVERT: B  364 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8733 (mm)
REVERT: B  380 GLN cc_start: 0.8603 (tm-30) cc_final: 0.8318 (pp30)
REVERT: B  448 VAL cc_start: 0.8596 (m) cc_final: 0.8241 (p)
REVERT: B  674 SER cc_start: 0.9124 (t) cc_final: 0.8824 (p)
REVERT: B  705 PHE cc_start: 0.8009 (OUTLIER) cc_final: 0.7765 (m-80)
  outliers start: 54
  outliers final: 39
  residues processed: 260
  average time/residue: 0.0829
  time to fit residues: 33.3538
Evaluate side-chains
  265 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 222
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  423 SER
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  790 LEU
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  373 LYS
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  432 TRP
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain B residue  529 PHE
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 1 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 121 optimal weight:    8.9990
   chunk 28 optimal weight:    1.9990
   chunk 10 optimal weight:    0.8980
   chunk 85 optimal weight:    4.9990
   chunk 58 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 11 optimal weight:    2.9990
   chunk 114 optimal weight:    0.0980
   chunk 87 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 506 ASN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 765 ASN
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 310 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.133035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.108708 restraints weight = 29904.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.111539 restraints weight = 16315.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.113270 restraints weight = 10776.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.114232 restraints weight = 8192.474|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.114976 restraints weight = 6980.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7611
moved from start:          0.2717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10414  Z= 0.134
  Angle     :  0.696  14.075  14068  Z= 0.338
  Chirality :  0.043   0.322   1639
  Planarity :  0.005   0.056   1687
  Dihedral  : 13.373 168.798   1604
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 13.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  4.56 %
    Allowed  : 25.98 %
    Favored  : 69.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.24), residues: 1247
  helix:  0.61 (0.17), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.97 (0.35), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 213 
 TYR   0.047   0.001   TYR A 458 
 PHE   0.031   0.002   PHE B 529 
 TRP   0.015   0.002   TRP A 460 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (10414)
  covalent geometry    : angle       0.69576 (14068)
  hydrogen bonds       : bond        0.04556 (  649)
  hydrogen bonds       : angle       5.11347 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  291 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 241
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ILE cc_start: 0.7341 (OUTLIER) cc_final: 0.6977 (mm)
REVERT: A  413 MET cc_start: 0.6853 (mtm) cc_final: 0.6452 (mpp)
REVERT: A  429 MET cc_start: 0.8786 (tpt) cc_final: 0.8419 (tpt)
REVERT: A  430 MET cc_start: 0.8895 (OUTLIER) cc_final: 0.8518 (mpp)
REVERT: A  447 PHE cc_start: 0.7488 (p90) cc_final: 0.7160 (p90)
REVERT: A  459 LEU cc_start: 0.9074 (OUTLIER) cc_final: 0.8786 (mm)
REVERT: A  471 LEU cc_start: 0.3865 (OUTLIER) cc_final: 0.3460 (mm)
REVERT: A  657 ARG cc_start: 0.7880 (mtt180) cc_final: 0.7554 (mtt180)
REVERT: A  759 ARG cc_start: 0.8274 (tmm-80) cc_final: 0.8071 (tmm-80)
REVERT: A  797 SER cc_start: 0.4656 (OUTLIER) cc_final: 0.4169 (p)
REVERT: B  178 MET cc_start: 0.8266 (mmm) cc_final: 0.7518 (ttt)
REVERT: B  299 GLU cc_start: 0.7152 (mm-30) cc_final: 0.6420 (tm-30)
REVERT: B  364 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8668 (mm)
REVERT: B  448 VAL cc_start: 0.8677 (m) cc_final: 0.8320 (p)
REVERT: B  521 MET cc_start: 0.8222 (ttt) cc_final: 0.7540 (tpt)
REVERT: B  674 SER cc_start: 0.9138 (t) cc_final: 0.8860 (p)
REVERT: B  705 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7686 (m-80)
  outliers start: 50
  outliers final: 32
  residues processed: 268
  average time/residue: 0.0796
  time to fit residues: 32.4773
Evaluate side-chains
  261 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 222
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  373 LYS
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  519 GLU
Chi-restraints excluded: chain B residue  529 PHE
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 98 optimal weight:    0.6980
   chunk 27 optimal weight:    7.9990
   chunk 40 optimal weight:   10.0000
   chunk 106 optimal weight:    6.9990
   chunk 49 optimal weight:    1.9990
   chunk 96 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9990
   chunk 78 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 34 optimal weight:    4.9990
   chunk 84 optimal weight:    0.7980
   overall best weight:    1.0986

