Starting phenix.real_space_refine
on Tue Apr 29 20:10:28 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuy_50782/04_2025/9fuy_50782.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuy_50782/04_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_50782/04_2025/9fuy_50782.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuy_50782/04_2025/9fuy_50782.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuy_50782/04_2025/9fuy_50782.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuy_50782/04_2025/9fuy_50782.cif"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.41, per 1000 atoms: 0.73
  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: 2.29
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.85
  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: 2.48

  Time building geometry restraints manager: 2.70 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: 0.04
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:             3.300
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.370
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.480
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.410
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (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
 TRP   0.003   0.001   TRP A  91 
 HIS   0.022   0.003   HIS A 107 
 PHE   0.030   0.002   PHE B 230 
 TYR   0.026   0.001   TYR A 439 
 ARG   0.007   0.001   ARG A 517 

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

*********************** 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  : 1.039 
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: 0.2028
  time to fit residues: 67.0704
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  : 1.131 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.6980
   chunk 84 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 28 optimal weight:    0.9980
   chunk 57 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 87 optimal weight:    6.9990
   chunk 33 optimal weight:    5.9990
   chunk 53 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9980
   chunk 101 optimal weight:    1.9990
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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
B 568 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.075478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.056197 restraints weight = 34182.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.058421 restraints weight = 20360.247|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.060073 restraints weight = 14037.711|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8268
moved from start:          0.2339

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8950  Z= 0.159
  Angle     :  0.661   9.497  12092  Z= 0.347
  Chirality :  0.043   0.186   1440
  Planarity :  0.004   0.045   1532
  Dihedral  :  4.616  23.528   1238
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.14 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.79 %
    Favored  : 97.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1134
  helix:  1.18 (0.19), residues: 690
  sheet: -0.19 (0.79), residues: 44
  loop : -1.26 (0.33), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 165 
 HIS   0.006   0.001   HIS B 107 
 PHE   0.061   0.002   PHE B 230 
 TYR   0.011   0.001   TYR A 439 
 ARG   0.007   0.001   ARG A 538 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04820 (  553)
  hydrogen bonds       : angle       4.93031 ( 1653)
  covalent geometry    : bond        0.00326 ( 8950)
  covalent geometry    : angle       0.66104 (12092)

*********************** 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
  259 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 258
  time to evaluate  : 1.122 
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: 0.9169 (tpp) cc_final: 0.8872 (tpp)
REVERT: A  107 HIS cc_start: 0.8582 (t-90) cc_final: 0.7786 (t-170)
REVERT: A  109 MET cc_start: 0.9302 (mmp) cc_final: 0.8968 (mmp)
REVERT: A  216 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8931 (pt0)
REVERT: A  218 LEU cc_start: 0.9644 (mt) cc_final: 0.9355 (mt)
REVERT: A  244 MET cc_start: 0.9266 (ppp) cc_final: 0.8987 (ppp)
REVERT: A  261 LEU cc_start: 0.9625 (mm) cc_final: 0.9422 (mm)
REVERT: A  263 LEU cc_start: 0.9704 (tt) cc_final: 0.9457 (tt)
REVERT: A  312 MET cc_start: 0.7293 (ttt) cc_final: 0.6873 (tpt)
REVERT: A  382 LYS cc_start: 0.7917 (mmpt) cc_final: 0.7251 (mmtm)
REVERT: A  405 HIS cc_start: 0.8992 (m90) cc_final: 0.8727 (m90)
REVERT: A  523 LEU cc_start: 0.9045 (mt) cc_final: 0.8802 (mt)
REVERT: B   47 LEU cc_start: 0.9377 (mt) cc_final: 0.9131 (mt)
REVERT: B   62 SER cc_start: 0.8729 (t) cc_final: 0.8436 (p)
REVERT: B  111 MET cc_start: 0.9035 (ttt) cc_final: 0.8826 (ttt)
REVERT: B  131 ASP cc_start: 0.9290 (m-30) cc_final: 0.9084 (m-30)
REVERT: B  149 GLU cc_start: 0.9123 (mm-30) cc_final: 0.8424 (mp0)
REVERT: B  196 MET cc_start: 0.9226 (mmm) cc_final: 0.8903 (mmm)
REVERT: B  210 MET cc_start: 0.8980 (tpp) cc_final: 0.8667 (tpp)
REVERT: B  244 MET cc_start: 0.9289 (ppp) cc_final: 0.9002 (ppp)
REVERT: B  456 MET cc_start: 0.9125 (pmm) cc_final: 0.8870 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1892
  time to fit residues: 71.7948
Evaluate side-chains
  204 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 79 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 46 optimal weight:    0.0040
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 52 optimal weight:    0.9980
   chunk 16 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 82 optimal weight:    0.0770
   overall best weight:    0.5752

