Starting phenix.real_space_refine
on Sat May  2 19:54:24 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9m7s_63692/05_2026/9m7s_63692.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9m7s_63692/05_2026/9m7s_63692.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9m7s_63692/05_2026/9m7s_63692.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9m7s_63692/05_2026/9m7s_63692.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9m7s_63692/05_2026/9m7s_63692.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9m7s_63692/05_2026/9m7s_63692.cif"
  }
  resolution = 3.18
  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=   0.000 sd=   0.082
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      58      5.16       5
     C    5545      2.51       5
     N    1292      2.21       5
     O    1340      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8235
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 2528
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 317, 2528
          Classifications: {'peptide': 317}
          Link IDs: {'PTRANS': 14, 'TRANS': 302}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 2877
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2877
          Classifications: {'peptide': 358}
          Link IDs: {'PTRANS': 22, 'TRANS': 335}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2830
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2830
          Classifications: {'peptide': 352}
          Link IDs: {'PTRANS': 22, 'TRANS': 329}
          Chain breaks: 2
  Time building chain proxies: 1.99, per 1000 atoms: 0.24
  Number of scatterers: 8235
  At special positions: 0
  Unit cell: (75.6, 105.84, 96.12, 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      58     16.00
     O    1340      8.00
     N    1292      7.00
     C    5545      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: 0.83
  Conformation dependent library (CDL) restraints added in 320.9 milliseconds
  

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1966

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 1 sheets defined
      78.8% alpha, 0.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.23
  Creating SS restraints...
    Processing helix  chain 'C' and resid 31 through 41
    Processing helix  chain 'C' and resid 42 through 44
      No H-bonds generated for 'chain 'C' and resid 42 through 44'
    Processing helix  chain 'C' and resid 45 through 63
      removed outlier: 4.302A  pdb=" N   SER C  49 " --> pdb=" O   TYR C  45 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE C  63 " --> pdb=" O   TRP C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 67 through 72
      removed outlier: 4.347A  pdb=" N   MET C  70 " --> pdb=" O   SER C  67 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   SER C  71 " --> pdb=" O   PRO C  68 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   HIS C  72 " --> pdb=" O   SER C  69 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 67 through 72'
    Processing helix  chain 'C' and resid 76 through 82
      removed outlier: 3.849A  pdb=" N   MET C  80 " --> pdb=" O   LYS C  76 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 82 through 107
    Processing helix  chain 'C' and resid 107 through 117
      removed outlier: 3.756A  pdb=" N   VAL C 111 " --> pdb=" O   PHE C 107 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 119 through 124
    Processing helix  chain 'C' and resid 125 through 137
    Processing helix  chain 'C' and resid 145 through 167
      removed outlier: 3.795A  pdb=" N   GLN C 149 " --> pdb=" O   SER C 145 " (cutoff:3.500A)
      Proline residue:  C 158  - end of helix
    Processing helix  chain 'C' and resid 183 through 185
      No H-bonds generated for 'chain 'C' and resid 183 through 185'
    Processing helix  chain 'C' and resid 186 through 204
      removed outlier: 4.177A  pdb=" N   VAL C 190 " --> pdb=" O   SER C 186 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   ALA C 201 " --> pdb=" O   ALA C 197 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   GLU C 202 " --> pdb=" O   ARG C 198 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 205 through 230
    Processing helix  chain 'C' and resid 242 through 245
    Processing helix  chain 'C' and resid 246 through 264
      Proline residue:  C 252  - end of helix
      removed outlier: 3.591A  pdb=" N   CYS C 263 " --> pdb=" O   TRP C 259 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 267 through 286
    Processing helix  chain 'C' and resid 287 through 293
      removed outlier: 4.105A  pdb=" N   PHE C 291 " --> pdb=" O   ARG C 287 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   LYS C 293 " --> pdb=" O   ASN C 289 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 294 through 296
      No H-bonds generated for 'chain 'C' and resid 294 through 296'
    Processing helix  chain 'C' and resid 299 through 304
    Processing helix  chain 'C' and resid 305 through 324
      removed outlier: 4.234A  pdb=" N   LEU C 309 " --> pdb=" O   TYR C 305 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLN C 318 " --> pdb=" O   LEU C 314 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLN C 321 " --> pdb=" O   VAL C 317 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   GLU C 322 " --> pdb=" O   GLN C 318 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 330 through 352
    Processing helix  chain 'A' and resid 222 through 228
      removed outlier: 3.782A  pdb=" N   TYR A 226 " --> pdb=" O   PRO A 222 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 262
    Processing helix  chain 'A' and resid 263 through 282