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 380 GLN
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.131642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.106983 restraints weight = 30604.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.109706 restraints weight = 16749.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.111460 restraints weight = 11130.952|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.112562 restraints weight = 8485.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.113032 restraints weight = 7125.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7655
moved from start:          0.2946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  10414  Z= 0.151
  Angle     :  0.712  12.945  14068  Z= 0.349
  Chirality :  0.043   0.243   1639
  Planarity :  0.005   0.055   1687
  Dihedral  : 13.303 164.872   1602
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 14.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  5.65 %
    Allowed  : 26.25 %
    Favored  : 68.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.24), residues: 1247
  helix:  0.59 (0.17), residues: 947
  sheet:  None (None), residues: 0
  loop : -1.89 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 213 
 TYR   0.046   0.001   TYR A 458 
 PHE   0.033   0.002   PHE B 529 
 TRP   0.019   0.002   TRP A 460 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00340 (10414)
  covalent geometry    : angle       0.71219 (14068)
  hydrogen bonds       : bond        0.04632 (  649)
  hydrogen bonds       : angle       5.16034 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  298 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 236
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 ILE cc_start: 0.7345 (OUTLIER) cc_final: 0.6998 (mm)
REVERT: A  447 PHE cc_start: 0.7524 (p90) cc_final: 0.7192 (p90)
REVERT: A  459 LEU cc_start: 0.9075 (OUTLIER) cc_final: 0.8784 (mm)
REVERT: A  471 LEU cc_start: 0.3971 (OUTLIER) cc_final: 0.3588 (mm)
REVERT: A  657 ARG cc_start: 0.7869 (mtt180) cc_final: 0.7624 (mtt180)
REVERT: A  703 GLN cc_start: 0.8104 (mm-40) cc_final: 0.7893 (mm-40)
REVERT: A  797 SER cc_start: 0.4594 (OUTLIER) cc_final: 0.4065 (p)
REVERT: B  178 MET cc_start: 0.8306 (mmm) cc_final: 0.7526 (ttt)
REVERT: B  364 LEU cc_start: 0.9002 (OUTLIER) cc_final: 0.8764 (mm)
REVERT: B  380 GLN cc_start: 0.8635 (tm-30) cc_final: 0.8357 (pp30)
REVERT: B  521 MET cc_start: 0.8245 (ttt) cc_final: 0.7901 (tpt)
REVERT: B  674 SER cc_start: 0.8964 (t) cc_final: 0.8673 (p)
REVERT: B  705 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.7882 (m-80)
  outliers start: 62
  outliers final: 42
  residues processed: 274
  average time/residue: 0.0834
  time to fit residues: 34.4998
Evaluate side-chains
  270 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 222
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  457 THR
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  471 LEU
Chi-restraints excluded: chain A residue  489 TRP
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  765 ASN
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  373 LYS
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  516 TYR
Chi-restraints excluded: chain B residue  529 PHE
Chi-restraints excluded: chain B residue  661 LEU
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  696 CYS
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 124 optimal weight:    0.7980
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 68 optimal weight:    5.9990
   chunk 58 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 72 optimal weight:    0.7980
   chunk 17 optimal weight:    5.9990
   chunk 113 optimal weight:    8.9990