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.076525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.056919 restraints weight = 33991.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.059160 restraints weight = 20392.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.060812 restraints weight = 14087.598|
|-----------------------------------------------------------------------------|
r_work (final): 0.3134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.2996

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8950  Z= 0.130
  Angle     :  0.635   7.186  12092  Z= 0.326
  Chirality :  0.042   0.167   1440
  Planarity :  0.004   0.034   1532
  Dihedral  :  4.497  23.246   1238
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.06 %
    Favored  : 95.86 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.41 %
    Favored  : 96.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.25), residues: 1134
  helix:  1.31 (0.19), residues: 692
  sheet: -0.54 (0.93), residues: 34
  loop : -1.26 (0.32), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  91 
 HIS   0.004   0.001   HIS B 568 
 PHE   0.025   0.002   PHE B 319 
 TYR   0.015   0.001   TYR B 439 
 ARG   0.005   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04189 (  553)
  hydrogen bonds       : angle       4.65138 ( 1653)
  covalent geometry    : bond        0.00266 ( 8950)
  covalent geometry    : angle       0.63464 (12092)

*********************** 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
  250 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 1.058 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9122 (tpp) cc_final: 0.8766 (tpp)
REVERT: A  107 HIS cc_start: 0.8647 (t-90) cc_final: 0.7758 (t-170)
REVERT: A  127 ARG cc_start: 0.9297 (mmt90) cc_final: 0.8893 (mmm160)
REVERT: A  149 GLU cc_start: 0.9032 (mp0) cc_final: 0.8694 (mp0)
REVERT: A  216 GLU cc_start: 0.9269 (mt-10) cc_final: 0.8896 (pt0)
REVERT: A  244 MET cc_start: 0.9272 (ppp) cc_final: 0.8979 (ppp)
REVERT: A  261 LEU cc_start: 0.9622 (mm) cc_final: 0.9383 (mm)
REVERT: A  312 MET cc_start: 0.7185 (ttt) cc_final: 0.6713 (tpt)
REVERT: A  322 LEU cc_start: 0.9569 (tp) cc_final: 0.9321 (tp)
REVERT: A  382 LYS cc_start: 0.7777 (mmpt) cc_final: 0.7182 (mmtm)
REVERT: A  402 MET cc_start: 0.8424 (mmm) cc_final: 0.8198 (mmm)
REVERT: A  405 HIS cc_start: 0.8877 (m90) cc_final: 0.8609 (m90)
REVERT: A  456 MET cc_start: 0.9131 (pmm) cc_final: 0.8852 (pmm)
REVERT: A  517 ARG cc_start: 0.9067 (mtm110) cc_final: 0.8822 (mtm110)
REVERT: B   47 LEU cc_start: 0.9383 (mt) cc_final: 0.9127 (mt)
REVERT: B   62 SER cc_start: 0.8704 (t) cc_final: 0.8426 (p)
REVERT: B   90 SER cc_start: 0.9273 (m) cc_final: 0.8554 (p)
REVERT: B  131 ASP cc_start: 0.9324 (m-30) cc_final: 0.9076 (m-30)
REVERT: B  149 GLU cc_start: 0.9034 (mm-30) cc_final: 0.8281 (mp0)
REVERT: B  196 MET cc_start: 0.9261 (mmm) cc_final: 0.8984 (mmm)
REVERT: B  218 LEU cc_start: 0.9250 (mm) cc_final: 0.9044 (mm)
REVERT: B  244 MET cc_start: 0.9306 (ppp) cc_final: 0.8992 (ppp)
REVERT: B  439 TYR cc_start: 0.8016 (t80) cc_final: 0.7802 (t80)
REVERT: B  456 MET cc_start: 0.9055 (pmm) cc_final: 0.8846 (pmm)
REVERT: B  460 MET cc_start: 0.8655 (tmm) cc_final: 0.8407 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 250
  average time/residue: 0.1770
  time to fit residues: 63.6912
Evaluate side-chains
  194 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 5 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   chunk 39 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 92 optimal weight:    0.5980
   chunk 99 optimal weight:    0.8980
   chunk 107 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 77 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.076737 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.056834 restraints weight = 34650.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.059026 restraints weight = 21436.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.060678 restraints weight = 15090.990|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8256
moved from start:          0.3316