      removed outlier: 3.842A  pdb=" N   LEU A 267 " --> pdb=" O   PHE A 263 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   GLY A 268 " --> pdb=" O   GLY A 264 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   SER A 271 " --> pdb=" O   LEU A 267 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ALA A 280 " --> pdb=" O   TRP A 276 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 320
    Processing helix  chain 'A' and resid 320 through 329
    Processing helix  chain 'A' and resid 334 through 337
    Processing helix  chain 'A' and resid 338 through 350
    Processing helix  chain 'A' and resid 360 through 382
      removed outlier: 4.326A  pdb=" N   TRP A 364 " --> pdb=" O   PRO A 360 " (cutoff:3.500A)
      removed outlier: 4.510A  pdb=" N   TYR A 365 " --> pdb=" O   HIS A 361 " (cutoff:3.500A)
      Proline residue:  A 370  - end of helix
      removed outlier: 3.759A  pdb=" N   CYS A 373 " --> pdb=" O   PHE A 369 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   LEU A 374 " --> pdb=" O   PRO A 370 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   TYR A 379 " --> pdb=" O   GLU A 375 " (cutoff:3.500A)
      removed outlier: 4.208A  pdb=" N   GLY A 380 " --> pdb=" O   LEU A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 416
      removed outlier: 4.057A  pdb=" N   VAL A 402 " --> pdb=" O   ASN A 398 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   GLY A 404 " --> pdb=" O   LEU A 400 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   ASN A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   PHE A 406 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 441
      removed outlier: 3.519A  pdb=" N   HIS A 431 " --> pdb=" O   VAL A 427 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   TYR A 440 " --> pdb=" O   PHE A 436 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 457
    Processing helix  chain 'A' and resid 458 through 476
      removed outlier: 3.914A  pdb=" N   ALA A 462 " --> pdb=" O   PHE A 458 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   ALA A 463 " --> pdb=" O   LEU A 459 " (cutoff:3.500A)
      Proline residue:  A 464  - end of helix
      removed outlier: 3.575A  pdb=" N   MET A 469 " --> pdb=" O   SER A 465 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 500
      removed outlier: 3.650A  pdb=" N   CYS A 485 " --> pdb=" O   GLY A 481 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 509 through 515
    Processing helix  chain 'A' and resid 516 through 533
    Processing helix  chain 'A' and resid 535 through 565
      removed outlier: 3.531A  pdb=" N   ILE A 540 " --> pdb=" O   THR A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 574 through 579
      removed outlier: 3.700A  pdb=" N   ILE A 577 " --> pdb=" O   ASP A 574 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   ILE A 579 " --> pdb=" O   ALA A 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 222 through 230
      removed outlier: 3.754A  pdb=" N   TYR B 226 " --> pdb=" O   PRO B 222 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 260 through 262
      No H-bonds generated for 'chain 'B' and resid 260 through 262'
    Processing helix  chain 'B' and resid 263 through 282
      removed outlier: 3.590A  pdb=" N   LEU B 267 " --> pdb=" O   PHE B 263 " (cutoff:3.500A)
      removed outlier: 3.975A  pdb=" N   GLN B 272 " --> pdb=" O   GLY B 268 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA B 280 " --> pdb=" O   TRP B 276 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 287
      removed outlier: 4.461A  pdb=" N   PHE B 287 " --> pdb=" O   PRO B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 292 through 320
    Processing helix  chain 'B' and resid 320 through 330
    Processing helix  chain 'B' and resid 332 through 337
    Processing helix  chain 'B' and resid 338 through 350
    Processing helix  chain 'B' and resid 360 through 368
      removed outlier: 4.130A  pdb=" N   TRP B 364 " --> pdb=" O   PRO B 360 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   TYR B 365 " --> pdb=" O   HIS B 361 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 368 through 384
      removed outlier: 3.529A  pdb=" N   MET B 383 " --> pdb=" O   TYR B 379 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   SER B 384 " --> pdb=" O   GLY B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 395 through 397
      No H-bonds generated for 'chain 'B' and resid 395 through 397'
    Processing helix  chain 'B' and resid 398 through 416
      removed outlier: 4.152A  pdb=" N   VAL B 402 " --> pdb=" O   ASN B 398 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   GLY B 404 " --> pdb=" O   LEU B 400 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 441
      removed outlier: 3.634A  pdb=" N   PHE B 423 " --> pdb=" O   GLU B 419 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   PHE B 424 " --> pdb=" O   GLY B 420 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   TYR B 440 " --> pdb=" O   PHE B 436 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   GLN B 441 " --> pdb=" O   VAL B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 460
    Processing helix  chain 'B' and resid 461 through 476
      removed outlier: 3.561A  pdb=" N   ALA B 472 " --> pdb=" O   SER B 468 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 479 through 500
    Processing helix  chain 'B' and resid 509 through 515
    Processing helix  chain 'B' and resid 516 through 533
      removed outlier: 4.016A  pdb=" N   THR B 520 " --> pdb=" O   THR B 516 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL B 532 " --> pdb=" O   ARG B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 535 through 566
    Processing helix  chain 'B' and resid 574 through 579
      removed outlier: 4.058A  pdb=" N   ILE B 579 " --> pdb=" O   ALA B 576 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 230 through 231