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 703 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4105 r_free = 0.4105 target = 0.131978 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.107416 restraints weight = 30372.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.110157 restraints weight = 16731.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.111879 restraints weight = 11161.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.112811 restraints weight = 8549.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.113587 restraints weight = 7316.334|
|-----------------------------------------------------------------------------|
r_work (final): 0.3774
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  10414  Z= 0.156
  Angle     :  0.746  12.144  14068  Z= 0.364
  Chirality :  0.045   0.228   1639
  Planarity :  0.005   0.060   1687
  Dihedral  : 13.183 161.944   1602
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 14.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  5.29 %
    Allowed  : 28.26 %
    Favored  : 66.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.11 (0.24), residues: 1247
  helix:  0.57 (0.17), residues: 953
  sheet:  None (None), residues: 0
  loop : -2.03 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.044   0.001   TYR A 458 
 PHE   0.029   0.002   PHE B 529 
 TRP   0.017   0.002   TRP A 789 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 (10414)
  covalent geometry    : angle       0.74562 (14068)
  hydrogen bonds       : bond        0.04643 (  649)
  hydrogen bonds       : angle       5.25047 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  292 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 58
    poor density    : 234
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 TRP cc_start: 0.5425 (OUTLIER) cc_final: 0.4159 (m-10)
REVERT: A  151 TYR cc_start: 0.8495 (t80) cc_final: 0.8145 (t80)
REVERT: A  219 ILE cc_start: 0.7421 (OUTLIER) cc_final: 0.7055 (mm)
REVERT: A  318 PHE cc_start: 0.8044 (t80) cc_final: 0.7767 (t80)
REVERT: A  447 PHE cc_start: 0.7497 (p90) cc_final: 0.7152 (p90)
REVERT: A  459 LEU cc_start: 0.9054 (OUTLIER) cc_final: 0.8756 (mm)
REVERT: A  797 SER cc_start: 0.4320 (OUTLIER) cc_final: 0.3830 (p)
REVERT: B  299 GLU cc_start: 0.7183 (mm-30) cc_final: 0.6509 (tm-30)
REVERT: B  364 LEU cc_start: 0.8999 (OUTLIER) cc_final: 0.8765 (mm)
REVERT: B  380 GLN cc_start: 0.8614 (tm-30) cc_final: 0.8331 (pp30)
REVERT: B  430 MET cc_start: 0.8619 (mpt) cc_final: 0.8418 (mpt)
REVERT: B  521 MET cc_start: 0.8257 (ttt) cc_final: 0.7981 (tpt)
REVERT: B  674 SER cc_start: 0.8957 (t) cc_final: 0.8654 (p)
REVERT: B  705 PHE cc_start: 0.8216 (OUTLIER) cc_final: 0.7927 (m-80)
  outliers start: 58
  outliers final: 41
  residues processed: 270
  average time/residue: 0.0872
  time to fit residues: 35.4591
Evaluate side-chains
  267 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 220
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue   89 ASN
Chi-restraints excluded: chain A residue  100 TRP
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  207 VAL
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  268 ILE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  489 TRP
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  711 PHE
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  370 MET
Chi-restraints excluded: chain B residue  379 ILE
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  446 VAL
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  516 TYR
Chi-restraints excluded: chain B residue  529 PHE
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  696 CYS
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 116 optimal weight:    0.0270
   chunk 95 optimal weight:    0.1980
   chunk 81 optimal weight:    0.9980
   chunk 112 optimal weight:    0.9990
   chunk 97 optimal weight:    0.7980
   chunk 94 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 34 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0570
   chunk 69 optimal weight:    0.0370
   overall best weight:    0.2234

