Starting phenix.real_space_refine
on Tue Sep 24 02:38:11 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ro0_24584/09_2024/7ro0_24584.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ro0_24584/09_2024/7ro0_24584.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.75
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ro0_24584/09_2024/7ro0_24584.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ro0_24584/09_2024/7ro0_24584.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ro0_24584/09_2024/7ro0_24584.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ro0_24584/09_2024/7ro0_24584.cif"
  }
  resolution = 3.75
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.045
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    4426      2.51       5
     N    1138      2.21       5
     O    1138      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib"
  Total number of atoms: 6742
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3371
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 19, 'TRANS': 429}
    Chain: "B"
      Number of atoms: 3371
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 449, 3371
          Classifications: {'peptide': 449}
          Link IDs: {'PTRANS': 19, 'TRANS': 429}
  Time building chain proxies: 5.00, per 1000 atoms: 0.74
  Number of scatterers: 6742
  At special positions: 0
  Unit cell: (77, 73.7, 114.4, 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    1138      8.00
     N    1138      7.00
     C    4426      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.63
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1568

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      75.6% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 25
      removed outlier: 3.877A  pdb=" N   ARG A  23 " --> pdb=" O   ARG A  19 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 32 through 69
      removed outlier: 4.474A  pdb=" N   ALA A  40 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   VAL A  41 " --> pdb=" O   PHE A  37 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   ALA A  67 " --> pdb=" O   GLN A  63 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   LEU A  68 " --> pdb=" O   ARG A  64 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   VAL A  69 " --> pdb=" O   MET A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 74 through 101
      removed outlier: 4.145A  pdb=" N   THR A  80 " --> pdb=" O   PRO A  76 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   SER A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 4.331A  pdb=" N   LEU A  89 " --> pdb=" O   CYS A  85 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   ALA A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   VAL A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 102 through 105
      removed outlier: 3.853A  pdb=" N   GLY A 105 " --> pdb=" O   PRO A 102 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 102 through 105'
    Processing helix  chain 'A' and resid 108 through 116
    Processing helix  chain 'A' and resid 127 through 141
      removed outlier: 4.779A  pdb=" N   PHE A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   LEU A 136 " --> pdb=" O   PHE A 132 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   GLY A 141 " --> pdb=" O   GLY A 137 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 148 through 167
      removed outlier: 3.576A  pdb=" N   GLN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   ILE A 154 " --> pdb=" O   PRO A 150 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASN A 157 " --> pdb=" O   GLN A 153 " (cutoff:3.500A)
      removed outlier: 4.092A  pdb=" N   ILE A 158 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 185
      removed outlier: 3.931A  pdb=" N   GLY A 181 " --> pdb=" O   LEU A 177 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   ALA A 182 " --> pdb=" O   LEU A 178 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 194 through 203
      removed outlier: 3.843A  pdb=" N   ILE A 200 " --> pdb=" O   GLY A 196 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   GLU A 202 " --> pdb=" O   LEU A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 214 through 233
      removed outlier: 3.890A  pdb=" N   ILE A 220 " --> pdb=" O   LYS A 216 " (cutoff:3.500A)
      removed outlier: 4.970A  pdb=" N   GLY A 221 " --> pdb=" O   ALA A 217 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 222 " --> pdb=" O   VAL A 218 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   ILE A 223 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 5.986A  pdb=" N   MET A 224 " --> pdb=" O   ILE A 220 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   MET A 228 " --> pdb=" O   MET A 224 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   PHE A 232 " --> pdb=" O   MET A 228 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 253 through 280
      removed outlier: 3.821A  pdb=" N   ILE A 257 " --> pdb=" O   TRP A 253 " (cutoff:3.500A)
      Proline residue:  A 267  - end of helix
      removed outlier: 4.330A  pdb=" N   ASP A 278 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 306
      removed outlier: 3.656A  pdb=" N   LEU A 301 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   CYS A 302 " --> pdb=" O   ILE A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 319
      removed outlier: 4.089A  pdb=" N   LEU A 319 " --> pdb=" O   GLY A 316 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 316 through 319'
    Processing helix  chain 'A' and resid 320 through 325
      removed outlier: 4.225A  pdb=" N   ALA A 325 " --> pdb=" O   PRO A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 348
      removed outlier: 3.772A  pdb=" N   PHE A 337 " --> pdb=" O   LEU A 333 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   ARG A 340 " --> pdb=" O   ILE A 336 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   LEU A 346 " --> pdb=" O   ILE A 342 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 356 through 376
      removed outlier: 3.714A  pdb=" N   THR A 365 " --> pdb=" O   LEU A 361 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   VAL A 366 " --> pdb=" O   ALA A 362 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   LEU A 367 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      removed outlier: 3.691A  pdb=" N   VAL A 374 " --> pdb=" O   ALA A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 383
      removed outlier: 3.705A  pdb=" N   TYR A 382 " --> pdb=" O   PHE A 379 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   HIS A 383 " --> pdb=" O   PRO A 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 379 through 383'
    Processing helix  chain 'A' and resid 387 through 393
      removed outlier: 3.685A  pdb=" N   ILE A 391 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 393 through 401
      removed outlier: 4.611A  pdb=" N   LEU A 397 " --> pdb=" O   GLY A 393 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   LEU A 398 " --> pdb=" O   MET A 394 " (cutoff:3.500A)
