Starting phenix.real_space_refine
on Fri Aug 22 17:29:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n9w_24263/08_2025/7n9w_24263.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n9w_24263/08_2025/7n9w_24263.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n9w_24263/08_2025/7n9w_24263.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n9w_24263/08_2025/7n9w_24263.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n9w_24263/08_2025/7n9w_24263.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n9w_24263/08_2025/7n9w_24263.map"
  }
  resolution = 4.16
  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=   0.003 sd=   0.028
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    4317      2.51       5
     N    1087      2.21       5
     O    1117      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6561
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3277
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3277
          Classifications: {'peptide': 445}
          Incomplete info: {'truncation_to_alanine': 14}
          Link IDs: {'PTRANS': 19, 'TRANS': 425}
          Unresolved non-hydrogen bonds: 65
          Unresolved non-hydrogen angles: 80
          Unresolved non-hydrogen dihedrals: 52
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 3, 'GLU:plan': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 47
    Chain: "B"
      Number of atoms: 3284
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 445, 3284
          Classifications: {'peptide': 445}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 19, 'TRANS': 425}
          Unresolved non-hydrogen bonds: 57
          Unresolved non-hydrogen angles: 70
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ARG:plan': 5, 'GLN:plan1': 2, 'GLU:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
  Time building chain proxies: 1.78, per 1000 atoms: 0.27
  Number of scatterers: 6561
  At special positions: 0
  Unit cell: (92.224, 111.088, 75.456, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    1117      8.00
     N    1087      7.00
     C    4317      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 379.9 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1552

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 1 sheets defined
      73.1% alpha, 0.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 27
    Processing helix  chain 'A' and resid 36 through 46
      removed outlier: 3.529A  pdb=" N   LEU A  45 " --> pdb=" O   VAL A  41 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   VAL A  46 " --> pdb=" O   VAL A  42 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 70
    Processing helix  chain 'A' and resid 74 through 100
      removed outlier: 4.028A  pdb=" N   LEU A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   THR A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   LEU A  84 " --> pdb=" O   THR A  80 " (cutoff:3.500A)
      removed outlier: 4.178A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 4.437A  pdb=" N   ALA A  87 " --> pdb=" O   PHE A  83 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   LEU A  96 " --> pdb=" O   PHE A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 117
      removed outlier: 3.599A  pdb=" N   GLY A 114 " --> pdb=" O   PRO A 110 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   ALA A 115 " --> pdb=" O   GLU A 111 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   LEU A 116 " --> pdb=" O   ILE A 112 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 134
      removed outlier: 3.697A  pdb=" N   LEU A 128 " --> pdb=" O   TRP A 124 " (cutoff:3.500A)
      Proline residue:  A 129  - end of helix
    Processing helix  chain 'A' and resid 135 through 140
    Processing helix  chain 'A' and resid 148 through 167
      removed outlier: 4.213A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   GLY A 159 " --> pdb=" O   GLY A 155 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG A 160 " --> pdb=" O   GLY A 156 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ILE A 165 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 172 through 177
    Processing helix  chain 'A' and resid 178 through 190
      removed outlier: 5.821A  pdb=" N   ALA A 184 " --> pdb=" O   THR A 180 " (cutoff:3.500A)
      removed outlier: 4.413A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 3.779A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 233
      removed outlier: 4.136A  pdb=" N   PHE A 219 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 4.121A  pdb=" N   MET A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 251 through 282
      removed outlier: 4.199A  pdb=" N   TYR A 255 " --> pdb=" O   THR A 251 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ILE A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 4.078A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   LEU A 279 " --> pdb=" O   GLY A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 305
      removed outlier: 3.508A  pdb=" N   TRP A 291 " --> pdb=" O   ASN A 287 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   LEU A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 324
      removed outlier: 3.638A  pdb=" N   THR A 324 " --> pdb=" O   ILE A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 337
    Processing helix  chain 'A' and resid 340 through 345
    Processing helix  chain 'A' and resid 357 through 362
    Processing helix  chain 'A' and resid 363 through 378
      removed outlier: 3.686A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 383
      removed outlier: 4.487A  pdb=" N   TYR A 382 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 395
      removed outlier: 3.649A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   ALA A 392 " --> pdb=" O   THR A 388 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   GLY A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   GLY A 395 " --> pdb=" O   ILE A 391 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 396 through 401
    Processing helix  chain 'A' and resid 404 through 408
    Processing helix  chain 'A' and resid 410 through 415
    Processing helix  chain 'A' and resid 421 through 430
      removed outlier: 3.664A  pdb=" N   MET A 425 " --> pdb=" O   LEU A 421 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 439
      removed outlier: 3.956A  pdb=" N   PHE A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 459
      removed outlier: 4.949A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS A 455 " --> pdb=" O   ARG A 451 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 28
    Processing helix  chain 'B' and resid 29 through 70
      removed outlier: 3.592A  pdb=" N   LEU B  33 " --> pdb=" O   ASP B  29 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ILE B  35 " --> pdb=" O   THR B  31 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU B  36 " --> pdb=" O   PRO B  32 " (cutoff:3.500A)
      removed outlier: 5.006A  pdb=" N   GLY B  47 " --> pdb=" O   GLY B  43 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU B  48 " --> pdb=" O   THR B  44 " (cutoff:3.500A)
      removed outlier: 5.899A  pdb=" N   ALA B  50 " --> pdb=" O   VAL B  46 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   LEU B  68 " --> pdb=" O   ARG B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 4.029A  pdb=" N   LEU B  78 " --> pdb=" O   ASN B  74 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   PHE B  83 " --> pdb=" O   LEU B  79 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU B  84 " --> pdb=" O   THR B  80 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ALA B  87 " --> pdb=" O   PHE B  83 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   VAL B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   LEU B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LYS B  99 " --> pdb=" O   PHE B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 109 through 114
      removed outlier: 4.228A  pdb=" N   GLY B 114 " --> pdb=" O   PRO B 110 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 126
      removed outlier: 3.685A  pdb=" N   ARG B 126 " --> pdb=" O   ARG B 123 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 123 through 126'
    Processing helix  chain 'B' and resid 127 through 138
      removed outlier: 3.964A  pdb=" N   PHE B 133 " --> pdb=" O   PRO B 129 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 147 through 165
      removed outlier: 4.172A  pdb=" N   THR B 151 " --> pdb=" O   ARG B 147 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 177
      removed outlier: 3.788A  pdb=" N   HIS B 175 " --> pdb=" O   ASP B 171 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 178 through 190
      removed outlier: 3.608A  pdb=" N   ALA B 184 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   PHE B 190 " --> pdb=" O   LEU B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 192 through 202
      removed outlier: 3.569A  pdb=" N   PHE B 199 " --> pdb=" O   ALA B 195 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 233
      removed outlier: 3.800A  pdb=" N   ILE B 215 " --> pdb=" O   THR B 211 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   PHE B 232 " --> pdb=" O   MET B 228 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 284
      removed outlier: 3.871A  pdb=" N   LEU B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 3.969A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   HIS B 281 " --> pdb=" O   GLN B 277 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   HIS B 284 " --> pdb=" O   LEU B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 308
      removed outlier: 4.322A  pdb=" N   LEU B 293 " --> pdb=" O   THR B 289 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 347
      removed outlier: 3.794A  pdb=" N   VAL B 338 " --> pdb=" O   VAL B 334 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 379
      removed outlier: 3.986A  pdb=" N   ALA B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 389 through 395
      removed outlier: 3.695A  pdb=" N   GLY B 395 " --> pdb=" O   ILE B 391 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 401
    Processing helix  chain 'B' and resid 405 through 416
      removed outlier: 4.057A  pdb=" N   LEU B 411 " --> pdb=" O   THR B 407 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   VAL B 412 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 421 through 430
      removed outlier: 3.835A  pdb=" N   MET B 425 " --> pdb=" O   LEU B 421 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   ILE B 427 " --> pdb=" O   LEU B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 432 through 440
    Processing helix  chain 'B' and resid 443 through 459
      removed outlier: 3.679A  pdb=" N   LYS B 455 " --> pdb=" O   ARG B 451 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 210 through 211

