Starting phenix.real_space_refine
on Wed Sep 17 13:33:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuy_50782/09_2025/9fuy_50782.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuy_50782/09_2025/9fuy_50782.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fuy_50782/09_2025/9fuy_50782.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuy_50782/09_2025/9fuy_50782.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuy_50782/09_2025/9fuy_50782.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuy_50782/09_2025/9fuy_50782.cif"
  }
  resolution = 4.1
  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=   0.001 sd=   0.009
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      54      5.16       5
     C    5590      2.51       5
     N    1536      2.21       5
     O    1642      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 25 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8822
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
    Chain: "B"
      Number of atoms: 4411
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 569, 4411
          Classifications: {'peptide': 569}
          Link IDs: {'PTRANS': 13, 'TRANS': 555}
  Time building chain proxies: 2.23, per 1000 atoms: 0.25
  Number of scatterers: 8822
  At special positions: 0
  Unit cell: (119, 98.6, 136, 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      54     16.00
     O    1642      8.00
     N    1536      7.00
     C    5590      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: 0.82
  Conformation dependent library (CDL) restraints added in 351.4 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2128

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 5 sheets defined
      67.5% alpha, 7.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 16 through 21
      removed outlier: 4.072A  pdb=" N   ILE A  20 " --> pdb=" O   LEU A  16 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 23 through 53
      removed outlier: 3.537A  pdb=" N   LEU A  27 " --> pdb=" O   PHE A  23 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   LYS A  49 " --> pdb=" O   LEU A  45 " (cutoff:3.500A)
      Proline residue:  A  50  - end of helix
      removed outlier: 3.500A  pdb=" N   ASP A  53 " --> pdb=" O   LYS A  49 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 110
      removed outlier: 4.219A  pdb=" N   LEU A  69 " --> pdb=" O   VAL A  65 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   GLY A 110 " --> pdb=" O   GLY A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 129
      removed outlier: 3.590A  pdb=" N   LEU A 125 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   SER A 126 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 164
      removed outlier: 4.003A  pdb=" N   ALA A 136 " --> pdb=" O   SER A 132 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 213
      Proline residue:  A 176  - end of helix
      removed outlier: 3.577A  pdb=" N   THR A 199 " --> pdb=" O   ASN A 195 " (cutoff:3.500A)
      removed outlier: 4.083A  pdb=" N   GLY A 213 " --> pdb=" O   GLN A 209 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 220
    Processing helix  chain 'A' and resid 223 through 270
      removed outlier: 4.050A  pdb=" N   ASP A 252 " --> pdb=" O   SER A 248 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.733A  pdb=" N   ALA A 270 " --> pdb=" O   VAL A 266 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 324
      removed outlier: 4.297A  pdb=" N   VAL A 286 " --> pdb=" O   GLY A 282 " (cutoff:3.500A)
      removed outlier: 4.432A  pdb=" N   ARG A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      Proline residue:  A 297  - end of helix
      removed outlier: 4.731A  pdb=" N   ASN A 305 " --> pdb=" O   LEU A 301 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ALA A 306 " --> pdb=" O   THR A 302 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 391
      removed outlier: 4.527A  pdb=" N   ILE A 389 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR A 390 " --> pdb=" O   ALA A 386 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
      removed outlier: 3.711A  pdb=" N   GLN A 418 " --> pdb=" O   SER A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 432 through 438
    Processing helix  chain 'A' and resid 446 through 457
    Processing helix  chain 'A' and resid 459 through 466
    Processing helix  chain 'A' and resid 482 through 498
    Processing helix  chain 'A' and resid 514 through 527
      removed outlier: 3.922A  pdb=" N   ALA A 518 " --> pdb=" O   GLU A 514 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 545
    Processing helix  chain 'A' and resid 561 through 568
    Processing helix  chain 'A' and resid 571 through 580
      removed outlier: 3.622A  pdb=" N   PHE A 580 " --> pdb=" O   HIS A 576 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 16 through 21
    Processing helix  chain 'B' and resid 23 through 47
    Processing helix  chain 'B' and resid 47 through 54
      removed outlier: 3.561A  pdb=" N   LEU B  51 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 61 through 111
      removed outlier: 3.807A  pdb=" N   VAL B  65 " --> pdb=" O   ARG B  61 " (cutoff:3.500A)
      Proline residue:  B  68  - end of helix
      removed outlier: 3.841A  pdb=" N   GLY B 110 " --> pdb=" O   GLY B 106 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 121 through 129
      removed outlier: 3.647A  pdb=" N   LEU B 125 " --> pdb=" O   THR B 121 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER B 126 " --> pdb=" O   GLY B 122 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 129 through 164
      removed outlier: 3.790A  pdb=" N   ALA B 136 " --> pdb=" O   SER B 132 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 166 through 213
      Proline residue:  B 176  - end of helix
      removed outlier: 4.564A  pdb=" N   GLY B 213 " --> pdb=" O   GLN B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 221
    Processing helix  chain 'B' and resid 222 through 272
      removed outlier: 3.578A  pdb=" N   THR B 227 " --> pdb=" O   GLN B 223 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   LYS B 228 " --> pdb=" O   GLU B 224 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ASP B 252 " --> pdb=" O   SER B 248 " (cutoff:3.500A)
      Proline residue:  B 253  - end of helix
      removed outlier: 4.059A  pdb=" N   SER B 271 " --> pdb=" O   LEU B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 282 through 323
      removed outlier: 4.215A  pdb=" N   ARG B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      Proline residue:  B 297  - end of helix
      removed outlier: 4.552A  pdb=" N   ASN B 305 " --> pdb=" O   LEU B 301 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   ALA B 306 " --> pdb=" O   THR B 302 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ILE B 321 " --> pdb=" O   THR B 317 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 381 through 391
      removed outlier: 4.104A  pdb=" N   ALA B 386 " --> pdb=" O   LYS B 382 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER B 387 " --> pdb=" O   SER B 383 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   ILE B 389 " --> pdb=" O   ILE B 385 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   THR B 390 " --> pdb=" O   ALA B 386 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 418
    Processing helix  chain 'B' and resid 432 through 438
    Processing helix  chain 'B' and resid 446 through 458
      removed outlier: 3.681A  pdb=" N   MET B 456 " --> pdb=" O   GLU B 452 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   ALA B 457 " --> pdb=" O   ALA B 453 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   TYR B 458 " --> pdb=" O   ALA B 454 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 459 through 465
      removed outlier: 4.469A  pdb=" N   ILE B 463 " --> pdb=" O   ALA B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 468 through 472
      removed outlier: 3.771A  pdb=" N   ASP B 471 " --> pdb=" O   ASN B 468 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   THR B 472 " --> pdb=" O   GLY B 469 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 468 through 472'
    Processing helix  chain 'B' and resid 482 through 498
      removed outlier: 3.651A  pdb=" N   LEU B 496 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   ARG B 497 " --> pdb=" O   ARG B 493 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 514 through 527
      removed outlier: 3.944A  pdb=" N   ALA B 518 " --> pdb=" O   GLU B 514 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 538 through 545
    Processing helix  chain 'B' and resid 561 through 568
    Processing helix  chain 'B' and resid 571 through 580
      removed outlier: 3.776A  pdb=" N   LYS B 577 " --> pdb=" O   ALA B 573 " (cutoff:3.500A)
      removed outlier: 4.043A  pdb=" N   MET B 578 " --> pdb=" O   GLN B 574 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   PHE B 580 " --> pdb=" O   HIS B 576 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 359
    Processing sheet with id=AA2, first strand: chain 'A' and resid 357 through 359
      removed outlier: 3.864A  pdb=" N   GLU A 343 " --> pdb=" O   LEU A 401 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   GLU A 399 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 4.732A  pdb=" N   VAL A 347 " --> pdb=" O   GLU A 397 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   GLU A 397 " --> pdb=" O   VAL A 347 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 422
      removed outlier: 6.125A  pdb=" N   ALA A 420 " --> pdb=" O   ILE A 503 " (cutoff:3.500A)
      removed outlier: 6.800A  pdb=" N   LEU A 502 " --> pdb=" O   LEU A 533 " (cutoff:3.500A)
      removed outlier: 6.432A  pdb=" N   THR A 371 " --> pdb=" O   GLU A 547 " (cutoff:3.500A)
      removed outlier: 7.840A  pdb=" N   VAL A 549 " --> pdb=" O   THR A 371 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   ALA A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
      removed outlier: 8.039A  pdb=" N   VAL A 551 " --> pdb=" O   ALA A 373 " (cutoff:3.500A)
      removed outlier: 7.934A  pdb=" N   VAL A 375 " --> pdb=" O   VAL A 551 " (cutoff:3.500A)
      removed outlier: 6.386A  pdb=" N   ILE A 548 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 4.175A  pdb=" N   ARG A 559 " --> pdb=" O   ILE A 548 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL A 550 " --> pdb=" O   VAL A 557 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 365 through 366
      removed outlier: 3.656A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 366 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   PHE B 344 " --> pdb=" O   LEU B 401 " (cutoff:3.500A)
      removed outlier: 6.820A  pdb=" N   LEU B 401 " --> pdb=" O   PHE B 344 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   ASN B 346 " --> pdb=" O   GLU B 399 " (cutoff:3.500A)
      removed outlier: 5.582A  pdb=" N   GLU B 399 " --> pdb=" O   ASN B 346 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 419 through 422
      removed outlier: 6.283A  pdb=" N   LEU B 502 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 7.744A  pdb=" N   ILE B 535 " --> pdb=" O   LEU B 502 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   LEU B 504 " --> pdb=" O   ILE B 535 " (cutoff:3.500A)
      removed outlier: 6.450A  pdb=" N   VAL B 372 " --> pdb=" O   VAL B 534 " (cutoff:3.500A)
      removed outlier: 6.854A  pdb=" N   THR B 371 " --> pdb=" O   GLU B 547 " (cutoff:3.500A)
      removed outlier: 8.244A  pdb=" N   VAL B 549 " --> pdb=" O   THR B 371 " (cutoff:3.500A)
      removed outlier: 5.695A  pdb=" N   ALA B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 7.146A  pdb=" N   VAL B 551 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 6.527A  pdb=" N   ILE B 548 " --> pdb=" O   ARG B 559 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   ARG B 559 " --> pdb=" O   ILE B 548 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   VAL B 550 " --> pdb=" O   VAL B 557 " (cutoff:3.500A)