      removed outlier: 4.495A  pdb=" N   ALA A 399 " --> pdb=" O   GLY A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 417
    Processing helix  chain 'A' and resid 418 through 420
      No H-bonds generated for 'chain 'A' and resid 418 through 420'
    Processing helix  chain 'A' and resid 421 through 437
      removed outlier: 4.152A  pdb=" N   THR A 433 " --> pdb=" O   GLY A 429 " (cutoff:3.500A)
      removed outlier: 3.821A  pdb=" N   LEU A 435 " --> pdb=" O   GLY A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 444 through 458
      removed outlier: 4.124A  pdb=" N   ALA A 450 " --> pdb=" O   SER A 446 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLN A 456 " --> pdb=" O   THR A 452 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 13 through 27
      removed outlier: 3.953A  pdb=" N   ARG B  23 " --> pdb=" O   ARG B  19 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   GLN B  24 " --> pdb=" O   GLN B  20 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   GLU B  27 " --> pdb=" O   ARG B  23 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 32 through 48
      removed outlier: 3.745A  pdb=" N   MET B  38 " --> pdb=" O   ALA B  34 " (cutoff:3.500A)
      removed outlier: 4.750A  pdb=" N   ALA B  40 " --> pdb=" O   LEU B  36 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   VAL B  41 " --> pdb=" O   PHE B  37 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   VAL B  46 " --> pdb=" O   VAL B  42 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 70
      removed outlier: 3.878A  pdb=" N   GLY B  56 " --> pdb=" O   ALA B  52 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LEU B  68 " --> pdb=" O   ARG B  64 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   VAL B  69 " --> pdb=" O   MET B  65 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   HIS B  70 " --> pdb=" O   GLY B  66 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 101
      removed outlier: 4.264A  pdb=" N   SER B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.521A  pdb=" N   LEU B  89 " --> pdb=" O   CYS B  85 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   GLY B  93 " --> pdb=" O   LEU B  89 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LEU B  96 " --> pdb=" O   PHE B  92 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   VAL B  97 " --> pdb=" O   GLY B  93 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 108 through 116
    Processing helix  chain 'B' and resid 127 through 141
      removed outlier: 4.586A  pdb=" N   PHE B 133 " --> pdb=" O   PRO B 129 " (cutoff:3.500A)
      removed outlier: 4.109A  pdb=" N   LEU B 136 " --> pdb=" O   PHE B 132 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   GLY B 137 " --> pdb=" O   PHE B 133 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 148 through 166
      removed outlier: 3.668A  pdb=" N   GLN B 153 " --> pdb=" O   GLY B 149 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   ILE B 154 " --> pdb=" O   PRO B 150 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   GLY B 159 " --> pdb=" O   GLY B 155 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ARG B 160 " --> pdb=" O   GLY B 156 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   MET B 161 " --> pdb=" O   ASN B 157 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 171 through 191
      removed outlier: 3.701A  pdb=" N   HIS B 175 " --> pdb=" O   ASP B 171 " (cutoff:3.500A)
      removed outlier: 4.216A  pdb=" N   LEU B 178 " --> pdb=" O   ARG B 174 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   ALA B 179 " --> pdb=" O   HIS B 175 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLY B 181 " --> pdb=" O   LEU B 177 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ALA B 184 " --> pdb=" O   THR B 180 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU B 186 " --> pdb=" O   ALA B 182 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 194 through 203
      removed outlier: 3.821A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 194 " (cutoff:3.500A)
      removed outlier: 4.151A  pdb=" N   GLU B 202 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 233
      removed outlier: 4.772A  pdb=" N   GLY B 221 " --> pdb=" O   ALA B 217 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   VAL B 222 " --> pdb=" O   VAL B 218 " (cutoff:3.500A)
      removed outlier: 4.157A  pdb=" N   ILE B 223 " --> pdb=" O   PHE B 219 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   MET B 224 " --> pdb=" O   ILE B 220 " (cutoff:3.500A)
      removed outlier: 4.225A  pdb=" N   MET B 228 " --> pdb=" O   MET B 224 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 253 through 285
      removed outlier: 3.802A  pdb=" N   ILE B 257 " --> pdb=" O   TRP B 253 " (cutoff:3.500A)
      Proline residue:  B 267  - end of helix
      removed outlier: 4.295A  pdb=" N   LYS B 271 " --> pdb=" O   PRO B 267 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLN B 277 " --> pdb=" O   VAL B 273 " (cutoff:3.500A)
      removed outlier: 4.176A  pdb=" N   ASP B 278 " --> pdb=" O   LEU B 274 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   VAL B 283 " --> pdb=" O   LEU B 279 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 287 through 306
    Processing helix  chain 'B' and resid 319 through 324
    Processing helix  chain 'B' and resid 329 through 349
      removed outlier: 3.623A  pdb=" N   ILE B 342 " --> pdb=" O   VAL B 338 " (cutoff:3.500A)
      removed outlier: 4.215A  pdb=" N   THR B 343 " --> pdb=" O   ALA B 339 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 356 through 379
      removed outlier: 4.246A  pdb=" N   THR B 365 " --> pdb=" O   LEU B 361 " (cutoff:3.500A)
      removed outlier: 4.139A  pdb=" N   VAL B 366 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 363 " (cutoff:3.500A)
      removed outlier: 4.081A  pdb=" N   VAL B 374 " --> pdb=" O   ALA B 370 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   GLU B 377 " --> pdb=" O   MET B 373 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   PHE B 379 " --> pdb=" O   ALA B 375 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 380 through 383
      removed outlier: 3.833A  pdb=" N   HIS B 383 " --> pdb=" O   PRO B 380 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 380 through 383'
    Processing helix  chain 'B' and resid 385 through 394
      removed outlier: 4.355A  pdb=" N   PHE B 389 " --> pdb=" O   GLU B 385 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   ALA B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 396 through 401
    Processing helix  chain 'B' and resid 404 through 417
    Processing helix  chain 'B' and resid 422 through 432
      removed outlier: 3.791A  pdb=" N   LEU B 430 " --> pdb=" O   ILE B 426 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 438
    Processing helix  chain 'B' and resid 444 through 457
      removed outlier: 3.847A  pdb=" N   LEU B 449 " --> pdb=" O   TYR B 445 " (cutoff:3.500A)
      removed outlier: 4.261A  pdb=" N   ALA B 450 " --> pdb=" O   SER B 446 " (cutoff:3.500A)

