Starting phenix.real_space_refine
on Tue Mar  3 14:44:26 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7rq7_24629/03_2026/7rq7_24629.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7rq7_24629/03_2026/7rq7_24629.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7rq7_24629/03_2026/7rq7_24629.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7rq7_24629/03_2026/7rq7_24629.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7rq7_24629/03_2026/7rq7_24629.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7rq7_24629/03_2026/7rq7_24629.map"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.030
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    4206      2.51       5
     N    1049      2.21       5
     O    1085      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6380
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3186
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 430, 3186
          Classifications: {'peptide': 430}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 410}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 15
    Chain: "B"
      Number of atoms: 3194
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 431, 3194
          Classifications: {'peptide': 431}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 19, 'TRANS': 411}
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'ARG:plan': 1, 'GLN:plan1': 1, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 15
  Time building chain proxies: 1.62, per 1000 atoms: 0.25
  Number of scatterers: 6380
  At special positions: 0
  Unit cell: (85.936, 111.088, 73.36, 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    1085      8.00
     N    1049      7.00
     C    4206      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.56
  Conformation dependent library (CDL) restraints added in 242.8 milliseconds
  

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1494

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 0 sheets defined
      78.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 34 through 71
      removed outlier: 3.869A  pdb=" N   THR A  71 " --> pdb=" O   ALA A  67 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 85
      removed outlier: 3.564A  pdb=" N   LEU A  78 " --> pdb=" O   ASN A  74 " (cutoff:3.500A)
      removed outlier: 3.693A  pdb=" N   CYS A  85 " --> pdb=" O   VAL A  81 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 101
      removed outlier: 3.556A  pdb=" N   LYS A  99 " --> pdb=" O   PHE A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.528A  pdb=" N   GLU A 117 " --> pdb=" O   GLU A 113 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 126 through 141
      removed outlier: 3.911A  pdb=" N   VAL A 130 " --> pdb=" O   ARG A 126 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE A 132 " --> pdb=" O   LEU A 128 " (cutoff:3.500A)
      removed outlier: 5.476A  pdb=" N   GLY A 137 " --> pdb=" O   PHE A 133 " (cutoff:3.500A)
      removed outlier: 4.291A  pdb=" N   THR A 138 " --> pdb=" O   GLY A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 165
      removed outlier: 3.615A  pdb=" N   GLN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   GLY A 156 " --> pdb=" O   VAL A 152 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   LEU A 163 " --> pdb=" O   GLY A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 171 through 188
      removed outlier: 3.749A  pdb=" N   HIS A 175 " --> pdb=" O   ASP A 171 " (cutoff:3.500A)
      removed outlier: 4.020A  pdb=" N   THR A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLY A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 4.270A  pdb=" N   LEU A 186 " --> pdb=" O   ALA A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 192 through 202
      removed outlier: 3.650A  pdb=" N   LEU A 198 " --> pdb=" O   LEU A 194 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 233
      removed outlier: 3.556A  pdb=" N   GLY A 221 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 248 through 251
    Processing helix  chain 'A' and resid 252 through 284
      removed outlier: 3.664A  pdb=" N   LEU A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 3.813A  pdb=" N   ASN A 270 " --> pdb=" O   GLY A 266 " (cutoff:3.500A)
      removed outlier: 4.896A  pdb=" N   LYS A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   LEU A 279 " --> pdb=" O   GLY A 275 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   HIS A 284 " --> pdb=" O   LEU A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 309
      removed outlier: 4.124A  pdb=" N   LEU A 293 " --> pdb=" O   THR A 289 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   LEU A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   CYS A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   PHE A 307 " --> pdb=" O   GLY A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 325
      removed outlier: 3.940A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 347
      removed outlier: 3.703A  pdb=" N   VAL A 334 " --> pdb=" O   MET A 330 " (cutoff:3.500A)
      removed outlier: 4.398A  pdb=" N   PHE A 335 " --> pdb=" O   GLY A 331 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 359 through 379
      removed outlier: 4.146A  pdb=" N   THR A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 380 through 383
      removed outlier: 3.890A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 380 through 383'
    Processing helix  chain 'A' and resid 385 through 392
      removed outlier: 4.176A  pdb=" N   PHE A 389 " --> pdb=" O   GLU A 385 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 402
      removed outlier: 3.998A  pdb=" N   LEU A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ILE A 402 " --> pdb=" O   LEU A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 408 through 416
    Processing helix  chain 'A' and resid 422 through 431
      removed outlier: 3.617A  pdb=" N   ILE A 427 " --> pdb=" O   LEU A 423 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   THR A 428 " --> pdb=" O   PRO A 424 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 431 through 440
      removed outlier: 3.536A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 3.782A  pdb=" N   LEU A 449 " --> pdb=" O   TYR A 445 " (cutoff:3.500A)
      removed outlier: 4.229A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLU A 457 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 459 through 460
      No H-bonds generated for 'chain 'A' and resid 459 through 460'
    Processing helix  chain 'B' and resid 31 through 31
      No H-bonds generated for 'chain 'B' and resid 31 through 31'
    Processing helix  chain 'B' and resid 32 through 46
    Processing helix  chain 'B' and resid 47 through 71
      removed outlier: 3.988A  pdb=" N   THR B  71 " --> pdb=" O   ALA B  67 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 75 through 85
      removed outlier: 3.823A  pdb=" N   THR B  80 " --> pdb=" O   PRO B  76 " (cutoff:3.500A)
      removed outlier: 4.470A  pdb=" N   VAL B  81 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 87 through 100
      removed outlier: 3.557A  pdb=" N   GLY B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 101 through 105
      removed outlier: 3.625A  pdb=" N   GLY B 105 " --> pdb=" O   PRO B 102 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 116
      removed outlier: 3.775A  pdb=" N   ILE B 112 " --> pdb=" O   GLY B 108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 123 through 136
      Proline residue:  B 129  - end of helix
      removed outlier: 3.907A  pdb=" N   PHE B 132 " --> pdb=" O   LEU B 128 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   PHE B 133 " --> pdb=" O   PRO B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 136 through 141
    Processing helix  chain 'B' and resid 148 through 166
      removed outlier: 3.822A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   LEU B 163 " --> pdb=" O   GLY B 159 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   ASP B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 177 through 190
      removed outlier: 3.601A  pdb=" N   GLY B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   ALA B 187 " --> pdb=" O   ALA B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 202
      removed outlier: 3.805A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   PHE B 199 " --> pdb=" O   ALA B 195 " (cutoff:3.500A)
      removed outlier: 4.710A  pdb=" N   ILE B 200 " --> pdb=" O   GLY B 196 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 231
      removed outlier: 3.591A  pdb=" N   GLY B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TYR B 229 " --> pdb=" O   SER B 225 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 248 through 250
      No H-bonds generated for 'chain 'B' and resid 248 through 250'
    Processing helix  chain 'B' and resid 251 through 284
      removed outlier: 4.192A  pdb=" N   TYR B 255 " --> pdb=" O   THR B 251 " (cutoff:3.500A)
      removed outlier: 3.880A  pdb=" N   LEU B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
    Processing helix  chain 'B' and resid 287 through 309
      removed outlier: 3.688A  pdb=" N   CYS B 302 " --> pdb=" O   ILE B 298 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 325
      removed outlier: 3.692A  pdb=" N   ALA B 325 " --> pdb=" O   PRO B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 329 through 349
      removed outlier: 3.762A  pdb=" N   LEU B 345 " --> pdb=" O   VAL B 341 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 358 through 379
      removed outlier: 3.802A  pdb=" N   ALA B 362 " --> pdb=" O   ALA B 358 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
    Processing helix  chain 'B' and resid 386 through 392
      removed outlier: 4.092A  pdb=" N   ALA B 392 " --> pdb=" O   THR B 388 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 393 through 401
      removed outlier: 3.865A  pdb=" N   LEU B 397 " --> pdb=" O   GLY B 393 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   LEU B 398 " --> pdb=" O   MET B 394 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   ALA B 399 " --> pdb=" O   GLY B 395 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 407
    Processing helix  chain 'B' and resid 408 through 416
      removed outlier: 3.872A  pdb=" N   VAL B 412 " --> pdb=" O   GLY B 408 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   LEU B 413 " --> pdb=" O   ILE B 409 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 440
    Processing helix  chain 'B' and resid 443 through 460
      removed outlier: 4.080A  pdb=" N   LEU B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLU B 457 " --> pdb=" O   LEU B 453 " (cutoff:3.500A)

