Starting phenix.real_space_refine
on Thu Feb  5 07:40:58 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ow8_13095/02_2026/7ow8_13095.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ow8_13095/02_2026/7ow8_13095.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ow8_13095/02_2026/7ow8_13095.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ow8_13095/02_2026/7ow8_13095.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ow8_13095/02_2026/7ow8_13095.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ow8_13095/02_2026/7ow8_13095.cif"
  }
  resolution = 3.5
  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=   0.076
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 8748 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     Mg      2      5.21       5
     S      36      5.16       5
     C    5714      2.51       5
     N    1490      2.21       5
     O    1694      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8942
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 577, 4439
          Classifications: {'peptide': 577}
          Link IDs: {'PTRANS': 17, 'TRANS': 559}
    Chain: "B"
      Number of atoms: 4439
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 577, 4439
          Classifications: {'peptide': 577}
          Link IDs: {'PTRANS': 17, 'TRANS': 559}
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.00, per 1000 atoms: 0.22
  Number of scatterers: 8942
  At special positions: 0
  Unit cell: (74.692, 85.212, 135.708, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      36     16.00
     P       6     15.00
     Mg      2     11.99
     O    1694      8.00
     N    1490      7.00
     C    5714      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: 0.56
  Conformation dependent library (CDL) restraints added in 339.6 milliseconds
  

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2124

  Finding SS restraints...
    Secondary structure from input PDB file:
      56 helices and 6 sheets defined
      71.7% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 22
      removed outlier: 3.651A  pdb=" N   PHE A  15 " --> pdb=" O   LYS A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 50
      removed outlier: 4.236A  pdb=" N   PHE A  31 " --> pdb=" O   GLY A  27 " (cutoff:3.500A)
      Proline residue:  A  47  - end of helix
    Processing helix  chain 'A' and resid 52 through 64
      removed outlier: 4.158A  pdb=" N   SER A  58 " --> pdb=" O   VAL A  54 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 108
      removed outlier: 3.713A  pdb=" N   LEU A  69 " --> pdb=" O   THR A  65 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLY A  79 " --> pdb=" O   PHE A  75 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASN A  91 " --> pdb=" O   ALA A  87 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   SER A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   GLU A 101 " --> pdb=" O   SER A  97 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LYS A 105 " --> pdb=" O   GLU A 101 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE A 108 " --> pdb=" O   TRP A 104 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 118
      removed outlier: 4.046A  pdb=" N   PHE A 115 " --> pdb=" O   PRO A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 126
      removed outlier: 3.876A  pdb=" N   THR A 123 " --> pdb=" O   ALA A 119 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   SER A 125 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 130 through 140
      removed outlier: 4.559A  pdb=" N   GLU A 136 " --> pdb=" O   MET A 132 " (cutoff:3.500A)
      removed outlier: 4.757A  pdb=" N   LEU A 137 " --> pdb=" O   VAL A 133 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   ILE A 138 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 163
      removed outlier: 3.695A  pdb=" N   GLY A 144 " --> pdb=" O   THR A 140 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   MET A 162 " --> pdb=" O   ILE A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 210
      Proline residue:  A 175  - end of helix
      Proline residue:  A 183  - end of helix
      removed outlier: 4.159A  pdb=" N   GLU A 194 " --> pdb=" O   SER A 190 " (cutoff:3.500A)
      removed outlier: 4.496A  pdb=" N   ALA A 200 " --> pdb=" O   GLN A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 219
    Processing helix  chain 'A' and resid 221 through 248
      removed outlier: 3.840A  pdb=" N   GLU A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
      removed outlier: 3.555A  pdb=" N   ALA A 244 " --> pdb=" O   GLY A 240 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   LYS A 245 " --> pdb=" O   VAL A 241 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 277
      removed outlier: 3.883A  pdb=" N   LEU A 253 " --> pdb=" O   LEU A 249 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE A 254 " --> pdb=" O   VAL A 250 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   SER A 255 " --> pdb=" O   GLY A 251 " (cutoff:3.500A)
      removed outlier: 4.523A  pdb=" N   MET A 271 " --> pdb=" O   GLY A 267 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   SER A 274 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 293
      removed outlier: 3.519A  pdb=" N   LEU A 283 " --> pdb=" O   THR A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 293 through 315
      removed outlier: 3.560A  pdb=" N   MET A 297 " --> pdb=" O   ILE A 293 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 323
      removed outlier: 3.690A  pdb=" N   ALA A 322 " --> pdb=" O   GLU A 319 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   GLU A 323 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 319 through 323'
    Processing helix  chain 'A' and resid 380 through 387
    Processing helix  chain 'A' and resid 404 through 408
    Processing helix  chain 'A' and resid 409 through 415
    Processing helix  chain 'A' and resid 430 through 437
    Processing helix  chain 'A' and resid 444 through 455
      removed outlier: 3.520A  pdb=" N   LYS A 450 " --> pdb=" O   ALA A 446 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 462
      removed outlier: 3.775A  pdb=" N   LYS A 462 " --> pdb=" O   LEU A 458 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 473 through 477
      removed outlier: 3.782A  pdb=" N   GLY A 476 " --> pdb=" O   GLY A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 482 through 495
      removed outlier: 4.131A  pdb=" N   ARG A 495 " --> pdb=" O   ARG A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 510 through 525
    Processing helix  chain 'A' and resid 536 through 540
      removed outlier: 3.780A  pdb=" N   THR A 539 " --> pdb=" O   ARG A 536 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL A 540 " --> pdb=" O   LEU A 537 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 536 through 540'
    Processing helix  chain 'A' and resid 559 through 567
    Processing helix  chain 'A' and resid 570 through 586