    525 hydrogen bonds defined for protein.
    1485 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: 1.01

  Time building geometry restraints manager: 1.08 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1186
        1.30 -     1.43: 2455
        1.43 -     1.55: 4750
        1.55 -     1.68: 5
        1.68 -     1.81: 99
  Bond restraints: 8495
  Sorted by residual:
  bond pdb=" CA  TYR A 379 "
       pdb=" C   TYR A 379 "
    ideal  model  delta    sigma   weight residual
    1.523  1.407  0.117 1.30e-02 5.92e+03 8.06e+01
  bond pdb=" CA  ASN A 395 "
       pdb=" C   ASN A 395 "
    ideal  model  delta    sigma   weight residual
    1.522  1.442  0.080 1.26e-02 6.30e+03 4.04e+01
  bond pdb=" C   ASN A 395 "
       pdb=" O   ASN A 395 "
    ideal  model  delta    sigma   weight residual
    1.244  1.187  0.057 9.80e-03 1.04e+04 3.38e+01
  bond pdb=" C   TYR A 379 "
       pdb=" O   TYR A 379 "
    ideal  model  delta    sigma   weight residual
    1.237  1.172  0.064 1.17e-02 7.31e+03 3.03e+01
  bond pdb=" CA  TRP A 382 "
       pdb=" C   TRP A 382 "
    ideal  model  delta    sigma   weight residual
    1.522  1.447  0.076 1.40e-02 5.10e+03 2.93e+01
  ... (remaining 8490 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.59: 11361
        2.59 -     5.19: 180
        5.19 -     7.78: 27
        7.78 -    10.37: 6
       10.37 -    12.97: 2
  Bond angle restraints: 11576
  Sorted by residual:
  angle pdb=" C   ASN A 395 "
        pdb=" N   PRO A 396 "
        pdb=" CA  PRO A 396 "
      ideal   model   delta    sigma   weight residual
     119.84  108.69   11.15 1.25e+00 6.40e-01 7.96e+01
  angle pdb=" N   ALA B 394 "
        pdb=" CA  ALA B 394 "
        pdb=" C   ALA B 394 "
      ideal   model   delta    sigma   weight residual
     111.07  119.13   -8.06 1.07e+00 8.73e-01 5.68e+01
  angle pdb=" N   GLY A 380 "
        pdb=" CA  GLY A 380 "
        pdb=" C   GLY A 380 "
      ideal   model   delta    sigma   weight residual
     112.73  120.66   -7.93 1.20e+00 6.94e-01 4.36e+01
  angle pdb=" N   ASN C 260 "
        pdb=" CA  ASN C 260 "
        pdb=" C   ASN C 260 "
      ideal   model   delta    sigma   weight residual
     111.69  104.35    7.34 1.23e+00 6.61e-01 3.56e+01
  angle pdb=" N   VAL B 393 "
        pdb=" CA  VAL B 393 "
        pdb=" C   VAL B 393 "
      ideal   model   delta    sigma   weight residual
     113.00  105.99    7.01 1.30e+00 5.92e-01 2.91e+01
  ... (remaining 11571 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 4499
       17.93 -    35.86: 355
       35.86 -    53.80: 52
       53.80 -    71.73: 7
       71.73 -    89.66: 3
  Dihedral angle restraints: 4916
    sinusoidal: 1887
      harmonic: 3029
  Sorted by residual:
  dihedral pdb=" CA  TRP B 276 "
           pdb=" C   TRP B 276 "
           pdb=" N   LYS B 277 "
           pdb=" CA  LYS B 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.74   18.26     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" C   TRP A 382 "
           pdb=" N   TRP A 382 "
           pdb=" CA  TRP A 382 "
           pdb=" CB  TRP A 382 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -113.76   -8.84     0      2.50e+00 1.60e-01 1.25e+01
  dihedral pdb=" CA  TYR C 305 "
           pdb=" C   TYR C 305 "
           pdb=" N   SER C 306 "
           pdb=" CA  SER C 306 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -163.69  -16.31     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 4913 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.071: 1199
       0.071 -    0.142: 102
       0.142 -    0.214: 16
       0.214 -    0.285: 6
       0.285 -    0.356: 3
  Chirality restraints: 1326
  Sorted by residual:
  chirality pdb=" CA  ASN A 395 "
            pdb=" N   ASN A 395 "
            pdb=" C   ASN A 395 "
            pdb=" CB  ASN A 395 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" CA  GLN B 381 "
            pdb=" N   GLN B 381 "
            pdb=" C   GLN B 381 "
            pdb=" CB  GLN B 381 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.90e+00
  chirality pdb=" CA  PRO A 396 "
            pdb=" N   PRO A 396 "
            pdb=" C   PRO A 396 "
            pdb=" CB  PRO A 396 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.39    0.33 2.00e-01 2.50e+01 2.72e+00
  ... (remaining 1323 not shown)

  Planarity restraints: 1397
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU B 375 "   -0.021 2.00e-02 2.50e+03   4.16e-02 1.73e+01
        pdb=" C   GLU B 375 "    0.072 2.00e-02 2.50e+03
        pdb=" O   GLU B 375 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   LEU B 376 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 420 "    0.042 5.00e-02 4.00e+02   6.42e-02 6.60e+00
        pdb=" N   PRO B 421 "   -0.111 5.00e-02 4.00e+02
        pdb=" CA  PRO B 421 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 421 "    0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 454 "   -0.037 5.00e-02 4.00e+02   5.65e-02 5.11e+00
        pdb=" N   PRO B 455 "    0.098 5.00e-02 4.00e+02
        pdb=" CA  PRO B 455 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO B 455 "   -0.031 5.00e-02 4.00e+02
  ... (remaining 1394 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 257
        2.71 -     3.26: 8884
        3.26 -     3.81: 13735
        3.81 -     4.35: 17619
        4.35 -     4.90: 29277
  Nonbonded interactions: 69772
  Sorted by model distance:
  nonbonded pdb=" O   SER B 465 "
            pdb=" OG  SER B 468 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   TYR B 258 "
            pdb=" NZ  LYS B 316 "
     model   vdw
     2.292 3.120
  nonbonded pdb=" O   VAL A 461 "
            pdb=" OG  SER A 465 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" OD1 ASN C 183 "
            pdb=" OG  SER C 186 "
     model   vdw
     2.375 3.040
  nonbonded pdb=" O   PHE C 291 "
            pdb=" OG  SER C 294 "
     model   vdw
     2.383 3.040
  ... (remaining 69767 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 218 through 384 or resid 391 through 583))
  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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.590
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     8.910
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7587
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      :  0.006   0.117   8495  Z= 0.432
  Angle     :  0.798  12.967  11576  Z= 0.486
  Chirality :  0.050   0.356   1326
  Planarity :  0.007   0.064   1397
  Dihedral  : 12.888  89.660   2950
  Min Nonbonded Distance : 2.166

Molprobity Statistics.
  All-atom Clashscore : 6.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  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 (0.27), residues: 1011
  helix:  0.65 (0.20), residues: 704
  sheet:  None (None), residues: 0
  loop : -0.28 (0.36), residues: 307

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 297 
 TYR   0.014   0.001   TYR A 258 
 PHE   0.018   0.001   PHE A 424 
 TRP   0.011   0.001   TRP C  86 
 HIS   0.004   0.001   HIS B 399 