    555 hydrogen bonds defined for protein.
    1653 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: 1.37

  Time building geometry restraints manager: 1.06 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 2603
        1.34 -     1.46: 1408
        1.46 -     1.58: 4835
        1.58 -     1.70: 0
        1.70 -     1.82: 104
  Bond restraints: 8950
  Sorted by residual:
  bond pdb=" N   ASP B 252 "
       pdb=" CA  ASP B 252 "
    ideal  model  delta    sigma   weight residual
    1.463  1.491 -0.028 6.90e-03 2.10e+04 1.59e+01
  bond pdb=" N   PHE B 272 "
       pdb=" CA  PHE B 272 "
    ideal  model  delta    sigma   weight residual
    1.463  1.490 -0.026 6.90e-03 2.10e+04 1.46e+01
  bond pdb=" N   ASP A 252 "
       pdb=" CA  ASP A 252 "
    ideal  model  delta    sigma   weight residual
    1.461  1.492 -0.031 9.20e-03 1.18e+04 1.14e+01
  bond pdb=" N   VAL B 245 "
       pdb=" CA  VAL B 245 "
    ideal  model  delta    sigma   weight residual
    1.460  1.494 -0.034 1.19e-02 7.06e+03 8.05e+00
  bond pdb=" N   LEU A 211 "
       pdb=" CA  LEU A 211 "
    ideal  model  delta    sigma   weight residual
    1.459  1.491 -0.032 1.21e-02 6.83e+03 7.05e+00
  ... (remaining 8945 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.16: 11521
        2.16 -     4.33: 439
        4.33 -     6.49: 106
        6.49 -     8.65: 18
        8.65 -    10.82: 8
  Bond angle restraints: 12092
  Sorted by residual:
  angle pdb=" C   THR A 145 "
        pdb=" CA  THR A 145 "
        pdb=" CB  THR A 145 "
      ideal   model   delta    sigma   weight residual
     110.85  120.05   -9.20 1.70e+00 3.46e-01 2.93e+01
  angle pdb=" CA  ASP B 252 "
        pdb=" C   ASP B 252 "
        pdb=" N   PRO B 253 "
      ideal   model   delta    sigma   weight residual
     120.58  123.81   -3.23 7.40e-01 1.83e+00 1.90e+01
  angle pdb=" CA  GLU A 149 "
        pdb=" CB  GLU A 149 "
        pdb=" CG  GLU A 149 "
      ideal   model   delta    sigma   weight residual
     114.10  122.14   -8.04 2.00e+00 2.50e-01 1.62e+01
  angle pdb=" CA  MET A 578 "
        pdb=" CB  MET A 578 "
        pdb=" CG  MET A 578 "
      ideal   model   delta    sigma   weight residual
     114.10  121.37   -7.27 2.00e+00 2.50e-01 1.32e+01
  angle pdb=" CA  MET B 160 "
        pdb=" CB  MET B 160 "
        pdb=" CG  MET B 160 "
      ideal   model   delta    sigma   weight residual
     114.10  121.32   -7.22 2.00e+00 2.50e-01 1.30e+01
  ... (remaining 12087 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 4698
       17.84 -    35.68: 564
       35.68 -    53.52: 157
       53.52 -    71.37: 24
       71.37 -    89.21: 11
  Dihedral angle restraints: 5454
    sinusoidal: 2164
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" C   THR A 145 "
           pdb=" N   THR A 145 "
           pdb=" CA  THR A 145 "
           pdb=" CB  THR A 145 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -135.05   13.05     0      2.50e+00 1.60e-01 2.72e+01
  dihedral pdb=" CA  SER A 271 "
           pdb=" C   SER A 271 "
           pdb=" N   PHE A 272 "
           pdb=" CA  PHE A 272 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.26  -25.74     0      5.00e+00 4.00e-02 2.65e+01
  dihedral pdb=" CA  ASP B 117 "
           pdb=" C   ASP B 117 "
           pdb=" N   LYS B 118 "
           pdb=" CA  LYS B 118 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -156.23  -23.77     0      5.00e+00 4.00e-02 2.26e+01
  ... (remaining 5451 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1253
       0.070 -    0.141: 167
       0.141 -    0.211: 15
       0.211 -    0.281: 4
       0.281 -    0.352: 1
  Chirality restraints: 1440
  Sorted by residual:
  chirality pdb=" CA  THR A 145 "
            pdb=" N   THR A 145 "
            pdb=" C   THR A 145 "
            pdb=" CB  THR A 145 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.17    0.35 2.00e-01 2.50e+01 3.09e+00
  chirality pdb=" CB  VAL A  96 "
            pdb=" CA  VAL A  96 "
            pdb=" CG1 VAL A  96 "
            pdb=" CG2 VAL A  96 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.37   -0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  ILE A 144 "
            pdb=" CA  ILE A 144 "
            pdb=" CG1 ILE A 144 "
            pdb=" CG2 ILE A 144 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.54e+00
  ... (remaining 1437 not shown)