      removed outlier: 3.598A  pdb=" N   ALA A 574 " --> pdb=" O   TYR A 570 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLN A 577 " --> pdb=" O   PHE A 573 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   LEU A 584 " --> pdb=" O   MET A 580 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 22
      removed outlier: 3.652A  pdb=" N   PHE B  15 " --> pdb=" O   LYS B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 50
      removed outlier: 4.236A  pdb=" N   PHE B  31 " --> pdb=" O   GLY B  27 " (cutoff:3.500A)
      Proline residue:  B  47  - end of helix
    Processing helix  chain 'B' and resid 52 through 64
      removed outlier: 4.158A  pdb=" N   SER B  58 " --> pdb=" O   VAL B  54 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 108
      removed outlier: 3.713A  pdb=" N   LEU B  69 " --> pdb=" O   THR B  65 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLY B  79 " --> pdb=" O   PHE B  75 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASN B  91 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   SER B  97 " --> pdb=" O   GLN B  93 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLU B 101 " --> pdb=" O   SER B  97 " (cutoff:3.500A)
      removed outlier: 4.167A  pdb=" N   LYS B 105 " --> pdb=" O   GLU B 101 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE B 108 " --> pdb=" O   TRP B 104 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 118
      removed outlier: 4.046A  pdb=" N   PHE B 115 " --> pdb=" O   PRO B 111 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 129
      removed outlier: 3.699A  pdb=" N   THR B 123 " --> pdb=" O   ALA B 119 " (cutoff:3.500A)
      removed outlier: 4.558A  pdb=" N   SER B 125 " --> pdb=" O   GLY B 121 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   VAL B 127 " --> pdb=" O   THR B 123 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 130 through 133
    Processing helix  chain 'B' and resid 134 through 140
      removed outlier: 3.935A  pdb=" N   ILE B 138 " --> pdb=" O   VAL B 134 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 163
      removed outlier: 3.749A  pdb=" N   MET B 162 " --> pdb=" O   ILE B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 206
      Proline residue:  B 175  - end of helix
      Proline residue:  B 183  - end of helix
      removed outlier: 4.159A  pdb=" N   GLU B 194 " --> pdb=" O   SER B 190 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   ALA B 200 " --> pdb=" O   GLN B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 211
      No H-bonds generated for 'chain 'B' and resid 209 through 211'
    Processing helix  chain 'B' and resid 212 through 219
    Processing helix  chain 'B' and resid 221 through 248
      removed outlier: 3.959A  pdb=" N   GLU B 243 " --> pdb=" O   LEU B 239 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ALA B 244 " --> pdb=" O   GLY B 240 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 277
      removed outlier: 3.883A  pdb=" N   LEU B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ILE B 254 " --> pdb=" O   VAL B 250 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   SER B 255 " --> pdb=" O   GLY B 251 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   MET B 271 " --> pdb=" O   GLY B 267 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   SER B 274 " --> pdb=" O   GLY B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 279 through 293
      removed outlier: 3.519A  pdb=" N   LEU B 283 " --> pdb=" O   THR B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 293 through 315
      removed outlier: 3.560A  pdb=" N   MET B 297 " --> pdb=" O   ILE B 293 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 323
      removed outlier: 3.690A  pdb=" N   ALA B 322 " --> pdb=" O   GLU B 319 " (cutoff:3.500A)
      removed outlier: 4.127A  pdb=" N   GLU B 323 " --> pdb=" O   ILE B 320 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 319 through 323'
    Processing helix  chain 'B' and resid 380 through 387
    Processing helix  chain 'B' and resid 404 through 408
    Processing helix  chain 'B' and resid 409 through 415
    Processing helix  chain 'B' and resid 430 through 437
    Processing helix  chain 'B' and resid 445 through 455
    Processing helix  chain 'B' and resid 457 through 462
      removed outlier: 3.775A  pdb=" N   LYS B 462 " --> pdb=" O   LEU B 458 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 473 through 477
      removed outlier: 3.783A  pdb=" N   GLY B 476 " --> pdb=" O   GLY B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 482 through 495
      removed outlier: 4.132A  pdb=" N   ARG B 495 " --> pdb=" O   ARG B 491 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 510 through 525
    Processing helix  chain 'B' and resid 536 through 540
      removed outlier: 3.780A  pdb=" N   THR B 539 " --> pdb=" O   ARG B 536 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   VAL B 540 " --> pdb=" O   LEU B 537 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 536 through 540'
    Processing helix  chain 'B' and resid 559 through 567
    Processing helix  chain 'B' and resid 570 through 586
      removed outlier: 3.597A  pdb=" N   ALA B 574 " --> pdb=" O   TYR B 570 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   GLN B 577 " --> pdb=" O   PHE B 573 " (cutoff:3.500A)
      removed outlier: 4.706A  pdb=" N   LEU B 584 " --> pdb=" O   MET B 580 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 363 through 364
    Processing sheet with id=AA2, first strand: chain 'A' and resid 346 through 348
      removed outlier: 4.997A  pdb=" N   VAL A 346 " --> pdb=" O   GLU A 359 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 417 through 420
      removed outlier: 6.295A  pdb=" N   LEU A 500 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   ILE A 533 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.971A  pdb=" N   LEU A 502 " --> pdb=" O   ILE A 533 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU A 546 " --> pdb=" O   ARG A 557 " (cutoff:3.500A)
      removed outlier: 4.254A  pdb=" N   ARG A 557 " --> pdb=" O   LEU A 546 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   PHE A 548 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 363 through 364
    Processing sheet with id=AA5, first strand: chain 'B' and resid 346 through 348
      removed outlier: 4.997A  pdb=" N   VAL B 346 " --> pdb=" O   GLU B 359 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 417 through 420
      removed outlier: 6.295A  pdb=" N   LEU B 500 " --> pdb=" O   ILE B 531 " (cutoff:3.500A)
      removed outlier: 8.028A  pdb=" N   ILE B 533 " --> pdb=" O   LEU B 500 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   LEU B 502 " --> pdb=" O   ILE B 533 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   LEU B 546 " --> pdb=" O   ARG B 557 " (cutoff:3.500A)
      removed outlier: 4.255A  pdb=" N   ARG B 557 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   PHE B 548 " --> pdb=" O   THR B 555 " (cutoff:3.500A)