    366 hydrogen bonds defined for protein.
    1083 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: 0.94

  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:
        1.22 -     1.34: 1942
        1.34 -     1.46: 1085
        1.46 -     1.57: 3603
        1.57 -     1.69: 0
        1.69 -     1.81: 74
  Bond restraints: 6704
  Sorted by residual:
  bond pdb=" C   THR A  31 "
       pdb=" N   PRO A  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.380 -0.047 8.40e-03 1.42e+04 3.12e+01
  bond pdb=" C   THR B  31 "
       pdb=" N   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.335  1.383 -0.048 1.30e-02 5.92e+03 1.38e+01
  bond pdb=" N   ILE B 200 "
       pdb=" CA  ILE B 200 "
    ideal  model  delta    sigma   weight residual
    1.460  1.499 -0.039 1.26e-02 6.30e+03 9.52e+00
  bond pdb=" N   ILE B 197 "
       pdb=" CA  ILE B 197 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.034 1.21e-02 6.83e+03 7.95e+00
  bond pdb=" N   ILE B 201 "
       pdb=" CA  ILE B 201 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.30e-02 5.92e+03 7.30e+00
  ... (remaining 6699 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.22: 8678
        2.22 -     4.45: 363
        4.45 -     6.67: 48
        6.67 -     8.89: 20
        8.89 -    11.12: 5
  Bond angle restraints: 9114
  Sorted by residual:
  angle pdb=" N   VAL B 162 "
        pdb=" CA  VAL B 162 "
        pdb=" C   VAL B 162 "
      ideal   model   delta    sigma   weight residual
     112.29  105.57    6.72 9.40e-01 1.13e+00 5.11e+01
  angle pdb=" N   ILE B 322 "
        pdb=" CA  ILE B 322 "
        pdb=" C   ILE B 322 "
      ideal   model   delta    sigma   weight residual
     112.83  106.50    6.33 9.90e-01 1.02e+00 4.09e+01
  angle pdb=" C   LYS B  30 "
        pdb=" N   THR B  31 "
        pdb=" CA  THR B  31 "
      ideal   model   delta    sigma   weight residual
     120.58  126.56   -5.98 1.32e+00 5.74e-01 2.05e+01
  angle pdb=" N   VAL B 236 "
        pdb=" CA  VAL B 236 "
        pdb=" C   VAL B 236 "
      ideal   model   delta    sigma   weight residual
     110.21  105.36    4.85 1.13e+00 7.83e-01 1.84e+01
  angle pdb=" C   GLY B 108 "
        pdb=" N   ILE B 109 "
        pdb=" CA  ILE B 109 "
      ideal   model   delta    sigma   weight residual
     122.13  129.90   -7.77 1.85e+00 2.92e-01 1.76e+01
  ... (remaining 9109 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.07: 3422
       17.07 -    34.13: 354
       34.13 -    51.20: 85
       51.20 -    68.27: 7
       68.27 -    85.34: 3
  Dihedral angle restraints: 3871
    sinusoidal: 1413
      harmonic: 2458
  Sorted by residual:
  dihedral pdb=" CA  ALA A 237 "
           pdb=" C   ALA A 237 "
           pdb=" N   LEU A 238 "
           pdb=" CA  LEU A 238 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.21  -27.79     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" CA  VAL B 162 "
           pdb=" C   VAL B 162 "
           pdb=" N   LEU B 163 "
           pdb=" CA  LEU B 163 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.96   24.04     0      5.00e+00 4.00e-02 2.31e+01
  dihedral pdb=" CA  PRO A 359 "
           pdb=" C   PRO A 359 "
           pdb=" N   MET A 360 "
           pdb=" CA  MET A 360 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.24   22.76     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 3868 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.077: 899
       0.077 -    0.153: 165
       0.153 -    0.230: 15
       0.230 -    0.307: 2
       0.307 -    0.384: 1
  Chirality restraints: 1082
  Sorted by residual:
  chirality pdb=" CB  ILE A 320 "
            pdb=" CA  ILE A 320 "
            pdb=" CG1 ILE A 320 "
            pdb=" CG2 ILE A 320 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.26    0.38 2.00e-01 2.50e+01 3.68e+00
  chirality pdb=" CA  ILE B 197 "
            pdb=" N   ILE B 197 "
            pdb=" C   ILE B 197 "
            pdb=" CB  ILE B 197 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.70   -0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  ILE B 201 "
            pdb=" N   ILE B 201 "
            pdb=" C   ILE B 201 "
            pdb=" CB  ILE B 201 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.67   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 1079 not shown)