    389 hydrogen bonds defined for protein.
    1167 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.83

  Time building geometry restraints manager: 1.91 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1050
        1.31 -     1.43: 1771
        1.43 -     1.56: 3991
        1.56 -     1.68: 0
        1.68 -     1.81: 74
  Bond restraints: 6886
  Sorted by residual:
  bond pdb=" C   TYR A  75 "
       pdb=" N   PRO A  76 "
    ideal  model  delta    sigma   weight residual
    1.335  1.396 -0.062 1.19e-02 7.06e+03 2.68e+01
  bond pdb=" C   VAL B 127 "
       pdb=" O   VAL B 127 "
    ideal  model  delta    sigma   weight residual
    1.237  1.191  0.046 9.80e-03 1.04e+04 2.22e+01
  bond pdb=" C   TRP B 124 "
       pdb=" O   TRP B 124 "
    ideal  model  delta    sigma   weight residual
    1.236  1.180  0.056 1.28e-02 6.10e+03 1.91e+01
  bond pdb=" N   VAL B 127 "
       pdb=" CA  VAL B 127 "
    ideal  model  delta    sigma   weight residual
    1.452  1.486 -0.034 1.18e-02 7.18e+03 8.15e+00
  bond pdb=" C   ARG B 126 "
       pdb=" O   ARG B 126 "
    ideal  model  delta    sigma   weight residual
    1.237  1.209  0.028 1.10e-02 8.26e+03 6.41e+00
  ... (remaining 6881 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.83: 9133
        2.83 -     5.66: 172
        5.66 -     8.49: 32
        8.49 -    11.32: 3
       11.32 -    14.14: 4
  Bond angle restraints: 9344
  Sorted by residual:
  angle pdb=" N   VAL B 127 "
        pdb=" CA  VAL B 127 "
        pdb=" C   VAL B 127 "
      ideal   model   delta    sigma   weight residual
     112.96  105.66    7.30 1.00e+00 1.00e+00 5.33e+01
  angle pdb=" C   ARG B 126 "
        pdb=" N   VAL B 127 "
        pdb=" CA  VAL B 127 "
      ideal   model   delta    sigma   weight residual
     121.84  116.41    5.43 1.13e+00 7.83e-01 2.31e+01
  angle pdb=" C   SER A 329 "
        pdb=" N   MET A 330 "
        pdb=" CA  MET A 330 "
      ideal   model   delta    sigma   weight residual
     121.54  130.10   -8.56 1.91e+00 2.74e-01 2.01e+01
  angle pdb=" C   PHE B 166 "
        pdb=" N   ARG B 167 "
        pdb=" CA  ARG B 167 "
      ideal   model   delta    sigma   weight residual
     122.46  128.20   -5.74 1.41e+00 5.03e-01 1.66e+01
  angle pdb=" CA  TRP B 124 "
        pdb=" C   TRP B 124 "
        pdb=" N   TRP B 125 "
      ideal   model   delta    sigma   weight residual
     118.08  123.34   -5.26 1.30e+00 5.92e-01 1.64e+01
  ... (remaining 9339 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.86: 3424
       15.86 -    31.72: 449
       31.72 -    47.57: 113
       47.57 -    63.43: 9
       63.43 -    79.29: 7
  Dihedral angle restraints: 4002
    sinusoidal: 1520
      harmonic: 2482
  Sorted by residual:
  dihedral pdb=" CA  PHE B 219 "
           pdb=" C   PHE B 219 "
           pdb=" N   ILE B 220 "
           pdb=" CA  ILE B 220 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.21   28.79     0      5.00e+00 4.00e-02 3.32e+01
  dihedral pdb=" CA  ASP B 118 "
           pdb=" C   ASP B 118 "
           pdb=" N   GLN B 119 "
           pdb=" CA  GLN B 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.09   23.91     0      5.00e+00 4.00e-02 2.29e+01
  dihedral pdb=" CA  ASP A 118 "
           pdb=" C   ASP A 118 "
           pdb=" N   GLN A 119 "
           pdb=" CA  GLN A 119 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.31   23.69     0      5.00e+00 4.00e-02 2.25e+01
  ... (remaining 3999 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 802
       0.059 -    0.118: 240
       0.118 -    0.176: 48
       0.176 -    0.235: 6
       0.235 -    0.294: 2
  Chirality restraints: 1098
  Sorted by residual:
  chirality pdb=" CA  TRP B 124 "
            pdb=" N   TRP B 124 "
            pdb=" C   TRP B 124 "
            pdb=" CB  TRP B 124 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.29 2.00e-01 2.50e+01 2.16e+00
  chirality pdb=" CB  THR A 324 "
            pdb=" CA  THR A 324 "
            pdb=" OG1 THR A 324 "
            pdb=" CG2 THR A 324 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.31    0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" CB  ILE A 154 "
            pdb=" CA  ILE A 154 "
            pdb=" CG1 ILE A 154 "
            pdb=" CG2 ILE A 154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.86   -0.21 2.00e-01 2.50e+01 1.14e+00
  ... (remaining 1095 not shown)