    559 hydrogen bonds defined for protein.
    1632 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: 1.29

  Time building geometry restraints manager: 0.74 seconds

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

  Histogram of bond lengths:
        1.15 -     1.28: 1471
        1.28 -     1.42: 2086
        1.42 -     1.55: 5426
        1.55 -     1.68: 25
        1.68 -     1.81: 70
  Bond restraints: 9078
  Sorted by residual:
  bond pdb=" C4  ATP A 601 "
       pdb=" C5  ATP A 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.460 -0.072 1.00e-02 1.00e+04 5.15e+01
  bond pdb=" C4  ATP B 601 "
       pdb=" C5  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.459 -0.071 1.00e-02 1.00e+04 5.04e+01
  bond pdb=" C   ARG B 201 "
       pdb=" O   ARG B 201 "
    ideal  model  delta    sigma   weight residual
    1.236  1.151  0.085 1.25e-02 6.40e+03 4.62e+01
  bond pdb=" C   THR A 131 "
       pdb=" O   THR A 131 "
    ideal  model  delta    sigma   weight residual
    1.237  1.310 -0.073 1.17e-02 7.31e+03 3.91e+01
  bond pdb=" CA  SER A 421 "
       pdb=" CB  SER A 421 "
    ideal  model  delta    sigma   weight residual
    1.528  1.437  0.091 1.48e-02 4.57e+03 3.75e+01
  ... (remaining 9073 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.54: 11996
        4.54 -     9.09: 262
        9.09 -    13.63: 37
       13.63 -    18.17: 3
       18.17 -    22.72: 4
  Bond angle restraints: 12302
  Sorted by residual:
  angle pdb=" PB  ATP A 601 "
        pdb=" O3B ATP A 601 "
        pdb=" PG  ATP A 601 "
      ideal   model   delta    sigma   weight residual
     139.87  117.15   22.72 1.00e+00 1.00e+00 5.16e+02
  angle pdb=" PB  ATP B 601 "
        pdb=" O3B ATP B 601 "
        pdb=" PG  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     139.87  117.17   22.70 1.00e+00 1.00e+00 5.15e+02
  angle pdb=" PA  ATP A 601 "
        pdb=" O3A ATP A 601 "
        pdb=" PB  ATP A 601 "
      ideal   model   delta    sigma   weight residual
     136.83  117.62   19.21 1.00e+00 1.00e+00 3.69e+02
  angle pdb=" PA  ATP B 601 "
        pdb=" O3A ATP B 601 "
        pdb=" PB  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     136.83  117.63   19.20 1.00e+00 1.00e+00 3.69e+02
  angle pdb=" N   THR A 203 "
        pdb=" CA  THR A 203 "
        pdb=" C   THR A 203 "
      ideal   model   delta    sigma   weight residual
     112.90   97.66   15.24 1.31e+00 5.83e-01 1.35e+02
  ... (remaining 12297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.92: 4701
       16.92 -    33.83: 607
       33.83 -    50.75: 159
       50.75 -    67.66: 37
       67.66 -    84.58: 20
  Dihedral angle restraints: 5524
    sinusoidal: 2218
      harmonic: 3306
  Sorted by residual:
  dihedral pdb=" C   LYS A 238 "
           pdb=" N   LYS A 238 "
           pdb=" CA  LYS A 238 "
           pdb=" CB  LYS A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -150.91   28.31     0      2.50e+00 1.60e-01 1.28e+02
  dihedral pdb=" N   LYS A 238 "
           pdb=" C   LYS A 238 "
           pdb=" CA  LYS A 238 "
           pdb=" CB  LYS A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  146.89  -24.09     0      2.50e+00 1.60e-01 9.28e+01
  dihedral pdb=" C   PHE B 202 "
           pdb=" N   PHE B 202 "
           pdb=" CA  PHE B 202 "
           pdb=" CB  PHE B 202 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -145.76   23.16     0      2.50e+00 1.60e-01 8.58e+01
  ... (remaining 5521 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.218: 1435
       0.218 -    0.435: 38
       0.435 -    0.653: 9
       0.653 -    0.870: 0
       0.870 -    1.088: 2
  Chirality restraints: 1484
  Sorted by residual:
  chirality pdb=" CA  LYS A 238 "
            pdb=" N   LYS A 238 "
            pdb=" C   LYS A 238 "
            pdb=" CB  LYS A 238 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.42    1.09 2.00e-01 2.50e+01 2.96e+01
  chirality pdb=" CA  PHE B 202 "
            pdb=" N   PHE B 202 "
            pdb=" C   PHE B 202 "
            pdb=" CB  PHE B 202 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.62    0.89 2.00e-01 2.50e+01 1.99e+01
  chirality pdb=" CA  LYS B 230 "
            pdb=" N   LYS B 230 "
            pdb=" C   LYS B 230 "
            pdb=" CB  LYS B 230 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.88    0.63 2.00e-01 2.50e+01 9.80e+00
  ... (remaining 1481 not shown)

  Planarity restraints: 1536
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN B 118 "    0.028 2.00e-02 2.50e+03   5.80e-02 3.37e+01
        pdb=" C   ASN B 118 "   -0.100 2.00e-02 2.50e+03
        pdb=" O   ASN B 118 "    0.038 2.00e-02 2.50e+03
        pdb=" N   ALA B 119 "    0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 202 "   -0.028 2.00e-02 2.50e+03   5.46e-02 2.98e+01
        pdb=" C   PHE A 202 "    0.095 2.00e-02 2.50e+03
        pdb=" O   PHE A 202 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   THR A 203 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 227 "    0.027 2.00e-02 2.50e+03   5.03e-02 2.53e+01
        pdb=" C   GLY A 227 "   -0.087 2.00e-02 2.50e+03
        pdb=" O   GLY A 227 "    0.031 2.00e-02 2.50e+03
        pdb=" N   ARG A 228 "    0.029 2.00e-02 2.50e+03
  ... (remaining 1533 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.57: 97
        2.57 -     3.15: 7301
        3.15 -     3.73: 14031
        3.73 -     4.32: 18876
        4.32 -     4.90: 30161
  Nonbonded interactions: 70466
  Sorted by model distance:
  nonbonded pdb=" O2B ATP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     1.983 2.170
  nonbonded pdb=" O2B ATP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     1.984 2.170
  nonbonded pdb=" OE1 GLN A 422 "
            pdb="MG    MG A 602 "
     model   vdw
     2.038 2.170
  nonbonded pdb=" OE1 GLN B 422 "
            pdb="MG    MG B 602 "
     model   vdw
     2.038 2.170
  nonbonded pdb=" O2G ATP A 601 "
            pdb="MG    MG A 602 "
     model   vdw
     2.046 2.170
  ... (remaining 70461 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: 0.02
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             1.040
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.040
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.700
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.170
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.250
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7092
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.011   0.091   9078  Z= 0.641
  Angle     :  1.608  22.715  12302  Z= 1.079
  Chirality :  0.097   1.088   1484
  Planarity :  0.010   0.078   1536
  Dihedral  : 17.116  84.579   3400
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  6.26 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  4.22 %
    Allowed  :  8.13 %
    Favored  : 87.65 %
  Cbeta Deviations :  2.26 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.72 %