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= 0.127
  Angle     :  0.620   7.624  12092  Z= 0.317
  Chirality :  0.042   0.166   1440
  Planarity :  0.003   0.026   1532
  Dihedral  :  4.354  22.291   1238
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.67 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.86 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.26), residues: 1134
  helix:  1.38 (0.19), residues: 694
  sheet: -1.25 (0.73), residues: 54
  loop : -1.26 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A  91 
 HIS   0.005   0.001   HIS B 568 
 PHE   0.027   0.002   PHE B 230 
 TYR   0.009   0.001   TYR B 393 
 ARG   0.006   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03989 (  553)
  hydrogen bonds       : angle       4.45535 ( 1653)
  covalent geometry    : bond        0.00268 ( 8950)
  covalent geometry    : angle       0.62011 (12092)

*********************** 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
  246 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8556 (t-90) cc_final: 0.7910 (t-90)
REVERT: A  218 LEU cc_start: 0.9611 (mt) cc_final: 0.9310 (mt)
REVERT: A  224 GLU cc_start: 0.8963 (mp0) cc_final: 0.8714 (pm20)
REVERT: A  244 MET cc_start: 0.9269 (ppp) cc_final: 0.8946 (ppp)
REVERT: A  261 LEU cc_start: 0.9630 (mm) cc_final: 0.9395 (mm)
REVERT: A  310 ARG cc_start: 0.9354 (ptm160) cc_final: 0.9045 (ptm-80)
REVERT: A  312 MET cc_start: 0.7141 (ttt) cc_final: 0.6645 (tpt)
REVERT: A  382 LYS cc_start: 0.7639 (mmpt) cc_final: 0.7124 (mmtm)
REVERT: A  405 HIS cc_start: 0.8855 (m90) cc_final: 0.8564 (m90)
REVERT: A  456 MET cc_start: 0.9176 (pmm) cc_final: 0.8884 (pmm)
REVERT: A  517 ARG cc_start: 0.9058 (mtm110) cc_final: 0.8330 (ptp-110)
REVERT: B   47 LEU cc_start: 0.9364 (mt) cc_final: 0.9104 (mt)
REVERT: B   62 SER cc_start: 0.8747 (t) cc_final: 0.8486 (p)
REVERT: B   90 SER cc_start: 0.9250 (m) cc_final: 0.8576 (p)
REVERT: B  111 MET cc_start: 0.8878 (ttt) cc_final: 0.8324 (tmm)
REVERT: B  116 PHE cc_start: 0.9324 (m-80) cc_final: 0.9042 (m-80)
REVERT: B  131 ASP cc_start: 0.9328 (m-30) cc_final: 0.9043 (m-30)
REVERT: B  149 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8779 (mm-30)
REVERT: B  196 MET cc_start: 0.9292 (mmm) cc_final: 0.8987 (mmm)
REVERT: B  218 LEU cc_start: 0.9255 (mm) cc_final: 0.9048 (mm)
REVERT: B  244 MET cc_start: 0.9318 (ppp) cc_final: 0.8987 (ppp)
REVERT: B  432 THR cc_start: 0.9356 (p) cc_final: 0.9111 (t)
REVERT: B  456 MET cc_start: 0.9119 (pmm) cc_final: 0.8896 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 245
  average time/residue: 0.2111
  time to fit residues: 75.9719
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  : 1.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 35 optimal weight:    8.9990
   chunk 89 optimal weight:    6.9990
   chunk 57 optimal weight:    4.9990
   chunk 11 optimal weight:    0.6980
   chunk 70 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 9 optimal weight:    0.4980
   chunk 60 optimal weight:    3.9990
   chunk 66 optimal weight:    0.2980
   overall best weight:    1.0982

-------------------------------------------------------------------------------
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 = 0.3442 r_free = 0.3442 target = 0.075728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3038 r_free = 0.3038 target = 0.055910 restraints weight = 34782.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.058104 restraints weight = 21533.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.059742 restraints weight = 15201.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8291
moved from start:          0.3500

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   8950  Z= 0.134
  Angle     :  0.611   7.065  12092  Z= 0.316
  Chirality :  0.042   0.172   1440
  Planarity :  0.003   0.027   1532
  Dihedral  :  4.253  21.448   1238
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 12.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.62 (0.26), residues: 1134
  helix:  1.48 (0.20), residues: 692
  sheet: -1.38 (0.71), residues: 54
  loop : -1.29 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  17 
 HIS   0.003   0.001   HIS B 214 
 PHE   0.024   0.002   PHE B 230 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.005   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03927 (  553)
  hydrogen bonds       : angle       4.39829 ( 1653)
  covalent geometry    : bond        0.00280 ( 8950)
  covalent geometry    : angle       0.61084 (12092)