  Planarity restraints: 1143
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "   -0.049 5.00e-02 4.00e+02   7.43e-02 8.83e+00
        pdb=" N   PRO A 150 "    0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "   -0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "   -0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 406 "    0.014 2.00e-02 2.50e+03   2.77e-02 7.69e+00
        pdb=" C   LEU B 406 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LEU B 406 "    0.018 2.00e-02 2.50e+03
        pdb=" N   THR B 407 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 423 "    0.046 5.00e-02 4.00e+02   6.89e-02 7.59e+00
        pdb=" N   PRO B 424 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO B 424 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 424 "    0.039 5.00e-02 4.00e+02
  ... (remaining 1140 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 1621
        2.79 -     3.32: 6249
        3.32 -     3.84: 10814
        3.84 -     4.37: 12137
        4.37 -     4.90: 20550
  Nonbonded interactions: 51371
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 107 "
            pdb=" O   GLY A 354 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" O   LEU A 435 "
            pdb=" OG1 THR A 439 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" OH  TYR A  94 "
            pdb=" OG  SER A 350 "
     model   vdw
     2.296 3.040
  nonbonded pdb=" O   PRO A 206 "
            pdb=" OH  TYR A 210 "
     model   vdw
     2.326 3.040
  nonbonded pdb=" OE2 GLU A 103 "
            pdb=" OE2 GLU A 111 "
     model   vdw
     2.328 3.040
  ... (remaining 51366 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and ((resid 17 through 29 and (name N or name CA or name C or name O  \ 
or name CB )) or resid 30 through 461))
  selection = (chain 'B' and (resid 17 through 206 or (resid 207 through 208 and (name N or na \ 
me CA or name C or name O or name CB )) or resid 209 through 461))
}

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:             0.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.010
  Process input model:                     7.700
  Find NCS groups from input model:        0.100
  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:1.030
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.480
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7669
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      :  0.005   0.060   6704  Z= 0.267
  Angle     :  1.079  11.119   9114  Z= 0.598
  Chirality :  0.060   0.384   1082
  Planarity :  0.007   0.074   1143
  Dihedral  : 14.637  85.335   2319
  Min Nonbonded Distance : 2.258

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.66 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  : 10.08 %
    Favored  : 88.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -5.14 (0.21), residues: 886
  helix: -3.34 (0.14), residues: 574
  sheet:  None (None), residues: 0
  loop : -3.21 (0.31), residues: 312

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.011   0.002   TYR A 100 
 PHE   0.027   0.002   PHE B 357 
 TRP   0.014   0.002   TRP B 291 
 HIS   0.003   0.001   HIS B  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 ( 6704)
  covalent geometry    : angle       1.07856 ( 9114)
  hydrogen bonds       : bond        0.13979 (  366)
  hydrogen bonds       : angle       6.47745 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 201
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   33 LEU cc_start: 0.7373 (OUTLIER) cc_final: 0.7153 (tt)
REVERT: A   55 LYS cc_start: 0.8757 (mttt) cc_final: 0.8446 (mtmt)
REVERT: A  148 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7611 (tm-30)
REVERT: A  202 GLU cc_start: 0.6820 (tp30) cc_final: 0.6455 (tp30)
REVERT: A  235 GLU cc_start: 0.8001 (tt0) cc_final: 0.7729 (tt0)
REVERT: A  246 ASP cc_start: 0.6429 (t0) cc_final: 0.6062 (t0)
REVERT: A  277 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7975 (tm-30)
REVERT: A  278 ASP cc_start: 0.8257 (p0) cc_final: 0.8013 (p0)
REVERT: A  279 LEU cc_start: 0.8845 (mp) cc_final: 0.8332 (tt)
REVERT: A  294 MET cc_start: 0.8943 (tmm) cc_final: 0.8691 (tmm)
REVERT: A  329 SER cc_start: 0.7621 (m) cc_final: 0.6904 (t)
REVERT: A  360 MET cc_start: 0.8399 (mtp) cc_final: 0.7468 (mtp)
REVERT: A  418 ASN cc_start: 0.9254 (m-40) cc_final: 0.8768 (m-40)
REVERT: A  434 LEU cc_start: 0.8637 (tt) cc_final: 0.8416 (tt)
REVERT: A  456 GLN cc_start: 0.8739 (tp40) cc_final: 0.8166 (tm-30)
REVERT: B   35 ILE cc_start: 0.9261 (tt) cc_final: 0.8993 (tp)
REVERT: B   55 LYS cc_start: 0.7375 (tmtt) cc_final: 0.7089 (tmtt)
REVERT: B   59 TRP cc_start: 0.8608 (t60) cc_final: 0.8118 (t60)
REVERT: B  161 MET cc_start: 0.7420 (ttt) cc_final: 0.7139 (ttm)
REVERT: B  208 PHE cc_start: 0.6564 (m-80) cc_final: 0.6152 (m-10)
REVERT: B  210 TYR cc_start: 0.7105 (m-10) cc_final: 0.6875 (m-10)
REVERT: B  276 MET cc_start: 0.8975 (tpp) cc_final: 0.8643 (tpt)
REVERT: B  277 GLN cc_start: 0.8177 (tm-30) cc_final: 0.7259 (tm-30)
REVERT: B  278 ASP cc_start: 0.8125 (t0) cc_final: 0.7789 (p0)
REVERT: B  291 TRP cc_start: 0.7849 (t-100) cc_final: 0.7561 (t-100)
REVERT: B  332 MET cc_start: 0.7899 (tpp) cc_final: 0.7406 (tpp)
REVERT: B  342 ILE cc_start: 0.9037 (tt) cc_final: 0.8826 (tp)
REVERT: B  382 TYR cc_start: 0.8635 (m-80) cc_final: 0.8242 (m-80)
REVERT: B  410 ILE cc_start: 0.8471 (mm) cc_final: 0.8116 (mm)
  outliers start: 9
  outliers final: 3
  residues processed: 206
  average time/residue: 0.0700
  time to fit residues: 19.4566
Evaluate side-chains
  165 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 161
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    6.9990
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    6.9990
   chunk 74 optimal weight:    2.9990
   overall best weight:    1.7784

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

Flipped N/Q/H residues before XYZ refinement:
B 270 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.142525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3232 r_free = 0.3232 target = 0.116618 restraints weight = 11362.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.119958 restraints weight = 7329.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.122293 restraints weight = 5407.977|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.123610 restraints weight = 4378.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.124891 restraints weight = 3818.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   6704  Z= 0.196
  Angle     :  0.737   8.890   9114  Z= 0.376
  Chirality :  0.044   0.196   1082
  Planarity :  0.006   0.054   1143
  Dihedral  :  5.875  28.632    938
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 11.56
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.66 %
    Favored  : 93.23 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  8.22 %
    Favored  : 91.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.46 (0.25), residues: 886
  helix: -1.90 (0.19), residues: 572
  sheet:  None (None), residues: 0
  loop : -2.83 (0.30), residues: 314