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 are not related in a simple way.
  whole: -3.90 (0.19), residues: 1150
  helix: -2.36 (0.14), residues: 750
  sheet: -1.83 (0.55), residues: 66
  loop : -2.81 (0.27), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 484 
 TYR   0.032   0.003   TYR B 419 
 PHE   0.032   0.003   PHE A 384 
 TRP   0.007   0.002   TRP B 104 
 HIS   0.004   0.002   HIS B 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.01109 ( 9078)
  covalent geometry    : angle       1.60777 (12302)
  hydrogen bonds       : bond        0.17789 (  559)
  hydrogen bonds       : angle       8.17112 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 191
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.8761 (tp) cc_final: 0.8560 (tp)
REVERT: A  105 LYS cc_start: 0.8344 (ttmt) cc_final: 0.8026 (tttm)
REVERT: A  129 ASN cc_start: 0.7975 (m-40) cc_final: 0.7693 (m110)
REVERT: A  207 ASN cc_start: 0.8377 (OUTLIER) cc_final: 0.7815 (t0)
REVERT: A  231 MET cc_start: 0.7551 (OUTLIER) cc_final: 0.7338 (mtp)
REVERT: A  238 LYS cc_start: 0.7368 (OUTLIER) cc_final: 0.7147 (mtpt)
REVERT: A  315 GLU cc_start: 0.8271 (tm-30) cc_final: 0.8058 (tm-30)
REVERT: A  316 ARG cc_start: 0.7635 (mmt180) cc_final: 0.7149 (mmm160)
REVERT: A  334 ILE cc_start: 0.8714 (OUTLIER) cc_final: 0.8384 (mm)
REVERT: A  365 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7800 (tm-30)
REVERT: A  408 TYR cc_start: 0.8690 (m-80) cc_final: 0.8117 (m-80)
REVERT: A  447 GLU cc_start: 0.7661 (tp30) cc_final: 0.7453 (tp30)
REVERT: A  453 GLU cc_start: 0.8301 (tm-30) cc_final: 0.7729 (tp30)
REVERT: A  506 THR cc_start: 0.7604 (p) cc_final: 0.7337 (t)
REVERT: A  514 GLU cc_start: 0.7897 (tt0) cc_final: 0.7607 (tt0)
REVERT: A  551 LYS cc_start: 0.8871 (mttt) cc_final: 0.8274 (mptt)
REVERT: B   33 LEU cc_start: 0.8783 (mp) cc_final: 0.8557 (mp)
REVERT: B   80 LEU cc_start: 0.8802 (tp) cc_final: 0.8581 (tp)
REVERT: B  105 LYS cc_start: 0.8297 (ttmt) cc_final: 0.8003 (tptp)
REVERT: B  129 ASN cc_start: 0.7836 (OUTLIER) cc_final: 0.7610 (m-40)
REVERT: B  136 GLU cc_start: 0.8022 (pt0) cc_final: 0.7612 (tp30)
REVERT: B  207 ASN cc_start: 0.8452 (t0) cc_final: 0.8052 (t0)
REVERT: B  231 MET cc_start: 0.7615 (ttm) cc_final: 0.7311 (mtp)
REVERT: B  234 SER cc_start: 0.7406 (OUTLIER) cc_final: 0.7077 (m)
REVERT: B  315 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7925 (tm-30)
REVERT: B  316 ARG cc_start: 0.7533 (mmt180) cc_final: 0.7145 (mmm160)
REVERT: B  365 GLU cc_start: 0.8204 (tm-30) cc_final: 0.7911 (tm-30)
REVERT: B  447 GLU cc_start: 0.7606 (tp30) cc_final: 0.7142 (tp30)
REVERT: B  453 GLU cc_start: 0.8300 (tm-30) cc_final: 0.7942 (tp30)
REVERT: B  514 GLU cc_start: 0.7857 (tt0) cc_final: 0.7633 (tt0)
REVERT: B  551 LYS cc_start: 0.8893 (mttt) cc_final: 0.8304 (mptt)
REVERT: B  572 ASP cc_start: 0.7970 (m-30) cc_final: 0.7640 (m-30)
  outliers start: 41
  outliers final: 12
  residues processed: 225
  average time/residue: 0.0992
  time to fit residues: 29.4645
Evaluate side-chains
  165 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 147
  time to evaluate  : 0.324 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  140 THR
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  207 ASN
Chi-restraints excluded: chain A residue  231 MET
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  239 LEU
Chi-restraints excluded: chain A residue  257 VAL
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  531 ILE
Chi-restraints excluded: chain B residue  129 ASN
Chi-restraints excluded: chain B residue  140 THR
Chi-restraints excluded: chain B residue  146 ILE
Chi-restraints excluded: chain B residue  234 SER
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  257 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    3.9990
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 65 optimal weight:    0.5980
   chunk 62 optimal weight:   20.0000
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
A 141 HIS
A 220 ASN
A 247 GLN
B  91 ASN
B 129 ASN
B 220 ASN
B 519 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.200410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.152436 restraints weight = 10281.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.151806 restraints weight = 7734.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.154382 restraints weight = 7164.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.154082 restraints weight = 4905.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.154651 restraints weight = 5086.123|
|-----------------------------------------------------------------------------|
r_work (final): 0.3757
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7415
moved from start:          0.1939

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9078  Z= 0.194
  Angle     :  0.698   7.060  12302  Z= 0.374
  Chirality :  0.044   0.165   1484
  Planarity :  0.005   0.070   1536
  Dihedral  : 10.610  85.876   1333
  Min Nonbonded Distance : 1.884

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.70 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  4.12 %
    Allowed  : 12.76 %
    Favored  : 83.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.36 %

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 are not related in a simple way.
  whole: -1.99 (0.23), residues: 1150
  helix: -0.69 (0.18), residues: 748
  sheet: -1.43 (0.59), residues: 66
  loop : -2.50 (0.27), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 345 
 TYR   0.015   0.002   TYR B 419 
 PHE   0.018   0.002   PHE A 573 
 TRP   0.008   0.001   TRP B 164 
 HIS   0.005   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00435 ( 9078)
  covalent geometry    : angle       0.69804 (12302)
  hydrogen bonds       : bond        0.04819 (  559)
  hydrogen bonds       : angle       5.60058 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 151
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.8770 (tp) cc_final: 0.8395 (tt)
REVERT: A  127 VAL cc_start: 0.8024 (OUTLIER) cc_final: 0.7663 (m)
REVERT: A  238 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7339 (mtpt)
REVERT: A  315 GLU cc_start: 0.8208 (tm-30) cc_final: 0.7934 (tm-30)
REVERT: A  427 MET cc_start: 0.8477 (mtp) cc_final: 0.8202 (mtt)
REVERT: A  453 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7610 (tp30)
REVERT: A  551 LYS cc_start: 0.8755 (mttt) cc_final: 0.8277 (mptt)
REVERT: B   80 LEU cc_start: 0.8851 (tp) cc_final: 0.8608 (tp)
REVERT: B  241 VAL cc_start: 0.8242 (OUTLIER) cc_final: 0.7236 (m)
REVERT: B  427 MET cc_start: 0.8521 (mtp) cc_final: 0.8313 (mtp)
REVERT: B  453 GLU cc_start: 0.8271 (tm-30) cc_final: 0.7773 (tp30)
REVERT: B  551 LYS cc_start: 0.8879 (mttt) cc_final: 0.8432 (mptt)
  outliers start: 40
  outliers final: 16
  residues processed: 181
  average time/residue: 0.0926
  time to fit residues: 23.2716
Evaluate side-chains
  153 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 134
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  220 ASN
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  290 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  423 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 109 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 90 optimal weight:    2.9990
   chunk 60 optimal weight:    5.9990
   chunk 53 optimal weight:    4.9990
   chunk 112 optimal weight:    4.9990
   chunk 31 optimal weight:    0.3980
   chunk 47 optimal weight:    0.5980
   chunk 35 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   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 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 308 GLN
A 333 GLN
A 338 HIS
** B 220 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 338 HIS
B 519 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.202139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.153684 restraints weight = 10259.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3733 r_free = 0.3733 target = 0.152093 restraints weight = 7690.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.154343 restraints weight = 7426.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.154817 restraints weight = 5072.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.155153 restraints weight = 5106.569|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.2426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9078  Z= 0.152
  Angle     :  0.626   7.707  12302  Z= 0.332
  Chirality :  0.042   0.159   1484
  Planarity :  0.005   0.070   1536
  Dihedral  :  9.711  80.044   1313
  Min Nonbonded Distance : 1.879