    397 hydrogen bonds defined for protein.
    1179 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.67

  Time building geometry restraints manager: 0.72 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 1549
        1.33 -     1.45: 1247
        1.45 -     1.57: 3651
        1.57 -     1.69: 1
        1.69 -     1.81: 74
  Bond restraints: 6522
  Sorted by residual:
  bond pdb=" C   THR A  31 "
       pdb=" N   PRO A  32 "
    ideal  model  delta    sigma   weight residual
    1.334  1.391 -0.057 2.34e-02 1.83e+03 6.00e+00
  bond pdb=" N   LEU B  33 "
       pdb=" CA  LEU B  33 "
    ideal  model  delta    sigma   weight residual
    1.458  1.489 -0.030 1.27e-02 6.20e+03 5.64e+00
  bond pdb=" CA  LEU B 421 "
       pdb=" CB  LEU B 421 "
    ideal  model  delta    sigma   weight residual
    1.531  1.595 -0.065 3.28e-02 9.30e+02 3.89e+00
  bond pdb=" C   LEU A 423 "
       pdb=" N   PRO A 424 "
    ideal  model  delta    sigma   weight residual
    1.334  1.375 -0.041 2.34e-02 1.83e+03 3.14e+00
  bond pdb=" C   PRO B  32 "
       pdb=" O   PRO B  32 "
    ideal  model  delta    sigma   weight residual
    1.237  1.216  0.022 1.26e-02 6.30e+03 2.95e+00
  ... (remaining 6517 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.23: 8564
        2.23 -     4.46: 242
        4.46 -     6.69: 36
        6.69 -     8.93: 22
        8.93 -    11.16: 3
  Bond angle restraints: 8867
  Sorted by residual:
  angle pdb=" N   VAL A 144 "
        pdb=" CA  VAL A 144 "
        pdb=" C   VAL A 144 "
      ideal   model   delta    sigma   weight residual
     111.91  107.45    4.46 8.90e-01 1.26e+00 2.52e+01
  angle pdb=" C   CYS A  85 "
        pdb=" N   SER A  86 "
        pdb=" CA  SER A  86 "
      ideal   model   delta    sigma   weight residual
     121.54  130.25   -8.71 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" C   GLY B 106 "
        pdb=" N   SER B 107 "
        pdb=" CA  SER B 107 "
      ideal   model   delta    sigma   weight residual
     121.54  129.01   -7.47 1.91e+00 2.74e-01 1.53e+01
  angle pdb=" N   ILE B 109 "
        pdb=" CA  ILE B 109 "
        pdb=" C   ILE B 109 "
      ideal   model   delta    sigma   weight residual
     108.88  116.73   -7.85 2.16e+00 2.14e-01 1.32e+01
  angle pdb=" CA  ILE B 109 "
        pdb=" C   ILE B 109 "
        pdb=" N   PRO B 110 "
      ideal   model   delta    sigma   weight residual
     118.88  124.40   -5.52 1.54e+00 4.22e-01 1.28e+01
  ... (remaining 8862 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.83: 3350
       17.83 -    35.66: 336
       35.66 -    53.49: 61
       53.49 -    71.32: 5
       71.32 -    89.16: 5
  Dihedral angle restraints: 3757
    sinusoidal: 1386
      harmonic: 2371
  Sorted by residual:
  dihedral pdb=" CA  ILE B 239 "
           pdb=" C   ILE B 239 "
           pdb=" N   ASP B 240 "
           pdb=" CA  ASP B 240 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -153.80  -26.20     0      5.00e+00 4.00e-02 2.75e+01
  dihedral pdb=" CA  ILE A 109 "
           pdb=" C   ILE A 109 "
           pdb=" N   PRO A 110 "
           pdb=" CA  PRO A 110 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.50   25.50     0      5.00e+00 4.00e-02 2.60e+01
  dihedral pdb=" CA  ALA B 311 "
           pdb=" C   ALA B 311 "
           pdb=" N   THR B 312 "
           pdb=" CA  THR B 312 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.58   23.42     0      5.00e+00 4.00e-02 2.19e+01
  ... (remaining 3754 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 691
       0.047 -    0.095: 262
       0.095 -    0.142: 82
       0.142 -    0.189: 15
       0.189 -    0.237: 2
  Chirality restraints: 1052
  Sorted by residual:
  chirality pdb=" CB  VAL A 144 "
            pdb=" CA  VAL A 144 "
            pdb=" CG1 VAL A 144 "
            pdb=" CG2 VAL A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.39   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CB  ILE A 356 "
            pdb=" CA  ILE A 356 "
            pdb=" CG1 ILE A 356 "
            pdb=" CG2 ILE A 356 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.87   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CB  VAL B  97 "
            pdb=" CA  VAL B  97 "
            pdb=" CG1 VAL B  97 "
            pdb=" CG2 VAL B  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.26e-01
  ... (remaining 1049 not shown)