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 160 
 TYR   0.011   0.002   TYR A 210 
 PHE   0.017   0.001   PHE B 357 
 TRP   0.012   0.002   TRP B  59 
 HIS   0.005   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00457 ( 6704)
  covalent geometry    : angle       0.73723 ( 9114)
  hydrogen bonds       : bond        0.03530 (  366)
  hydrogen bonds       : angle       4.75807 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  197 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 196
  time to evaluate  : 0.141 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 VAL cc_start: 0.9042 (m) cc_final: 0.8717 (t)
REVERT: A  148 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7751 (tm-30)
REVERT: A  202 GLU cc_start: 0.6858 (tp30) cc_final: 0.6570 (tp30)
REVERT: A  219 PHE cc_start: 0.8239 (m-80) cc_final: 0.8016 (m-80)
REVERT: A  246 ASP cc_start: 0.6362 (t0) cc_final: 0.5950 (t0)
REVERT: A  279 LEU cc_start: 0.8863 (mp) cc_final: 0.8437 (tt)
REVERT: A  294 MET cc_start: 0.8974 (tmm) cc_final: 0.8559 (tmm)
REVERT: A  342 ILE cc_start: 0.8760 (tp) cc_final: 0.8493 (tp)
REVERT: A  360 MET cc_start: 0.8392 (mtp) cc_final: 0.7715 (mtp)
REVERT: A  391 ILE cc_start: 0.9330 (mm) cc_final: 0.9085 (mm)
REVERT: A  456 GLN cc_start: 0.8672 (tp40) cc_final: 0.8110 (tm-30)
REVERT: B   55 LYS cc_start: 0.7399 (tmtt) cc_final: 0.7089 (tmtt)
REVERT: B   59 TRP cc_start: 0.8645 (t60) cc_final: 0.8039 (t60)
REVERT: B   61 GLN cc_start: 0.8546 (mt0) cc_final: 0.7794 (mp10)
REVERT: B  136 LEU cc_start: 0.9007 (mt) cc_final: 0.8781 (mt)
REVERT: B  191 ASN cc_start: 0.8246 (t0) cc_final: 0.7909 (t0)
REVERT: B  276 MET cc_start: 0.8974 (tpp) cc_final: 0.8715 (tpt)
REVERT: B  356 ILE cc_start: 0.9048 (tt) cc_final: 0.8805 (tt)
REVERT: B  438 PHE cc_start: 0.7896 (t80) cc_final: 0.7689 (t80)
  outliers start: 1
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0632
  time to fit residues: 17.2159
Evaluate side-chains
  161 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   chunk 35 optimal weight:    0.8980
   chunk 67 optimal weight:    3.9990
   chunk 42 optimal weight:    0.5980
   chunk 47 optimal weight:    4.9990
   chunk 16 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 82 optimal weight:    4.9990
   chunk 56 optimal weight:    0.7980
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
B  63 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.145685 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.119902 restraints weight = 11048.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.123097 restraints weight = 7155.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.125589 restraints weight = 5328.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.127024 restraints weight = 4315.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.127935 restraints weight = 3744.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.2376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6704  Z= 0.135
  Angle     :  0.673   7.958   9114  Z= 0.339
  Chirality :  0.042   0.141   1082
  Planarity :  0.005   0.055   1143
  Dihedral  :  5.371  25.212    938
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  4.81 %
    Favored  : 94.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.67 (0.26), residues: 886
  helix: -1.29 (0.21), residues: 580
  sheet:  None (None), residues: 0
  loop : -2.52 (0.32), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 120 
 TYR   0.007   0.001   TYR B 255 
 PHE   0.019   0.001   PHE B 357 
 TRP   0.012   0.001   TRP A  59 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 6704)
  covalent geometry    : angle       0.67348 ( 9114)
  hydrogen bonds       : bond        0.03232 (  366)
  hydrogen bonds       : angle       4.46365 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 208
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.6360 (m-30) cc_final: 0.6158 (m-30)
REVERT: A   88 VAL cc_start: 0.9006 (m) cc_final: 0.8720 (t)
REVERT: A  148 GLU cc_start: 0.7910 (tm-30) cc_final: 0.7623 (tm-30)
REVERT: A  202 GLU cc_start: 0.6880 (tp30) cc_final: 0.6518 (tp30)
REVERT: A  219 PHE cc_start: 0.8210 (m-80) cc_final: 0.7968 (m-80)
REVERT: A  279 LEU cc_start: 0.8814 (mp) cc_final: 0.8415 (tt)
REVERT: A  342 ILE cc_start: 0.8678 (tp) cc_final: 0.8377 (tp)
REVERT: A  360 MET cc_start: 0.8396 (mtp) cc_final: 0.8190 (mtp)
REVERT: A  456 GLN cc_start: 0.8617 (tp40) cc_final: 0.8050 (tm-30)
REVERT: B   35 ILE cc_start: 0.9187 (tp) cc_final: 0.8974 (tp)
REVERT: B   55 LYS cc_start: 0.7386 (tmtt) cc_final: 0.7073 (tmtt)
REVERT: B   59 TRP cc_start: 0.8552 (t60) cc_final: 0.8174 (t60)
REVERT: B   61 GLN cc_start: 0.8514 (mt0) cc_final: 0.7801 (mp10)
REVERT: B   63 GLN cc_start: 0.9356 (OUTLIER) cc_final: 0.9078 (mp-120)
REVERT: B  124 TRP cc_start: 0.7675 (p-90) cc_final: 0.7323 (p-90)
REVERT: B  132 PHE cc_start: 0.8673 (t80) cc_final: 0.8460 (t80)
REVERT: B  136 LEU cc_start: 0.8981 (mt) cc_final: 0.8764 (mt)
REVERT: B  191 ASN cc_start: 0.8119 (t0) cc_final: 0.7878 (t0)
REVERT: B  197 ILE cc_start: 0.8394 (mt) cc_final: 0.8144 (mt)
REVERT: B  270 ASN cc_start: 0.9179 (m-40) cc_final: 0.8306 (m110)
REVERT: B  277 GLN cc_start: 0.8074 (tm-30) cc_final: 0.7423 (tm-30)
  outliers start: 2
  outliers final: 0
  residues processed: 209
  average time/residue: 0.0620
  time to fit residues: 17.8773
Evaluate side-chains
  166 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    0.0570
   chunk 30 optimal weight:    0.0980
   chunk 39 optimal weight:    0.0980
   chunk 72 optimal weight:    5.9990
   chunk 1 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 86 optimal weight:    0.6980
   chunk 63 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 78 optimal weight:    0.7980
   overall best weight:    0.3498