Details of bonding type rmsd
  covalent geometry    : bond        0.00626 ( 8495)
  covalent geometry    : angle       0.79847 (11576)
  hydrogen bonds       : bond        0.17778 (  525)
  hydrogen bonds       : angle       6.69131 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  217 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 217
  time to evaluate  : 0.211 
Fit side-chains
REVERT: C  110 LYS cc_start: 0.7150 (mmmt) cc_final: 0.6818 (mtmt)
REVERT: C  343 PHE cc_start: 0.7180 (t80) cc_final: 0.6859 (t80)
REVERT: A  322 GLU cc_start: 0.6148 (pm20) cc_final: 0.5244 (pm20)
REVERT: A  395 ASN cc_start: 0.8151 (t0) cc_final: 0.7794 (t0)
REVERT: A  460 PHE cc_start: 0.8804 (m-80) cc_final: 0.8566 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 217
  average time/residue: 0.0981
  time to fit residues: 28.4292
Evaluate side-chains
  153 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.267 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 97 optimal weight:    2.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.8980
   chunk 100 optimal weight:    0.0020
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.6588

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

Flipped N/Q/H residues before XYZ refinement:
C 193 ASN
C 260 ASN
A 405 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.167880 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.139179 restraints weight = 9252.203|
|-----------------------------------------------------------------------------|
r_work (start): 0.3444 rms_B_bonded: 1.61
r_work: 0.3303 rms_B_bonded: 2.31 restraints_weight: 0.5000
r_work: 0.3177 rms_B_bonded: 3.77 restraints_weight: 0.2500
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.2364

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   8495  Z= 0.152
  Angle     :  0.574   6.823  11576  Z= 0.295
  Chirality :  0.041   0.172   1326
  Planarity :  0.006   0.068   1397
  Dihedral  :  4.093  17.236   1100
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  :  5.76 %
    Favored  : 92.54 %
  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:  1.23 (0.27), residues: 1011
  helix:  1.19 (0.20), residues: 717
  sheet:  None (None), residues: 0
  loop :  0.11 (0.37), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 388 
 TYR   0.013   0.002   TYR B 432 
 PHE   0.016   0.002   PHE A 424 
 TRP   0.020   0.001   TRP C  86 
 HIS   0.005   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 8495)
  covalent geometry    : angle       0.57376 (11576)
  hydrogen bonds       : bond        0.04335 (  525)
  hydrogen bonds       : angle       4.39685 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 166
  time to evaluate  : 0.293 
Fit side-chains
REVERT: C   50 LEU cc_start: 0.8472 (OUTLIER) cc_final: 0.8123 (tt)
REVERT: C  110 LYS cc_start: 0.7067 (mmmt) cc_final: 0.6506 (mtmt)
REVERT: C  218 VAL cc_start: 0.9244 (m) cc_final: 0.9039 (t)
REVERT: A  234 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7917 (mp0)
REVERT: A  322 GLU cc_start: 0.6510 (pm20) cc_final: 0.5411 (pm20)
REVERT: A  395 ASN cc_start: 0.8329 (t0) cc_final: 0.7811 (t0)
REVERT: A  499 ARG cc_start: 0.6909 (ttp-170) cc_final: 0.6588 (ptp-170)
REVERT: A  565 PHE cc_start: 0.7715 (m-10) cc_final: 0.7435 (m-10)
REVERT: B  327 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8658 (mt-10)
REVERT: B  383 MET cc_start: 0.7270 (mtm) cc_final: 0.6743 (mtp)
REVERT: B  510 LEU cc_start: 0.8848 (mt) cc_final: 0.8596 (mp)
  outliers start: 15
  outliers final: 8
  residues processed: 176
  average time/residue: 0.0853
  time to fit residues: 20.8268
Evaluate side-chains
  155 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 145
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  240 LYS
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  567 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0670
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    0.0060
   chunk 83 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 59 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 89 optimal weight:    1.9990
   chunk 55 optimal weight:    0.5980
   overall best weight:    0.4134

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

Flipped N/Q/H residues before XYZ refinement:
A 405 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.169852 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3525 r_free = 0.3525 target = 0.140822 restraints weight = 9086.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.61
r_work: 0.3254 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.3129 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8053
moved from start:          0.2746

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8495  Z= 0.119
  Angle     :  0.510   6.520  11576  Z= 0.260
  Chirality :  0.039   0.147   1326
  Planarity :  0.005   0.067   1397
  Dihedral  :  3.905  15.572   1100
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 10.17 %
    Favored  : 88.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.27), residues: 1011
  helix:  1.64 (0.20), residues: 695
  sheet:  None (None), residues: 0
  loop :  0.37 (0.38), residues: 316

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 287 
 TYR   0.011   0.001   TYR C 220 
 PHE   0.017   0.001   PHE C  98 
 TRP   0.012   0.001   TRP C  86 
 HIS   0.003   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 8495)
  covalent geometry    : angle       0.51000 (11576)
  hydrogen bonds       : bond        0.03865 (  525)
  hydrogen bonds       : angle       4.12527 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 154
  time to evaluate  : 0.191 
Fit side-chains
REVERT: C  321 GLN cc_start: 0.7680 (tp40) cc_final: 0.7425 (mm-40)
REVERT: A  234 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7879 (mp0)
REVERT: A  322 GLU cc_start: 0.6564 (pm20) cc_final: 0.5429 (pm20)
REVERT: A  395 ASN cc_start: 0.8343 (t0) cc_final: 0.7834 (t0)
REVERT: A  551 LEU cc_start: 0.8875 (mt) cc_final: 0.8620 (mt)
REVERT: B  286 LYS cc_start: 0.8346 (tptt) cc_final: 0.7952 (mtpp)
REVERT: B  327 GLU cc_start: 0.8941 (mt-10) cc_final: 0.8550 (mt-10)
REVERT: B  383 MET cc_start: 0.7270 (mtm) cc_final: 0.6879 (mtm)
REVERT: B  510 LEU cc_start: 0.8838 (mt) cc_final: 0.8602 (mp)
  outliers start: 11
  outliers final: 7
  residues processed: 163
  average time/residue: 0.0882
  time to fit residues: 19.8112
Evaluate side-chains
  151 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 143
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  561 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  506 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 30 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 93 optimal weight:    4.9990
   chunk 49 optimal weight:    2.9990
   chunk 94 optimal weight:    0.5980
   chunk 59 optimal weight:    0.1980
   chunk 31 optimal weight:    3.9990
   chunk 21 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.168150 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.137252 restraints weight = 9338.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.3317 rms_B_bonded: 1.61
r_work: 0.3187 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3059 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8124
moved from start:          0.3124