  Planarity restraints: 1174
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 330 "   -0.018 2.00e-02 2.50e+03   3.55e-02 1.26e+01
        pdb=" C   MET A 330 "    0.061 2.00e-02 2.50e+03
        pdb=" O   MET A 330 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   GLY A 331 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA B 358 "   -0.056 5.00e-02 4.00e+02   8.42e-02 1.14e+01
        pdb=" N   PRO B 359 "    0.146 5.00e-02 4.00e+02
        pdb=" CA  PRO B 359 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO B 359 "   -0.047 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 266 "    0.051 5.00e-02 4.00e+02   7.76e-02 9.63e+00
        pdb=" N   PRO B 267 "   -0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO B 267 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 267 "    0.042 5.00e-02 4.00e+02
  ... (remaining 1171 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 719
        2.74 -     3.28: 6401
        3.28 -     3.82: 10899
        3.82 -     4.36: 12102
        4.36 -     4.90: 22058
  Nonbonded interactions: 52179
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 103 "
            pdb=" NH2 ARG B 123 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OD1 ASN A 270 "
            pdb=" OG  SER A 401 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" OE1 GLU A 414 "
            pdb=" OH  TYR B 419 "
     model   vdw
     2.308 3.040
  nonbonded pdb=" OH  TYR A 419 "
            pdb=" OE1 GLU B 414 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OD1 ASN A 287 "
            pdb=" OG1 THR A 289 "
     model   vdw
     2.317 3.040
  ... (remaining 52174 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'
}