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.09 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 17.28 %
    Favored  : 79.42 %
  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 are not related in a simple way.
  whole: -1.06 (0.24), residues: 1150
  helix: -0.01 (0.19), residues: 754
  sheet: -0.95 (0.65), residues: 64
  loop : -2.10 (0.30), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 345 
 TYR   0.013   0.001   TYR A  83 
 PHE   0.017   0.001   PHE A 573 
 TRP   0.007   0.001   TRP B 164 
 HIS   0.021   0.002   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 9078)
  covalent geometry    : angle       0.62568 (12302)
  hydrogen bonds       : bond        0.04186 (  559)
  hydrogen bonds       : angle       5.09071 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 151
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.8833 (tp) cc_final: 0.8614 (tp)
REVERT: A  127 VAL cc_start: 0.7971 (OUTLIER) cc_final: 0.7576 (p)
REVERT: A  238 LYS cc_start: 0.7669 (OUTLIER) cc_final: 0.7434 (mtpt)
REVERT: A  315 GLU cc_start: 0.8171 (tm-30) cc_final: 0.7930 (tm-30)
REVERT: A  453 GLU cc_start: 0.8293 (tm-30) cc_final: 0.7591 (tm-30)
REVERT: A  454 MET cc_start: 0.8104 (ttm) cc_final: 0.7563 (ttm)
REVERT: A  551 LYS cc_start: 0.8809 (mttt) cc_final: 0.8350 (mptt)
REVERT: B   80 LEU cc_start: 0.8826 (tp) cc_final: 0.8573 (tp)
REVERT: B  241 VAL cc_start: 0.8299 (OUTLIER) cc_final: 0.7220 (m)
REVERT: B  368 LYS cc_start: 0.8674 (mttp) cc_final: 0.8350 (mttm)
REVERT: B  453 GLU cc_start: 0.8284 (tm-30) cc_final: 0.7913 (tm-30)
REVERT: B  551 LYS cc_start: 0.8865 (mttt) cc_final: 0.8446 (mptt)
  outliers start: 32
  outliers final: 19
  residues processed: 175
  average time/residue: 0.0954
  time to fit residues: 22.7910
Evaluate side-chains
  159 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 137
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  136 GLU
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain A residue  436 CYS
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  257 VAL
Chi-restraints excluded: chain B residue  259 MET
Chi-restraints excluded: chain B residue  318 ILE
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  423 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 53 optimal weight:    6.9990
   chunk 7 optimal weight:    0.6980
   chunk 6 optimal weight:    4.9990
   chunk 90 optimal weight:    0.6980
   chunk 38 optimal weight:    0.7980
   chunk 103 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 35 optimal weight:    8.9990
   chunk 113 optimal weight:    6.9990
   chunk 98 optimal weight:    0.3980
   chunk 62 optimal weight:    6.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 208 GLN
B 220 ASN
B 338 HIS
B 577 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.202259 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.153355 restraints weight = 10508.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.152600 restraints weight = 7776.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.155102 restraints weight = 7196.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.155306 restraints weight = 5080.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.156023 restraints weight = 4845.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7397
moved from start:          0.2906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9078  Z= 0.149
  Angle     :  0.600   7.484  12302  Z= 0.317
  Chirality :  0.042   0.165   1484
  Planarity :  0.004   0.068   1536
  Dihedral  :  9.292  80.624   1313
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.26 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 17.28 %
    Favored  : 79.32 %
  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 are not related in a simple way.
  whole: -0.35 (0.25), residues: 1150
  helix:  0.51 (0.19), residues: 748
  sheet: -0.67 (0.69), residues: 64
  loop : -1.70 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 345 
 TYR   0.012   0.001   TYR B  83 
 PHE   0.027   0.002   PHE B  31 
 TRP   0.006   0.001   TRP A 164 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9078)
  covalent geometry    : angle       0.60002 (12302)
  hydrogen bonds       : bond        0.03895 (  559)
  hydrogen bonds       : angle       4.82122 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 154
  time to evaluate  : 0.263 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8811 (tp) cc_final: 0.8581 (tp)
REVERT: A  127 VAL cc_start: 0.8058 (OUTLIER) cc_final: 0.7387 (t)
REVERT: A  238 LYS cc_start: 0.7665 (OUTLIER) cc_final: 0.7416 (mtpt)
REVERT: A  299 GLN cc_start: 0.7563 (mm110) cc_final: 0.7326 (mm-40)
REVERT: A  315 GLU cc_start: 0.8247 (tm-30) cc_final: 0.8008 (tm-30)
REVERT: A  453 GLU cc_start: 0.8260 (tm-30) cc_final: 0.7598 (tm-30)
REVERT: A  454 MET cc_start: 0.8143 (ttm) cc_final: 0.7606 (ttm)
REVERT: A  533 ILE cc_start: 0.8778 (OUTLIER) cc_final: 0.8483 (mt)
REVERT: A  551 LYS cc_start: 0.8788 (mttt) cc_final: 0.8357 (mptt)
REVERT: B   80 LEU cc_start: 0.8819 (tp) cc_final: 0.8563 (tp)
REVERT: B  201 ARG cc_start: 0.7351 (OUTLIER) cc_final: 0.7125 (ttp-170)
REVERT: B  241 VAL cc_start: 0.8353 (OUTLIER) cc_final: 0.7094 (m)
REVERT: B  243 GLU cc_start: 0.7896 (tm-30) cc_final: 0.7597 (tm-30)
REVERT: B  299 GLN cc_start: 0.7473 (mm110) cc_final: 0.7271 (mm-40)
REVERT: B  368 LYS cc_start: 0.8642 (mttp) cc_final: 0.8406 (mttm)
REVERT: B  453 GLU cc_start: 0.8288 (tm-30) cc_final: 0.7612 (tm-30)
REVERT: B  487 ILE cc_start: 0.7498 (OUTLIER) cc_final: 0.6601 (tt)
REVERT: B  536 ARG cc_start: 0.6071 (mtp180) cc_final: 0.5491 (mtp180)
REVERT: B  551 LYS cc_start: 0.8828 (mttt) cc_final: 0.8439 (mptt)
REVERT: B  577 GLN cc_start: 0.8046 (OUTLIER) cc_final: 0.7844 (mm-40)
  outliers start: 33
  outliers final: 16
  residues processed: 179
  average time/residue: 0.0859
  time to fit residues: 21.2883
Evaluate side-chains
  163 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 140
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  199 THR
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  370 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain A residue  533 ILE
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  201 ARG
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  423 GLU
Chi-restraints excluded: chain B residue  487 ILE
Chi-restraints excluded: chain B residue  577 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 48 optimal weight:    0.1980
   chunk 55 optimal weight:    5.9990
   chunk 15 optimal weight:    9.9990
   chunk 64 optimal weight:    0.6980
   chunk 26 optimal weight:    0.1980
   chunk 56 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 58 optimal weight:    0.0770
   chunk 79 optimal weight:    0.4980
   chunk 106 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9990
   overall best weight:    0.3338

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS
** A 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 220 ASN
B 308 GLN
B 338 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.204375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.150917 restraints weight = 10332.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.151836 restraints weight = 7038.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.153388 restraints weight = 5227.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.155606 restraints weight = 4715.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.156158 restraints weight = 4067.102|
|-----------------------------------------------------------------------------|
r_work (final): 0.3732
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.3185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9078  Z= 0.125
  Angle     :  0.577   6.911  12302  Z= 0.305
  Chirality :  0.041   0.185   1484
  Planarity :  0.004   0.067   1536
  Dihedral  :  9.017  84.503   1313
  Min Nonbonded Distance : 1.927