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

Flipped N/Q/H residues before XYZ refinement:
A 153 GLN
A 157 ASN
B 175 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.147530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.121786 restraints weight = 11151.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.125240 restraints weight = 7136.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.127452 restraints weight = 5233.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.129221 restraints weight = 4240.250|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.130481 restraints weight = 3613.992|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7686
moved from start:          0.2809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027   6704  Z= 0.113
  Angle     :  0.650   7.106   9114  Z= 0.323
  Chirality :  0.042   0.148   1082
  Planarity :  0.005   0.045   1143
  Dihedral  :  4.970  18.949    938
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.64 %
    Favored  : 94.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.15 (0.27), residues: 886
  helix: -0.97 (0.21), residues: 582
  sheet:  None (None), residues: 0
  loop : -2.14 (0.35), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B  64 
 TYR   0.013   0.001   TYR B 210 
 PHE   0.025   0.001   PHE A 307 
 TRP   0.019   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6704)
  covalent geometry    : angle       0.64952 ( 9114)
  hydrogen bonds       : bond        0.03011 (  366)
  hydrogen bonds       : angle       4.26074 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8388 (mmp) cc_final: 0.7791 (tpp)
REVERT: A   88 VAL cc_start: 0.9028 (m) cc_final: 0.8744 (t)
REVERT: A  148 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7617 (tm-30)
REVERT: A  153 GLN cc_start: 0.8302 (tt0) cc_final: 0.8093 (tt0)
REVERT: A  219 PHE cc_start: 0.8038 (m-80) cc_final: 0.7771 (m-80)
REVERT: A  228 MET cc_start: 0.7557 (mtt) cc_final: 0.7314 (mtp)
REVERT: A  329 SER cc_start: 0.7726 (m) cc_final: 0.7232 (t)
REVERT: A  342 ILE cc_start: 0.8676 (tp) cc_final: 0.8403 (tp)
REVERT: A  360 MET cc_start: 0.8341 (mtp) cc_final: 0.7870 (mtm)
REVERT: A  456 GLN cc_start: 0.8556 (tp40) cc_final: 0.8049 (tm-30)
REVERT: B   35 ILE cc_start: 0.9208 (tp) cc_final: 0.8967 (tp)
REVERT: B   38 MET cc_start: 0.8493 (mmt) cc_final: 0.8195 (mmt)
REVERT: B   55 LYS cc_start: 0.7421 (tmtt) cc_final: 0.7128 (tmtt)
REVERT: B   59 TRP cc_start: 0.8704 (t60) cc_final: 0.8307 (t60)
REVERT: B   61 GLN cc_start: 0.8597 (mt0) cc_final: 0.7811 (mp10)
REVERT: B  124 TRP cc_start: 0.7813 (p-90) cc_final: 0.7216 (p-90)
REVERT: B  132 PHE cc_start: 0.8585 (t80) cc_final: 0.8254 (t80)
REVERT: B  160 ARG cc_start: 0.7397 (tpt-90) cc_final: 0.7127 (tpt90)
REVERT: B  197 ILE cc_start: 0.8614 (mt) cc_final: 0.8292 (mt)
REVERT: B  270 ASN cc_start: 0.9131 (m-40) cc_final: 0.8308 (m110)
REVERT: B  332 MET cc_start: 0.7505 (tpp) cc_final: 0.7209 (tpp)
REVERT: B  410 ILE cc_start: 0.8733 (mm) cc_final: 0.8512 (mm)
REVERT: B  418 ASN cc_start: 0.8749 (m-40) cc_final: 0.8343 (t0)
  outliers start: 0
  outliers final: 0
  residues processed: 210
  average time/residue: 0.0620
  time to fit residues: 17.9200
Evaluate side-chains
  169 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    4.9990
   chunk 35 optimal weight:    0.5980
   chunk 25 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9990
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 51 optimal weight:    6.9990
   chunk 6 optimal weight:    0.0970
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 153 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.144380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.117935 restraints weight = 11352.788|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.121328 restraints weight = 7355.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.123452 restraints weight = 5446.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.125222 restraints weight = 4459.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.126460 restraints weight = 3814.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.3005

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   6704  Z= 0.136
  Angle     :  0.669   7.676   9114  Z= 0.330
  Chirality :  0.042   0.129   1082
  Planarity :  0.004   0.044   1143
  Dihedral  :  4.943  19.003    938
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.21 %
    Favored  : 93.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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 aren not related in a simple way.
  whole: -1.80 (0.28), residues: 886
  helix: -0.72 (0.22), residues: 580
  sheet:  None (None), residues: 0
  loop : -1.94 (0.35), residues: 306