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:             0.650
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.060
  Process input model:                     19.600
  Find NCS groups from input model:        0.180
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.670
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.500
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8219
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      :  0.008   0.070   6886  Z= 0.498
  Angle     :  1.029  14.144   9344  Z= 0.548
  Chirality :  0.059   0.294   1098
  Planarity :  0.009   0.084   1174
  Dihedral  : 14.947  79.288   2434
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 5.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.43 %
    Favored  : 86.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -5.18 (0.19), residues: 894
  helix: -3.11 (0.14), residues: 638
  sheet:  None (None), residues: 0
  loop : -3.74 (0.29), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.034   0.003   TRP A 291 
 HIS   0.016   0.002   HIS A 284 
 PHE   0.030   0.002   PHE A 357 
 TYR   0.021   0.002   TYR B 419 
 ARG   0.005   0.000   ARG A 147 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 132
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   22 ILE cc_start: 0.8579 (tt) cc_final: 0.8335 (tt)
REVERT: A   29 ASP cc_start: 0.8243 (t70) cc_final: 0.7978 (t70)
REVERT: A   38 MET cc_start: 0.8859 (mmt) cc_final: 0.8336 (mmt)
REVERT: A  165 ILE cc_start: 0.8158 (mm) cc_final: 0.7834 (mt)
REVERT: A  298 ILE cc_start: 0.8759 (tt) cc_final: 0.8486 (tt)
REVERT: A  332 MET cc_start: 0.7307 (tpt) cc_final: 0.6926 (tpp)
REVERT: A  360 MET cc_start: 0.8271 (mtm) cc_final: 0.7956 (mtt)
REVERT: B   20 GLN cc_start: 0.8690 (tm-30) cc_final: 0.7763 (tm-30)
REVERT: B   54 ASP cc_start: 0.8919 (t0) cc_final: 0.8628 (t0)
REVERT: B   75 TYR cc_start: 0.8242 (t80) cc_final: 0.7740 (t80)
REVERT: B  113 GLU cc_start: 0.8113 (tt0) cc_final: 0.7854 (tm-30)
REVERT: B  279 LEU cc_start: 0.8944 (tp) cc_final: 0.8707 (tp)
REVERT: B  391 ILE cc_start: 0.9150 (tp) cc_final: 0.8882 (tp)
  outliers start: 5
  outliers final: 4
  residues processed: 137
  average time/residue: 0.2029
  time to fit residues: 35.8798
Evaluate side-chains
  112 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 108
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  126 ARG
Chi-restraints excluded: chain B residue  127 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 66 optimal weight:    0.6980
   chunk 37 optimal weight:    3.9990
   chunk 22 optimal weight:    0.4980
   chunk 44 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 68 optimal weight:    0.9990
   chunk 26 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 207 GLN
B 207 GLN
B 418 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8173
moved from start:          0.1360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   6886  Z= 0.180
  Angle     :  0.597   9.049   9344  Z= 0.297
  Chirality :  0.040   0.129   1098
  Planarity :  0.006   0.064   1174
  Dihedral  :  5.469  36.179    966
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 18.20 %
    Favored  : 80.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.96 (0.26), residues: 894
  helix: -1.33 (0.19), residues: 644
  sheet:  None (None), residues: 0
  loop : -3.35 (0.33), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 291 
 HIS   0.009   0.001   HIS B 284 
 PHE   0.020   0.001   PHE A  92 
 TYR   0.021   0.001   TYR B 419 
 ARG   0.007   0.001   ARG A 282 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 114
  time to evaluate  : 0.695 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7946 (ttp-110) cc_final: 0.7697 (ttm110)
REVERT: A   29 ASP cc_start: 0.8258 (t70) cc_final: 0.8054 (t70)
REVERT: A   38 MET cc_start: 0.8862 (mmt) cc_final: 0.8169 (mmt)
REVERT: A   54 ASP cc_start: 0.9001 (t0) cc_final: 0.8724 (t0)
REVERT: A  165 ILE cc_start: 0.8329 (mm) cc_final: 0.8061 (mt)
REVERT: A  298 ILE cc_start: 0.8584 (tt) cc_final: 0.8381 (tt)
REVERT: A  332 MET cc_start: 0.6980 (tpt) cc_final: 0.6701 (mmt)
REVERT: A  360 MET cc_start: 0.8221 (mtm) cc_final: 0.7992 (mtt)
REVERT: A  423 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8482 (mt)
REVERT: A  430 LEU cc_start: 0.8854 (tp) cc_final: 0.8296 (tt)
REVERT: B   20 GLN cc_start: 0.8666 (tm-30) cc_final: 0.7640 (tm-30)
REVERT: B   54 ASP cc_start: 0.8751 (t0) cc_final: 0.8433 (t0)
REVERT: B  136 LEU cc_start: 0.8640 (tp) cc_final: 0.8309 (tp)
REVERT: B  148 GLU cc_start: 0.8278 (pp20) cc_final: 0.8063 (pp20)
REVERT: B  391 ILE cc_start: 0.9081 (tp) cc_final: 0.8806 (tp)
  outliers start: 12
  outliers final: 8
  residues processed: 122
  average time/residue: 0.1438
  time to fit residues: 25.5233
Evaluate side-chains
  112 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 103
  time to evaluate  : 0.748 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 MET
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  423 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  350 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 44 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 66 optimal weight:    0.9990
   chunk 54 optimal weight:    0.1980
   chunk 22 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9980
   chunk 86 optimal weight:    0.3980
   chunk 71 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 64 optimal weight:    0.9980
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8156
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   6886  Z= 0.169
  Angle     :  0.565   9.033   9344  Z= 0.276
  Chirality :  0.040   0.121   1098
  Planarity :  0.005   0.058   1174
  Dihedral  :  4.909  34.331    962
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 20.71 %
    Favored  : 76.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.28), residues: 894
  helix: -0.62 (0.21), residues: 648
  sheet:  None (None), residues: 0
  loop : -3.07 (0.35), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 291 
 HIS   0.007   0.001   HIS B 284 
 PHE   0.016   0.001   PHE A  92 
 TYR   0.012   0.001   TYR B 419 
 ARG   0.004   0.000   ARG A 282 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 117
  time to evaluate  : 0.768 
Fit side-chains
REVERT: A   38 MET cc_start: 0.8928 (mmt) cc_final: 0.8227 (mmt)
REVERT: A   54 ASP cc_start: 0.9066 (t0) cc_final: 0.8721 (t0)
REVERT: A  298 ILE cc_start: 0.8626 (tt) cc_final: 0.8398 (tt)
REVERT: A  409 ILE cc_start: 0.8782 (mm) cc_final: 0.8550 (mt)
REVERT: B   20 GLN cc_start: 0.8696 (tm-30) cc_final: 0.7596 (tm-30)
REVERT: B   54 ASP cc_start: 0.8727 (t0) cc_final: 0.8379 (t0)
REVERT: B  113 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7143 (tm-30)
REVERT: B  136 LEU cc_start: 0.8564 (tp) cc_final: 0.8242 (tp)
REVERT: B  144 VAL cc_start: 0.8926 (OUTLIER) cc_final: 0.8686 (p)
REVERT: B  148 GLU cc_start: 0.8335 (pp20) cc_final: 0.8134 (pp20)
REVERT: B  391 ILE cc_start: 0.9087 (tp) cc_final: 0.8774 (tp)
  outliers start: 18
  outliers final: 14
  residues processed: 129
  average time/residue: 0.1333
  time to fit residues: 25.4157
Evaluate side-chains
  125 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 110
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 38 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 80 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 76 optimal weight:    0.8980
   chunk 22 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   overall best weight:    1.7186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.1840

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   6886  Z= 0.314
  Angle     :  0.633   8.828   9344  Z= 0.310
  Chirality :  0.044   0.133   1098
  Planarity :  0.006   0.062   1174
  Dihedral  :  5.046  28.844    961
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 6.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.26 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.60 %
    Favored  : 74.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.69 (0.28), residues: 894
  helix: -0.41 (0.21), residues: 650
  sheet:  None (None), residues: 0
  loop : -2.87 (0.37), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 291 
 HIS   0.009   0.001   HIS B 284 
 PHE   0.016   0.001   PHE A  92 
 TYR   0.011   0.001   TYR B 419 
 ARG   0.008   0.000   ARG A  23 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.776 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7761 (ttm110)
REVERT: A   38 MET cc_start: 0.8961 (mmt) cc_final: 0.8454 (mmt)
REVERT: A   54 ASP cc_start: 0.9088 (t0) cc_final: 0.8748 (t0)
REVERT: A  276 MET cc_start: 0.7889 (tpp) cc_final: 0.7661 (ttp)
REVERT: A  298 ILE cc_start: 0.8706 (tt) cc_final: 0.8437 (tt)
REVERT: A  328 PHE cc_start: 0.7559 (OUTLIER) cc_final: 0.7348 (m-10)
REVERT: B   20 GLN cc_start: 0.8752 (tm-30) cc_final: 0.7686 (tm-30)
REVERT: B   54 ASP cc_start: 0.8818 (t0) cc_final: 0.8495 (t0)
REVERT: B  113 GLU cc_start: 0.7695 (tm-30) cc_final: 0.6900 (tm-30)
REVERT: B  144 VAL cc_start: 0.9057 (OUTLIER) cc_final: 0.8835 (p)
REVERT: B  148 GLU cc_start: 0.8495 (pp20) cc_final: 0.8160 (pp20)
REVERT: B  391 ILE cc_start: 0.9263 (tp) cc_final: 0.8895 (tp)
  outliers start: 26
  outliers final: 19
  residues processed: 121
  average time/residue: 0.1323
  time to fit residues: 23.7021
Evaluate side-chains
  123 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 0.751 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue   84 LEU
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  127 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  365 THR
Chi-restraints excluded: chain B residue  376 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 48 optimal weight:    0.5980
   chunk 1 optimal weight:    0.0570
   chunk 63 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 72 optimal weight:    6.9990
   chunk 58 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 76 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.6298