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 700 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.135342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.110810 restraints weight = 30282.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.113666 restraints weight = 16552.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.115453 restraints weight = 10995.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.116407 restraints weight = 8414.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.117223 restraints weight = 7208.968|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
moved from start:          0.3352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056  10414  Z= 0.141
  Angle     :  0.767  12.150  14068  Z= 0.368
  Chirality :  0.045   0.305   1639
  Planarity :  0.004   0.058   1687
  Dihedral  : 12.730 165.621   1602
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 13.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 28.99 %
    Favored  : 66.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.05 (0.24), residues: 1247
  helix:  0.62 (0.17), residues: 945
  sheet:  None (None), residues: 0
  loop : -1.98 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.046   0.001   TYR A 458 
 PHE   0.029   0.002   PHE A 367 
 TRP   0.030   0.002   TRP A 789 
 HIS   0.003   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 (10414)
  covalent geometry    : angle       0.76668 (14068)
  hydrogen bonds       : bond        0.04487 (  649)
  hydrogen bonds       : angle       5.15854 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  295 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 246
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 TRP cc_start: 0.5288 (OUTLIER) cc_final: 0.4030 (m-10)
REVERT: A  179 MET cc_start: 0.7300 (mmm) cc_final: 0.7050 (mmm)
REVERT: A  219 ILE cc_start: 0.7150 (OUTLIER) cc_final: 0.6878 (mm)
REVERT: A  413 MET cc_start: 0.6762 (mtm) cc_final: 0.6495 (mpp)
REVERT: A  429 MET cc_start: 0.8805 (tpt) cc_final: 0.8458 (tpt)
REVERT: A  430 MET cc_start: 0.8859 (OUTLIER) cc_final: 0.8538 (mpp)
REVERT: A  447 PHE cc_start: 0.7378 (p90) cc_final: 0.7015 (p90)
REVERT: A  459 LEU cc_start: 0.9052 (OUTLIER) cc_final: 0.8765 (mm)
REVERT: A  657 ARG cc_start: 0.7885 (mtt180) cc_final: 0.7571 (mtt180)
REVERT: A  789 TRP cc_start: 0.6518 (t60) cc_final: 0.6210 (t60)
REVERT: A  797 SER cc_start: 0.4241 (OUTLIER) cc_final: 0.3747 (p)
REVERT: B  178 MET cc_start: 0.8202 (mmm) cc_final: 0.7478 (ttt)
REVERT: B  299 GLU cc_start: 0.7161 (mm-30) cc_final: 0.6433 (tm-30)
REVERT: B  364 LEU cc_start: 0.8964 (OUTLIER) cc_final: 0.8604 (mm)
REVERT: B  380 GLN cc_start: 0.8593 (tm-30) cc_final: 0.8314 (pp30)
REVERT: B  505 HIS cc_start: 0.6457 (p-80) cc_final: 0.6216 (p-80)
REVERT: B  521 MET cc_start: 0.8217 (ttt) cc_final: 0.7976 (tpt)
REVERT: B  674 SER cc_start: 0.8891 (t) cc_final: 0.8610 (p)
REVERT: B  705 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7835 (m-80)
  outliers start: 49
  outliers final: 32
  residues processed: 277
  average time/residue: 0.0832
  time to fit residues: 35.1018
Evaluate side-chains
  272 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 233
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  100 TRP
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  516 TYR
Chi-restraints excluded: chain B residue  661 LEU
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    8.9990
   chunk 79 optimal weight:    0.9980
   chunk 73 optimal weight:    0.0770
   chunk 3 optimal weight:    0.9980
   chunk 88 optimal weight:    1.9990
   chunk 112 optimal weight:    0.9990
   chunk 109 optimal weight:    6.9990
   chunk 53 optimal weight:   10.0000
   chunk 124 optimal weight:    0.9990
   overall best weight:    0.7540

