Starting phenix.real_space_refine
on Tue Mar 11 17:59:14 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7n9w_24263/03_2025/7n9w_24263.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7n9w_24263/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7n9w_24263/03_2025/7n9w_24263.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7n9w_24263/03_2025/7n9w_24263.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7n9w_24263/03_2025/7n9w_24263.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7n9w_24263/03_2025/7n9w_24263.cif"
  }
  resolution = 4.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: {'GLN:plan1': 3, 'GLU:plan': 1, 'ARG:plan': 5, '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: {'GLN:plan1': 2, 'GLU:plan': 1, 'ARG:plan': 5, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 40
  Time building chain proxies: 4.18, per 1000 atoms: 0.64
  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: 1.47
  Conformation dependent library (CDL) restraints added in 941.5 milliseconds
  

  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: 0.61
  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: 1.57

  Time building geometry restraints manager: 1.76 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:             0.310
  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:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     17.930
  Find NCS groups from input model:        0.240
  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:2.930
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.800
-------------------------------------------------------------------------------
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= 0.339
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.014   0.002   TRP B 291 
 HIS   0.003   0.001   HIS B  70 
 PHE   0.027   0.002   PHE B 357 
 TYR   0.011   0.002   TYR A 100 
 ARG   0.003   0.000   ARG A 403 

*********************** 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  : 0.812 
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: 0.1793
  time to fit residues: 49.1456
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  : 0.775 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    2.9990
   chunk 66 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 22 optimal weight:    2.9990
   chunk 44 optimal weight:   30.0000
   chunk 35 optimal weight:    0.9990
   chunk 68 optimal weight:    4.9990
   chunk 26 optimal weight:    9.9990
   chunk 41 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.144635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.118912 restraints weight = 11132.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.122265 restraints weight = 7182.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.124632 restraints weight = 5295.753|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.1885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6704  Z= 0.242
  Angle     :  0.702   8.365   9114  Z= 0.357
  Chirality :  0.043   0.198   1082
  Planarity :  0.006   0.052   1143
  Dihedral  :  5.745  28.404    938
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  6.21 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  7.13 %
    Favored  : 92.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.39 (0.25), residues: 886
  helix: -1.91 (0.19), residues: 570
  sheet:  None (None), residues: 0
  loop : -2.66 (0.31), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP A  59 
 HIS   0.004   0.001   HIS A 284 
 PHE   0.015   0.001   PHE B 357 
 TYR   0.011   0.001   TYR A 210 
 ARG   0.003   0.000   ARG B 174 