  Planarity restraints: 1109
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY A 149 "    0.045 5.00e-02 4.00e+02   6.73e-02 7.24e+00
        pdb=" N   PRO A 150 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 150 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A 150 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN B 157 "    0.013 2.00e-02 2.50e+03   2.61e-02 6.80e+00
        pdb=" CG  ASN B 157 "   -0.045 2.00e-02 2.50e+03
        pdb=" OD1 ASN B 157 "    0.017 2.00e-02 2.50e+03
        pdb=" ND2 ASN B 157 "    0.015 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU B 128 "   -0.040 5.00e-02 4.00e+02   5.98e-02 5.72e+00
        pdb=" N   PRO B 129 "    0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO B 129 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 129 "   -0.034 5.00e-02 4.00e+02
  ... (remaining 1106 not shown)

  Histogram of nonbonded interaction distances:
        2.35 -     2.86: 2184
        2.86 -     3.37: 6372
        3.37 -     3.88: 10484
        3.88 -     4.39: 11817
        4.39 -     4.90: 19870
  Nonbonded interactions: 50727
  Sorted by model distance:
  nonbonded pdb=" O   ILE B 320 "
            pdb=" OG1 THR B 324 "
     model   vdw
     2.353 3.040
  nonbonded pdb=" OD1 ASN B 270 "
            pdb=" OG  SER B 401 "
     model   vdw
     2.359 3.040
  nonbonded pdb=" N   THR B  31 "
            pdb=" CD  PRO B  32 "
     model   vdw
     2.363 3.520
  nonbonded pdb=" O   SER A 446 "
            pdb=" OG  SER A 446 "
     model   vdw
     2.364 3.040
  nonbonded pdb=" OG1 THR B 365 "
            pdb=" O   ALA B 390 "
     model   vdw
     2.368 3.040
  ... (remaining 50722 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'
  selection = (chain 'B' and resid 31 through 460)
}

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:             0.440
  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:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.640
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7947
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   0.065   6522  Z= 0.222
  Angle     :  0.950  11.158   8867  Z= 0.496
  Chirality :  0.055   0.237   1052
  Planarity :  0.007   0.067   1109
  Dihedral  : 14.605  89.155   2263
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  8.16 %
    Favored  : 91.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.29 (0.19), residues: 857
  helix: -3.13 (0.13), residues: 616
  sheet:  None (None), residues: 0
  loop : -4.01 (0.28), residues: 241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 147 
 TYR   0.010   0.001   TYR A 445 
 PHE   0.017   0.001   PHE B 357 
 TRP   0.012   0.001   TRP B  59 
 HIS   0.005   0.001   HIS B 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 6522)
  covalent geometry    : angle       0.95003 ( 8867)
  hydrogen bonds       : bond        0.13550 (  397)
  hydrogen bonds       : angle       5.95514 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 218
  time to evaluate  : 0.182 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8369 (mmmt)
REVERT: A   94 TYR cc_start: 0.8957 (m-80) cc_final: 0.8631 (m-10)
REVERT: A  166 PHE cc_start: 0.8206 (m-80) cc_final: 0.7924 (m-10)
REVERT: A  250 ASN cc_start: 0.7779 (m110) cc_final: 0.7478 (m-40)
REVERT: A  293 LEU cc_start: 0.8672 (mm) cc_final: 0.8117 (pp)
REVERT: A  336 ILE cc_start: 0.8967 (mt) cc_final: 0.8713 (mt)
REVERT: A  342 ILE cc_start: 0.9005 (tp) cc_final: 0.8706 (tp)
REVERT: A  420 GLN cc_start: 0.8767 (pm20) cc_final: 0.8373 (pm20)
REVERT: B   62 ASN cc_start: 0.8663 (t0) cc_final: 0.8442 (t0)
REVERT: B   96 LEU cc_start: 0.8646 (mt) cc_final: 0.8288 (mm)
REVERT: B  271 LYS cc_start: 0.9205 (mttt) cc_final: 0.8945 (mmtp)
REVERT: B  414 GLU cc_start: 0.7777 (tp30) cc_final: 0.7577 (tp30)
REVERT: B  434 LEU cc_start: 0.8806 (tt) cc_final: 0.8549 (pp)
  outliers start: 2
  outliers final: 1
  residues processed: 220
  average time/residue: 0.0678
  time to fit residues: 20.0237
Evaluate side-chains
  164 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 163
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 74 optimal weight:    0.6980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
** A 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 233 ASN
A 250 ASN
A 456 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.128550 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.107458 restraints weight = 12018.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.110418 restraints weight = 7410.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.112228 restraints weight = 5383.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.113644 restraints weight = 4388.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.114446 restraints weight = 3800.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7996
moved from start:          0.1807