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.91 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 19.55 %
    Favored  : 77.47 %
  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 are not related in a simple way.
  whole: -0.01 (0.25), residues: 1150
  helix:  0.82 (0.20), residues: 748
  sheet: -0.58 (0.70), residues: 64
  loop : -1.67 (0.32), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 345 
 TYR   0.011   0.001   TYR B  83 
 PHE   0.030   0.002   PHE A 573 
 TRP   0.006   0.001   TRP A 164 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00252 ( 9078)
  covalent geometry    : angle       0.57692 (12302)
  hydrogen bonds       : bond        0.03710 (  559)
  hydrogen bonds       : angle       4.60124 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  178 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 149
  time to evaluate  : 0.343 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8768 (tp) cc_final: 0.8527 (tp)
REVERT: A  127 VAL cc_start: 0.8046 (OUTLIER) cc_final: 0.7671 (m)
REVERT: A  238 LYS cc_start: 0.7585 (OUTLIER) cc_final: 0.7306 (mtpt)
REVERT: A  299 GLN cc_start: 0.7493 (mm110) cc_final: 0.7261 (mm-40)
REVERT: A  315 GLU cc_start: 0.8302 (tm-30) cc_final: 0.8051 (tm-30)
REVERT: A  453 GLU cc_start: 0.8235 (tm-30) cc_final: 0.7568 (tm-30)
REVERT: A  454 MET cc_start: 0.8160 (ttm) cc_final: 0.7656 (ttm)
REVERT: A  551 LYS cc_start: 0.8773 (mttt) cc_final: 0.8315 (mptt)
REVERT: B   80 LEU cc_start: 0.8791 (tp) cc_final: 0.8534 (tp)
REVERT: B  243 GLU cc_start: 0.7846 (tm-30) cc_final: 0.7614 (tm-30)
REVERT: B  299 GLN cc_start: 0.7433 (mm110) cc_final: 0.7232 (mm-40)
REVERT: B  365 GLU cc_start: 0.7894 (tm-30) cc_final: 0.7634 (tm-30)
REVERT: B  368 LYS cc_start: 0.8637 (mttp) cc_final: 0.8383 (mttm)
REVERT: B  453 GLU cc_start: 0.8251 (tm-30) cc_final: 0.7585 (tm-30)
REVERT: B  506 THR cc_start: 0.8427 (m) cc_final: 0.7737 (p)
REVERT: B  551 LYS cc_start: 0.8825 (mttt) cc_final: 0.8412 (mptt)
  outliers start: 29
  outliers final: 20
  residues processed: 169
  average time/residue: 0.0960
  time to fit residues: 22.1564
Evaluate side-chains
  157 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 135
  time to evaluate  : 0.277 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  208 GLN
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  241 VAL
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  423 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 102 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 24 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 110 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 105 optimal weight:    0.9990
   chunk 106 optimal weight:    0.9980
   chunk 113 optimal weight:    3.9990
   chunk 46 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
A 338 HIS
A 577 GLN
B 338 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.200677 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.151260 restraints weight = 10348.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.149944 restraints weight = 7917.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.152772 restraints weight = 6878.660|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.153116 restraints weight = 4972.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.153286 restraints weight = 4799.647|
|-----------------------------------------------------------------------------|
r_work (final): 0.3736
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.3315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   9078  Z= 0.192
  Angle     :  0.623   6.998  12302  Z= 0.328
  Chirality :  0.043   0.178   1484
  Planarity :  0.005   0.066   1536
  Dihedral  :  9.283  85.395   1312
  Min Nonbonded Distance : 1.783

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.61 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 19.65 %
    Favored  : 76.65 %
  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 are not related in a simple way.
  whole:  0.10 (0.25), residues: 1150
  helix:  0.91 (0.20), residues: 744
  sheet: -0.67 (0.69), residues: 66
  loop : -1.60 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 345 
 TYR   0.013   0.001   TYR B  83 
 PHE   0.034   0.002   PHE B  31 
 TRP   0.004   0.001   TRP A 104 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 9078)
  covalent geometry    : angle       0.62259 (12302)
  hydrogen bonds       : bond        0.03871 (  559)
  hydrogen bonds       : angle       4.66558 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 144
  time to evaluate  : 0.340 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8783 (tp) cc_final: 0.8525 (tp)
REVERT: A  127 VAL cc_start: 0.8161 (OUTLIER) cc_final: 0.7508 (t)
REVERT: A  238 LYS cc_start: 0.7701 (OUTLIER) cc_final: 0.7317 (mtpt)
REVERT: A  299 GLN cc_start: 0.7593 (mm110) cc_final: 0.7383 (mm-40)
REVERT: A  315 GLU cc_start: 0.8253 (tm-30) cc_final: 0.8000 (tm-30)
REVERT: A  453 GLU cc_start: 0.8241 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: A  454 MET cc_start: 0.8023 (ttm) cc_final: 0.7536 (ttm)
REVERT: A  551 LYS cc_start: 0.8781 (mttt) cc_final: 0.8409 (mptt)
REVERT: B   80 LEU cc_start: 0.8830 (tp) cc_final: 0.8591 (tp)
REVERT: B  243 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7607 (tm-30)
REVERT: B  453 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7588 (tm-30)
REVERT: B  536 ARG cc_start: 0.6580 (mtp180) cc_final: 0.6031 (mtt180)
REVERT: B  551 LYS cc_start: 0.8787 (mttt) cc_final: 0.8490 (mptt)
  outliers start: 36
  outliers final: 25
  residues processed: 168
  average time/residue: 0.1015
  time to fit residues: 23.2872
Evaluate side-chains
  159 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 132
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  231 MET
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  370 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  423 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 72 optimal weight:    6.9990
   chunk 33 optimal weight:    3.9990
   chunk 105 optimal weight:    0.9980
   chunk 15 optimal weight:    6.9990
   chunk 109 optimal weight:    0.8980
   chunk 0 optimal weight:    2.9990
   chunk 48 optimal weight:    0.4980
   chunk 112 optimal weight:    0.9980
   chunk 91 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
A 118 ASN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
A 338 HIS
A 577 GLN
B  91 ASN
B 208 GLN
B 220 ASN
B 338 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.202788 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.152721 restraints weight = 10501.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.153578 restraints weight = 7972.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.155404 restraints weight = 6638.840|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.155382 restraints weight = 4587.072|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.155750 restraints weight = 4305.310|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7448
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   9078  Z= 0.157
  Angle     :  0.603   7.153  12302  Z= 0.318
  Chirality :  0.042   0.159   1484
  Planarity :  0.004   0.066   1536
  Dihedral  :  8.984  86.509   1311
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.17 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  3.91 %
    Allowed  : 20.99 %
    Favored  : 75.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.31 (0.25), residues: 1150
  helix:  1.08 (0.20), residues: 740
  sheet: -0.24 (0.71), residues: 60
  loop : -1.59 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 345 
 TYR   0.011   0.001   TYR A  83 
 PHE   0.032   0.002   PHE A  31 
 TRP   0.004   0.001   TRP B 104 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 9078)
  covalent geometry    : angle       0.60304 (12302)
  hydrogen bonds       : bond        0.03672 (  559)
  hydrogen bonds       : angle       4.52835 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  175 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 137
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8729 (tp) cc_final: 0.8459 (tp)
REVERT: A  127 VAL cc_start: 0.8096 (OUTLIER) cc_final: 0.7483 (t)
REVERT: A  238 LYS cc_start: 0.7593 (OUTLIER) cc_final: 0.7243 (mtpt)
REVERT: A  368 LYS cc_start: 0.8639 (mttm) cc_final: 0.8402 (mttm)
REVERT: A  453 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7593 (tm-30)
REVERT: A  454 MET cc_start: 0.8048 (ttm) cc_final: 0.7556 (ttm)
REVERT: A  551 LYS cc_start: 0.8842 (mttt) cc_final: 0.8428 (mptt)
REVERT: B   80 LEU cc_start: 0.8776 (tp) cc_final: 0.8527 (tp)
REVERT: B  243 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7593 (tm-30)
REVERT: B  453 GLU cc_start: 0.8282 (tm-30) cc_final: 0.7622 (tm-30)
REVERT: B  536 ARG cc_start: 0.6403 (mtp180) cc_final: 0.5849 (mtt180)
REVERT: B  551 LYS cc_start: 0.8792 (mttt) cc_final: 0.8472 (mptt)
  outliers start: 38
  outliers final: 26
  residues processed: 159
  average time/residue: 0.0959
  time to fit residues: 21.1836
Evaluate side-chains
  162 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 134
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  423 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 110 optimal weight:    2.9990
   chunk 93 optimal weight:    0.9980
   chunk 85 optimal weight:    0.9990
   chunk 47 optimal weight:    0.5980
   chunk 28 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   chunk 41 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 96 optimal weight:    5.9990
   chunk 69 optimal weight:    0.9990
   chunk 102 optimal weight:    0.0050
   overall best weight:    0.6794