*********************** 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
  198 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.733 
Fit side-chains
   revert: symmetry clash
REVERT: A   88 VAL cc_start: 0.9008 (m) cc_final: 0.8722 (t)
REVERT: A   91 MET cc_start: 0.8033 (mpp) cc_final: 0.7808 (mpp)
REVERT: A  148 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7636 (tm-30)
REVERT: A  202 GLU cc_start: 0.6843 (tp30) cc_final: 0.6521 (tp30)
REVERT: A  219 PHE cc_start: 0.8233 (m-80) cc_final: 0.7983 (m-80)
REVERT: A  246 ASP cc_start: 0.6337 (t0) cc_final: 0.5902 (t0)
REVERT: A  279 LEU cc_start: 0.8855 (mp) cc_final: 0.8436 (tt)
REVERT: A  294 MET cc_start: 0.8968 (tmm) cc_final: 0.8572 (tmm)
REVERT: A  342 ILE cc_start: 0.8693 (tp) cc_final: 0.8423 (tp)
REVERT: A  360 MET cc_start: 0.8445 (mtp) cc_final: 0.7984 (mtp)
REVERT: A  382 TYR cc_start: 0.7582 (m-80) cc_final: 0.7354 (m-80)
REVERT: A  391 ILE cc_start: 0.9327 (mm) cc_final: 0.9097 (mm)
REVERT: A  456 GLN cc_start: 0.8661 (tp40) cc_final: 0.8138 (tm-30)
REVERT: B   55 LYS cc_start: 0.7369 (tmtt) cc_final: 0.7046 (tmtt)
REVERT: B   59 TRP cc_start: 0.8627 (t60) cc_final: 0.8032 (t60)
REVERT: B   61 GLN cc_start: 0.8523 (mt0) cc_final: 0.7735 (mp10)
REVERT: B   65 MET cc_start: 0.8090 (tmm) cc_final: 0.7463 (tmm)
REVERT: B  136 LEU cc_start: 0.8984 (mt) cc_final: 0.8759 (mt)
REVERT: B  191 ASN cc_start: 0.8201 (t0) cc_final: 0.7850 (t0)
REVERT: B  197 ILE cc_start: 0.8489 (mt) cc_final: 0.8231 (mt)
REVERT: B  276 MET cc_start: 0.8928 (tpp) cc_final: 0.8650 (tpt)
REVERT: B  277 GLN cc_start: 0.8201 (tm-30) cc_final: 0.7233 (tm-30)
REVERT: B  293 LEU cc_start: 0.8708 (mm) cc_final: 0.8488 (mm)
REVERT: B  457 GLU cc_start: 0.7596 (mm-30) cc_final: 0.7298 (mm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 198
  average time/residue: 0.1643
  time to fit residues: 44.6086
Evaluate side-chains
  154 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 79 optimal weight:    1.9990
   chunk 49 optimal weight:    0.5980
   chunk 9 optimal weight:    2.9990
   chunk 41 optimal weight:    3.9990
   chunk 27 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 69 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 55 optimal weight:    0.6980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.3633 r_free = 0.3633 target = 0.147826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.122200 restraints weight = 11250.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.125525 restraints weight = 7232.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.127683 restraints weight = 5361.812|
|-----------------------------------------------------------------------------|
r_work (final): 0.3348
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7769
moved from start:          0.2352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6704  Z= 0.188
  Angle     :  0.658   7.591   9114  Z= 0.330
  Chirality :  0.042   0.162   1082
  Planarity :  0.005   0.051   1143
  Dihedral  :  5.238  24.625    938
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  5.27 %
    Favored  : 94.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.57 (0.27), residues: 886
  helix: -1.28 (0.21), residues: 582
  sheet:  None (None), residues: 0
  loop : -2.33 (0.34), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  59 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.017   0.001   PHE B 357 
 TYR   0.008   0.001   TYR A 210 
 ARG   0.003   0.000   ARG B 174 