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6522  Z= 0.140
  Angle     :  0.687   8.026   8867  Z= 0.341
  Chirality :  0.041   0.212   1052
  Planarity :  0.005   0.046   1109
  Dihedral  :  5.514  50.670    909
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 18.52 %
    Favored  : 79.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.90 (0.25), residues: 857
  helix: -1.32 (0.19), residues: 618
  sheet:  None (None), residues: 0
  loop : -3.24 (0.31), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  64 
 TYR   0.007   0.001   TYR A 445 
 PHE   0.017   0.001   PHE B 379 
 TRP   0.019   0.001   TRP B 124 
 HIS   0.003   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 6522)
  covalent geometry    : angle       0.68711 ( 8867)
  hydrogen bonds       : bond        0.03631 (  397)
  hydrogen bonds       : angle       4.35739 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  199 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 186
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8541 (mmmt)
REVERT: A  293 LEU cc_start: 0.8726 (mm) cc_final: 0.8244 (pp)
REVERT: A  305 LEU cc_start: 0.8673 (OUTLIER) cc_final: 0.8446 (mp)
REVERT: A  420 GLN cc_start: 0.8759 (pm20) cc_final: 0.7993 (pm20)
REVERT: B   62 ASN cc_start: 0.8603 (t0) cc_final: 0.8370 (t0)
REVERT: B   91 MET cc_start: 0.8227 (mpp) cc_final: 0.7886 (mpp)
REVERT: B  117 GLU cc_start: 0.6823 (mt-10) cc_final: 0.6569 (mm-30)
REVERT: B  153 GLN cc_start: 0.8893 (tt0) cc_final: 0.8016 (tm-30)
REVERT: B  250 ASN cc_start: 0.7624 (t0) cc_final: 0.7326 (t0)
REVERT: B  271 LYS cc_start: 0.9189 (mttt) cc_final: 0.8954 (mmtp)
REVERT: B  382 TYR cc_start: 0.7527 (m-80) cc_final: 0.6918 (m-80)
REVERT: B  414 GLU cc_start: 0.7957 (tp30) cc_final: 0.7590 (tp30)
REVERT: B  442 LYS cc_start: 0.8524 (mppt) cc_final: 0.8301 (mppt)
  outliers start: 13
  outliers final: 7
  residues processed: 195
  average time/residue: 0.0669
  time to fit residues: 17.9251
Evaluate side-chains
  175 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 167
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   70 HIS
Chi-restraints excluded: chain A residue  276 MET
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  363 LEU
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 55 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 40 optimal weight:    0.0870
   chunk 26 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   overall best weight:    0.6758

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

Flipped N/Q/H residues before XYZ refinement:
** A 270 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 284 HIS ** 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 = 0.3514 r_free = 0.3514 target = 0.130098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.108522 restraints weight = 12003.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.111397 restraints weight = 7612.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.112865 restraints weight = 5648.216|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.114623 restraints weight = 4736.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.115471 restraints weight = 4060.528|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7984
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6522  Z= 0.133
  Angle     :  0.672   9.322   8867  Z= 0.330
  Chirality :  0.041   0.131   1052
  Planarity :  0.004   0.038   1109
  Dihedral  :  5.249  48.958    909
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 21.51 %
    Favored  : 75.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.89 (0.27), residues: 857
  helix: -0.51 (0.21), residues: 615
  sheet:  None (None), residues: 0
  loop : -3.03 (0.33), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  64 
 TYR   0.007   0.001   TYR A  94 
 PHE   0.022   0.001   PHE B 379 
 TRP   0.022   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 6522)
  covalent geometry    : angle       0.67210 ( 8867)
  hydrogen bonds       : bond        0.03302 (  397)
  hydrogen bonds       : angle       4.16820 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 178
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8786 (mmtt) cc_final: 0.8380 (mmmt)
REVERT: A  293 LEU cc_start: 0.8637 (mm) cc_final: 0.8101 (pp)
REVERT: A  305 LEU cc_start: 0.8685 (OUTLIER) cc_final: 0.8468 (mp)
REVERT: A  420 GLN cc_start: 0.8675 (pm20) cc_final: 0.7906 (pm20)
REVERT: B   62 ASN cc_start: 0.8612 (t0) cc_final: 0.8371 (t0)
REVERT: B   91 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7769 (mpp)
REVERT: B  153 GLN cc_start: 0.8825 (tt0) cc_final: 0.7954 (tm-30)
REVERT: B  250 ASN cc_start: 0.7508 (t0) cc_final: 0.6976 (t0)
REVERT: B  271 LYS cc_start: 0.9144 (mttt) cc_final: 0.8853 (mmtp)
REVERT: B  276 MET cc_start: 0.8887 (tpp) cc_final: 0.8651 (tpp)
REVERT: B  382 TYR cc_start: 0.7357 (m-80) cc_final: 0.6778 (m-80)
REVERT: B  414 GLU cc_start: 0.8099 (tp30) cc_final: 0.7791 (tp30)
REVERT: B  416 THR cc_start: 0.8625 (OUTLIER) cc_final: 0.8353 (p)
REVERT: B  442 LYS cc_start: 0.8324 (mppt) cc_final: 0.8072 (mppt)
  outliers start: 20
  outliers final: 8
  residues processed: 191
  average time/residue: 0.0622
  time to fit residues: 16.4811
Evaluate side-chains
  178 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 167
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  313 SER
Chi-restraints excluded: chain A residue  391 ILE
Chi-restraints excluded: chain A residue  406 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  312 THR
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 60 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 64 optimal weight:    0.0170
   chunk 28 optimal weight:    0.8980
   chunk 59 optimal weight:    0.6980
   chunk 43 optimal weight:    8.9990
   chunk 45 optimal weight:    0.8980
   chunk 55 optimal weight:    0.5980
   chunk 70 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.5818