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8153
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   6886  Z= 0.164
  Angle     :  0.555   9.182   9344  Z= 0.270
  Chirality :  0.040   0.123   1098
  Planarity :  0.005   0.055   1174
  Dihedral  :  4.655  25.437    961
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.55 %
    Allowed  : 22.04 %
    Favored  : 74.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.24 (0.29), residues: 894
  helix: -0.04 (0.22), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.77 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 291 
 HIS   0.007   0.001   HIS B 284 
 PHE   0.013   0.001   PHE A  92 
 TYR   0.008   0.001   TYR B 419 
 ARG   0.006   0.000   ARG A  23 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 108
  time to evaluate  : 0.545 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7691 (ttm110)
REVERT: A   38 MET cc_start: 0.8943 (mmt) cc_final: 0.8406 (mmt)
REVERT: A   54 ASP cc_start: 0.9074 (t0) cc_final: 0.8717 (t0)
REVERT: A  276 MET cc_start: 0.7755 (tpp) cc_final: 0.7478 (ttp)
REVERT: A  298 ILE cc_start: 0.8503 (tt) cc_final: 0.8247 (tt)
REVERT: A  328 PHE cc_start: 0.7207 (OUTLIER) cc_final: 0.6980 (m-10)
REVERT: B   20 GLN cc_start: 0.8750 (tm-30) cc_final: 0.7670 (tm-30)
REVERT: B   54 ASP cc_start: 0.8714 (t0) cc_final: 0.8352 (t0)
REVERT: B  113 GLU cc_start: 0.7741 (tm-30) cc_final: 0.7320 (tm-30)
REVERT: B  136 LEU cc_start: 0.8570 (tp) cc_final: 0.8236 (tp)
REVERT: B  144 VAL cc_start: 0.9003 (OUTLIER) cc_final: 0.8779 (p)
REVERT: B  148 GLU cc_start: 0.8397 (pp20) cc_final: 0.8179 (pp20)
REVERT: B  391 ILE cc_start: 0.9137 (tp) cc_final: 0.8822 (tp)
  outliers start: 24
  outliers final: 16
  residues processed: 126
  average time/residue: 0.1315
  time to fit residues: 24.2430
Evaluate side-chains
  121 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  292 VAL
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  357 PHE
Chi-restraints excluded: chain B residue  365 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 76 optimal weight:    0.7980
   chunk 16 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 20 optimal weight:    1.9990
   chunk 85 optimal weight:    0.8980
   chunk 70 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0980
   chunk 7 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 44 optimal weight:    0.9980
   chunk 82 optimal weight:    0.0980
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8136
moved from start:          0.2242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6886  Z= 0.157
  Angle     :  0.544   9.114   9344  Z= 0.264
  Chirality :  0.039   0.125   1098
  Planarity :  0.005   0.053   1174
  Dihedral  :  4.432  24.619    961
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 23.67 %
    Favored  : 73.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.98 (0.29), residues: 894
  helix:  0.15 (0.22), residues: 642
  sheet:  None (None), residues: 0
  loop : -2.65 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 291 
 HIS   0.006   0.000   HIS B 284 
 PHE   0.012   0.001   PHE A  92 
 TYR   0.009   0.001   TYR B 419 
 ARG   0.005   0.000   ARG A  23 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 111
  time to evaluate  : 0.716 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7880 (ttm-80) cc_final: 0.7571 (ttm110)
REVERT: A   38 MET cc_start: 0.8933 (mmt) cc_final: 0.8359 (mmt)
REVERT: A   54 ASP cc_start: 0.9079 (t0) cc_final: 0.8721 (t0)
REVERT: A  276 MET cc_start: 0.7746 (tpp) cc_final: 0.7474 (ttp)
REVERT: A  298 ILE cc_start: 0.8647 (tt) cc_final: 0.8276 (tt)
REVERT: A  328 PHE cc_start: 0.6970 (OUTLIER) cc_final: 0.6723 (m-10)
REVERT: B   54 ASP cc_start: 0.8690 (t0) cc_final: 0.8314 (t0)
REVERT: B  113 GLU cc_start: 0.7739 (tm-30) cc_final: 0.7310 (tm-30)
REVERT: B  136 LEU cc_start: 0.8513 (tp) cc_final: 0.8195 (tp)
REVERT: B  144 VAL cc_start: 0.8996 (OUTLIER) cc_final: 0.8773 (p)
REVERT: B  148 GLU cc_start: 0.8393 (pp20) cc_final: 0.8082 (pp20)
REVERT: B  391 ILE cc_start: 0.9226 (tp) cc_final: 0.8808 (tp)
  outliers start: 21
  outliers final: 15
  residues processed: 127
  average time/residue: 0.1371
  time to fit residues: 25.6269
Evaluate side-chains
  123 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 106
  time to evaluate  : 0.721 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 LEU
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue  122 VAL
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 48 optimal weight:    0.6980
   chunk 62 optimal weight:    0.0470
   chunk 71 optimal weight:    7.9990
   chunk 47 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 51 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.7082