*********************** 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
  207 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 0.666 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8377 (mttt) cc_final: 0.8176 (mttt)
REVERT: A   88 VAL cc_start: 0.9005 (m) cc_final: 0.8793 (t)
REVERT: A  148 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7611 (tm-30)
REVERT: A  202 GLU cc_start: 0.6892 (tp30) cc_final: 0.6545 (tp30)
REVERT: A  219 PHE cc_start: 0.8154 (m-80) cc_final: 0.7894 (m-80)
REVERT: A  224 MET cc_start: 0.8326 (tpt) cc_final: 0.7992 (tpp)
REVERT: A  228 MET cc_start: 0.7744 (mtt) cc_final: 0.7430 (mtp)
REVERT: A  279 LEU cc_start: 0.8834 (mp) cc_final: 0.8442 (tt)
REVERT: A  342 ILE cc_start: 0.8682 (tp) cc_final: 0.8427 (tp)
REVERT: A  360 MET cc_start: 0.8373 (mtp) cc_final: 0.8125 (mtp)
REVERT: A  456 GLN cc_start: 0.8645 (tp40) cc_final: 0.8071 (tm-30)
REVERT: B   55 LYS cc_start: 0.7410 (tmtt) cc_final: 0.7091 (tmtt)
REVERT: B   59 TRP cc_start: 0.8579 (t60) cc_final: 0.8103 (t60)
REVERT: B   61 GLN cc_start: 0.8536 (mt0) cc_final: 0.7808 (mp10)
REVERT: B  124 TRP cc_start: 0.7891 (p-90) cc_final: 0.7336 (p-90)
REVERT: B  191 ASN cc_start: 0.8088 (t0) cc_final: 0.7864 (t0)
REVERT: B  197 ILE cc_start: 0.8445 (mt) cc_final: 0.8232 (mt)
REVERT: B  270 ASN cc_start: 0.9129 (m-40) cc_final: 0.8271 (m110)
REVERT: B  276 MET cc_start: 0.8888 (tpp) cc_final: 0.8661 (tpp)
REVERT: B  330 MET cc_start: 0.7506 (mpp) cc_final: 0.6904 (tpt)
REVERT: B  413 LEU cc_start: 0.8577 (mm) cc_final: 0.8369 (mt)
  outliers start: 1
  outliers final: 0
  residues processed: 206
  average time/residue: 0.1644
  time to fit residues: 46.0105
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  : 0.707 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 27 optimal weight:    6.9990
   chunk 11 optimal weight:    0.3980
   chunk 62 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 80 optimal weight:    0.8980
   chunk 58 optimal weight:    0.9980
   chunk 55 optimal weight:    0.5980
   chunk 63 optimal weight:    0.6980
   chunk 0 optimal weight:   50.0000
   chunk 26 optimal weight:    0.7980
   chunk 69 optimal weight:    3.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.145882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.120162 restraints weight = 11290.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.123563 restraints weight = 7192.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.125781 restraints weight = 5275.752|
|-----------------------------------------------------------------------------|
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7755
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6704  Z= 0.183
  Angle     :  0.649   7.227   9114  Z= 0.323
  Chirality :  0.042   0.155   1082
  Planarity :  0.005   0.045   1143
  Dihedral  :  5.016  20.230    938
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.27), residues: 886
  helix: -0.98 (0.21), residues: 584
  sheet:  None (None), residues: 0
  loop : -2.15 (0.34), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 272 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.018   0.001   PHE A 307 
 TYR   0.014   0.001   TYR B 210 
 ARG   0.004   0.000   ARG B  64 

*********************** 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
  199 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   88 VAL cc_start: 0.8974 (m) cc_final: 0.8716 (t)
REVERT: A   91 MET cc_start: 0.8053 (mpp) cc_final: 0.7852 (mpp)
REVERT: A  148 GLU cc_start: 0.7855 (tm-30) cc_final: 0.7626 (tm-30)
REVERT: A  219 PHE cc_start: 0.8089 (m-80) cc_final: 0.7815 (m-80)
REVERT: A  342 ILE cc_start: 0.8682 (tp) cc_final: 0.8365 (tp)
REVERT: A  360 MET cc_start: 0.8379 (mtp) cc_final: 0.7889 (mtm)
REVERT: A  456 GLN cc_start: 0.8647 (tp40) cc_final: 0.8056 (tm-30)
REVERT: B   38 MET cc_start: 0.8579 (mmt) cc_final: 0.8118 (mmt)
REVERT: B   55 LYS cc_start: 0.7338 (tmtt) cc_final: 0.6999 (tmtt)
REVERT: B   59 TRP cc_start: 0.8525 (t60) cc_final: 0.8096 (t60)
REVERT: B   61 GLN cc_start: 0.8600 (mt0) cc_final: 0.7797 (mp10)
REVERT: B  124 TRP cc_start: 0.7808 (p-90) cc_final: 0.7263 (p-90)
REVERT: B  197 ILE cc_start: 0.8449 (mt) cc_final: 0.8216 (mt)
REVERT: B  270 ASN cc_start: 0.9139 (m-40) cc_final: 0.8261 (m110)
REVERT: B  330 MET cc_start: 0.7121 (mpp) cc_final: 0.6812 (tpt)
REVERT: B  332 MET cc_start: 0.7687 (tpp) cc_final: 0.7305 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 199
  average time/residue: 0.1601
  time to fit residues: 43.6517
Evaluate side-chains
  159 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.782 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 58 optimal weight:    0.8980
   chunk 81 optimal weight:    4.9990
   chunk 24 optimal weight:    3.9990
   chunk 67 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 22 optimal weight:    0.3980
   chunk 4 optimal weight:    4.9990
   chunk 73 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.0584