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

Flipped N/Q/H residues before XYZ refinement:
A  63 ASN
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.134071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.109811 restraints weight = 30005.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.112629 restraints weight = 16436.426|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.114350 restraints weight = 10906.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.115447 restraints weight = 8355.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.116016 restraints weight = 7036.561|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.3468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  10414  Z= 0.150
  Angle     :  0.808  12.794  14068  Z= 0.387
  Chirality :  0.046   0.310   1639
  Planarity :  0.005   0.059   1687
  Dihedral  : 12.646 160.302   1602
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 15.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  4.10 %
    Allowed  : 29.63 %
    Favored  : 66.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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:  0.02 (0.24), residues: 1247
  helix:  0.66 (0.17), residues: 942
  sheet:  None (None), residues: 0
  loop : -1.89 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 213 
 TYR   0.048   0.001   TYR A 458 
 PHE   0.051   0.002   PHE B 469 
 TRP   0.022   0.002   TRP A 789 
 HIS   0.002   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00343 (10414)
  covalent geometry    : angle       0.80750 (14068)
  hydrogen bonds       : bond        0.04567 (  649)
  hydrogen bonds       : angle       5.24217 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  276 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 231
  time to evaluate  : 0.430 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 TRP cc_start: 0.5243 (OUTLIER) cc_final: 0.3986 (m-10)
REVERT: A  179 MET cc_start: 0.7392 (mmm) cc_final: 0.7143 (mmm)
REVERT: A  219 ILE cc_start: 0.7209 (OUTLIER) cc_final: 0.6915 (mm)
REVERT: A  413 MET cc_start: 0.6648 (mtm) cc_final: 0.6396 (mpp)
REVERT: A  447 PHE cc_start: 0.7463 (p90) cc_final: 0.7129 (p90)
REVERT: A  459 LEU cc_start: 0.9049 (OUTLIER) cc_final: 0.8772 (mm)
REVERT: A  657 ARG cc_start: 0.7872 (mtt180) cc_final: 0.7572 (mtt180)
REVERT: A  790 LEU cc_start: 0.7930 (mt) cc_final: 0.7719 (mt)
REVERT: A  797 SER cc_start: 0.4228 (OUTLIER) cc_final: 0.3722 (p)
REVERT: B  178 MET cc_start: 0.8244 (mmm) cc_final: 0.7466 (ttt)
REVERT: B  364 LEU cc_start: 0.8986 (OUTLIER) cc_final: 0.8666 (mm)
REVERT: B  380 GLN cc_start: 0.8577 (tm-30) cc_final: 0.8310 (pp30)
REVERT: B  505 HIS cc_start: 0.6372 (p-80) cc_final: 0.6163 (p-80)
REVERT: B  521 MET cc_start: 0.8299 (ttt) cc_final: 0.8031 (tpt)
REVERT: B  674 SER cc_start: 0.8919 (t) cc_final: 0.8647 (p)
REVERT: B  705 PHE cc_start: 0.8149 (OUTLIER) cc_final: 0.7923 (m-80)
  outliers start: 45
  outliers final: 34
  residues processed: 259
  average time/residue: 0.0854
  time to fit residues: 33.5835
Evaluate side-chains
  269 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 229
  time to evaluate  : 0.405 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  100 TRP
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  423 SER
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  516 TYR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  661 LEU
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 112 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 110 optimal weight:    4.9990
   chunk 121 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 56 optimal weight:    0.0060
   chunk 87 optimal weight:    0.9980
   chunk 124 optimal weight:    0.0970
   overall best weight:    0.5194

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.135406 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.111240 restraints weight = 29789.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.114052 restraints weight = 16318.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.115816 restraints weight = 10800.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.116804 restraints weight = 8243.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.117563 restraints weight = 7019.117|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7560
moved from start:          0.3661

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063  10414  Z= 0.146
  Angle     :  0.818  14.147  14068  Z= 0.390
  Chirality :  0.046   0.318   1639
  Planarity :  0.005   0.059   1687
  Dihedral  : 12.389 154.889   1602
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 15.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  4.01 %
    Allowed  : 29.44 %
    Favored  : 66.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.01 (0.24), residues: 1247
  helix:  0.64 (0.17), residues: 942
  sheet:  None (None), residues: 0
  loop : -1.87 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 213 
 TYR   0.047   0.001   TYR A 458 
 PHE   0.060   0.002   PHE A 367 
 TRP   0.030   0.002   TRP A 789 
 HIS   0.002   0.001   HIS A 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 (10414)
  covalent geometry    : angle       0.81807 (14068)
  hydrogen bonds       : bond        0.04527 (  649)
  hydrogen bonds       : angle       5.16937 ( 1947)