*********************** 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
  242 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 242
  time to evaluate  : 1.006 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9099 (tpp) cc_final: 0.8867 (tpt)
REVERT: A  107 HIS cc_start: 0.8496 (t-90) cc_final: 0.7813 (t-90)
REVERT: A  149 GLU cc_start: 0.9150 (mp0) cc_final: 0.8875 (mp0)
REVERT: A  210 MET cc_start: 0.9295 (tpp) cc_final: 0.8783 (tpt)
REVERT: A  218 LEU cc_start: 0.9626 (mt) cc_final: 0.9324 (mt)
REVERT: A  244 MET cc_start: 0.9294 (ppp) cc_final: 0.9055 (ppp)
REVERT: A  261 LEU cc_start: 0.9645 (mm) cc_final: 0.9441 (mm)
REVERT: A  310 ARG cc_start: 0.9355 (ptm160) cc_final: 0.9123 (ptm-80)
REVERT: A  312 MET cc_start: 0.7173 (ttt) cc_final: 0.6651 (tpt)
REVERT: A  402 MET cc_start: 0.8541 (mmm) cc_final: 0.8165 (mmm)
REVERT: A  405 HIS cc_start: 0.8810 (m90) cc_final: 0.8503 (m90)
REVERT: A  456 MET cc_start: 0.9153 (pmm) cc_final: 0.8865 (pmm)
REVERT: A  517 ARG cc_start: 0.9021 (mtm110) cc_final: 0.8781 (mtm110)
REVERT: B   47 LEU cc_start: 0.9393 (mt) cc_final: 0.9113 (mt)
REVERT: B   62 SER cc_start: 0.8772 (t) cc_final: 0.8521 (p)
REVERT: B   67 MET cc_start: 0.9395 (ppp) cc_final: 0.9156 (ppp)
REVERT: B   90 SER cc_start: 0.9250 (m) cc_final: 0.8574 (p)
REVERT: B  116 PHE cc_start: 0.9322 (m-80) cc_final: 0.8914 (m-80)
REVERT: B  131 ASP cc_start: 0.9332 (m-30) cc_final: 0.9027 (m-30)
REVERT: B  149 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8846 (mm-30)
REVERT: B  196 MET cc_start: 0.9302 (mmm) cc_final: 0.9004 (mmm)
REVERT: B  244 MET cc_start: 0.9320 (ppp) cc_final: 0.8988 (ppp)
REVERT: B  432 THR cc_start: 0.9336 (p) cc_final: 0.9095 (t)
REVERT: B  456 MET cc_start: 0.9124 (pmm) cc_final: 0.8913 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 242
  average time/residue: 0.1634
  time to fit residues: 58.3378
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  : 0.988 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 63 optimal weight:    0.6980
   chunk 4 optimal weight:    0.3980
   chunk 86 optimal weight:    0.9990
   chunk 51 optimal weight:    7.9990
   chunk 55 optimal weight:   20.0000
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    5.9990
   chunk 101 optimal weight:    1.9990
   chunk 106 optimal weight:    9.9990
   chunk 7 optimal weight:    0.8980
   chunk 29 optimal weight:    0.9990
   overall best weight:    0.7984

-------------------------------------------------------------------------------
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 568 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.076489 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.056349 restraints weight = 34571.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.058530 restraints weight = 21585.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.060183 restraints weight = 15291.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8270
moved from start:          0.3684

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8950  Z= 0.122
  Angle     :  0.615   6.341  12092  Z= 0.314
  Chirality :  0.042   0.172   1440
  Planarity :  0.003   0.027   1532
  Dihedral  :  4.206  21.439   1238
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.03 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1134
  helix:  1.45 (0.20), residues: 692
  sheet: -1.37 (0.70), residues: 54
  loop : -1.31 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 568 
 PHE   0.044   0.002   PHE B 319 
 TYR   0.007   0.001   TYR A 572 
 ARG   0.007   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03861 (  553)
  hydrogen bonds       : angle       4.34858 ( 1653)
  covalent geometry    : bond        0.00256 ( 8950)
  covalent geometry    : angle       0.61499 (12092)