-------------------------------------------------------------------------------
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 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.143718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.117343 restraints weight = 11285.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.120571 restraints weight = 7253.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.123106 restraints weight = 5391.529|
|-----------------------------------------------------------------------------|
r_work (final): 0.3335
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6704  Z= 0.218
  Angle     :  0.664   7.513   9114  Z= 0.329
  Chirality :  0.043   0.153   1082
  Planarity :  0.005   0.045   1143
  Dihedral  :  4.943  19.066    938
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.77 (0.28), residues: 886
  helix: -0.69 (0.22), residues: 584
  sheet:  None (None), residues: 0
  loop : -1.93 (0.36), residues: 302

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.018   0.001   PHE B 357 
 TYR   0.008   0.001   TYR A 210 
 ARG   0.007   0.000   ARG B 120 

*********************** 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
  183 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.673 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.6420 (m-30) cc_final: 0.6205 (m-30)
REVERT: A   38 MET cc_start: 0.8416 (mmp) cc_final: 0.7715 (tpp)
REVERT: A  148 GLU cc_start: 0.7927 (tm-30) cc_final: 0.7649 (tm-30)
REVERT: A  202 GLU cc_start: 0.6802 (tp30) cc_final: 0.6581 (tp30)
REVERT: A  219 PHE cc_start: 0.8181 (m-80) cc_final: 0.7893 (m-80)
REVERT: A  224 MET cc_start: 0.8365 (tpt) cc_final: 0.8162 (tpp)
REVERT: A  228 MET cc_start: 0.7756 (mtt) cc_final: 0.7427 (mtp)
REVERT: A  279 LEU cc_start: 0.8827 (mt) cc_final: 0.8608 (tt)
REVERT: A  294 MET cc_start: 0.8851 (tmm) cc_final: 0.8564 (tpp)
REVERT: A  342 ILE cc_start: 0.8726 (tp) cc_final: 0.8446 (tp)
REVERT: A  456 GLN cc_start: 0.8637 (tp40) cc_final: 0.8070 (tm-30)
REVERT: B   55 LYS cc_start: 0.7412 (tmtt) cc_final: 0.7058 (tmtt)
REVERT: B   59 TRP cc_start: 0.8846 (t60) cc_final: 0.8481 (t60)
REVERT: B  120 ARG cc_start: 0.8383 (mtp85) cc_final: 0.8175 (tpp80)
REVERT: B  169 LYS cc_start: 0.7925 (mmtt) cc_final: 0.7649 (mmtm)
REVERT: B  270 ASN cc_start: 0.9159 (m-40) cc_final: 0.8322 (m110)
REVERT: B  276 MET cc_start: 0.8509 (tpt) cc_final: 0.7953 (tpp)
REVERT: B  332 MET cc_start: 0.7565 (tpp) cc_final: 0.7309 (tpp)
REVERT: B  413 LEU cc_start: 0.8582 (mt) cc_final: 0.8232 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.1570
  time to fit residues: 39.5751
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  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 67 optimal weight:    3.9990
   chunk 48 optimal weight:    7.9990
   chunk 54 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 9 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0170
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 43 optimal weight:    0.7980
   chunk 69 optimal weight:    2.9990
   overall best weight:    1.2822

-------------------------------------------------------------------------------
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 ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.144881 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.119178 restraints weight = 11161.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.121726 restraints weight = 7283.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.124266 restraints weight = 5565.536|
|-----------------------------------------------------------------------------|
r_work (final): 0.3326
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.3040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6704  Z= 0.245
  Angle     :  0.680   8.591   9114  Z= 0.339
  Chirality :  0.043   0.159   1082
  Planarity :  0.005   0.044   1143
  Dihedral  :  4.996  19.385    938
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.88 %
    Favored  : 93.12 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.64 (0.28), residues: 886
  helix: -0.54 (0.22), residues: 576
  sheet:  None (None), residues: 0
  loop : -2.00 (0.35), residues: 310

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.019   0.001   PHE A 307 
 TYR   0.018   0.002   TYR B 210 
 ARG   0.005   0.000   ARG B 120 