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

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

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2494 Ramachandran restraints generated.
    1247 Oldfield, 0 Emsley, 1247 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  287 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 243
  time to evaluate  : 0.400 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 TRP cc_start: 0.5208 (OUTLIER) cc_final: 0.4010 (m-10)
REVERT: A  179 MET cc_start: 0.7354 (mmm) cc_final: 0.7128 (mmm)
REVERT: A  219 ILE cc_start: 0.7098 (OUTLIER) cc_final: 0.6840 (mm)
REVERT: A  413 MET cc_start: 0.6645 (mtm) cc_final: 0.6320 (mpp)
REVERT: A  429 MET cc_start: 0.8831 (tpt) cc_final: 0.8502 (tpt)
REVERT: A  430 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8540 (mpp)
REVERT: A  447 PHE cc_start: 0.7360 (p90) cc_final: 0.7086 (p90)
REVERT: A  459 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8779 (mm)
REVERT: A  797 SER cc_start: 0.4447 (OUTLIER) cc_final: 0.3878 (p)
REVERT: B  178 MET cc_start: 0.8170 (mmm) cc_final: 0.7370 (ttt)
REVERT: B  364 LEU cc_start: 0.8975 (OUTLIER) cc_final: 0.8631 (mm)
REVERT: B  380 GLN cc_start: 0.8552 (tm-30) cc_final: 0.8285 (pp30)
REVERT: B  521 MET cc_start: 0.8297 (ttt) cc_final: 0.8058 (tpt)
REVERT: B  674 SER cc_start: 0.8909 (t) cc_final: 0.8657 (p)
REVERT: B  705 PHE cc_start: 0.8188 (OUTLIER) cc_final: 0.7965 (m-80)
  outliers start: 44
  outliers final: 31
  residues processed: 268
  average time/residue: 0.0832
  time to fit residues: 34.4940
Evaluate side-chains
  268 residues out of total 1097 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 230
  time to evaluate  : 0.401 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   42 LEU
Chi-restraints excluded: chain A residue  100 TRP
Chi-restraints excluded: chain A residue  124 VAL
Chi-restraints excluded: chain A residue  206 ILE
Chi-restraints excluded: chain A residue  219 ILE
Chi-restraints excluded: chain A residue  241 VAL
Chi-restraints excluded: chain A residue  325 VAL
Chi-restraints excluded: chain A residue  381 ASN
Chi-restraints excluded: chain A residue  388 ILE
Chi-restraints excluded: chain A residue  430 MET
Chi-restraints excluded: chain A residue  459 LEU
Chi-restraints excluded: chain A residue  672 ASN
Chi-restraints excluded: chain A residue  797 SER
Chi-restraints excluded: chain A residue  803 VAL
Chi-restraints excluded: chain A residue  810 VAL
Chi-restraints excluded: chain A residue  818 ILE
Chi-restraints excluded: chain B residue   39 ILE
Chi-restraints excluded: chain B residue  219 ILE
Chi-restraints excluded: chain B residue  220 VAL
Chi-restraints excluded: chain B residue  265 VAL
Chi-restraints excluded: chain B residue  277 VAL
Chi-restraints excluded: chain B residue  302 ASP
Chi-restraints excluded: chain B residue  319 LEU
Chi-restraints excluded: chain B residue  335 GLN
Chi-restraints excluded: chain B residue  364 LEU
Chi-restraints excluded: chain B residue  389 VAL
Chi-restraints excluded: chain B residue  413 MET
Chi-restraints excluded: chain B residue  432 TRP
Chi-restraints excluded: chain B residue  447 PHE
Chi-restraints excluded: chain B residue  450 LEU
Chi-restraints excluded: chain B residue  451 TYR
Chi-restraints excluded: chain B residue  496 VAL
Chi-restraints excluded: chain B residue  502 THR
Chi-restraints excluded: chain B residue  516 TYR
Chi-restraints excluded: chain B residue  540 MET
Chi-restraints excluded: chain B residue  664 LEU
Chi-restraints excluded: chain B residue  695 PHE
Chi-restraints excluded: chain B residue  705 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 125
   random chunks:
   chunk 82 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 116 optimal weight:    8.9990
   chunk 60 optimal weight:    3.9990
   chunk 16 optimal weight:    9.9990
   chunk 86 optimal weight:    6.9990
   chunk 45 optimal weight:    0.2980
   chunk 41 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 335 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 520 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.134911 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.110765 restraints weight = 30245.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.113562 restraints weight = 16600.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.115327 restraints weight = 11016.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.116430 restraints weight = 8396.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.117053 restraints weight = 7067.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.3760

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  10414  Z= 0.150
  Angle     :  0.838  13.869  14068  Z= 0.398
  Chirality :  0.047   0.316   1639
  Planarity :  0.005   0.058   1687
  Dihedral  : 12.333 146.751   1602
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 30.26 %
    Favored  : 66.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -0.01 (0.24), residues: 1247
  helix:  0.62 (0.17), residues: 942
  sheet:  None (None), residues: 0
  loop : -1.82 (0.36), residues: 305

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 759 
 TYR   0.048   0.001   TYR A 458 
 PHE   0.057   0.002   PHE A 367 
 TRP   0.029   0.002   TRP A 789 
 HIS   0.003   0.001   HIS B 658 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (10414)
  covalent geometry    : angle       0.83777 (14068)
  hydrogen bonds       : bond        0.04542 (  649)
  hydrogen bonds       : angle       5.22884 ( 1947)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2152.97 seconds
wall clock time: 38 minutes 9.08 seconds (2289.08 seconds total)