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8138
moved from start:          0.2329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   6886  Z= 0.172
  Angle     :  0.549   9.084   9344  Z= 0.267
  Chirality :  0.040   0.121   1098
  Planarity :  0.005   0.053   1174
  Dihedral  :  4.386  26.300    961
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 23.96 %
    Favored  : 72.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.29), residues: 894
  helix:  0.19 (0.22), residues: 646
  sheet:  None (None), residues: 0
  loop : -2.57 (0.37), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 125 
 HIS   0.006   0.000   HIS B 284 
 PHE   0.011   0.001   PHE A  92 
 TYR   0.024   0.001   TYR B 419 
 ARG   0.005   0.000   ARG A  23 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.725 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7896 (ttm-80) cc_final: 0.7550 (ttm110)
REVERT: A   38 MET cc_start: 0.8942 (mmt) cc_final: 0.8368 (mmt)
REVERT: A   54 ASP cc_start: 0.9103 (t0) cc_final: 0.8719 (t0)
REVERT: A  298 ILE cc_start: 0.8645 (tt) cc_final: 0.8263 (tt)
REVERT: B   54 ASP cc_start: 0.8688 (t0) cc_final: 0.8303 (t0)
REVERT: B  113 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7289 (tm-30)
REVERT: B  144 VAL cc_start: 0.9005 (OUTLIER) cc_final: 0.8780 (p)
REVERT: B  148 GLU cc_start: 0.8411 (pp20) cc_final: 0.8096 (pp20)
REVERT: B  391 ILE cc_start: 0.9264 (tp) cc_final: 0.8833 (tp)
  outliers start: 22
  outliers final: 18
  residues processed: 122
  average time/residue: 0.1333
  time to fit residues: 24.0765
Evaluate side-chains
  124 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  330 MET
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 50 optimal weight:    6.9990
   chunk 25 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 57 optimal weight:    5.9990
   chunk 41 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 66 optimal weight:    0.3980
   chunk 77 optimal weight:    0.7980
   chunk 81 optimal weight:    3.9990
   chunk 74 optimal weight:    5.9990
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8142
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6886  Z= 0.184
  Angle     :  0.579  10.227   9344  Z= 0.275
  Chirality :  0.041   0.260   1098
  Planarity :  0.005   0.053   1174
  Dihedral  :  4.370  26.640    960
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 25.00 %
    Favored  : 71.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.87 (0.29), residues: 894
  helix:  0.21 (0.22), residues: 648
  sheet:  None (None), residues: 0
  loop : -2.59 (0.37), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 125 
 HIS   0.006   0.000   HIS B 284 
 PHE   0.011   0.001   PHE A  92 
 TYR   0.037   0.002   TYR B 419 
 ARG   0.004   0.000   ARG A  23 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.713 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7568 (ttm110)
REVERT: A   38 MET cc_start: 0.8947 (mmt) cc_final: 0.8354 (mmt)
REVERT: A   54 ASP cc_start: 0.9112 (t0) cc_final: 0.8720 (t0)
REVERT: A  298 ILE cc_start: 0.8660 (tt) cc_final: 0.8276 (tt)
REVERT: A  328 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6556 (m-10)
REVERT: B   38 MET cc_start: 0.7935 (mmt) cc_final: 0.7413 (mmt)
REVERT: B   54 ASP cc_start: 0.8690 (t0) cc_final: 0.8316 (t0)
REVERT: B  113 GLU cc_start: 0.7727 (tm-30) cc_final: 0.7272 (tm-30)
REVERT: B  144 VAL cc_start: 0.8997 (OUTLIER) cc_final: 0.8767 (p)
REVERT: B  148 GLU cc_start: 0.8421 (pp20) cc_final: 0.8094 (pp20)
REVERT: B  391 ILE cc_start: 0.9237 (tp) cc_final: 0.8815 (tp)
  outliers start: 21
  outliers final: 19
  residues processed: 122
  average time/residue: 0.1338
  time to fit residues: 24.2206
Evaluate side-chains
  125 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  328 PHE
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0870
   chunk 62 optimal weight:    0.0670
   chunk 24 optimal weight:    1.9990
   chunk 71 optimal weight:    7.9990
   chunk 74 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 83 optimal weight:    0.7980
   overall best weight:    0.5696