*********************** 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
  246 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 245
  time to evaluate  : 1.096 
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: A   98 MET cc_start: 0.9074 (tpp) cc_final: 0.8774 (tpt)
REVERT: A  107 HIS cc_start: 0.8437 (t-90) cc_final: 0.7732 (t-90)
REVERT: A  149 GLU cc_start: 0.9117 (mp0) cc_final: 0.8752 (mp0)
REVERT: A  210 MET cc_start: 0.9300 (tpp) cc_final: 0.8701 (tpt)
REVERT: A  218 LEU cc_start: 0.9598 (mt) cc_final: 0.9348 (mt)
REVERT: A  224 GLU cc_start: 0.8944 (mp0) cc_final: 0.8685 (pm20)
REVERT: A  229 ARG cc_start: 0.9312 (mtp180) cc_final: 0.8913 (mtp180)
REVERT: A  244 MET cc_start: 0.9348 (ppp) cc_final: 0.9027 (ppp)
REVERT: A  261 LEU cc_start: 0.9635 (mm) cc_final: 0.9414 (mm)
REVERT: A  310 ARG cc_start: 0.9351 (ptm160) cc_final: 0.9060 (ptm-80)
REVERT: A  312 MET cc_start: 0.7052 (ttt) cc_final: 0.6683 (tpt)
REVERT: A  382 LYS cc_start: 0.7768 (mmpt) cc_final: 0.7304 (mmtm)
REVERT: A  402 MET cc_start: 0.8565 (mmm) cc_final: 0.8204 (mmm)
REVERT: A  405 HIS cc_start: 0.8810 (m90) cc_final: 0.8491 (m90)
REVERT: B   47 LEU cc_start: 0.9378 (mt) cc_final: 0.9110 (mt)
REVERT: B   62 SER cc_start: 0.8763 (t) cc_final: 0.8502 (p)
REVERT: B   90 SER cc_start: 0.9276 (m) cc_final: 0.8716 (p)
REVERT: B   98 MET cc_start: 0.9229 (tpp) cc_final: 0.8849 (tpp)
REVERT: B  109 MET cc_start: 0.8708 (tmm) cc_final: 0.8267 (tmm)
REVERT: B  116 PHE cc_start: 0.9298 (m-80) cc_final: 0.8909 (m-80)
REVERT: B  131 ASP cc_start: 0.9350 (m-30) cc_final: 0.9011 (m-30)
REVERT: B  196 MET cc_start: 0.9304 (mmm) cc_final: 0.9028 (mmm)
REVERT: B  244 MET cc_start: 0.9323 (ppp) cc_final: 0.8979 (ppp)
REVERT: B  432 THR cc_start: 0.9335 (p) cc_final: 0.9086 (t)
REVERT: B  456 MET cc_start: 0.9149 (pmm) cc_final: 0.8912 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 245
  average time/residue: 0.1682
  time to fit residues: 60.2797
Evaluate side-chains
  194 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 194
  time to evaluate  : 1.043 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 103 optimal weight:    0.9990
   chunk 100 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 104 optimal weight:    0.6980
   chunk 40 optimal weight:    3.9990
   chunk 70 optimal weight:    0.5980
   chunk 74 optimal weight:    4.9990
   chunk 71 optimal weight:    1.9990
   chunk 59 optimal weight:    0.8980
   chunk 30 optimal weight:    2.9990
   chunk 67 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.076829 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.056746 restraints weight = 34811.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.058975 restraints weight = 21674.950|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.060639 restraints weight = 15313.029|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.3837

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= 0.121
  Angle     :  0.611   6.512  12092  Z= 0.312
  Chirality :  0.042   0.160   1440
  Planarity :  0.003   0.028   1532
  Dihedral  :  4.165  21.072   1238
  Min Nonbonded Distance : 2.594

Molprobity Statistics.
  All-atom Clashscore : 11.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.32 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.26), residues: 1134
  helix:  1.46 (0.20), residues: 692
  sheet: -1.31 (0.63), residues: 64
  loop : -1.35 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  17 
 HIS   0.003   0.001   HIS A 214 
 PHE   0.031   0.002   PHE B 319 
 TYR   0.017   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  553)
  hydrogen bonds       : angle       4.30214 ( 1653)
  covalent geometry    : bond        0.00254 ( 8950)
  covalent geometry    : angle       0.61111 (12092)