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8495  Z= 0.134
  Angle     :  0.526   5.838  11576  Z= 0.266
  Chirality :  0.040   0.193   1326
  Planarity :  0.005   0.067   1397
  Dihedral  :  3.905  14.757   1100
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 10.40 %
    Favored  : 88.25 %
  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:  1.73 (0.27), residues: 1011
  helix:  1.62 (0.19), residues: 700
  sheet:  None (None), residues: 0
  loop :  0.20 (0.38), residues: 311

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 287 
 TYR   0.012   0.001   TYR C 220 
 PHE   0.015   0.001   PHE A 517 
 TRP   0.014   0.001   TRP C  86 
 HIS   0.005   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 8495)
  covalent geometry    : angle       0.52585 (11576)
  hydrogen bonds       : bond        0.03898 (  525)
  hydrogen bonds       : angle       4.05560 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 148
  time to evaluate  : 0.291 
Fit side-chains
REVERT: A  234 GLU cc_start: 0.8135 (OUTLIER) cc_final: 0.7854 (mp0)
REVERT: A  322 GLU cc_start: 0.6567 (pm20) cc_final: 0.5421 (pm20)
REVERT: A  395 ASN cc_start: 0.8425 (t0) cc_final: 0.7931 (t0)
REVERT: A  418 ARG cc_start: 0.7710 (ttp80) cc_final: 0.7403 (ttm110)
REVERT: A  551 LEU cc_start: 0.8932 (mt) cc_final: 0.8633 (mt)
REVERT: A  565 PHE cc_start: 0.7521 (m-10) cc_final: 0.7234 (m-10)
REVERT: B  286 LYS cc_start: 0.8474 (tptt) cc_final: 0.8171 (mtpp)
REVERT: B  327 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8577 (mt-10)
REVERT: B  362 PHE cc_start: 0.8626 (p90) cc_final: 0.8364 (p90)
REVERT: B  383 MET cc_start: 0.7239 (mtm) cc_final: 0.6899 (mtm)
REVERT: B  510 LEU cc_start: 0.8898 (mt) cc_final: 0.8634 (mp)
  outliers start: 12
  outliers final: 11
  residues processed: 155
  average time/residue: 0.0888
  time to fit residues: 18.9118
Evaluate side-chains
  155 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 143
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  240 LYS
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  541 MET
Chi-restraints excluded: chain A residue  561 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  506 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 44 optimal weight:    0.8980
   chunk 3 optimal weight:    3.9990
   chunk 1 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   chunk 75 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 97 optimal weight:    1.9990
   chunk 56 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 289 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.164681 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.133785 restraints weight = 9263.440|
|-----------------------------------------------------------------------------|
r_work (start): 0.3292 rms_B_bonded: 1.58
r_work: 0.3159 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3027 rms_B_bonded: 4.15 restraints_weight: 0.2500
r_work (final): 0.3027
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8169
moved from start:          0.3419

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   8495  Z= 0.158
  Angle     :  0.554   8.101  11576  Z= 0.279
  Chirality :  0.041   0.190   1326
  Planarity :  0.005   0.067   1397
  Dihedral  :  3.956  15.057   1100
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.51 %
    Favored  : 87.46 %
  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:  1.77 (0.27), residues: 1011
  helix:  1.64 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.31 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 287 
 TYR   0.014   0.001   TYR C 220 
 PHE   0.015   0.002   PHE A 517 
 TRP   0.012   0.001   TRP C  86 
 HIS   0.005   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 8495)
  covalent geometry    : angle       0.55397 (11576)
  hydrogen bonds       : bond        0.04098 (  525)
  hydrogen bonds       : angle       4.10712 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 156
  time to evaluate  : 0.241 
Fit side-chains
REVERT: A  234 GLU cc_start: 0.8484 (OUTLIER) cc_final: 0.8225 (mp0)
REVERT: A  322 GLU cc_start: 0.6477 (pm20) cc_final: 0.5367 (pm20)
REVERT: A  395 ASN cc_start: 0.8453 (t0) cc_final: 0.7960 (t0)
REVERT: B  286 LYS cc_start: 0.8500 (tptt) cc_final: 0.8168 (mtpp)
REVERT: B  327 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8741 (mt-10)
REVERT: B  362 PHE cc_start: 0.8766 (p90) cc_final: 0.8462 (p90)
REVERT: B  418 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.6585 (ttm-80)
REVERT: B  510 LEU cc_start: 0.8923 (mt) cc_final: 0.8629 (mp)
  outliers start: 18
  outliers final: 12
  residues processed: 164
  average time/residue: 0.0939
  time to fit residues: 21.0391
Evaluate side-chains
  157 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 143
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  561 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  418 ARG
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    2.9990
   chunk 64 optimal weight:    1.9990
   chunk 56 optimal weight:    0.8980
   chunk 35 optimal weight:    0.4980
   chunk 76 optimal weight:    0.7980
   chunk 85 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   chunk 93 optimal weight:    0.0770
   chunk 61 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   overall best weight:    0.5538