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8118
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6886  Z= 0.160
  Angle     :  0.573  10.061   9344  Z= 0.273
  Chirality :  0.040   0.244   1098
  Planarity :  0.005   0.052   1174
  Dihedral  :  4.279  27.104    960
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 24.85 %
    Favored  : 71.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.30), residues: 894
  helix:  0.32 (0.22), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.32 (0.39), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 125 
 HIS   0.005   0.001   HIS B 284 
 PHE   0.010   0.001   PHE A  92 
 TYR   0.033   0.001   TYR B 419 
 ARG   0.004   0.000   ARG A  23 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 111
  time to evaluate  : 0.661 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7879 (ttm-80) cc_final: 0.7597 (ttm110)
REVERT: A   38 MET cc_start: 0.8932 (mmt) cc_final: 0.8348 (mmt)
REVERT: A   54 ASP cc_start: 0.9103 (t0) cc_final: 0.8717 (t0)
REVERT: A  165 ILE cc_start: 0.8576 (tp) cc_final: 0.8061 (tp)
REVERT: A  298 ILE cc_start: 0.8623 (tt) cc_final: 0.8250 (tt)
REVERT: B   54 ASP cc_start: 0.8678 (t0) cc_final: 0.8298 (t0)
REVERT: B  113 GLU cc_start: 0.7711 (tm-30) cc_final: 0.7251 (tm-30)
REVERT: B  144 VAL cc_start: 0.8983 (OUTLIER) cc_final: 0.8762 (p)
REVERT: B  148 GLU cc_start: 0.8389 (pp20) cc_final: 0.8087 (pp20)
REVERT: B  391 ILE cc_start: 0.9203 (tp) cc_final: 0.8822 (tp)
  outliers start: 23
  outliers final: 20
  residues processed: 127
  average time/residue: 0.1416
  time to fit residues: 26.6213
Evaluate side-chains
  129 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 0.686 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   22 ILE
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 51 optimal weight:    1.9990
   chunk 39 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 87 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 69 optimal weight:    0.5980
   chunk 7 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 42 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0070
   chunk 74 optimal weight:    4.9990
   overall best weight:    0.8000

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8134
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6886  Z= 0.186
  Angle     :  0.585  10.217   9344  Z= 0.279
  Chirality :  0.041   0.205   1098
  Planarity :  0.005   0.053   1174
  Dihedral  :  4.310  26.903    960
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 25.15 %
    Favored  : 71.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.29), residues: 894
  helix:  0.36 (0.22), residues: 646
  sheet:  None (None), residues: 0
  loop : -2.47 (0.38), residues: 248

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 125 
 HIS   0.005   0.000   HIS B 284 
 PHE   0.011   0.001   PHE A  92 
 TYR   0.043   0.001   TYR B 419 
 ARG   0.004   0.000   ARG A  23 

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

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

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1788 Ramachandran restraints generated.
    894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 110
  time to evaluate  : 0.671 
Fit side-chains
REVERT: A   23 ARG cc_start: 0.7861 (ttm-80) cc_final: 0.7618 (ttm110)
REVERT: A   38 MET cc_start: 0.8956 (mmt) cc_final: 0.8378 (mmt)
REVERT: A  165 ILE cc_start: 0.8600 (tp) cc_final: 0.8090 (tp)
REVERT: A  294 MET cc_start: 0.7718 (tmm) cc_final: 0.6886 (tmm)
REVERT: A  298 ILE cc_start: 0.8663 (tt) cc_final: 0.8284 (tt)
REVERT: B   54 ASP cc_start: 0.8783 (t0) cc_final: 0.8427 (t0)
REVERT: B   75 TYR cc_start: 0.8540 (t80) cc_final: 0.8265 (t80)
REVERT: B  113 GLU cc_start: 0.7735 (tm-30) cc_final: 0.7278 (tm-30)
REVERT: B  144 VAL cc_start: 0.8998 (OUTLIER) cc_final: 0.8770 (p)
REVERT: B  148 GLU cc_start: 0.8416 (pp20) cc_final: 0.8100 (pp20)
REVERT: B  391 ILE cc_start: 0.9255 (tp) cc_final: 0.8823 (tp)
  outliers start: 23
  outliers final: 19
  residues processed: 127
  average time/residue: 0.1437
  time to fit residues: 26.8325
Evaluate side-chains
  128 residues out of total 676 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 0.735 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  200 ILE
Chi-restraints excluded: chain A residue  214 SER
Chi-restraints excluded: chain A residue  219 PHE
Chi-restraints excluded: chain A residue  264 ILE
Chi-restraints excluded: chain A residue  283 VAL
Chi-restraints excluded: chain A residue  312 THR
Chi-restraints excluded: chain A residue  374 VAL
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  425 MET
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  197 ILE
Chi-restraints excluded: chain B residue  212 LEU
Chi-restraints excluded: chain B residue  215 ILE
Chi-restraints excluded: chain B residue  219 PHE
Chi-restraints excluded: chain B residue  222 VAL
Chi-restraints excluded: chain B residue  223 ILE
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  328 PHE
Chi-restraints excluded: chain B residue  357 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 88
   random chunks:
   chunk 21 optimal weight:    3.9990
   chunk 64 optimal weight:    0.4980
   chunk 10 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9990
   chunk 69 optimal weight:    0.1980
   chunk 29 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   chunk 8 optimal weight:    0.6980
   chunk 12 optimal weight:    0.5980
   chunk 61 optimal weight:    0.9980
   chunk 3 optimal weight:    3.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 191 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.114821 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.095670 restraints weight = 9731.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.2963 r_free = 0.2963 target = 0.098617 restraints weight = 5766.409|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2991 r_free = 0.2991 target = 0.100618 restraints weight = 4008.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.2998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
moved from start:          0.2643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   6886  Z= 0.159
  Angle     :  0.579  10.556   9344  Z= 0.276
  Chirality :  0.040   0.197   1098
  Planarity :  0.005   0.052   1174
  Dihedral  :  4.215  27.019    960
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 25.59 %
    Favored  : 71.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.30), residues: 894
  helix:  0.49 (0.22), residues: 644
  sheet:  None (None), residues: 0
  loop : -2.30 (0.40), residues: 250

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 125 
 HIS   0.005   0.000   HIS B 284 
 PHE   0.010   0.001   PHE B 166 
 TYR   0.038   0.001   TYR B 419 
 ARG   0.005   0.000   ARG A  23 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1389.76 seconds
wall clock time: 29 minutes 4.85 seconds (1744.85 seconds total)