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

Flipped N/Q/H residues before XYZ refinement:
A 157 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.129167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.107414 restraints weight = 11969.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.110193 restraints weight = 7481.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.112340 restraints weight = 5546.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.113387 restraints weight = 4481.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.114431 restraints weight = 3952.547|
|-----------------------------------------------------------------------------|
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.2666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6522  Z= 0.125
  Angle     :  0.662   9.036   8867  Z= 0.321
  Chirality :  0.040   0.127   1052
  Planarity :  0.004   0.033   1109
  Dihedral  :  5.060  48.219    909
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 24.02 %
    Favored  : 73.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.25 (0.29), residues: 857
  helix: -0.02 (0.22), residues: 612
  sheet:  None (None), residues: 0
  loop : -2.81 (0.35), residues: 245

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 147 
 TYR   0.007   0.001   TYR A 255 
 PHE   0.022   0.001   PHE B 379 
 TRP   0.024   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6522)
  covalent geometry    : angle       0.66217 ( 8867)
  hydrogen bonds       : bond        0.03174 (  397)
  hydrogen bonds       : angle       4.02576 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 179
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8820 (mmtt) cc_final: 0.8420 (mmmt)
REVERT: A   65 MET cc_start: 0.7724 (mmp) cc_final: 0.7514 (ptp)
REVERT: A   83 PHE cc_start: 0.8300 (t80) cc_final: 0.8066 (t80)
REVERT: A  253 TRP cc_start: 0.8149 (p-90) cc_final: 0.7907 (p-90)
REVERT: A  293 LEU cc_start: 0.8548 (mm) cc_final: 0.7986 (pp)
REVERT: A  294 MET cc_start: 0.8613 (tmm) cc_final: 0.8352 (tmm)
REVERT: A  305 LEU cc_start: 0.8621 (OUTLIER) cc_final: 0.8385 (mp)
REVERT: A  420 GLN cc_start: 0.8632 (pm20) cc_final: 0.7883 (pm20)
REVERT: B   62 ASN cc_start: 0.8652 (t0) cc_final: 0.8395 (t0)
REVERT: B  147 ARG cc_start: 0.8652 (ptm-80) cc_final: 0.7223 (ptp-170)
REVERT: B  153 GLN cc_start: 0.8787 (tt0) cc_final: 0.8359 (tm-30)
REVERT: B  250 ASN cc_start: 0.7449 (t0) cc_final: 0.6905 (t0)
REVERT: B  271 LYS cc_start: 0.9115 (mttt) cc_final: 0.8832 (mmtp)
REVERT: B  276 MET cc_start: 0.8847 (tpp) cc_final: 0.8632 (tpp)
REVERT: B  382 TYR cc_start: 0.7282 (m-80) cc_final: 0.6659 (m-80)
  outliers start: 17
  outliers final: 10
  residues processed: 189
  average time/residue: 0.0696
  time to fit residues: 17.8383
Evaluate side-chains
  177 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 166
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  305 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 24 optimal weight:    0.7980
   chunk 66 optimal weight:    3.9990
   chunk 34 optimal weight:    5.9990
   chunk 7 optimal weight:    0.3980
   chunk 12 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   chunk 10 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   chunk 67 optimal weight:    0.8980
   chunk 53 optimal weight:    1.9990
   chunk 50 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:
** A 270 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 = 0.3513 r_free = 0.3513 target = 0.129731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.108164 restraints weight = 12063.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.111050 restraints weight = 7621.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.113090 restraints weight = 5605.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.114200 restraints weight = 4545.439|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.115108 restraints weight = 3989.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3248
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7968
moved from start:          0.2916

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6522  Z= 0.131
  Angle     :  0.685  10.956   8867  Z= 0.330
  Chirality :  0.041   0.127   1052
  Planarity :  0.004   0.038   1109
  Dihedral  :  5.009  46.571    909
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 27.00 %
    Favored  : 71.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.92 (0.29), residues: 857
  helix:  0.22 (0.22), residues: 614
  sheet:  None (None), residues: 0
  loop : -2.68 (0.36), residues: 243

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 403 
 TYR   0.008   0.001   TYR A 255 
 PHE   0.030   0.001   PHE B 379 
 TRP   0.029   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 ( 6522)
  covalent geometry    : angle       0.68530 ( 8867)
  hydrogen bonds       : bond        0.03208 (  397)
  hydrogen bonds       : angle       4.00743 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 170
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
REVERT: A   55 LYS cc_start: 0.8905 (mmtt) cc_final: 0.8406 (mmmt)
REVERT: A   83 PHE cc_start: 0.8223 (t80) cc_final: 0.7939 (t80)
REVERT: A  253 TRP cc_start: 0.8180 (p-90) cc_final: 0.7854 (p-90)
REVERT: A  293 LEU cc_start: 0.8458 (mm) cc_final: 0.7866 (pp)
REVERT: A  420 GLN cc_start: 0.8554 (pm20) cc_final: 0.7891 (pm20)
REVERT: B   62 ASN cc_start: 0.8633 (t0) cc_final: 0.8383 (t0)
REVERT: B   91 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.7870 (mpp)
REVERT: B   92 PHE cc_start: 0.8062 (t80) cc_final: 0.7843 (t80)
REVERT: B  147 ARG cc_start: 0.8640 (ptm-80) cc_final: 0.7237 (ptp-170)
REVERT: B  157 ASN cc_start: 0.8905 (m-40) cc_final: 0.8488 (m110)
REVERT: B  250 ASN cc_start: 0.7408 (t0) cc_final: 0.6941 (t0)
REVERT: B  271 LYS cc_start: 0.9110 (mttt) cc_final: 0.8817 (mmtp)
REVERT: B  276 MET cc_start: 0.8723 (tpp) cc_final: 0.8487 (tpp)
REVERT: B  382 TYR cc_start: 0.7129 (m-80) cc_final: 0.6399 (m-80)
REVERT: B  414 GLU cc_start: 0.8207 (tp30) cc_final: 0.7894 (tp30)
REVERT: B  421 LEU cc_start: 0.9130 (OUTLIER) cc_final: 0.8756 (pp)
  outliers start: 12
  outliers final: 7
  residues processed: 177
  average time/residue: 0.0638
  time to fit residues: 15.6473
Evaluate side-chains
  174 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 165
  time to evaluate  : 0.193 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  421 LEU
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 19 optimal weight:    0.0970
   chunk 30 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 61 optimal weight:    0.6980
   chunk 41 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 33 optimal weight:    0.8980
   chunk 74 optimal weight:    0.0770
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.4736