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

Flipped N/Q/H residues before XYZ refinement:
C 353 ASN
** B 398 ASN ** 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 = 0.3729 r_free = 0.3729 target = 0.159535 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.128249 restraints weight = 9444.368|
|-----------------------------------------------------------------------------|
r_work (start): 0.3321 rms_B_bonded: 1.80
r_work: 0.3175 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3043 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8133
moved from start:          0.3601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8495  Z= 0.129
  Angle     :  0.533   8.421  11576  Z= 0.267
  Chirality :  0.039   0.191   1326
  Planarity :  0.005   0.066   1397
  Dihedral  :  3.956  17.489   1100
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.64 %
    Favored  : 86.55 %
  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: 1011
  helix:  1.72 (0.19), residues: 692
  sheet:  None (None), residues: 0
  loop :  0.35 (0.37), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 287 
 TYR   0.012   0.001   TYR C 220 
 PHE   0.015   0.001   PHE A 517 
 TRP   0.029   0.001   TRP C  86 
 HIS   0.004   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8495)
  covalent geometry    : angle       0.53273 (11576)
  hydrogen bonds       : bond        0.03781 (  525)
  hydrogen bonds       : angle       4.04642 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 0.294 
Fit side-chains
REVERT: C   73 MET cc_start: 0.3424 (tpt) cc_final: 0.3184 (tpt)
REVERT: A  322 GLU cc_start: 0.6469 (pm20) cc_final: 0.5294 (pm20)
REVERT: A  327 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8355 (mt-10)
REVERT: A  395 ASN cc_start: 0.8423 (t0) cc_final: 0.7937 (t0)
REVERT: A  565 PHE cc_start: 0.7617 (m-10) cc_final: 0.7276 (m-10)
REVERT: B  286 LYS cc_start: 0.8456 (tptt) cc_final: 0.8132 (mtpp)
REVERT: B  307 LEU cc_start: 0.8131 (mp) cc_final: 0.7918 (mt)
REVERT: B  327 GLU cc_start: 0.9006 (mt-10) cc_final: 0.8599 (mt-10)
REVERT: B  362 PHE cc_start: 0.8747 (p90) cc_final: 0.8459 (p90)
REVERT: B  367 LEU cc_start: 0.8795 (mt) cc_final: 0.8420 (mp)
REVERT: B  418 ARG cc_start: 0.7710 (OUTLIER) cc_final: 0.6549 (ttm-80)
REVERT: B  510 LEU cc_start: 0.8892 (mt) cc_final: 0.8611 (mp)
  outliers start: 16
  outliers final: 12
  residues processed: 160
  average time/residue: 0.0890
  time to fit residues: 19.6804
Evaluate side-chains
  155 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 142
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  240 LYS
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  541 MET
Chi-restraints excluded: chain A residue  561 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  418 ARG
Chi-restraints excluded: chain B residue  506 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 69 optimal weight:    0.4980
   chunk 41 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 68 optimal weight:   10.0000
   chunk 85 optimal weight:    0.8980
   chunk 95 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 80 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 353 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.156394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.124155 restraints weight = 9620.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 1.73
r_work: 0.3150 rms_B_bonded: 2.62 restraints_weight: 0.5000
r_work: 0.3020 rms_B_bonded: 4.26 restraints_weight: 0.2500
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8172
moved from start:          0.3735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8495  Z= 0.140
  Angle     :  0.542   8.869  11576  Z= 0.272
  Chirality :  0.040   0.190   1326
  Planarity :  0.005   0.066   1397
  Dihedral  :  3.914  14.891   1100
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 12.54 %
    Favored  : 85.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.84 (0.27), residues: 1011
  helix:  1.70 (0.19), residues: 691
  sheet:  None (None), residues: 0
  loop :  0.32 (0.37), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 287 
 TYR   0.013   0.001   TYR C 220 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.010   0.001   TRP B 512 
 HIS   0.005   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 8495)
  covalent geometry    : angle       0.54176 (11576)
  hydrogen bonds       : bond        0.03874 (  525)
  hydrogen bonds       : angle       4.03425 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 145
  time to evaluate  : 0.304 
Fit side-chains
REVERT: C  102 LEU cc_start: 0.8436 (mt) cc_final: 0.8105 (mp)
REVERT: C  353 ASN cc_start: 0.7514 (t0) cc_final: 0.6957 (t0)
REVERT: A  234 GLU cc_start: 0.8376 (OUTLIER) cc_final: 0.7577 (mp0)
REVERT: A  322 GLU cc_start: 0.6399 (pm20) cc_final: 0.5296 (pm20)
REVERT: A  395 ASN cc_start: 0.8453 (t0) cc_final: 0.7952 (t0)
REVERT: A  565 PHE cc_start: 0.7589 (m-10) cc_final: 0.7225 (m-10)
REVERT: B  307 LEU cc_start: 0.8110 (mp) cc_final: 0.7909 (mt)
REVERT: B  327 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8613 (mt-10)
REVERT: B  362 PHE cc_start: 0.8733 (p90) cc_final: 0.8409 (p90)
REVERT: B  367 LEU cc_start: 0.8760 (mt) cc_final: 0.8386 (mp)
REVERT: B  418 ARG cc_start: 0.7735 (OUTLIER) cc_final: 0.6627 (ttm-80)
REVERT: B  510 LEU cc_start: 0.8894 (mt) cc_final: 0.8615 (mp)
  outliers start: 18
  outliers final: 13
  residues processed: 155
  average time/residue: 0.0909
  time to fit residues: 19.3671
Evaluate side-chains
  157 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  332 MET
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  541 MET
Chi-restraints excluded: chain A residue  561 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  355 ILE
Chi-restraints excluded: chain B residue  418 ARG
Chi-restraints excluded: chain B residue  506 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 93 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 85 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9990
   chunk 84 optimal weight:    0.5980
   chunk 11 optimal weight:    0.5980
   chunk 79 optimal weight:    0.7980
   chunk 4 optimal weight:    2.9990
   chunk 33 optimal weight:    0.2980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** C 321 GLN ** 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 = 0.3764 r_free = 0.3764 target = 0.162363 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.130227 restraints weight = 9357.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3282 rms_B_bonded: 1.65
r_work: 0.3155 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.3022 rms_B_bonded: 4.23 restraints_weight: 0.2500
r_work (final): 0.3022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.3818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8495  Z= 0.128
  Angle     :  0.529   8.919  11576  Z= 0.265
  Chirality :  0.039   0.193   1326
  Planarity :  0.005   0.066   1397
  Dihedral  :  3.846  14.612   1100
  Min Nonbonded Distance : 2.599