*********************** 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
  182 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.6449 (m-30) cc_final: 0.6234 (m-30)
REVERT: A   38 MET cc_start: 0.8427 (mmp) cc_final: 0.7660 (tpp)
REVERT: A   88 VAL cc_start: 0.9036 (t) cc_final: 0.8749 (t)
REVERT: A  148 GLU cc_start: 0.7889 (tm-30) cc_final: 0.7600 (tm-30)
REVERT: A  202 GLU cc_start: 0.6780 (tp30) cc_final: 0.6546 (tp30)
REVERT: A  219 PHE cc_start: 0.8149 (m-80) cc_final: 0.7942 (m-80)
REVERT: A  224 MET cc_start: 0.8350 (tpt) cc_final: 0.8134 (tpp)
REVERT: A  279 LEU cc_start: 0.8896 (mt) cc_final: 0.8670 (tt)
REVERT: A  294 MET cc_start: 0.8857 (tmm) cc_final: 0.8519 (tpp)
REVERT: A  342 ILE cc_start: 0.8709 (tp) cc_final: 0.8404 (tp)
REVERT: A  456 GLN cc_start: 0.8658 (tp40) cc_final: 0.8045 (tm-30)
REVERT: B   38 MET cc_start: 0.8369 (mmt) cc_final: 0.8098 (mmt)
REVERT: B   55 LYS cc_start: 0.7426 (tmtt) cc_final: 0.7088 (tmtt)
REVERT: B   59 TRP cc_start: 0.8914 (t60) cc_final: 0.8459 (t60)
REVERT: B  169 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7738 (mmtm)
REVERT: B  197 ILE cc_start: 0.8650 (mt) cc_final: 0.8388 (mt)
REVERT: B  270 ASN cc_start: 0.9155 (m-40) cc_final: 0.8300 (m110)
REVERT: B  278 ASP cc_start: 0.8310 (t0) cc_final: 0.8098 (p0)
REVERT: B  332 MET cc_start: 0.7488 (tpp) cc_final: 0.7236 (tpp)
REVERT: B  346 LEU cc_start: 0.8214 (tp) cc_final: 0.7897 (tp)
REVERT: B  413 LEU cc_start: 0.8629 (mt) cc_final: 0.8321 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.1512
  time to fit residues: 38.2496
Evaluate side-chains
  151 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 0.740 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 62 optimal weight:    0.7980
   chunk 45 optimal weight:    0.5980
   chunk 71 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9980
   chunk 2 optimal weight:    0.9980
   chunk 5 optimal weight:    0.1980
   chunk 84 optimal weight:    0.2980
   chunk 67 optimal weight:    0.9990
   chunk 10 optimal weight:    0.8980
   chunk 17 optimal weight:    7.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B  62 ASN
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.148700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.123195 restraints weight = 11135.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.126538 restraints weight = 7148.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.128728 restraints weight = 5265.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7731
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6704  Z= 0.178
  Angle     :  0.662   7.583   9114  Z= 0.326
  Chirality :  0.042   0.155   1082
  Planarity :  0.004   0.042   1143
  Dihedral  :  4.758  18.985    938
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.98 %
    Favored  : 94.02 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.43 (0.29), residues: 886
  helix: -0.42 (0.22), residues: 582
  sheet:  None (None), residues: 0
  loop : -1.82 (0.36), residues: 304

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.018   0.001   PHE B 357 
 TYR   0.018   0.001   TYR B 210 
 ARG   0.005   0.000   ARG B 120 