  Planarity restraints: 1532
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 250 "    0.016 2.00e-02 2.50e+03   3.28e-02 1.07e+01
        pdb=" C   ILE A 250 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   ILE A 250 "    0.021 2.00e-02 2.50e+03
        pdb=" N   SER A 251 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET A  67 "   -0.044 5.00e-02 4.00e+02   6.59e-02 6.95e+00
        pdb=" N   PRO A  68 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO A  68 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO A  68 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL B 146 "   -0.012 2.00e-02 2.50e+03   2.48e-02 6.13e+00
        pdb=" C   VAL B 146 "    0.043 2.00e-02 2.50e+03
        pdb=" O   VAL B 146 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   VAL B 147 "   -0.015 2.00e-02 2.50e+03
  ... (remaining 1529 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 907
        2.74 -     3.28: 10078
        3.28 -     3.82: 14984
        3.82 -     4.36: 17162
        4.36 -     4.90: 27287
  Nonbonded interactions: 70418
  Sorted by model distance:
  nonbonded pdb=" O   GLU A 149 "
            pdb=" OG  SER A 152 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O   VAL A 287 "
            pdb=" OG  SER A 290 "
     model   vdw
     2.220 3.040
  nonbonded pdb=" O   GLN A 209 "
            pdb=" NE2 HIS B 427 "
     model   vdw
     2.238 3.120
  nonbonded pdb=" O   ALA A 358 "
            pdb=" NZ  LYS A 382 "
     model   vdw
     2.242 3.120
  nonbonded pdb=" OG  SER A 378 "
            pdb=" OE1 GLU A 552 "
     model   vdw
     2.278 3.040
  ... (remaining 70413 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: 0.02
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:             4.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     9.500
  Find NCS groups from input model:        0.120
  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:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051   8950  Z= 0.271
  Angle     :  1.040  10.819  12092  Z= 0.560
  Chirality :  0.049   0.352   1440
  Planarity :  0.005   0.066   1532
  Dihedral  : 17.015  89.208   3326
  Min Nonbonded Distance : 2.203

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.62 %
    Allowed  : 32.33 %
    Favored  : 67.05 %
  Cbeta Deviations :  0.09 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.02 (0.25), residues: 1134
  helix:  0.80 (0.20), residues: 668
  sheet: -0.62 (0.63), residues: 64
  loop : -1.14 (0.33), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 517 
 TYR   0.026   0.001   TYR A 439 
 PHE   0.030   0.002   PHE B 230 
 TRP   0.003   0.001   TRP A  91 
 HIS   0.022   0.003   HIS A 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00527 ( 8950)
  covalent geometry    : angle       1.04033 (12092)
  hydrogen bonds       : bond        0.12751 (  553)
  hydrogen bonds       : angle       6.31081 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 220
  time to evaluate  : 0.265 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9079 (tpp) cc_final: 0.8444 (tpt)
REVERT: A  105 PHE cc_start: 0.9196 (m-80) cc_final: 0.8960 (m-80)
REVERT: A  127 ARG cc_start: 0.9167 (mmt90) cc_final: 0.8865 (mmm160)
REVERT: A  218 LEU cc_start: 0.9578 (mt) cc_final: 0.9283 (mp)
REVERT: A  382 LYS cc_start: 0.7352 (mmpt) cc_final: 0.7063 (mmmt)
REVERT: A  428 LEU cc_start: 0.9421 (mt) cc_final: 0.9195 (mt)
REVERT: A  456 MET cc_start: 0.9266 (pmm) cc_final: 0.8821 (pmm)
REVERT: B   84 VAL cc_start: 0.9377 (m) cc_final: 0.9110 (p)
REVERT: B  100 MET cc_start: 0.9374 (tpp) cc_final: 0.9063 (mmm)
REVERT: B  107 HIS cc_start: 0.8653 (t70) cc_final: 0.8300 (t70)
REVERT: B  131 ASP cc_start: 0.8983 (m-30) cc_final: 0.8724 (p0)
REVERT: B  196 MET cc_start: 0.9146 (mmm) cc_final: 0.8849 (mmm)
REVERT: B  210 MET cc_start: 0.8821 (mmt) cc_final: 0.8584 (tpp)
REVERT: B  244 MET cc_start: 0.9194 (ppp) cc_final: 0.8941 (ppp)
REVERT: B  439 TYR cc_start: 0.8403 (t80) cc_final: 0.7199 (t80)
  outliers start: 6
  outliers final: 4
  residues processed: 224
  average time/residue: 0.0677
  time to fit residues: 22.9597
Evaluate side-chains
  208 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 204
  time to evaluate  : 0.336 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 108 optimal weight:    6.9990
   chunk 49 optimal weight:    0.9980
   chunk 97 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    2.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    2.9990
   overall best weight:    2.1586