Molprobity Statistics.
  All-atom Clashscore : 7.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.69 %
    Allowed  : 13.11 %
    Favored  : 85.20 %
  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:  1.93 (0.27), residues: 1011
  helix:  1.76 (0.19), residues: 691
  sheet:  None (None), residues: 0
  loop :  0.36 (0.37), residues: 320

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 287 
 TYR   0.013   0.001   TYR C 220 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.014   0.001   TRP C  86 
 HIS   0.004   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 8495)
  covalent geometry    : angle       0.52907 (11576)
  hydrogen bonds       : bond        0.03718 (  525)
  hydrogen bonds       : angle       4.00272 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  161 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 146
  time to evaluate  : 0.276 
Fit side-chains
REVERT: C   63 ILE cc_start: 0.8180 (mt) cc_final: 0.7750 (pt)
REVERT: C  102 LEU cc_start: 0.8377 (mt) cc_final: 0.8055 (mp)
REVERT: C  180 MET cc_start: 0.4703 (tpp) cc_final: 0.4466 (tpp)
REVERT: A  234 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.7611 (mp0)
REVERT: A  322 GLU cc_start: 0.6361 (pm20) cc_final: 0.5229 (pm20)
REVERT: A  395 ASN cc_start: 0.8416 (t0) cc_final: 0.7897 (t0)
REVERT: A  565 PHE cc_start: 0.7627 (m-10) cc_final: 0.7281 (m-10)
REVERT: B  286 LYS cc_start: 0.8452 (tptt) cc_final: 0.8062 (mtpp)
REVERT: B  307 LEU cc_start: 0.8080 (mp) cc_final: 0.7877 (mt)
REVERT: B  327 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8593 (mt-10)
REVERT: B  362 PHE cc_start: 0.8691 (p90) cc_final: 0.8362 (p90)
REVERT: B  367 LEU cc_start: 0.8609 (mt) cc_final: 0.8308 (mp)
REVERT: B  510 LEU cc_start: 0.8903 (mt) cc_final: 0.8624 (mp)
  outliers start: 15
  outliers final: 14
  residues processed: 154
  average time/residue: 0.0926
  time to fit residues: 19.5861
Evaluate side-chains
  157 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 142
  time to evaluate  : 0.295 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   50 LEU
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  141 MET
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  240 LYS
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  332 MET
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  561 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  506 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 58 optimal weight:    1.9990
   chunk 99 optimal weight:    1.9990
   chunk 69 optimal weight:    0.7980
   chunk 46 optimal weight:    0.0970
   chunk 84 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 11 optimal weight:    0.6980
   chunk 65 optimal weight:    0.9980
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** C 321 GLN ** 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 = 0.3747 r_free = 0.3747 target = 0.160836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.128333 restraints weight = 9424.485|
|-----------------------------------------------------------------------------|
r_work (start): 0.3269 rms_B_bonded: 1.67
r_work: 0.3144 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.3917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8495  Z= 0.135
  Angle     :  0.540   9.406  11576  Z= 0.271
  Chirality :  0.040   0.193   1326
  Planarity :  0.005   0.066   1397
  Dihedral  :  3.881  15.194   1100
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 13.22 %
    Favored  : 84.97 %
  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:  1.92 (0.27), residues: 1011
  helix:  1.75 (0.19), residues: 689
  sheet:  None (None), residues: 0
  loop :  0.36 (0.37), residues: 322

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 287 
 TYR   0.012   0.001   TYR C 220 
 PHE   0.017   0.001   PHE C  98 
 TRP   0.009   0.001   TRP C  86 
 HIS   0.005   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 8495)
  covalent geometry    : angle       0.54019 (11576)
  hydrogen bonds       : bond        0.03805 (  525)
  hydrogen bonds       : angle       4.02602 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 141
  time to evaluate  : 0.304 
Fit side-chains
REVERT: C   63 ILE cc_start: 0.8250 (mt) cc_final: 0.7861 (pt)
REVERT: C  102 LEU cc_start: 0.8388 (mt) cc_final: 0.8066 (mp)
REVERT: C  134 MET cc_start: 0.8437 (ttm) cc_final: 0.8227 (mtm)
REVERT: A  234 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7562 (mp0)
REVERT: A  322 GLU cc_start: 0.6381 (pm20) cc_final: 0.5249 (pm20)
REVERT: A  395 ASN cc_start: 0.8355 (t0) cc_final: 0.7795 (t0)
REVERT: A  565 PHE cc_start: 0.7651 (m-10) cc_final: 0.7317 (m-10)
REVERT: B  327 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8601 (mt-10)
REVERT: B  362 PHE cc_start: 0.8714 (p90) cc_final: 0.8371 (p90)
REVERT: B  367 LEU cc_start: 0.8614 (mt) cc_final: 0.8203 (mp)
REVERT: B  418 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.6512 (ttm-80)
REVERT: B  510 LEU cc_start: 0.8899 (mt) cc_final: 0.8611 (mp)
  outliers start: 16
  outliers final: 13
  residues processed: 148
  average time/residue: 0.1036
  time to fit residues: 20.8932
Evaluate side-chains
  155 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 140
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  141 MET
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  332 MET
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  439 LEU
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain A residue  561 ILE
Chi-restraints excluded: chain B residue  285 THR
Chi-restraints excluded: chain B residue  418 ARG
Chi-restraints excluded: chain B residue  506 ILE
Chi-restraints excluded: chain B residue  511 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 54 optimal weight:    0.0470
   chunk 22 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 88 optimal weight:    1.9990
   chunk 13 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 65 optimal weight:    0.0980
   chunk 4 optimal weight:    0.7980
   chunk 85 optimal weight:    0.0870
   chunk 49 optimal weight:    0.7980
   overall best weight:    0.3256