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

Flipped N/Q/H residues before XYZ refinement:
A 270 ASN
** A 284 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.130371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.108640 restraints weight = 11902.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.111510 restraints weight = 7486.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.113457 restraints weight = 5532.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.114634 restraints weight = 4516.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.115652 restraints weight = 3959.347|
|-----------------------------------------------------------------------------|
r_work (final): 0.3333
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7935
moved from start:          0.3143

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6522  Z= 0.123
  Angle     :  0.684  13.391   8867  Z= 0.326
  Chirality :  0.041   0.175   1052
  Planarity :  0.004   0.034   1109
  Dihedral  :  4.848  44.181    909
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Rotamer:
    Outliers :  2.35 %
    Allowed  : 26.37 %
    Favored  : 71.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.71 (0.29), residues: 857
  helix:  0.32 (0.22), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.53 (0.37), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 403 
 TYR   0.007   0.001   TYR A 255 
 PHE   0.027   0.001   PHE B 379 
 TRP   0.027   0.001   TRP B 124 
 HIS   0.002   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 6522)
  covalent geometry    : angle       0.68417 ( 8867)
  hydrogen bonds       : bond        0.03099 (  397)
  hydrogen bonds       : angle       4.00275 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 176
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A   83 PHE cc_start: 0.8016 (t80) cc_final: 0.7747 (t80)
REVERT: A  253 TRP cc_start: 0.8150 (p-90) cc_final: 0.7822 (p-90)
REVERT: A  293 LEU cc_start: 0.8409 (mm) cc_final: 0.7828 (pp)
REVERT: A  294 MET cc_start: 0.8654 (tmm) cc_final: 0.8356 (tmm)
REVERT: A  420 GLN cc_start: 0.8400 (pm20) cc_final: 0.7813 (pm20)
REVERT: A  421 LEU cc_start: 0.8546 (OUTLIER) cc_final: 0.8207 (pp)
REVERT: B   62 ASN cc_start: 0.8578 (t0) cc_final: 0.8341 (t0)
REVERT: B   91 MET cc_start: 0.8235 (OUTLIER) cc_final: 0.7859 (mpp)
REVERT: B  147 ARG cc_start: 0.8589 (ptm-80) cc_final: 0.7456 (ptp-170)
REVERT: B  250 ASN cc_start: 0.7413 (t0) cc_final: 0.7143 (t0)
REVERT: B  271 LYS cc_start: 0.9018 (mttt) cc_final: 0.8748 (mmtp)
REVERT: B  276 MET cc_start: 0.8678 (tpp) cc_final: 0.8450 (tpp)
REVERT: B  414 GLU cc_start: 0.8188 (tp30) cc_final: 0.7884 (tp30)
  outliers start: 15
  outliers final: 6
  residues processed: 184
  average time/residue: 0.0638
  time to fit residues: 16.1521
Evaluate side-chains
  169 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 161
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 LEU
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 43 optimal weight:    8.9990
   chunk 45 optimal weight:    0.6980
   chunk 20 optimal weight:    3.9990
   chunk 68 optimal weight:    5.9990
   chunk 44 optimal weight:    0.5980
   chunk 14 optimal weight:    0.9980
   chunk 74 optimal weight:    0.0870
   chunk 7 optimal weight:    0.6980
   chunk 30 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   overall best weight:    0.5958

-------------------------------------------------------------------------------
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 = 0.3538 r_free = 0.3538 target = 0.131498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.109821 restraints weight = 11893.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112731 restraints weight = 7522.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114505 restraints weight = 5563.544|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115951 restraints weight = 4574.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116628 restraints weight = 3971.057|
|-----------------------------------------------------------------------------|
r_work (final): 0.3271
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7943
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6522  Z= 0.128
  Angle     :  0.707  15.838   8867  Z= 0.333
  Chirality :  0.041   0.170   1052
  Planarity :  0.004   0.035   1109
  Dihedral  :  4.776  39.628    909
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 12.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.48 %
    Favored  : 94.52 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 28.10 %
    Favored  : 70.33 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.52 (0.30), residues: 857
  helix:  0.48 (0.22), residues: 619
  sheet:  None (None), residues: 0
  loop : -2.49 (0.37), residues: 238