*********************** 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
  239 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 239
  time to evaluate  : 1.102 
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: 0.9078 (tpp) cc_final: 0.8750 (tpt)
REVERT: A  116 PHE cc_start: 0.9015 (m-80) cc_final: 0.8660 (m-80)
REVERT: A  210 MET cc_start: 0.9312 (tpp) cc_final: 0.8681 (tpt)
REVERT: A  218 LEU cc_start: 0.9593 (mt) cc_final: 0.9338 (mt)
REVERT: A  224 GLU cc_start: 0.8949 (mp0) cc_final: 0.8745 (pm20)
REVERT: A  229 ARG cc_start: 0.9320 (mtp180) cc_final: 0.8922 (mtp180)
REVERT: A  244 MET cc_start: 0.9342 (ppp) cc_final: 0.9026 (ppp)
REVERT: A  261 LEU cc_start: 0.9640 (mm) cc_final: 0.9392 (mm)
REVERT: A  310 ARG cc_start: 0.9346 (ptm160) cc_final: 0.9065 (ptm-80)
REVERT: A  312 MET cc_start: 0.7028 (ttt) cc_final: 0.6659 (tpt)
REVERT: A  382 LYS cc_start: 0.7711 (mmpt) cc_final: 0.7324 (mmtm)
REVERT: A  402 MET cc_start: 0.8570 (mmm) cc_final: 0.8225 (mmm)
REVERT: A  405 HIS cc_start: 0.8750 (m90) cc_final: 0.8433 (m90)
REVERT: A  456 MET cc_start: 0.9156 (pmm) cc_final: 0.8889 (pmm)
REVERT: B   47 LEU cc_start: 0.9382 (mt) cc_final: 0.9101 (mt)
REVERT: B   62 SER cc_start: 0.8801 (t) cc_final: 0.8583 (p)
REVERT: B   64 LEU cc_start: 0.9333 (pp) cc_final: 0.9117 (pp)
REVERT: B   67 MET cc_start: 0.9359 (ppp) cc_final: 0.9121 (ppp)
REVERT: B   98 MET cc_start: 0.9227 (tpp) cc_final: 0.8785 (tpp)
REVERT: B  109 MET cc_start: 0.8690 (tmm) cc_final: 0.8262 (tmm)
REVERT: B  111 MET cc_start: 0.8919 (ttt) cc_final: 0.8485 (tmm)
REVERT: B  116 PHE cc_start: 0.9283 (m-80) cc_final: 0.9063 (m-10)
REVERT: B  131 ASP cc_start: 0.9321 (m-30) cc_final: 0.8967 (m-30)
REVERT: B  196 MET cc_start: 0.9297 (mmm) cc_final: 0.9035 (mmm)
REVERT: B  244 MET cc_start: 0.9343 (ppp) cc_final: 0.8982 (ppp)
REVERT: B  432 THR cc_start: 0.9337 (p) cc_final: 0.9086 (t)
REVERT: B  456 MET cc_start: 0.9161 (pmm) cc_final: 0.8921 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 239
  average time/residue: 0.1746
  time to fit residues: 61.3527
Evaluate side-chains
  199 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.064 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 40 optimal weight:    9.9990
   chunk 96 optimal weight:    5.9990
   chunk 51 optimal weight:    3.9990
   chunk 85 optimal weight:    0.9980
   chunk 43 optimal weight:    6.9990
   chunk 102 optimal weight:    5.9990
   chunk 99 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 86 optimal weight:    0.8980
   chunk 41 optimal weight:    8.9990
   chunk 49 optimal weight:    2.9990
   overall best weight:    1.5584

-------------------------------------------------------------------------------
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 = 0.3414 r_free = 0.3414 target = 0.074287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.054467 restraints weight = 35408.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.056620 restraints weight = 21672.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.058209 restraints weight = 15199.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3923

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   8950  Z= 0.158
  Angle     :  0.647   8.428  12092  Z= 0.334
  Chirality :  0.043   0.187   1440
  Planarity :  0.003   0.032   1532
  Dihedral  :  4.199  19.102   1238
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.25), residues: 1134
  helix:  1.52 (0.20), residues: 692
  sheet: -1.33 (0.62), residues: 64
  loop : -1.40 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP B  17 
 HIS   0.004   0.001   HIS A 427 
 PHE   0.026   0.002   PHE B  23 
 TYR   0.011   0.001   TYR B 393 
 ARG   0.007   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03922 (  553)
  hydrogen bonds       : angle       4.35264 ( 1653)
  covalent geometry    : bond        0.00331 ( 8950)
  covalent geometry    : angle       0.64701 (12092)