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 209 
 TYR   0.019   0.001   TYR B 210 
 PHE   0.018   0.001   PHE B 357 
 TRP   0.019   0.001   TRP B  59 
 HIS   0.004   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6704)
  covalent geometry    : angle       0.66946 ( 9114)
  hydrogen bonds       : bond        0.03024 (  366)
  hydrogen bonds       : angle       4.34661 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.6412 (m-30) cc_final: 0.6190 (m-30)
REVERT: A   38 MET cc_start: 0.8432 (mmp) cc_final: 0.7783 (tpp)
REVERT: A   88 VAL cc_start: 0.9024 (m) cc_final: 0.8734 (t)
REVERT: A   91 MET cc_start: 0.8125 (mpp) cc_final: 0.7921 (mpp)
REVERT: A  148 GLU cc_start: 0.7963 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: A  202 GLU cc_start: 0.6667 (tp30) cc_final: 0.6467 (tp30)
REVERT: A  219 PHE cc_start: 0.8097 (m-80) cc_final: 0.7829 (m-80)
REVERT: A  228 MET cc_start: 0.7782 (mtt) cc_final: 0.7412 (mtp)
REVERT: A  279 LEU cc_start: 0.8794 (mt) cc_final: 0.8579 (tt)
REVERT: A  329 SER cc_start: 0.7723 (m) cc_final: 0.7219 (t)
REVERT: A  342 ILE cc_start: 0.8725 (tp) cc_final: 0.8452 (tp)
REVERT: A  456 GLN cc_start: 0.8642 (tp40) cc_final: 0.8050 (tm-30)
REVERT: B   55 LYS cc_start: 0.7428 (tmtt) cc_final: 0.7128 (tmtt)
REVERT: B   59 TRP cc_start: 0.8772 (t60) cc_final: 0.8316 (t60)
REVERT: B   61 GLN cc_start: 0.8317 (mt0) cc_final: 0.7645 (mp10)
REVERT: B  119 GLN cc_start: 0.8346 (mp10) cc_final: 0.8110 (mp10)
REVERT: B  164 ASP cc_start: 0.8218 (m-30) cc_final: 0.8001 (m-30)
REVERT: B  197 ILE cc_start: 0.8657 (mt) cc_final: 0.8429 (mt)
REVERT: B  270 ASN cc_start: 0.9174 (m-40) cc_final: 0.8312 (m110)
REVERT: B  330 MET cc_start: 0.7419 (mpp) cc_final: 0.6708 (tpt)
REVERT: B  332 MET cc_start: 0.7587 (tpp) cc_final: 0.7264 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.0619
  time to fit residues: 16.5193
Evaluate side-chains
  155 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 41 optimal weight:    0.7980
   chunk 59 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 34 optimal weight:    0.9980
   chunk 49 optimal weight:    5.9990
   chunk 52 optimal weight:    5.9990
   chunk 57 optimal weight:    2.9990
   chunk 66 optimal weight:    3.9990
   overall best weight:    1.2982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.143608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.117511 restraints weight = 11269.012|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.120858 restraints weight = 7306.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.122989 restraints weight = 5420.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.124645 restraints weight = 4432.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.125856 restraints weight = 3845.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3370
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7763
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6704  Z= 0.163
  Angle     :  0.698   8.602   9114  Z= 0.344
  Chirality :  0.044   0.156   1082
  Planarity :  0.005   0.044   1143
  Dihedral  :  4.985  19.285    938
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.66 %
    Favored  : 93.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.71 (0.28), residues: 886
  helix: -0.61 (0.22), residues: 576
  sheet:  None (None), residues: 0
  loop : -1.98 (0.34), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 120 
 TYR   0.015   0.001   TYR B 210 
 PHE   0.019   0.001   PHE A 307 
 TRP   0.018   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6704)
  covalent geometry    : angle       0.69758 ( 9114)
  hydrogen bonds       : bond        0.03087 (  366)
  hydrogen bonds       : angle       4.39308 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8458 (mmp) cc_final: 0.7747 (tpp)
REVERT: A  148 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7616 (tm-30)
REVERT: A  202 GLU cc_start: 0.6726 (tp30) cc_final: 0.6513 (tp30)
REVERT: A  219 PHE cc_start: 0.8215 (m-80) cc_final: 0.7934 (m-80)
REVERT: A  279 LEU cc_start: 0.8814 (mt) cc_final: 0.8590 (tt)
REVERT: A  329 SER cc_start: 0.7792 (m) cc_final: 0.7263 (t)
REVERT: A  342 ILE cc_start: 0.8730 (tp) cc_final: 0.8419 (tp)
REVERT: A  373 MET cc_start: 0.8673 (ptm) cc_final: 0.7873 (ptm)
REVERT: A  456 GLN cc_start: 0.8573 (tp40) cc_final: 0.8092 (tm-30)
REVERT: B   38 MET cc_start: 0.8456 (mmt) cc_final: 0.8183 (mmt)
REVERT: B   55 LYS cc_start: 0.7426 (tmtt) cc_final: 0.7066 (tmtt)
REVERT: B   59 TRP cc_start: 0.8732 (t60) cc_final: 0.8302 (t60)
REVERT: B  160 ARG cc_start: 0.7472 (tpt-90) cc_final: 0.7205 (tpt-90)
REVERT: B  197 ILE cc_start: 0.8656 (mt) cc_final: 0.8437 (mt)
REVERT: B  270 ASN cc_start: 0.9212 (m-40) cc_final: 0.8401 (m110)
REVERT: B  332 MET cc_start: 0.7660 (tpp) cc_final: 0.7286 (tpp)
REVERT: B  346 LEU cc_start: 0.8105 (tp) cc_final: 0.7689 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 196
  average time/residue: 0.0594
  time to fit residues: 16.4018
Evaluate side-chains
  156 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 29 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 10 optimal weight:    0.8980
   chunk 4 optimal weight:    5.9990
   chunk 56 optimal weight:    0.0070
   chunk 53 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 66 optimal weight:    5.9990
   chunk 9 optimal weight:    0.1980
   chunk 62 optimal weight:    1.9990
   chunk 41 optimal weight:    0.5980
   overall best weight:    0.4998

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

Flipped N/Q/H residues before XYZ refinement:
B 418 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.147410 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.121582 restraints weight = 11084.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.124971 restraints weight = 7132.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.126731 restraints weight = 5270.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.128439 restraints weight = 4371.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.129829 restraints weight = 3801.888|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7689
moved from start:          0.3427