*********************** 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
  190 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.698 
Fit side-chains
   revert: symmetry clash
REVERT: A   29 ASP cc_start: 0.6255 (m-30) cc_final: 0.6051 (m-30)
REVERT: A   38 MET cc_start: 0.8420 (mmp) cc_final: 0.7975 (mmt)
REVERT: A   88 VAL cc_start: 0.9037 (t) cc_final: 0.8773 (t)
REVERT: A  148 GLU cc_start: 0.7812 (tm-30) cc_final: 0.7584 (tm-30)
REVERT: A  202 GLU cc_start: 0.6714 (tp30) cc_final: 0.6509 (tp30)
REVERT: A  219 PHE cc_start: 0.8021 (m-80) cc_final: 0.7615 (m-80)
REVERT: A  228 MET cc_start: 0.7374 (mtt) cc_final: 0.7084 (mtp)
REVERT: A  279 LEU cc_start: 0.8818 (mt) cc_final: 0.8588 (tt)
REVERT: A  294 MET cc_start: 0.8831 (tmm) cc_final: 0.8524 (tpp)
REVERT: A  446 SER cc_start: 0.8553 (p) cc_final: 0.8347 (p)
REVERT: A  456 GLN cc_start: 0.8602 (tp40) cc_final: 0.8090 (tm-30)
REVERT: B   38 MET cc_start: 0.8292 (mmt) cc_final: 0.7990 (mmt)
REVERT: B   55 LYS cc_start: 0.7346 (tmtt) cc_final: 0.6983 (tmtt)
REVERT: B   59 TRP cc_start: 0.8876 (t60) cc_final: 0.8604 (t60)
REVERT: B  118 ASP cc_start: 0.6923 (m-30) cc_final: 0.6675 (m-30)
REVERT: B  120 ARG cc_start: 0.8303 (mtp85) cc_final: 0.8051 (tpp80)
REVERT: B  132 PHE cc_start: 0.8609 (t80) cc_final: 0.8381 (t80)
REVERT: B  169 LYS cc_start: 0.7909 (mmtt) cc_final: 0.7648 (mmtm)
REVERT: B  197 ILE cc_start: 0.8561 (mt) cc_final: 0.8254 (mt)
REVERT: B  208 PHE cc_start: 0.5905 (m-80) cc_final: 0.5692 (m-10)
REVERT: B  270 ASN cc_start: 0.9113 (m-40) cc_final: 0.8238 (m110)
REVERT: B  346 LEU cc_start: 0.8276 (tp) cc_final: 0.7899 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 190
  average time/residue: 0.1451
  time to fit residues: 38.6964
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  : 0.705 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 67 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 15 optimal weight:    0.3980
   chunk 56 optimal weight:    0.0470
   chunk 84 optimal weight:    0.8980
   chunk 65 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0770
   chunk 81 optimal weight:    0.0000
   chunk 64 optimal weight:    0.8980
   overall best weight:    0.2840

-------------------------------------------------------------------------------
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 = 0.3672 r_free = 0.3672 target = 0.151016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.125783 restraints weight = 11059.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.129101 restraints weight = 7102.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.131330 restraints weight = 5246.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7674
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6704  Z= 0.163
  Angle     :  0.653   7.621   9114  Z= 0.319
  Chirality :  0.043   0.160   1082
  Planarity :  0.004   0.041   1143
  Dihedral  :  4.634  18.922    938
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.43 %
    Favored  : 93.57 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.29), residues: 886
  helix: -0.36 (0.22), residues: 588
  sheet:  None (None), residues: 0
  loop : -1.66 (0.37), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.021   0.001   PHE A 307 
 TYR   0.014   0.001   TYR B 210 
 ARG   0.005   0.000   ARG B 120 