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

Flipped N/Q/H residues before XYZ refinement:
A 107 HIS
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 520 GLN
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 529 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.073408 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2993 r_free = 0.2993 target = 0.054142 restraints weight = 35813.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.056310 restraints weight = 21321.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.057916 restraints weight = 14723.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.059088 restraints weight = 11097.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.059924 restraints weight = 8908.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3106
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
moved from start:          0.2394

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   8950  Z= 0.207
  Angle     :  0.679   7.931  12092  Z= 0.364
  Chirality :  0.044   0.189   1440
  Planarity :  0.004   0.047   1532
  Dihedral  :  4.656  22.126   1238
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.59 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.31 %
    Favored  : 96.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.26), residues: 1134
  helix:  1.21 (0.19), residues: 690
  sheet: -0.81 (0.64), residues: 64
  loop : -1.20 (0.34), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 229 
 TYR   0.016   0.001   TYR A 439 
 PHE   0.064   0.003   PHE B 230 
 TRP   0.011   0.001   TRP A 165 
 HIS   0.006   0.002   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00417 ( 8950)
  covalent geometry    : angle       0.67934 (12092)
  hydrogen bonds       : bond        0.05036 (  553)
  hydrogen bonds       : angle       5.01549 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  255 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 255
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.5939 (mtm180) cc_final: 0.5368 (mtt180)
REVERT: A   98 MET cc_start: 0.9138 (tpp) cc_final: 0.8831 (tpp)
REVERT: A  107 HIS cc_start: 0.8589 (t-90) cc_final: 0.7785 (t-170)
REVERT: A  109 MET cc_start: 0.9338 (mmp) cc_final: 0.9039 (mmp)
REVERT: A  216 GLU cc_start: 0.9308 (mt-10) cc_final: 0.8894 (pt0)
REVERT: A  218 LEU cc_start: 0.9654 (mt) cc_final: 0.9357 (mt)
REVERT: A  244 MET cc_start: 0.9266 (ppp) cc_final: 0.8978 (ppp)
REVERT: A  263 LEU cc_start: 0.9711 (tt) cc_final: 0.9469 (tt)
REVERT: A  312 MET cc_start: 0.7416 (ttt) cc_final: 0.7014 (tpt)
REVERT: A  322 LEU cc_start: 0.9601 (tp) cc_final: 0.9392 (tp)
REVERT: A  382 LYS cc_start: 0.7825 (mmpt) cc_final: 0.7199 (mmtm)
REVERT: A  405 HIS cc_start: 0.8976 (m90) cc_final: 0.8713 (m90)
REVERT: A  524 ASP cc_start: 0.9227 (t70) cc_final: 0.8992 (m-30)
REVERT: B   47 LEU cc_start: 0.9417 (mt) cc_final: 0.9171 (mt)
REVERT: B   53 ASP cc_start: 0.8623 (t0) cc_final: 0.8357 (m-30)
REVERT: B   71 VAL cc_start: 0.9287 (t) cc_final: 0.8906 (t)
REVERT: B  196 MET cc_start: 0.9260 (mmm) cc_final: 0.8942 (mmm)
REVERT: B  244 MET cc_start: 0.9285 (ppp) cc_final: 0.9000 (ppp)
REVERT: B  456 MET cc_start: 0.9158 (pmm) cc_final: 0.8780 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 255
  average time/residue: 0.0623
  time to fit residues: 23.8953
Evaluate side-chains
  196 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 51 optimal weight:    0.8980
   chunk 32 optimal weight:    8.9990
   chunk 17 optimal weight:    3.9990
   chunk 83 optimal weight:    1.9990
   chunk 73 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0170
   chunk 39 optimal weight:    0.4980
   chunk 55 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 96 optimal weight:    5.9990
   chunk 79 optimal weight:    0.8980
   overall best weight:    0.6618

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 485 GLN
B 529 ASN
B 568 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.075757 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.056165 restraints weight = 34184.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.058352 restraints weight = 20573.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.060011 restraints weight = 14267.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.061210 restraints weight = 10768.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.062166 restraints weight = 8639.914|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8230
moved from start:          0.2986

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8950  Z= 0.134
  Angle     :  0.639   9.203  12092  Z= 0.328
  Chirality :  0.042   0.165   1440
  Planarity :  0.004   0.036   1532
  Dihedral  :  4.504  23.471   1238
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 11.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.31 %
    Favored  : 96.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.25), residues: 1134
  helix:  1.35 (0.19), residues: 692
  sheet: -0.62 (0.93), residues: 34
  loop : -1.28 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 229 
 TYR   0.010   0.001   TYR A 572 
 PHE   0.023   0.002   PHE B  23 
 TRP   0.009   0.001   TRP A  91 
 HIS   0.004   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.63922 (12092)
  hydrogen bonds       : bond        0.04265 (  553)
  hydrogen bonds       : angle       4.70175 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 247
  time to evaluate  : 0.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9096 (tpp) cc_final: 0.8751 (tpp)
REVERT: A  107 HIS cc_start: 0.8641 (t-90) cc_final: 0.7758 (t-170)
REVERT: A  226 GLU cc_start: 0.8253 (mp0) cc_final: 0.7974 (mp0)
REVERT: A  244 MET cc_start: 0.9265 (ppp) cc_final: 0.8951 (ppp)
REVERT: A  263 LEU cc_start: 0.9698 (tt) cc_final: 0.9431 (tt)
REVERT: A  312 MET cc_start: 0.7290 (ttt) cc_final: 0.6786 (tpt)
REVERT: A  322 LEU cc_start: 0.9594 (tp) cc_final: 0.9307 (tp)
REVERT: A  382 LYS cc_start: 0.7672 (mmpt) cc_final: 0.7202 (mmtm)
REVERT: A  402 MET cc_start: 0.8441 (mmm) cc_final: 0.8214 (mmm)
REVERT: A  405 HIS cc_start: 0.8832 (m90) cc_final: 0.8558 (m90)
REVERT: A  524 ASP cc_start: 0.9216 (t70) cc_final: 0.8973 (m-30)
REVERT: B   47 LEU cc_start: 0.9354 (mt) cc_final: 0.9121 (mt)
REVERT: B   62 SER cc_start: 0.8706 (t) cc_final: 0.8432 (p)
REVERT: B   90 SER cc_start: 0.9256 (m) cc_final: 0.8753 (p)
REVERT: B  131 ASP cc_start: 0.9312 (m-30) cc_final: 0.9061 (m-30)
REVERT: B  149 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8283 (mp0)
REVERT: B  196 MET cc_start: 0.9267 (mmm) cc_final: 0.8957 (mmm)
REVERT: B  244 MET cc_start: 0.9298 (ppp) cc_final: 0.9003 (ppp)
REVERT: B  456 MET cc_start: 0.9111 (pmm) cc_final: 0.8754 (pmm)
REVERT: B  460 MET cc_start: 0.8583 (tmm) cc_final: 0.8321 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 248
  average time/residue: 0.0688
  time to fit residues: 25.1474
Evaluate side-chains
  197 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 89 optimal weight:    9.9990
   chunk 28 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 45 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0030
   chunk 36 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 53 optimal weight:    5.9990
   chunk 85 optimal weight:    0.8980
   overall best weight:    0.7194