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054   6704  Z= 0.121
  Angle     :  0.664   8.797   9114  Z= 0.326
  Chirality :  0.042   0.155   1082
  Planarity :  0.005   0.041   1143
  Dihedral  :  4.791  18.864    938
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.76 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.41 %
    Favored  : 96.59 %
  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 aren not related in a simple way.
  whole: -1.55 (0.28), residues: 886
  helix: -0.51 (0.22), residues: 586
  sheet:  None (None), residues: 0
  loop : -1.90 (0.36), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 120 
 TYR   0.014   0.001   TYR B 210 
 PHE   0.018   0.001   PHE B 357 
 TRP   0.015   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00283 ( 6704)
  covalent geometry    : angle       0.66373 ( 9114)
  hydrogen bonds       : bond        0.02926 (  366)
  hydrogen bonds       : angle       4.27669 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.234 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8424 (mmp) cc_final: 0.8021 (mmt)
REVERT: A   88 VAL cc_start: 0.9017 (t) cc_final: 0.8778 (t)
REVERT: A  148 GLU cc_start: 0.7970 (tm-30) cc_final: 0.7492 (tm-30)
REVERT: A  219 PHE cc_start: 0.8030 (m-80) cc_final: 0.7659 (m-80)
REVERT: A  228 MET cc_start: 0.7444 (mtt) cc_final: 0.7224 (mtp)
REVERT: A  279 LEU cc_start: 0.8883 (mt) cc_final: 0.8659 (tt)
REVERT: A  446 SER cc_start: 0.8538 (p) cc_final: 0.8338 (p)
REVERT: A  456 GLN cc_start: 0.8590 (tp40) cc_final: 0.8074 (tm-30)
REVERT: B   38 MET cc_start: 0.8414 (mmt) cc_final: 0.8147 (mmt)
REVERT: B   55 LYS cc_start: 0.7377 (tmtt) cc_final: 0.7035 (tmtt)
REVERT: B   59 TRP cc_start: 0.8758 (t60) cc_final: 0.8238 (t60)
REVERT: B   61 GLN cc_start: 0.8287 (mt0) cc_final: 0.7617 (mp10)
REVERT: B  160 ARG cc_start: 0.7253 (tpt-90) cc_final: 0.6951 (tpt90)
REVERT: B  197 ILE cc_start: 0.8570 (mt) cc_final: 0.8304 (mt)
REVERT: B  208 PHE cc_start: 0.5872 (m-80) cc_final: 0.5671 (m-10)
REVERT: B  270 ASN cc_start: 0.9176 (m-40) cc_final: 0.8332 (m110)
REVERT: B  291 TRP cc_start: 0.8015 (t-100) cc_final: 0.7714 (t-100)
REVERT: B  332 MET cc_start: 0.7598 (tpp) cc_final: 0.7216 (tpp)
REVERT: B  346 LEU cc_start: 0.8095 (tp) cc_final: 0.7632 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0519
  time to fit residues: 14.6951
Evaluate side-chains
  162 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 79 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0270
   chunk 44 optimal weight:    0.0870
   chunk 12 optimal weight:    0.0570
   chunk 60 optimal weight:    0.9990
   chunk 58 optimal weight:    0.8980
   chunk 74 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0870
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.2312

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

Flipped N/Q/H residues before XYZ refinement:
B  62 ASN
B 418 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.151519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.126483 restraints weight = 11082.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.129932 restraints weight = 7128.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.132293 restraints weight = 5201.303|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.133810 restraints weight = 4177.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.135139 restraints weight = 3586.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.3447
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.3658

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6704  Z= 0.116
  Angle     :  0.668   8.505   9114  Z= 0.325
  Chirality :  0.042   0.149   1082
  Planarity :  0.004   0.042   1143
  Dihedral  :  4.629  18.904    938
  Min Nonbonded Distance : 2.421

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.78 %
    Favored  : 99.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.50 (0.28), residues: 886
  helix: -0.48 (0.21), residues: 596
  sheet:  None (None), residues: 0
  loop : -1.90 (0.37), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 120 
 TYR   0.011   0.001   TYR B 255 
 PHE   0.031   0.001   PHE B 357 
 TRP   0.009   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 ( 6704)
  covalent geometry    : angle       0.66820 ( 9114)
  hydrogen bonds       : bond        0.02877 (  366)
  hydrogen bonds       : angle       4.24566 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 197
  time to evaluate  : 0.143 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8405 (mmp) cc_final: 0.7964 (mmt)
REVERT: A   88 VAL cc_start: 0.9027 (t) cc_final: 0.8817 (t)
REVERT: A  148 GLU cc_start: 0.7831 (tm-30) cc_final: 0.7347 (tm-30)
REVERT: A  154 ILE cc_start: 0.9162 (mt) cc_final: 0.8893 (mp)
REVERT: A  219 PHE cc_start: 0.7927 (m-80) cc_final: 0.7562 (m-80)
REVERT: A  228 MET cc_start: 0.7401 (mtt) cc_final: 0.7137 (mtp)
REVERT: A  446 SER cc_start: 0.8636 (p) cc_final: 0.8083 (m)
REVERT: A  456 GLN cc_start: 0.8499 (tp40) cc_final: 0.8060 (tm-30)
REVERT: B   38 MET cc_start: 0.8431 (mmt) cc_final: 0.8192 (mmt)
REVERT: B   55 LYS cc_start: 0.7316 (tmtt) cc_final: 0.6955 (tmtt)
REVERT: B   61 GLN cc_start: 0.8219 (mt0) cc_final: 0.7594 (mp10)
REVERT: B  160 ARG cc_start: 0.7180 (tpt-90) cc_final: 0.6927 (tpt170)
REVERT: B  197 ILE cc_start: 0.8538 (mt) cc_final: 0.8289 (mt)
REVERT: B  208 PHE cc_start: 0.5931 (m-80) cc_final: 0.5680 (m-10)
REVERT: B  270 ASN cc_start: 0.9086 (m-40) cc_final: 0.8278 (m110)
  outliers start: 1
  outliers final: 0
  residues processed: 197
  average time/residue: 0.0549
  time to fit residues: 15.1842
Evaluate side-chains
  165 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 165
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 45 optimal weight:    0.0270
   chunk 17 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 68 optimal weight:    0.8980
   chunk 55 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 4 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 25 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.5838

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.151543 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.126028 restraints weight = 11349.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.129363 restraints weight = 7356.139|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.131528 restraints weight = 5443.648|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.133332 restraints weight = 4434.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.134233 restraints weight = 3802.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7671
moved from start:          0.3785

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6704  Z= 0.123
  Angle     :  0.681   8.374   9114  Z= 0.332
  Chirality :  0.043   0.149   1082
  Planarity :  0.004   0.044   1143
  Dihedral  :  4.625  19.038    938
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.09 %
    Favored  : 98.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.28), residues: 886
  helix: -0.36 (0.22), residues: 586
  sheet:  None (None), residues: 0
  loop : -1.84 (0.35), residues: 300