*********************** 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
  192 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.709 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8403 (mmp) cc_final: 0.8087 (mmt)
REVERT: A   88 VAL cc_start: 0.9025 (t) cc_final: 0.8803 (t)
REVERT: A  148 GLU cc_start: 0.7827 (tm-30) cc_final: 0.7420 (tm-30)
REVERT: A  219 PHE cc_start: 0.7849 (m-80) cc_final: 0.7498 (m-80)
REVERT: A  228 MET cc_start: 0.7279 (mtt) cc_final: 0.7016 (mtp)
REVERT: A  294 MET cc_start: 0.8808 (tmm) cc_final: 0.8276 (tpp)
REVERT: A  446 SER cc_start: 0.8572 (p) cc_final: 0.8073 (m)
REVERT: A  456 GLN cc_start: 0.8486 (tp40) cc_final: 0.8062 (tm-30)
REVERT: B   38 MET cc_start: 0.8304 (mmt) cc_final: 0.7973 (mmt)
REVERT: B   55 LYS cc_start: 0.7354 (tmtt) cc_final: 0.6980 (tmtt)
REVERT: B   59 TRP cc_start: 0.8844 (t60) cc_final: 0.8544 (t60)
REVERT: B  118 ASP cc_start: 0.7041 (m-30) cc_final: 0.6837 (m-30)
REVERT: B  177 LEU cc_start: 0.8871 (mm) cc_final: 0.8559 (mm)
REVERT: B  197 ILE cc_start: 0.8497 (mt) cc_final: 0.8189 (mt)
REVERT: B  208 PHE cc_start: 0.5905 (m-80) cc_final: 0.5690 (m-10)
REVERT: B  270 ASN cc_start: 0.9108 (m-40) cc_final: 0.8309 (m110)
REVERT: B  276 MET cc_start: 0.8422 (tpt) cc_final: 0.7978 (tpp)
REVERT: B  291 TRP cc_start: 0.8066 (t-100) cc_final: 0.7701 (t-100)
  outliers start: 0
  outliers final: 0
  residues processed: 192
  average time/residue: 0.1573
  time to fit residues: 42.0776
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  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 2 optimal weight:    5.9990
   chunk 50 optimal weight:    0.8980
   chunk 13 optimal weight:    0.9980
   chunk 58 optimal weight:    3.9990
   chunk 26 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 67 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 23 optimal weight:    0.6980
   chunk 36 optimal weight:    4.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  70 HIS
A 157 ASN
B  62 ASN
** B 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 175 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.148985 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.124099 restraints weight = 10907.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.127499 restraints weight = 6932.223|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.129666 restraints weight = 5036.459|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.3660

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6704  Z= 0.211
  Angle     :  0.708   9.185   9114  Z= 0.347
  Chirality :  0.044   0.185   1082
  Planarity :  0.005   0.050   1143
  Dihedral  :  4.723  18.792    938
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.30 (0.29), residues: 886
  helix: -0.31 (0.22), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.86 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP B  59 
 HIS   0.004   0.001   HIS A 284 
 PHE   0.018   0.001   PHE B 357 
 TYR   0.014   0.001   TYR B 210 
 ARG   0.002   0.000   ARG B 160 

*********************** 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
  197 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.683 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 MET cc_start: 0.8405 (mmp) cc_final: 0.8192 (mmp)
REVERT: A  148 GLU cc_start: 0.7874 (tm-30) cc_final: 0.7554 (tm-30)
REVERT: A  219 PHE cc_start: 0.7994 (m-80) cc_final: 0.7680 (m-80)
REVERT: A  228 MET cc_start: 0.7645 (mtt) cc_final: 0.7348 (mtp)
REVERT: A  330 MET cc_start: 0.8845 (mmm) cc_final: 0.8635 (mmm)
REVERT: A  456 GLN cc_start: 0.8485 (tp40) cc_final: 0.8095 (tm-30)
REVERT: B   38 MET cc_start: 0.8290 (mmt) cc_final: 0.7934 (mmt)
REVERT: B   55 LYS cc_start: 0.7350 (tmtt) cc_final: 0.7021 (tmtt)
REVERT: B   59 TRP cc_start: 0.8849 (t60) cc_final: 0.8546 (t60)
REVERT: B  177 LEU cc_start: 0.8883 (mm) cc_final: 0.8651 (mm)
REVERT: B  197 ILE cc_start: 0.8519 (mt) cc_final: 0.8257 (mt)
REVERT: B  270 ASN cc_start: 0.9130 (m-40) cc_final: 0.8316 (m110)
REVERT: B  291 TRP cc_start: 0.8109 (t-100) cc_final: 0.7745 (t-100)
REVERT: B  332 MET cc_start: 0.7495 (tpp) cc_final: 0.7155 (tpp)
REVERT: B  346 LEU cc_start: 0.8296 (tp) cc_final: 0.7977 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.1514
  time to fit residues: 41.8181
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  : 0.684 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 81 optimal weight:    0.5980
   chunk 69 optimal weight:    0.9990
   chunk 76 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 28 optimal weight:    6.9990
   chunk 53 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9990
   chunk 33 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 157 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 = 0.3662 r_free = 0.3662 target = 0.149859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.124071 restraints weight = 11299.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.126726 restraints weight = 7345.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.129471 restraints weight = 5588.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.3722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6704  Z= 0.201
  Angle     :  0.701   9.175   9114  Z= 0.343
  Chirality :  0.044   0.171   1082
  Planarity :  0.005   0.078   1143
  Dihedral  :  4.718  19.273    938
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.28 (0.29), residues: 886
  helix: -0.29 (0.22), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.85 (0.37), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  59 
 HIS   0.003   0.001   HIS A 284 
 PHE   0.035   0.001   PHE B 357 
 TYR   0.011   0.001   TYR B 210 
 ARG   0.010   0.001   ARG B 160 