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.075686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.055990 restraints weight = 34622.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.058158 restraints weight = 21031.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 22)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.059778 restraints weight = 14687.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.061027 restraints weight = 11154.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.061946 restraints weight = 8960.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3157
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.3276

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   8950  Z= 0.126
  Angle     :  0.607   7.605  12092  Z= 0.315
  Chirality :  0.042   0.172   1440
  Planarity :  0.003   0.026   1532
  Dihedral  :  4.387  22.408   1238
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.79 %
    Favored  : 97.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.26), residues: 1134
  helix:  1.40 (0.20), residues: 694
  sheet: -1.25 (0.73), residues: 54
  loop : -1.27 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 102 
 TYR   0.009   0.001   TYR B 393 
 PHE   0.032   0.002   PHE B 230 
 TRP   0.009   0.001   TRP A  91 
 HIS   0.004   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 8950)
  covalent geometry    : angle       0.60692 (12092)
  hydrogen bonds       : bond        0.04019 (  553)
  hydrogen bonds       : angle       4.53889 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.286 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8537 (t-90) cc_final: 0.7905 (t-90)
REVERT: A  210 MET cc_start: 0.9291 (tpp) cc_final: 0.8787 (tpt)
REVERT: A  218 LEU cc_start: 0.9605 (mt) cc_final: 0.9288 (mt)
REVERT: A  244 MET cc_start: 0.9254 (ppp) cc_final: 0.8935 (ppp)
REVERT: A  261 LEU cc_start: 0.9640 (mm) cc_final: 0.9404 (mm)
REVERT: A  312 MET cc_start: 0.7286 (ttt) cc_final: 0.6837 (tpt)
REVERT: A  405 HIS cc_start: 0.8783 (m90) cc_final: 0.8509 (m90)
REVERT: A  524 ASP cc_start: 0.9218 (t70) cc_final: 0.8993 (m-30)
REVERT: B   47 LEU cc_start: 0.9394 (mt) cc_final: 0.9134 (mt)
REVERT: B   62 SER cc_start: 0.8732 (t) cc_final: 0.8462 (p)
REVERT: B   90 SER cc_start: 0.9470 (m) cc_final: 0.8885 (p)
REVERT: B  116 PHE cc_start: 0.9306 (m-80) cc_final: 0.8882 (m-80)
REVERT: B  131 ASP cc_start: 0.9320 (m-30) cc_final: 0.9041 (m-30)
REVERT: B  149 GLU cc_start: 0.8986 (mm-30) cc_final: 0.8757 (mm-30)
REVERT: B  196 MET cc_start: 0.9306 (mmm) cc_final: 0.8971 (mmm)
REVERT: B  244 MET cc_start: 0.9306 (ppp) cc_final: 0.8986 (ppp)
REVERT: B  456 MET cc_start: 0.9161 (pmm) cc_final: 0.8774 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.0639
  time to fit residues: 23.6320
Evaluate side-chains
  188 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.328 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 96 optimal weight:    6.9990
   chunk 111 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 83 optimal weight:    1.9990
   chunk 16 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   chunk 72 optimal weight:    0.9990
   chunk 47 optimal weight:    0.9980
   chunk 24 optimal weight:    0.7980
   chunk 99 optimal weight:    0.0270
   chunk 49 optimal weight:    9.9990
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 485 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.076645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.056507 restraints weight = 34777.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.058741 restraints weight = 21380.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3133 r_free = 0.3133 target = 0.060426 restraints weight = 14992.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.061655 restraints weight = 11425.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.062610 restraints weight = 9245.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.3534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8950  Z= 0.122
  Angle     :  0.611   6.491  12092  Z= 0.313
  Chirality :  0.042   0.176   1440
  Planarity :  0.003   0.028   1532
  Dihedral  :  4.306  22.021   1238
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 12.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.96 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.58 (0.26), residues: 1134
  helix:  1.46 (0.20), residues: 692
  sheet: -1.26 (0.72), residues: 54
  loop : -1.34 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 229 
 TYR   0.008   0.001   TYR B 393 
 PHE   0.022   0.001   PHE B 230 
 TRP   0.007   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 8950)
  covalent geometry    : angle       0.61109 (12092)
  hydrogen bonds       : bond        0.03887 (  553)
  hydrogen bonds       : angle       4.41744 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 242
  time to evaluate  : 0.289 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9054 (tpp) cc_final: 0.8813 (tpt)
REVERT: A  107 HIS cc_start: 0.8471 (t-90) cc_final: 0.7778 (t-90)
REVERT: A  210 MET cc_start: 0.9294 (tpp) cc_final: 0.8728 (tpt)
REVERT: A  218 LEU cc_start: 0.9598 (mt) cc_final: 0.9270 (mt)
REVERT: A  229 ARG cc_start: 0.9315 (mtp180) cc_final: 0.8936 (mtp180)
REVERT: A  244 MET cc_start: 0.9249 (ppp) cc_final: 0.9022 (ppp)
REVERT: A  261 LEU cc_start: 0.9645 (mm) cc_final: 0.9444 (mm)
REVERT: A  312 MET cc_start: 0.7180 (ttt) cc_final: 0.6700 (tpt)
REVERT: A  382 LYS cc_start: 0.7446 (mmpt) cc_final: 0.7136 (mmtm)
REVERT: A  402 MET cc_start: 0.8451 (mmm) cc_final: 0.8080 (mmm)
REVERT: A  405 HIS cc_start: 0.8762 (m90) cc_final: 0.8470 (m90)
REVERT: A  456 MET cc_start: 0.9100 (pmm) cc_final: 0.8848 (pmm)
REVERT: A  524 ASP cc_start: 0.9211 (t70) cc_final: 0.8986 (m-30)
REVERT: B   47 LEU cc_start: 0.9405 (mt) cc_final: 0.9145 (mt)
REVERT: B   62 SER cc_start: 0.8737 (t) cc_final: 0.8516 (p)
REVERT: B   90 SER cc_start: 0.9507 (m) cc_final: 0.8957 (p)
REVERT: B  111 MET cc_start: 0.8988 (ttt) cc_final: 0.8685 (ttt)
REVERT: B  116 PHE cc_start: 0.9322 (m-80) cc_final: 0.8850 (m-80)
REVERT: B  131 ASP cc_start: 0.9322 (m-30) cc_final: 0.9006 (m-30)
REVERT: B  149 GLU cc_start: 0.8985 (mm-30) cc_final: 0.8758 (mm-30)
REVERT: B  196 MET cc_start: 0.9291 (mmm) cc_final: 0.8990 (mmm)
REVERT: B  237 MET cc_start: 0.9074 (ppp) cc_final: 0.8838 (ptm)
REVERT: B  242 MET cc_start: 0.9534 (mmt) cc_final: 0.9272 (mmt)
REVERT: B  244 MET cc_start: 0.9310 (ppp) cc_final: 0.8980 (ppp)
REVERT: B  432 THR cc_start: 0.9369 (p) cc_final: 0.9110 (t)
REVERT: B  456 MET cc_start: 0.9136 (pmm) cc_final: 0.8801 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 242
  average time/residue: 0.0654
  time to fit residues: 23.9024
Evaluate side-chains
  198 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    0.9990
   chunk 95 optimal weight:    0.1980
   chunk 7 optimal weight:    0.6980
   chunk 108 optimal weight:    0.0980
   chunk 18 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 53 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 23 optimal weight:    2.9990
   chunk 58 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 485 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 = 0.3467 r_free = 0.3467 target = 0.076847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.057375 restraints weight = 34097.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.059596 restraints weight = 20990.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.061276 restraints weight = 14712.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.062435 restraints weight = 11165.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.063448 restraints weight = 9090.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3194
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.3743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8950  Z= 0.117
  Angle     :  0.609   6.277  12092  Z= 0.311
  Chirality :  0.042   0.155   1440
  Planarity :  0.003   0.027   1532
  Dihedral  :  4.222  21.716   1238
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.34 %
    Favored  : 98.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.56 (0.26), residues: 1134
  helix:  1.44 (0.20), residues: 692
  sheet: -1.34 (0.70), residues: 54
  loop : -1.33 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 229 
 TYR   0.014   0.001   TYR A 439 
 PHE   0.043   0.002   PHE B 319 
 TRP   0.008   0.001   TRP A  91 
 HIS   0.008   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 8950)
  covalent geometry    : angle       0.60940 (12092)
  hydrogen bonds       : bond        0.03780 (  553)
  hydrogen bonds       : angle       4.35299 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  239 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9023 (tpp) cc_final: 0.8721 (tpt)
REVERT: A  107 HIS cc_start: 0.8389 (t-90) cc_final: 0.7660 (t-90)
REVERT: A  210 MET cc_start: 0.9286 (tpp) cc_final: 0.8695 (tpt)
REVERT: A  218 LEU cc_start: 0.9591 (mt) cc_final: 0.9316 (mt)
REVERT: A  229 ARG cc_start: 0.9325 (mtp180) cc_final: 0.8940 (mtp180)
REVERT: A  244 MET cc_start: 0.9332 (ppp) cc_final: 0.9019 (ppp)
REVERT: A  261 LEU cc_start: 0.9624 (mm) cc_final: 0.9396 (mm)
REVERT: A  312 MET cc_start: 0.6920 (ttt) cc_final: 0.6565 (tpt)
REVERT: A  382 LYS cc_start: 0.7439 (mmpt) cc_final: 0.7152 (mmtm)
REVERT: A  402 MET cc_start: 0.8495 (mmm) cc_final: 0.8146 (mmm)
REVERT: A  405 HIS cc_start: 0.8683 (m90) cc_final: 0.8393 (m90)
REVERT: A  456 MET cc_start: 0.9176 (pmm) cc_final: 0.8871 (pmm)
REVERT: B   47 LEU cc_start: 0.9366 (mt) cc_final: 0.9074 (mt)
REVERT: B   62 SER cc_start: 0.8740 (t) cc_final: 0.8508 (p)
REVERT: B   67 MET cc_start: 0.9324 (ppp) cc_final: 0.9090 (ppp)
REVERT: B   98 MET cc_start: 0.9129 (tpp) cc_final: 0.7940 (tpp)
REVERT: B  102 ARG cc_start: 0.9272 (ttm110) cc_final: 0.8975 (mtm-85)
REVERT: B  109 MET cc_start: 0.8803 (tmm) cc_final: 0.8426 (tmm)
REVERT: B  116 PHE cc_start: 0.9279 (m-80) cc_final: 0.8815 (m-80)
REVERT: B  131 ASP cc_start: 0.9304 (m-30) cc_final: 0.8962 (m-30)
REVERT: B  196 MET cc_start: 0.9298 (mmm) cc_final: 0.9021 (mmm)
REVERT: B  218 LEU cc_start: 0.9195 (mm) cc_final: 0.8816 (tp)
REVERT: B  244 MET cc_start: 0.9323 (ppp) cc_final: 0.8977 (ppp)
REVERT: B  432 THR cc_start: 0.9371 (p) cc_final: 0.9107 (t)
REVERT: B  456 MET cc_start: 0.9124 (pmm) cc_final: 0.8873 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.0668
  time to fit residues: 24.0093
Evaluate side-chains
  196 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.398 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 60 optimal weight:    0.1980
   chunk 57 optimal weight:    1.9990
   chunk 104 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 65 optimal weight:    4.9990
   chunk 109 optimal weight:    6.9990
   chunk 36 optimal weight:   10.0000
   chunk 93 optimal weight:    1.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 485 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.076083 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.056072 restraints weight = 35216.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.058245 restraints weight = 21920.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.059861 restraints weight = 15525.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.061092 restraints weight = 11924.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.062040 restraints weight = 9670.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.3913