*********************** 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
  235 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 235
  time to evaluate  : 0.963 
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: A   74 LEU cc_start: 0.9417 (mt) cc_final: 0.9217 (mt)
REVERT: A  210 MET cc_start: 0.9359 (tpp) cc_final: 0.8741 (tpp)
REVERT: A  218 LEU cc_start: 0.9615 (mt) cc_final: 0.9375 (mt)
REVERT: A  224 GLU cc_start: 0.9012 (mp0) cc_final: 0.8755 (pm20)
REVERT: A  244 MET cc_start: 0.9348 (ppp) cc_final: 0.9041 (ppp)
REVERT: A  261 LEU cc_start: 0.9657 (mm) cc_final: 0.9447 (mm)
REVERT: A  291 MET cc_start: 0.9488 (mmp) cc_final: 0.9244 (mmm)
REVERT: A  310 ARG cc_start: 0.9382 (ptm160) cc_final: 0.9100 (ptm-80)
REVERT: A  312 MET cc_start: 0.7167 (ttt) cc_final: 0.6916 (tpt)
REVERT: A  382 LYS cc_start: 0.7654 (mmpt) cc_final: 0.7295 (mmmt)
REVERT: A  402 MET cc_start: 0.8597 (mmm) cc_final: 0.8291 (mmm)
REVERT: A  405 HIS cc_start: 0.8683 (m90) cc_final: 0.8346 (m90)
REVERT: B   47 LEU cc_start: 0.9423 (mt) cc_final: 0.9157 (mt)
REVERT: B   62 SER cc_start: 0.8800 (t) cc_final: 0.8592 (p)
REVERT: B  109 MET cc_start: 0.8723 (tmm) cc_final: 0.8332 (tmm)
REVERT: B  111 MET cc_start: 0.8970 (ttt) cc_final: 0.8507 (tmm)
REVERT: B  116 PHE cc_start: 0.9315 (m-80) cc_final: 0.9108 (m-10)
REVERT: B  131 ASP cc_start: 0.9325 (m-30) cc_final: 0.8969 (m-30)
REVERT: B  196 MET cc_start: 0.9333 (mmm) cc_final: 0.9029 (mmm)
REVERT: B  244 MET cc_start: 0.9366 (ppp) cc_final: 0.8995 (ppp)
REVERT: B  456 MET cc_start: 0.9223 (pmm) cc_final: 0.8969 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 235
  average time/residue: 0.1747
  time to fit residues: 59.7593
Evaluate side-chains
  193 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 74 optimal weight:    4.9990
   chunk 27 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9990
   chunk 78 optimal weight:    0.7980
   chunk 6 optimal weight:    1.9990
   chunk 79 optimal weight:    0.8980
   chunk 16 optimal weight:    0.5980
   chunk 87 optimal weight:    0.9980
   chunk 77 optimal weight:    2.9990
   chunk 49 optimal weight:    9.9990
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 240 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 = 0.3448 r_free = 0.3448 target = 0.076108 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.055980 restraints weight = 35030.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.058181 restraints weight = 21705.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.059830 restraints weight = 15329.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.4046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   8950  Z= 0.128
  Angle     :  0.658   8.580  12092  Z= 0.333
  Chirality :  0.043   0.185   1440
  Planarity :  0.003   0.030   1532
  Dihedral  :  4.207  20.023   1238
  Min Nonbonded Distance : 2.460

Molprobity Statistics.
  All-atom Clashscore : 12.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.25), residues: 1134
  helix:  1.50 (0.20), residues: 692
  sheet: -1.34 (0.62), residues: 64
  loop : -1.39 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B  17 
 HIS   0.011   0.002   HIS A 568 
 PHE   0.028   0.002   PHE A 105 
 TYR   0.015   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03768 (  553)
  hydrogen bonds       : angle       4.37856 ( 1653)
  covalent geometry    : bond        0.00278 ( 8950)
  covalent geometry    : angle       0.65838 (12092)