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

Flipped N/Q/H residues before XYZ refinement:
** C 321 GLN ** 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 = 0.3784 r_free = 0.3784 target = 0.164287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.132066 restraints weight = 9398.153|
|-----------------------------------------------------------------------------|
r_work (start): 0.3328 rms_B_bonded: 1.67
r_work: 0.3209 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3078 rms_B_bonded: 4.21 restraints_weight: 0.2500
r_work (final): 0.3078
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8081
moved from start:          0.3969

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8495  Z= 0.109
  Angle     :  0.514   9.191  11576  Z= 0.258
  Chirality :  0.039   0.201   1326
  Planarity :  0.005   0.066   1397
  Dihedral  :  3.781  18.282   1100
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.13 %
    Allowed  : 14.12 %
    Favored  : 84.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  2.22 (0.27), residues: 1011
  helix:  2.00 (0.19), residues: 681
  sheet:  None (None), residues: 0
  loop :  0.47 (0.37), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 287 
 TYR   0.012   0.001   TYR C 220 
 PHE   0.016   0.001   PHE A 517 
 TRP   0.013   0.001   TRP A 293 
 HIS   0.005   0.001   HIS C  74 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 8495)
  covalent geometry    : angle       0.51363 (11576)
  hydrogen bonds       : bond        0.03463 (  525)
  hydrogen bonds       : angle       3.93833 ( 1485)

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

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

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2022 Ramachandran restraints generated.
    1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 147
  time to evaluate  : 0.389 
Fit side-chains
REVERT: C   63 ILE cc_start: 0.8218 (mt) cc_final: 0.7862 (pt)
REVERT: C  102 LEU cc_start: 0.8325 (mt) cc_final: 0.8016 (mp)
REVERT: C  165 LYS cc_start: 0.7656 (tptt) cc_final: 0.7157 (tptp)
REVERT: A  234 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7406 (mp0)
REVERT: A  236 GLU cc_start: 0.7692 (mt-10) cc_final: 0.7451 (mt-10)
REVERT: A  322 GLU cc_start: 0.6443 (pm20) cc_final: 0.5556 (pm20)
REVERT: A  327 GLU cc_start: 0.8553 (mt-10) cc_final: 0.8334 (mt-10)
REVERT: A  395 ASN cc_start: 0.8299 (t0) cc_final: 0.7802 (t0)
REVERT: A  565 PHE cc_start: 0.7605 (m-10) cc_final: 0.7224 (m-10)
REVERT: B  307 LEU cc_start: 0.8086 (mp) cc_final: 0.7879 (mt)
REVERT: B  327 GLU cc_start: 0.8981 (mt-10) cc_final: 0.8542 (mt-10)
REVERT: B  362 PHE cc_start: 0.8598 (p90) cc_final: 0.8293 (p90)
REVERT: B  367 LEU cc_start: 0.8441 (mt) cc_final: 0.8064 (mp)
REVERT: B  510 LEU cc_start: 0.8880 (mt) cc_final: 0.8618 (mp)
  outliers start: 10
  outliers final: 9
  residues processed: 152
  average time/residue: 0.0972
  time to fit residues: 20.1786
Evaluate side-chains
  153 residues out of total 885 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 143
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  107 PHE
Chi-restraints excluded: chain C residue  141 MET
Chi-restraints excluded: chain C residue  189 SER
Chi-restraints excluded: chain C residue  285 VAL
Chi-restraints excluded: chain C residue  332 MET
Chi-restraints excluded: chain A residue  234 GLU
Chi-restraints excluded: chain A residue  314 LEU
Chi-restraints excluded: chain A residue  401 SER
Chi-restraints excluded: chain A residue  496 LEU
Chi-restraints excluded: chain B residue  285 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 101
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 19 optimal weight:    9.9990
   chunk 98 optimal weight:    0.7980
   chunk 90 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 63 optimal weight:    0.6980
   chunk 77 optimal weight:    2.9990
   chunk 33 optimal weight:    0.0370
   chunk 85 optimal weight:    0.0570
   chunk 79 optimal weight:    0.4980
   chunk 16 optimal weight:    0.8980
   overall best weight:    0.4176

-------------------------------------------------------------------------------
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 = 0.3764 r_free = 0.3764 target = 0.162218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.132580 restraints weight = 9413.462|
|-----------------------------------------------------------------------------|
r_work (start): 0.3346 rms_B_bonded: 1.56
r_work: 0.3196 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3072 rms_B_bonded: 4.07 restraints_weight: 0.2500
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8495  Z= 0.116
  Angle     :  0.519   9.757  11576  Z= 0.261
  Chirality :  0.039   0.201   1326
  Planarity :  0.005   0.066   1397
  Dihedral  :  3.773  19.161   1100
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 14.35 %
    Favored  : 84.41 %
  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:  2.16 (0.27), residues: 1011
  helix:  1.93 (0.19), residues: 688
  sheet:  None (None), residues: 0
  loop :  0.47 (0.37), residues: 323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C 287 
 TYR   0.012   0.001   TYR C 220 
 PHE   0.022   0.001   PHE C 115 
 TRP   0.013   0.001   TRP C  59 
 HIS   0.004   0.001   HIS B 431 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8495)
  covalent geometry    : angle       0.51893 (11576)
  hydrogen bonds       : bond        0.03557 (  525)
  hydrogen bonds       : angle       3.93943 ( 1485)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2175.68 seconds
wall clock time: 37 minutes 59.77 seconds (2279.77 seconds total)