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   8950  Z= 0.140
  Angle     :  0.622   8.049  12092  Z= 0.320
  Chirality :  0.042   0.170   1440
  Planarity :  0.003   0.028   1532
  Dihedral  :  4.196  20.015   1238
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  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 aren not related in a simple way.
  whole:  0.61 (0.25), residues: 1134
  helix:  1.51 (0.20), residues: 692
  sheet: -1.16 (0.65), residues: 64
  loop : -1.40 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 101 
 TYR   0.009   0.001   TYR B 393 
 PHE   0.037   0.002   PHE B 319 
 TRP   0.018   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 ( 8950)
  covalent geometry    : angle       0.62200 (12092)
  hydrogen bonds       : bond        0.03834 (  553)
  hydrogen bonds       : angle       4.35142 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9014 (tpp) cc_final: 0.8668 (tpt)
REVERT: A  107 HIS cc_start: 0.8383 (t-90) cc_final: 0.7649 (t-90)
REVERT: A  210 MET cc_start: 0.9323 (tpp) cc_final: 0.8769 (tpt)
REVERT: A  218 LEU cc_start: 0.9599 (mt) cc_final: 0.9330 (mt)
REVERT: A  244 MET cc_start: 0.9334 (ppp) cc_final: 0.9010 (ppp)
REVERT: A  261 LEU cc_start: 0.9641 (mm) cc_final: 0.9389 (mm)
REVERT: A  382 LYS cc_start: 0.7590 (mmpt) cc_final: 0.7274 (mmtm)
REVERT: A  402 MET cc_start: 0.8541 (mmm) cc_final: 0.8188 (mmm)
REVERT: A  405 HIS cc_start: 0.8661 (m90) cc_final: 0.8349 (m90)
REVERT: B   47 LEU cc_start: 0.9384 (mt) cc_final: 0.9126 (mt)
REVERT: B   62 SER cc_start: 0.8769 (t) cc_final: 0.8541 (p)
REVERT: B   98 MET cc_start: 0.9089 (tpp) cc_final: 0.8779 (tpp)
REVERT: B  111 MET cc_start: 0.8995 (ttt) cc_final: 0.8485 (tmm)
REVERT: B  116 PHE cc_start: 0.9295 (m-80) cc_final: 0.9079 (m-10)
REVERT: B  131 ASP cc_start: 0.9298 (m-30) cc_final: 0.8952 (m-30)
REVERT: B  196 MET cc_start: 0.9320 (mmm) cc_final: 0.9021 (mmm)
REVERT: B  244 MET cc_start: 0.9355 (ppp) cc_final: 0.8984 (ppp)
REVERT: B  432 THR cc_start: 0.9381 (p) cc_final: 0.9121 (t)
REVERT: B  456 MET cc_start: 0.9155 (pmm) cc_final: 0.8897 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.0666
  time to fit residues: 22.9346
Evaluate side-chains
  192 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 192
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 18 optimal weight:    8.9990
   chunk 53 optimal weight:    3.9990
   chunk 88 optimal weight:    8.9990
   chunk 33 optimal weight:    1.9990
   chunk 58 optimal weight:    0.9980
   chunk 37 optimal weight:    5.9990
   chunk 21 optimal weight:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 99 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   overall best weight:    2.1988