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

Flipped N/Q/H residues before XYZ refinement:
A 118 ASN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 HIS
B 208 GLN
B 220 ASN
B 338 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.203759 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.153299 restraints weight = 10468.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.154120 restraints weight = 7404.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.156501 restraints weight = 6138.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.156451 restraints weight = 4180.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3749 r_free = 0.3749 target = 0.156765 restraints weight = 4015.374|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7402
moved from start:          0.3707

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9078  Z= 0.145
  Angle     :  0.592   8.816  12302  Z= 0.310
  Chirality :  0.041   0.191   1484
  Planarity :  0.004   0.065   1536
  Dihedral  :  8.772  83.197   1311
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.35 %
    Favored  : 95.57 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 21.91 %
    Favored  : 74.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.43 (0.26), residues: 1150
  helix:  1.20 (0.20), residues: 740
  sheet: -0.36 (0.69), residues: 64
  loop : -1.55 (0.32), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 345 
 TYR   0.010   0.001   TYR B 408 
 PHE   0.040   0.002   PHE B  31 
 TRP   0.004   0.001   TRP A 104 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00325 ( 9078)
  covalent geometry    : angle       0.59195 (12302)
  hydrogen bonds       : bond        0.03567 (  559)
  hydrogen bonds       : angle       4.41809 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 135
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8690 (tp) cc_final: 0.8440 (tp)
REVERT: A  118 ASN cc_start: 0.8574 (OUTLIER) cc_final: 0.8311 (t0)
REVERT: A  127 VAL cc_start: 0.7999 (OUTLIER) cc_final: 0.7310 (t)
REVERT: A  238 LYS cc_start: 0.7580 (OUTLIER) cc_final: 0.7260 (mtpt)
REVERT: A  299 GLN cc_start: 0.7509 (mm110) cc_final: 0.7248 (mm-40)
REVERT: A  333 GLN cc_start: 0.8372 (mm-40) cc_final: 0.8097 (mt0)
REVERT: A  368 LYS cc_start: 0.8636 (mttm) cc_final: 0.8372 (mttm)
REVERT: A  453 GLU cc_start: 0.8240 (tm-30) cc_final: 0.7791 (tm-30)
REVERT: A  454 MET cc_start: 0.8095 (ttm) cc_final: 0.7755 (ttm)
REVERT: A  551 LYS cc_start: 0.8838 (mttt) cc_final: 0.8392 (mptt)
REVERT: B   80 LEU cc_start: 0.8769 (tp) cc_final: 0.8519 (tp)
REVERT: B  201 ARG cc_start: 0.7434 (ttp-170) cc_final: 0.7230 (ttp-170)
REVERT: B  243 GLU cc_start: 0.7836 (tm-30) cc_final: 0.7618 (tm-30)
REVERT: B  453 GLU cc_start: 0.8336 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: B  536 ARG cc_start: 0.6232 (mtp180) cc_final: 0.5769 (mtt180)
REVERT: B  551 LYS cc_start: 0.8824 (mttt) cc_final: 0.8437 (mptt)
  outliers start: 34
  outliers final: 30
  residues processed: 157
  average time/residue: 0.1010
  time to fit residues: 21.4892
Evaluate side-chains
  156 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 123
  time to evaluate  : 0.323 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  118 ASN
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  138 ILE
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  386 LEU
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  220 ASN
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  259 MET
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  386 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  423 GLU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 32 optimal weight:   10.0000
   chunk 89 optimal weight:    4.9990
   chunk 50 optimal weight:    4.9990
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 5 optimal weight:   20.0000
   chunk 27 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 HIS
A 535 HIS
B 333 GLN
B 338 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.192473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.141631 restraints weight = 10673.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.137922 restraints weight = 9246.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.140681 restraints weight = 8612.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.141617 restraints weight = 5870.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.141987 restraints weight = 5379.409|
|-----------------------------------------------------------------------------|
r_work (final): 0.3593
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7581
moved from start:          0.3628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.077   9078  Z= 0.386
  Angle     :  0.825   9.290  12302  Z= 0.430
  Chirality :  0.050   0.177   1484
  Planarity :  0.005   0.067   1536
  Dihedral  :  9.948  82.077   1311
  Min Nonbonded Distance : 1.672

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.74 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  3.70 %
    Allowed  : 22.63 %
    Favored  : 73.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.27 %

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 are not related in a simple way.
  whole: -0.27 (0.25), residues: 1150
  helix:  0.62 (0.19), residues: 736
  sheet: -0.27 (0.70), residues: 58
  loop : -1.78 (0.30), residues: 356

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B 126 
 TYR   0.023   0.002   TYR A  83 
 PHE   0.039   0.002   PHE B  31 
 TRP   0.012   0.002   TRP B 104 
 HIS   0.004   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00920 ( 9078)
  covalent geometry    : angle       0.82547 (12302)
  hydrogen bonds       : bond        0.04502 (  559)
  hydrogen bonds       : angle       5.02222 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 137
  time to evaluate  : 0.354 
Fit side-chains
REVERT: A   80 LEU cc_start: 0.8766 (tp) cc_final: 0.8477 (tp)
REVERT: A  127 VAL cc_start: 0.8185 (OUTLIER) cc_final: 0.7493 (t)
REVERT: A  238 LYS cc_start: 0.7757 (OUTLIER) cc_final: 0.7445 (mtpt)
REVERT: A  333 GLN cc_start: 0.8333 (mm-40) cc_final: 0.8061 (mt0)
REVERT: A  525 MET cc_start: 0.8726 (mmt) cc_final: 0.8105 (mmt)
REVERT: A  551 LYS cc_start: 0.8929 (mttt) cc_final: 0.8426 (mptt)
REVERT: B   80 LEU cc_start: 0.8848 (tp) cc_final: 0.8566 (tp)
REVERT: B  243 GLU cc_start: 0.8078 (tm-30) cc_final: 0.7696 (tm-30)
REVERT: B  453 GLU cc_start: 0.8368 (tm-30) cc_final: 0.7986 (tm-30)
REVERT: B  536 ARG cc_start: 0.6691 (mtp180) cc_final: 0.5903 (mtt180)
REVERT: B  551 LYS cc_start: 0.8903 (mttt) cc_final: 0.8416 (mptt)
  outliers start: 36
  outliers final: 28
  residues processed: 163
  average time/residue: 0.0844
  time to fit residues: 19.3079
Evaluate side-chains
  163 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 133
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  112 VAL
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  259 MET
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  334 ILE
Chi-restraints excluded: chain A residue  355 LEU
Chi-restraints excluded: chain A residue  370 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain A residue  417 ILE
Chi-restraints excluded: chain A residue  423 GLU
Chi-restraints excluded: chain B residue  112 VAL
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  203 THR
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  423 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 23 optimal weight:    0.8980
   chunk 32 optimal weight:    7.9990
   chunk 84 optimal weight:   10.0000
   chunk 106 optimal weight:    0.5980
   chunk 98 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   chunk 12 optimal weight:    0.4980
   chunk 51 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 76 optimal weight:    0.5980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  91 ASN
B 220 ASN
B 338 HIS
B 577 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4212 r_free = 0.4212 target = 0.201729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.152460 restraints weight = 10491.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.155242 restraints weight = 7309.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.156472 restraints weight = 6345.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.156173 restraints weight = 4434.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.156594 restraints weight = 4656.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3772
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7376
moved from start:          0.3853