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 120 
 TYR   0.011   0.001   TYR B 210 
 PHE   0.029   0.001   PHE B 357 
 TRP   0.012   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 6704)
  covalent geometry    : angle       0.68056 ( 9114)
  hydrogen bonds       : bond        0.02853 (  366)
  hydrogen bonds       : angle       4.26049 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8349 (mmp) cc_final: 0.8084 (mmt)
REVERT: A  148 GLU cc_start: 0.7808 (tm-30) cc_final: 0.7468 (tm-30)
REVERT: A  219 PHE cc_start: 0.7974 (m-80) cc_final: 0.7640 (m-80)
REVERT: A  228 MET cc_start: 0.7466 (mtt) cc_final: 0.7181 (mtp)
REVERT: A  456 GLN cc_start: 0.8518 (tp40) cc_final: 0.8073 (tm-30)
REVERT: B   38 MET cc_start: 0.8433 (mmt) cc_final: 0.8156 (mmt)
REVERT: B   55 LYS cc_start: 0.7334 (tmtt) cc_final: 0.7016 (tmtt)
REVERT: B   59 TRP cc_start: 0.8743 (t60) cc_final: 0.8287 (t60)
REVERT: B  160 ARG cc_start: 0.7176 (tpt-90) cc_final: 0.6862 (tpt170)
REVERT: B  177 LEU cc_start: 0.8814 (mm) cc_final: 0.8592 (mm)
REVERT: B  197 ILE cc_start: 0.8527 (mt) cc_final: 0.8325 (mt)
REVERT: B  202 GLU cc_start: 0.6746 (tp30) cc_final: 0.6433 (tp30)
REVERT: B  270 ASN cc_start: 0.9104 (m-40) cc_final: 0.8337 (m110)
REVERT: B  291 TRP cc_start: 0.7966 (t-100) cc_final: 0.7687 (t-100)
REVERT: B  346 LEU cc_start: 0.8013 (tp) cc_final: 0.7587 (tp)
REVERT: B  413 LEU cc_start: 0.8462 (mm) cc_final: 0.8166 (mp)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.0763
  time to fit residues: 20.8761
Evaluate side-chains
  163 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 16 optimal weight:    0.3980
   chunk 59 optimal weight:    3.9990
   chunk 33 optimal weight:    0.0060
   chunk 7 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 64 optimal weight:    0.7980
   chunk 6 optimal weight:    0.7980
   chunk 84 optimal weight:    0.7980
   chunk 40 optimal weight:    0.0970
   chunk 71 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   overall best weight:    0.4194

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

Flipped N/Q/H residues before XYZ refinement:
B  62 ASN
B 418 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.149882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.124930 restraints weight = 11131.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.128376 restraints weight = 7162.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.130750 restraints weight = 5235.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.131927 restraints weight = 4212.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.133159 restraints weight = 3686.873|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7640
moved from start:          0.3906

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6704  Z= 0.118
  Angle     :  0.676   7.985   9114  Z= 0.332
  Chirality :  0.042   0.139   1082
  Planarity :  0.004   0.044   1143
  Dihedral  :  4.621  19.355    938
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.87 %
    Favored  : 94.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.16 %
    Favored  : 99.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.35 (0.28), residues: 886
  helix: -0.30 (0.22), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.97 (0.35), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 209 
 TYR   0.013   0.001   TYR B 210 
 PHE   0.031   0.001   PHE B 357 
 TRP   0.014   0.001   TRP A 253 
 HIS   0.003   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 ( 6704)
  covalent geometry    : angle       0.67564 ( 9114)
  hydrogen bonds       : bond        0.02884 (  366)
  hydrogen bonds       : angle       4.26909 ( 1083)

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

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

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1772 Ramachandran restraints generated.
    886 Oldfield, 0 Emsley, 886 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8342 (mmp) cc_final: 0.8125 (mmp)
REVERT: A  148 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7235 (tm-30)
REVERT: A  219 PHE cc_start: 0.7954 (m-80) cc_final: 0.7646 (m-80)
REVERT: A  228 MET cc_start: 0.7447 (mtt) cc_final: 0.7116 (mtp)
REVERT: A  456 GLN cc_start: 0.8520 (tp40) cc_final: 0.8081 (tm-30)
REVERT: B   38 MET cc_start: 0.8397 (mmt) cc_final: 0.8124 (mmt)
REVERT: B   55 LYS cc_start: 0.7338 (tmtt) cc_final: 0.7000 (tmtt)
REVERT: B   59 TRP cc_start: 0.8664 (t60) cc_final: 0.8093 (t60)
REVERT: B   61 GLN cc_start: 0.8452 (mt0) cc_final: 0.7733 (mp10)
REVERT: B  160 ARG cc_start: 0.7140 (tpt-90) cc_final: 0.6894 (tpt170)
REVERT: B  177 LEU cc_start: 0.8810 (mm) cc_final: 0.8591 (mm)
REVERT: B  197 ILE cc_start: 0.8544 (mt) cc_final: 0.8333 (mt)
REVERT: B  202 GLU cc_start: 0.6793 (tp30) cc_final: 0.6517 (tp30)
REVERT: B  204 MET cc_start: 0.7684 (mmm) cc_final: 0.7415 (mmm)
REVERT: B  270 ASN cc_start: 0.9113 (m-40) cc_final: 0.8338 (m110)
REVERT: B  279 LEU cc_start: 0.8569 (tp) cc_final: 0.8281 (tp)
REVERT: B  282 ARG cc_start: 0.6172 (mtm180) cc_final: 0.5877 (mtm180)
REVERT: B  332 MET cc_start: 0.7268 (tpp) cc_final: 0.6950 (tpp)
REVERT: B  346 LEU cc_start: 0.7905 (tp) cc_final: 0.7542 (tp)
REVERT: B  413 LEU cc_start: 0.8422 (mm) cc_final: 0.8059 (mt)
REVERT: B  422 ILE cc_start: 0.7596 (tp) cc_final: 0.7181 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0712
  time to fit residues: 19.9268
Evaluate side-chains
  170 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 170
  time to evaluate  : 0.250 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 34 optimal weight:    0.9980
   chunk 84 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 76 optimal weight:    1.9990
   chunk 18 optimal weight:    0.1980
   chunk 11 optimal weight:    0.0770
   chunk 46 optimal weight:    3.9990
   chunk 56 optimal weight:    8.9990
   chunk 35 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 418 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.149050 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.123879 restraints weight = 11202.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.127299 restraints weight = 7127.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.129568 restraints weight = 5200.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.131358 restraints weight = 4193.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.132183 restraints weight = 3583.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3458
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7648
moved from start:          0.3981

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6704  Z= 0.125
  Angle     :  0.686   7.913   9114  Z= 0.338
  Chirality :  0.043   0.136   1082
  Planarity :  0.005   0.044   1143
  Dihedral  :  4.642  19.765    938
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 10.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.26 (0.28), residues: 886
  helix: -0.25 (0.22), residues: 592
  sheet:  None (None), residues: 0
  loop : -1.92 (0.36), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 209 
 TYR   0.016   0.001   TYR B 210 
 PHE   0.031   0.001   PHE B 357 
 TRP   0.027   0.002   TRP A 253 
 HIS   0.003   0.001   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6704)
  covalent geometry    : angle       0.68586 ( 9114)
  hydrogen bonds       : bond        0.02900 (  366)
  hydrogen bonds       : angle       4.30778 ( 1083)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1034.13 seconds
wall clock time: 18 minutes 30.24 seconds (1110.24 seconds total)