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

Flipped N/Q/H residues before XYZ refinement:
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.072133 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2966 r_free = 0.2966 target = 0.053031 restraints weight = 34915.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.055065 restraints weight = 21167.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.056617 restraints weight = 14827.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.057740 restraints weight = 11267.030|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.058620 restraints weight = 9075.515|
|-----------------------------------------------------------------------------|
r_work (final): 0.3085
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8322
moved from start:          0.3962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   8950  Z= 0.202
  Angle     :  0.673   7.054  12092  Z= 0.354
  Chirality :  0.044   0.199   1440
  Planarity :  0.004   0.033   1532
  Dihedral  :  4.334  18.126   1238
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 15.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  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 aren not related in a simple way.
  whole:  0.53 (0.25), residues: 1134
  helix:  1.46 (0.20), residues: 692
  sheet: -1.31 (0.63), residues: 64
  loop : -1.44 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 101 
 TYR   0.018   0.002   TYR A 439 
 PHE   0.043   0.002   PHE A 105 
 TRP   0.040   0.002   TRP B  17 
 HIS   0.016   0.002   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00411 ( 8950)
  covalent geometry    : angle       0.67286 (12092)
  hydrogen bonds       : bond        0.04149 (  553)
  hydrogen bonds       : angle       4.51052 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 227
  time to evaluate  : 0.271 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8411 (t-90) cc_final: 0.7633 (t-90)
REVERT: A  210 MET cc_start: 0.9368 (tpp) cc_final: 0.8721 (tpp)
REVERT: A  218 LEU cc_start: 0.9629 (mt) cc_final: 0.9355 (mt)
REVERT: A  244 MET cc_start: 0.9360 (ppp) cc_final: 0.9045 (ppp)
REVERT: A  261 LEU cc_start: 0.9663 (mm) cc_final: 0.9455 (mm)
REVERT: A  291 MET cc_start: 0.9493 (mmp) cc_final: 0.9279 (mmm)
REVERT: A  382 LYS cc_start: 0.7494 (mmpt) cc_final: 0.7153 (mmmt)
REVERT: A  402 MET cc_start: 0.8562 (mmm) cc_final: 0.8216 (mmm)
REVERT: A  405 HIS cc_start: 0.8706 (m90) cc_final: 0.8411 (m90)
REVERT: B   47 LEU cc_start: 0.9439 (mt) cc_final: 0.9159 (mt)
REVERT: B   64 LEU cc_start: 0.9499 (pp) cc_final: 0.9231 (pp)
REVERT: B   67 MET cc_start: 0.9347 (ppp) cc_final: 0.9077 (ppp)
REVERT: B  109 MET cc_start: 0.8637 (tmm) cc_final: 0.8337 (tmm)
REVERT: B  116 PHE cc_start: 0.9342 (m-80) cc_final: 0.8959 (m-80)
REVERT: B  131 ASP cc_start: 0.9324 (m-30) cc_final: 0.8981 (m-30)
REVERT: B  196 MET cc_start: 0.9358 (mmm) cc_final: 0.9019 (mmm)
REVERT: B  244 MET cc_start: 0.9367 (ppp) cc_final: 0.8991 (ppp)
REVERT: B  432 THR cc_start: 0.9378 (p) cc_final: 0.9112 (t)
REVERT: B  456 MET cc_start: 0.9220 (pmm) cc_final: 0.8896 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 227
  average time/residue: 0.0595
  time to fit residues: 20.9543
Evaluate side-chains
  185 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 185
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 109 optimal weight:    5.9990
   chunk 26 optimal weight:    3.9990
   chunk 1 optimal weight:    0.2980
   chunk 105 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 33 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   chunk 83 optimal weight:    0.6980
   chunk 89 optimal weight:    0.9990
   overall best weight:    0.9384

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

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 568 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.074306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3009 r_free = 0.3009 target = 0.054729 restraints weight = 34341.162|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.056905 restraints weight = 20855.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.058531 restraints weight = 14555.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.059627 restraints weight = 11057.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.060561 restraints weight = 9052.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8260
moved from start:          0.4091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052   8950  Z= 0.133
  Angle     :  0.652   7.750  12092  Z= 0.333
  Chirality :  0.043   0.199   1440
  Planarity :  0.003   0.031   1532
  Dihedral  :  4.309  20.045   1238
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 12.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.14 %
    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 aren not related in a simple way.
  whole:  0.49 (0.25), residues: 1134
  helix:  1.43 (0.20), residues: 692
  sheet: -1.28 (0.63), residues: 64
  loop : -1.46 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 101 
 TYR   0.006   0.001   TYR A 572 
 PHE   0.024   0.002   PHE B 319 
 TRP   0.022   0.001   TRP B  17 
 HIS   0.009   0.001   HIS A 568 