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9078  Z= 0.147
  Angle     :  0.643  10.846  12302  Z= 0.333
  Chirality :  0.043   0.291   1484
  Planarity :  0.004   0.065   1536
  Dihedral  :  8.948  83.639   1311
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.26 %
    Favored  : 95.65 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 24.18 %
    Favored  : 73.15 %
  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 are not related in a simple way.
  whole:  0.27 (0.25), residues: 1150
  helix:  1.07 (0.20), residues: 748
  sheet: -0.66 (0.66), residues: 66
  loop : -1.61 (0.31), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 536 
 TYR   0.011   0.001   TYR B 419 
 PHE   0.045   0.002   PHE B  31 
 TRP   0.006   0.001   TRP A 104 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 9078)
  covalent geometry    : angle       0.64259 (12302)
  hydrogen bonds       : bond        0.03611 (  559)
  hydrogen bonds       : angle       4.54591 ( 1632)

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

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

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2300 Ramachandran restraints generated.
    1150 Oldfield, 0 Emsley, 1150 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 130
  time to evaluate  : 0.318 
Fit side-chains
   revert: symmetry clash
REVERT: A   80 LEU cc_start: 0.8738 (tp) cc_final: 0.8470 (tp)
REVERT: A  118 ASN cc_start: 0.8732 (t0) cc_final: 0.8433 (t0)
REVERT: A  127 VAL cc_start: 0.8010 (OUTLIER) cc_final: 0.7662 (m)
REVERT: A  238 LYS cc_start: 0.7636 (OUTLIER) cc_final: 0.7295 (mtpt)
REVERT: A  453 GLU cc_start: 0.8316 (tm-30) cc_final: 0.7635 (tm-30)
REVERT: A  454 MET cc_start: 0.8105 (ttm) cc_final: 0.7844 (ttt)
REVERT: A  525 MET cc_start: 0.8648 (mmt) cc_final: 0.8034 (mmt)
REVERT: A  551 LYS cc_start: 0.8820 (mttt) cc_final: 0.8351 (mptt)
REVERT: B   80 LEU cc_start: 0.8785 (tp) cc_final: 0.8504 (tp)
REVERT: B  243 GLU cc_start: 0.7882 (tm-30) cc_final: 0.7657 (tm-30)
REVERT: B  453 GLU cc_start: 0.8374 (tm-30) cc_final: 0.8024 (tm-30)
REVERT: B  454 MET cc_start: 0.8334 (ttm) cc_final: 0.8107 (ttt)
REVERT: B  536 ARG cc_start: 0.6509 (mtp180) cc_final: 0.6167 (mtt180)
REVERT: B  551 LYS cc_start: 0.8818 (mttt) cc_final: 0.8417 (mmmt)
  outliers start: 26
  outliers final: 18
  residues processed: 150
  average time/residue: 0.0827
  time to fit residues: 17.1233
Evaluate side-chains
  144 residues out of total 972 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 124
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  116 ASP
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  133 VAL
Chi-restraints excluded: chain A residue  134 VAL
Chi-restraints excluded: chain A residue  159 LEU
Chi-restraints excluded: chain A residue  206 LEU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  238 LYS
Chi-restraints excluded: chain A residue  248 SER
Chi-restraints excluded: chain A residue  288 LEU
Chi-restraints excluded: chain A residue  370 THR
Chi-restraints excluded: chain A residue  400 LEU
Chi-restraints excluded: chain B residue  116 ASP
Chi-restraints excluded: chain B residue  159 LEU
Chi-restraints excluded: chain B residue  236 LEU
Chi-restraints excluded: chain B residue  248 SER
Chi-restraints excluded: chain B residue  288 LEU
Chi-restraints excluded: chain B residue  355 LEU
Chi-restraints excluded: chain B residue  400 LEU
Chi-restraints excluded: chain B residue  423 GLU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 9 optimal weight:    0.5980
   chunk 38 optimal weight:    0.8980
   chunk 34 optimal weight:    0.0060
   chunk 77 optimal weight:    0.9990
   chunk 8 optimal weight:    0.6980
   chunk 32 optimal weight:    4.9990
   chunk 3 optimal weight:    2.9990
   chunk 72 optimal weight:    8.9990
   chunk 20 optimal weight:    0.8980
   chunk 96 optimal weight:    0.7980
   chunk 51 optimal weight:    7.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 207 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 333 GLN
A 338 HIS
A 577 GLN
B 220 ASN
B 338 HIS
B 577 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.203152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.152136 restraints weight = 10453.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.153253 restraints weight = 7138.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.154939 restraints weight = 5603.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.155463 restraints weight = 4607.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.155912 restraints weight = 4128.297|
|-----------------------------------------------------------------------------|
r_work (final): 0.3727
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9078  Z= 0.143
  Angle     :  0.623  10.449  12302  Z= 0.321
  Chirality :  0.042   0.222   1484
  Planarity :  0.004   0.065   1536
  Dihedral  :  8.961  85.960   1311
  Min Nonbonded Distance : 1.854

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.61 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 24.38 %
    Favored  : 73.15 %
  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 are not related in a simple way.
  whole:  0.53 (0.26), residues: 1150
  helix:  1.24 (0.20), residues: 740
  sheet: -0.22 (0.70), residues: 60
  loop : -1.45 (0.32), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 345 
 TYR   0.011   0.001   TYR B  83 
 PHE   0.039   0.002   PHE B  31 
 TRP   0.005   0.001   TRP A 104 
 HIS   0.003   0.001   HIS B 141 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 9078)
  covalent geometry    : angle       0.62271 (12302)
  hydrogen bonds       : bond        0.03538 (  559)
  hydrogen bonds       : angle       4.43514 ( 1632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1371.45 seconds
wall clock time: 24 minutes 25.32 seconds (1465.32 seconds total)