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 147 
 TYR   0.007   0.001   TYR A 210 
 PHE   0.024   0.001   PHE B 438 
 TRP   0.023   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6522)
  covalent geometry    : angle       0.70666 ( 8867)
  hydrogen bonds       : bond        0.03125 (  397)
  hydrogen bonds       : angle       3.95326 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 170
  time to evaluate  : 0.196 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.9113 (tptm) cc_final: 0.8796 (tttt)
REVERT: A  253 TRP cc_start: 0.8176 (p-90) cc_final: 0.7852 (p-90)
REVERT: A  293 LEU cc_start: 0.8400 (mm) cc_final: 0.7784 (pp)
REVERT: A  294 MET cc_start: 0.8746 (tmm) cc_final: 0.8421 (tmm)
REVERT: A  342 ILE cc_start: 0.8996 (tp) cc_final: 0.8757 (tp)
REVERT: A  420 GLN cc_start: 0.8449 (pm20) cc_final: 0.7878 (pm20)
REVERT: A  421 LEU cc_start: 0.8542 (OUTLIER) cc_final: 0.8252 (pp)
REVERT: B  147 ARG cc_start: 0.8546 (ptm-80) cc_final: 0.7638 (ptp-170)
REVERT: B  157 ASN cc_start: 0.8455 (m-40) cc_final: 0.8071 (m110)
REVERT: B  271 LYS cc_start: 0.8990 (mttt) cc_final: 0.8726 (mmtp)
REVERT: B  414 GLU cc_start: 0.8186 (tp30) cc_final: 0.7858 (tp30)
  outliers start: 10
  outliers final: 6
  residues processed: 175
  average time/residue: 0.0670
  time to fit residues: 16.2727
Evaluate side-chains
  167 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 160
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9980
   chunk 22 optimal weight:    3.9990
   chunk 69 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 59 optimal weight:    0.8980
   chunk 3 optimal weight:    0.9980
   chunk 83 optimal weight:    0.7980
   chunk 84 optimal weight:    5.9990
   chunk 79 optimal weight:    0.1980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 = 0.3451 r_free = 0.3451 target = 0.125600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.105268 restraints weight = 11916.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3203 r_free = 0.3203 target = 0.107859 restraints weight = 7695.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.109524 restraints weight = 5748.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.110837 restraints weight = 4733.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.111557 restraints weight = 4108.012|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.3440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6522  Z= 0.133
  Angle     :  0.734  15.554   8867  Z= 0.344
  Chirality :  0.041   0.140   1052
  Planarity :  0.004   0.037   1109
  Dihedral  :  4.782  39.716    909
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.37 %
    Favored  : 94.63 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 29.67 %
    Favored  : 68.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.45 (0.30), residues: 857
  helix:  0.49 (0.22), residues: 621
  sheet:  None (None), residues: 0
  loop : -2.36 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 147 
 TYR   0.007   0.001   TYR A 255 
 PHE   0.031   0.001   PHE A  95 
 TRP   0.021   0.001   TRP B 124 
 HIS   0.001   0.000   HIS A  70 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6522)
  covalent geometry    : angle       0.73395 ( 8867)
  hydrogen bonds       : bond        0.03213 (  397)
  hydrogen bonds       : angle       3.95393 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 166
  time to evaluate  : 0.235 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.9144 (tptm) cc_final: 0.8878 (tttt)
REVERT: A  253 TRP cc_start: 0.8190 (p-90) cc_final: 0.7826 (p-90)
REVERT: A  293 LEU cc_start: 0.8391 (mm) cc_final: 0.7770 (pp)
REVERT: A  294 MET cc_start: 0.8814 (tmm) cc_final: 0.8512 (tmm)
REVERT: A  342 ILE cc_start: 0.9013 (tp) cc_final: 0.8750 (tp)
REVERT: A  420 GLN cc_start: 0.8449 (pm20) cc_final: 0.7875 (pm20)
REVERT: B  147 ARG cc_start: 0.8532 (ptm-80) cc_final: 0.7659 (ptp-170)
REVERT: B  157 ASN cc_start: 0.8536 (m-40) cc_final: 0.8135 (m110)
REVERT: B  271 LYS cc_start: 0.9013 (mttt) cc_final: 0.8731 (mmtp)
REVERT: B  414 GLU cc_start: 0.8163 (tp30) cc_final: 0.7882 (tp30)
  outliers start: 10
  outliers final: 9
  residues processed: 170
  average time/residue: 0.0646
  time to fit residues: 15.2678
Evaluate side-chains
  170 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 161
  time to evaluate  : 0.215 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  162 VAL
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  228 MET
Chi-restraints excluded: chain B residue  238 LEU
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  416 THR
Chi-restraints excluded: chain B residue  434 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    0.0270
   chunk 51 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 81 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 32 optimal weight:    0.0870
   chunk 79 optimal weight:    0.0970
   chunk 73 optimal weight:    0.3980
   chunk 7 optimal weight:    0.7980
   overall best weight:    0.2614

-------------------------------------------------------------------------------
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 = 0.3496 r_free = 0.3496 target = 0.128952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.108091 restraints weight = 11974.173|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.110760 restraints weight = 7450.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.112836 restraints weight = 5465.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.114012 restraints weight = 4391.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.115010 restraints weight = 3801.772|
|-----------------------------------------------------------------------------|
r_work (final): 0.3305
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
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   0.040   6522  Z= 0.126
  Angle     :  0.742  15.754   8867  Z= 0.344
  Chirality :  0.041   0.150   1052
  Planarity :  0.004   0.037   1109
  Dihedral  :  4.617  31.195    909
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 11.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.78 %
    Favored  : 95.22 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 30.46 %
    Favored  : 68.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.32 (0.30), residues: 857
  helix:  0.57 (0.22), residues: 622
  sheet:  None (None), residues: 0
  loop : -2.25 (0.39), residues: 235