Details of bonding type rmsd
  covalent geometry    : bond        0.00287 ( 8950)
  covalent geometry    : angle       0.65202 (12092)
  hydrogen bonds       : bond        0.03895 (  553)
  hydrogen bonds       : angle       4.44599 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.9432 (mt) cc_final: 0.9227 (mt)
REVERT: A  210 MET cc_start: 0.9361 (tpp) cc_final: 0.9145 (tpp)
REVERT: A  218 LEU cc_start: 0.9572 (mt) cc_final: 0.9329 (mt)
REVERT: A  244 MET cc_start: 0.9355 (ppp) cc_final: 0.9029 (ppp)
REVERT: A  261 LEU cc_start: 0.9632 (mm) cc_final: 0.9422 (mm)
REVERT: A  382 LYS cc_start: 0.7444 (mmpt) cc_final: 0.7045 (mmmt)
REVERT: A  402 MET cc_start: 0.8570 (mmm) cc_final: 0.8274 (mmm)
REVERT: A  405 HIS cc_start: 0.8644 (m90) cc_final: 0.8315 (m90)
REVERT: B   47 LEU cc_start: 0.9402 (mt) cc_final: 0.9122 (mt)
REVERT: B   64 LEU cc_start: 0.9463 (pp) cc_final: 0.9241 (pp)
REVERT: B   67 MET cc_start: 0.9354 (ppp) cc_final: 0.9094 (ppp)
REVERT: B  109 MET cc_start: 0.8618 (tmm) cc_final: 0.8322 (tmm)
REVERT: B  111 MET cc_start: 0.8986 (ttt) cc_final: 0.8484 (tmm)
REVERT: B  131 ASP cc_start: 0.9334 (m-30) cc_final: 0.8985 (m-30)
REVERT: B  196 MET cc_start: 0.9333 (mmm) cc_final: 0.9038 (mmm)
REVERT: B  244 MET cc_start: 0.9349 (ppp) cc_final: 0.8977 (ppp)
REVERT: B  432 THR cc_start: 0.9358 (p) cc_final: 0.9082 (t)
REVERT: B  456 MET cc_start: 0.9158 (pmm) cc_final: 0.8932 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 232
  average time/residue: 0.0604
  time to fit residues: 21.2460
Evaluate side-chains
  184 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 184
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 81 optimal weight:    0.8980
   chunk 82 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0270
   chunk 76 optimal weight:    0.4980
   chunk 61 optimal weight:    3.9990
   chunk 92 optimal weight:    0.9990
   chunk 108 optimal weight:    3.9990
   chunk 44 optimal weight:    6.9990
   chunk 109 optimal weight:    6.9990
   overall best weight:    0.6842

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.075004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.055526 restraints weight = 34187.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 21)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.057686 restraints weight = 20908.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.059341 restraints weight = 14693.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.060595 restraints weight = 11185.531|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.061536 restraints weight = 8963.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.4232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   8950  Z= 0.128
  Angle     :  0.682   9.202  12092  Z= 0.344
  Chirality :  0.043   0.169   1440
  Planarity :  0.004   0.093   1532
  Dihedral  :  4.337  19.513   1238
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 13.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.43 (0.25), residues: 1134
  helix:  1.39 (0.20), residues: 692
  sheet: -1.32 (0.62), residues: 64
  loop : -1.51 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 101 
 TYR   0.013   0.001   TYR B 393 
 PHE   0.037   0.002   PHE A 105 
 TRP   0.017   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 214 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 8950)
  covalent geometry    : angle       0.68182 (12092)
  hydrogen bonds       : bond        0.03804 (  553)
  hydrogen bonds       : angle       4.41447 ( 1653)

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

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

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2268 Ramachandran restraints generated.
    1134 Oldfield, 0 Emsley, 1134 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 228
  time to evaluate  : 0.251 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.9422 (mt) cc_final: 0.9213 (mt)
REVERT: A  149 GLU cc_start: 0.9084 (mp0) cc_final: 0.8707 (mp0)
REVERT: A  210 MET cc_start: 0.9349 (tpp) cc_final: 0.9113 (tpp)
REVERT: A  218 LEU cc_start: 0.9549 (mt) cc_final: 0.9348 (mm)
REVERT: A  244 MET cc_start: 0.9357 (ppp) cc_final: 0.9023 (ppp)
REVERT: A  261 LEU cc_start: 0.9624 (mm) cc_final: 0.9376 (mm)
REVERT: A  382 LYS cc_start: 0.7422 (mmpt) cc_final: 0.7070 (mmmt)
REVERT: A  402 MET cc_start: 0.8517 (mmm) cc_final: 0.8230 (mmm)
REVERT: A  405 HIS cc_start: 0.8614 (m90) cc_final: 0.8291 (m90)
REVERT: B   47 LEU cc_start: 0.9387 (mt) cc_final: 0.9111 (mt)
REVERT: B   67 MET cc_start: 0.9369 (ppp) cc_final: 0.9107 (ppp)
REVERT: B  109 MET cc_start: 0.8594 (tmm) cc_final: 0.8244 (tmm)
REVERT: B  111 MET cc_start: 0.8958 (ttt) cc_final: 0.8506 (tmm)
REVERT: B  131 ASP cc_start: 0.9327 (m-30) cc_final: 0.8973 (m-30)
REVERT: B  196 MET cc_start: 0.9322 (mmm) cc_final: 0.9033 (mmm)
REVERT: B  244 MET cc_start: 0.9345 (ppp) cc_final: 0.8976 (ppp)
REVERT: B  432 THR cc_start: 0.9364 (p) cc_final: 0.9098 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 228
  average time/residue: 0.0634
  time to fit residues: 21.6973
Evaluate side-chains
  183 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.245 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 104 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 49 optimal weight:    9.9990
   chunk 29 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0980
   chunk 5 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 94 optimal weight:    7.9990
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 209 GLN
A 436 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.075959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.056073 restraints weight = 34372.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.058269 restraints weight = 21416.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.059813 restraints weight = 15157.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.061097 restraints weight = 11792.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.062030 restraints weight = 9500.962|
|-----------------------------------------------------------------------------|
r_work (final): 0.3154
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.4324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   8950  Z= 0.129
  Angle     :  0.679   9.570  12092  Z= 0.344
  Chirality :  0.043   0.163   1440
  Planarity :  0.004   0.070   1532
  Dihedral  :  4.254  19.386   1238
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.44 (0.25), residues: 1134
  helix:  1.40 (0.20), residues: 692
  sheet: -1.69 (0.65), residues: 54
  loop : -1.45 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 101 
 TYR   0.006   0.001   TYR A 572 
 PHE   0.032   0.002   PHE A 105 
 TRP   0.016   0.001   TRP B  17 
 HIS   0.012   0.001   HIS B 107 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.67851 (12092)
  hydrogen bonds       : bond        0.03787 (  553)
  hydrogen bonds       : angle       4.39805 ( 1653)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1567.63 seconds
wall clock time: 27 minutes 51.51 seconds (1671.51 seconds total)