********************** 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
  191 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
REVERT: A  148 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7569 (tm-30)
REVERT: A  219 PHE cc_start: 0.8021 (m-80) cc_final: 0.7732 (m-80)
REVERT: A  228 MET cc_start: 0.7603 (mtt) cc_final: 0.7318 (mtp)
REVERT: A  456 GLN cc_start: 0.8486 (tp40) cc_final: 0.8133 (tm-30)
REVERT: B   38 MET cc_start: 0.8342 (mmt) cc_final: 0.7987 (mmt)
REVERT: B   55 LYS cc_start: 0.7336 (tmtt) cc_final: 0.7000 (tmtt)
REVERT: B   59 TRP cc_start: 0.8876 (t60) cc_final: 0.8546 (t60)
REVERT: B  118 ASP cc_start: 0.7382 (m-30) cc_final: 0.7103 (m-30)
REVERT: B  177 LEU cc_start: 0.8804 (mm) cc_final: 0.8595 (mm)
REVERT: B  197 ILE cc_start: 0.8501 (mt) cc_final: 0.8252 (mt)
REVERT: B  202 GLU cc_start: 0.6848 (tp30) cc_final: 0.6565 (tp30)
REVERT: B  270 ASN cc_start: 0.9122 (m-40) cc_final: 0.8297 (m110)
REVERT: B  276 MET cc_start: 0.8507 (tpt) cc_final: 0.7927 (tpp)
REVERT: B  291 TRP cc_start: 0.8117 (t-100) cc_final: 0.7712 (t-100)
REVERT: B  332 MET cc_start: 0.7486 (tpp) cc_final: 0.7158 (tpp)
REVERT: B  346 LEU cc_start: 0.8374 (tp) cc_final: 0.7875 (tp)
REVERT: B  422 ILE cc_start: 0.7836 (tp) cc_final: 0.7539 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 191
  average time/residue: 0.1449
  time to fit residues: 38.7230
Evaluate side-chains
  167 residues out of total 672 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.828 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 61 optimal weight:    0.5980
   chunk 75 optimal weight:    0.7980
   chunk 83 optimal weight:    0.5980
   chunk 26 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 18 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 47 optimal weight:    0.6980
   chunk 51 optimal weight:    5.9990
   chunk 16 optimal weight:    0.8980
   chunk 20 optimal weight:    0.5980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  70 HIS
B  62 ASN
B 175 HIS
** B 418 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.149894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.124326 restraints weight = 11204.580|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.127652 restraints weight = 7208.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.129759 restraints weight = 5315.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7712
moved from start:          0.3835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059   6704  Z= 0.191
  Angle     :  0.691   8.724   9114  Z= 0.339
  Chirality :  0.043   0.171   1082
  Planarity :  0.005   0.079   1143
  Dihedral  :  4.691  19.524    938
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.55 %
    Favored  : 93.45 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.22 (0.29), residues: 886
  helix: -0.24 (0.22), residues: 594
  sheet:  None (None), residues: 0
  loop : -1.84 (0.36), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 253 
 HIS   0.003   0.001   HIS A  70 
 PHE   0.034   0.001   PHE B 357 
 TYR   0.011   0.001   TYR B 210 
 ARG   0.002   0.000   ARG A 123 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2054.88 seconds
wall clock time: 36 minutes 19.80 seconds (2179.80 seconds total)