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  64 
 TYR   0.006   0.001   TYR A 255 
 PHE   0.028   0.001   PHE A  95 
 TRP   0.020   0.001   TRP B 124 
 HIS   0.001   0.000   HIS B 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 6522)
  covalent geometry    : angle       0.74216 ( 8867)
  hydrogen bonds       : bond        0.03152 (  397)
  hydrogen bonds       : angle       3.89831 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  185 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 176
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.9130 (tptm) cc_final: 0.8830 (tttt)
REVERT: A  293 LEU cc_start: 0.8352 (mm) cc_final: 0.7753 (pp)
REVERT: A  294 MET cc_start: 0.8846 (tmm) cc_final: 0.8546 (tmm)
REVERT: A  342 ILE cc_start: 0.8949 (tp) cc_final: 0.8720 (tp)
REVERT: A  344 THR cc_start: 0.8726 (t) cc_final: 0.8485 (t)
REVERT: B  147 ARG cc_start: 0.8530 (ptm-80) cc_final: 0.7634 (ptp-170)
REVERT: B  157 ASN cc_start: 0.8493 (m-40) cc_final: 0.7992 (m110)
REVERT: B  271 LYS cc_start: 0.8967 (mttt) cc_final: 0.8725 (mmtp)
REVERT: B  414 GLU cc_start: 0.8144 (tp30) cc_final: 0.7888 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 180
  average time/residue: 0.0636
  time to fit residues: 15.9465
Evaluate side-chains
  168 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 161
  time to evaluate  : 0.225 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 70 optimal weight:    9.9990
   chunk 38 optimal weight:    0.6980
   chunk 4 optimal weight:    3.9990
   chunk 74 optimal weight:    0.8980
   chunk 50 optimal weight:    0.0980
   chunk 71 optimal weight:    0.7980
   chunk 64 optimal weight:    9.9990
   chunk 9 optimal weight:    4.9990
   chunk 78 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.127769 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.106186 restraints weight = 12083.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.109149 restraints weight = 7510.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.111038 restraints weight = 5466.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.112451 restraints weight = 4430.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.113455 restraints weight = 3808.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7894
moved from start:          0.3880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6522  Z= 0.140
  Angle     :  0.782  15.974   8867  Z= 0.361
  Chirality :  0.042   0.194   1052
  Planarity :  0.004   0.036   1109
  Dihedral  :  4.619  24.750    909
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.90 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.41 %
    Allowed  : 32.18 %
    Favored  : 66.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.25 (0.30), residues: 857
  helix:  0.60 (0.22), residues: 620
  sheet:  None (None), residues: 0
  loop : -2.15 (0.39), residues: 237

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  64 
 TYR   0.008   0.001   TYR A 255 
 PHE   0.032   0.001   PHE A  95 
 TRP   0.022   0.001   TRP A 253 
 HIS   0.001   0.000   HIS A 284 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 6522)
  covalent geometry    : angle       0.78215 ( 8867)
  hydrogen bonds       : bond        0.03166 (  397)
  hydrogen bonds       : angle       3.92731 ( 1179)

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

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

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1714 Ramachandran restraints generated.
    857 Oldfield, 0 Emsley, 857 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 170
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   99 LYS cc_start: 0.9146 (tptm) cc_final: 0.8869 (tttt)
REVERT: A  204 MET cc_start: 0.7440 (mmp) cc_final: 0.7135 (mmt)
REVERT: A  294 MET cc_start: 0.8915 (tmm) cc_final: 0.8622 (tmm)
REVERT: A  342 ILE cc_start: 0.9004 (tp) cc_final: 0.8742 (tp)
REVERT: B   38 MET cc_start: 0.7339 (mmt) cc_final: 0.7020 (mmt)
REVERT: B   62 ASN cc_start: 0.8697 (t0) cc_final: 0.8431 (t0)
REVERT: B  147 ARG cc_start: 0.8561 (ptm-80) cc_final: 0.7702 (ptp-170)
REVERT: B  157 ASN cc_start: 0.8504 (m-40) cc_final: 0.8034 (m110)
REVERT: B  250 ASN cc_start: 0.7475 (t0) cc_final: 0.7188 (t0)
REVERT: B  271 LYS cc_start: 0.8996 (mttt) cc_final: 0.8611 (mmtp)
REVERT: B  414 GLU cc_start: 0.8199 (tp30) cc_final: 0.7913 (tp30)
  outliers start: 9
  outliers final: 7
  residues processed: 175
  average time/residue: 0.0586
  time to fit residues: 14.4367
Evaluate side-chains
  168 residues out of total 643 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 161
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   88 VAL
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  258 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue   91 MET
Chi-restraints excluded: chain B residue  260 ILE
Chi-restraints excluded: chain B residue  416 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 74 optimal weight:    0.9990
   chunk 68 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 8 optimal weight:    5.9990
   chunk 84 optimal weight:    0.0980
   chunk 11 optimal weight:    7.9990
   chunk 1 optimal weight:    0.6980
   chunk 41 optimal weight:    2.9990
   chunk 48 optimal weight:    0.7980
   chunk 83 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3473 r_free = 0.3473 target = 0.127354 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.107742 restraints weight = 11927.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3233 r_free = 0.3233 target = 0.110008 restraints weight = 7931.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.111625 restraints weight = 6075.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.112894 restraints weight = 5084.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.113473 restraints weight = 4418.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3902

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6522  Z= 0.140
  Angle     :  0.776  15.871   8867  Z= 0.358
  Chirality :  0.042   0.183   1052
  Planarity :  0.004   0.036   1109
  Dihedral  :  4.596  23.655    909
  Min Nonbonded Distance : 2.519

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.13 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 31.55 %
    Favored  : 66.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.13 (0.30), residues: 857
  helix:  0.70 (0.22), residues: 618
  sheet:  None (None), residues: 0
  loop : -2.10 (0.39), residues: 239

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  64 
 TYR   0.008   0.001   TYR A 210 
 PHE   0.033   0.001   PHE A  95 
 TRP   0.035   0.001   TRP A 253 
 HIS   0.001   0.000   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 ( 6522)
  covalent geometry    : angle       0.77599 ( 8867)
  hydrogen bonds       : bond        0.03157 (  397)
  hydrogen bonds       : angle       3.90856 ( 1179)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 969.33 seconds
wall clock time: 17 minutes 22.58 seconds (1042.58 seconds total)