*********************** 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
  229 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 228
  time to evaluate  : 2.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.9399 (mt) cc_final: 0.9197 (mt)
REVERT: A   98 MET cc_start: 0.9026 (tpp) cc_final: 0.8655 (tpt)
REVERT: A  210 MET cc_start: 0.9341 (tpp) cc_final: 0.8701 (tpp)
REVERT: A  218 LEU cc_start: 0.9577 (mt) cc_final: 0.9332 (mt)
REVERT: A  224 GLU cc_start: 0.9013 (mp0) cc_final: 0.8781 (pm20)
REVERT: A  244 MET cc_start: 0.9358 (ppp) cc_final: 0.9035 (ppp)
REVERT: A  261 LEU cc_start: 0.9632 (mm) cc_final: 0.9390 (mm)
REVERT: A  310 ARG cc_start: 0.9378 (ptm160) cc_final: 0.9114 (ptm-80)
REVERT: A  312 MET cc_start: 0.7026 (ttt) cc_final: 0.6154 (tpt)
REVERT: A  382 LYS cc_start: 0.7618 (mmpt) cc_final: 0.7359 (mptt)
REVERT: A  402 MET cc_start: 0.8545 (mmm) cc_final: 0.8267 (mmm)
REVERT: A  405 HIS cc_start: 0.8722 (m90) cc_final: 0.8410 (m90)
REVERT: B   47 LEU cc_start: 0.9375 (mt) cc_final: 0.9090 (mt)
REVERT: B   62 SER cc_start: 0.8829 (t) cc_final: 0.8624 (p)
REVERT: B   67 MET cc_start: 0.9339 (ppp) cc_final: 0.9079 (ppp)
REVERT: B  111 MET cc_start: 0.8944 (ttt) cc_final: 0.8466 (tmm)
REVERT: B  131 ASP cc_start: 0.9329 (m-30) cc_final: 0.8966 (m-30)
REVERT: B  196 MET cc_start: 0.9319 (mmm) cc_final: 0.9054 (mmm)
REVERT: B  242 MET cc_start: 0.9459 (mmt) cc_final: 0.9217 (mmt)
REVERT: B  244 MET cc_start: 0.9353 (ppp) cc_final: 0.8980 (ppp)
REVERT: B  432 THR cc_start: 0.9390 (p) cc_final: 0.9142 (t)
REVERT: B  456 MET cc_start: 0.9187 (pmm) cc_final: 0.8942 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 228
  average time/residue: 0.2345
  time to fit residues: 78.9212
Evaluate side-chains
  191 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 191
  time to evaluate  : 1.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 24 optimal weight:    0.0980
   chunk 95 optimal weight:    0.1980
   chunk 72 optimal weight:    0.8980
   chunk 70 optimal weight:    0.6980
   chunk 87 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 8 optimal weight:    1.9990
   chunk 88 optimal weight:    0.6980
   chunk 100 optimal weight:    5.9990
   chunk 68 optimal weight:    0.5980
   overall best weight:    0.4580

-------------------------------------------------------------------------------
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 = 0.3462 r_free = 0.3462 target = 0.076536 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.056887 restraints weight = 33822.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.059117 restraints weight = 20800.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 19)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.060765 restraints weight = 14587.605|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8246
moved from start:          0.4161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   8950  Z= 0.122
  Angle     :  0.659   8.635  12092  Z= 0.329
  Chirality :  0.043   0.169   1440
  Planarity :  0.003   0.030   1532
  Dihedral  :  4.161  19.861   1238
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.56 (0.25), residues: 1134
  helix:  1.46 (0.20), residues: 692
  sheet: -1.30 (0.62), residues: 64
  loop : -1.39 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B  17 
 HIS   0.007   0.001   HIS B 214 
 PHE   0.022   0.001   PHE A 105 
 TYR   0.006   0.001   TYR A 572 
 ARG   0.004   0.000   ARG B 229 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03723 (  553)
  hydrogen bonds       : angle       4.33630 ( 1653)
  covalent geometry    : bond        0.00259 ( 8950)
  covalent geometry    : angle       0.65937 (12092)

********************** 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
  240 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.022 
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: 0.9398 (mt) cc_final: 0.9182 (mt)
REVERT: A   90 SER cc_start: 0.9417 (t) cc_final: 0.9215 (t)
REVERT: A   98 MET cc_start: 0.9020 (tpp) cc_final: 0.8647 (tpt)
REVERT: A  210 MET cc_start: 0.9332 (tpp) cc_final: 0.9001 (tpp)
REVERT: A  218 LEU cc_start: 0.9555 (mt) cc_final: 0.9316 (mt)
REVERT: A  224 GLU cc_start: 0.9001 (mp0) cc_final: 0.8592 (tp30)
REVERT: A  244 MET cc_start: 0.9346 (ppp) cc_final: 0.9052 (ppp)
REVERT: A  261 LEU cc_start: 0.9610 (mm) cc_final: 0.9372 (mm)
REVERT: A  310 ARG cc_start: 0.9356 (ptm160) cc_final: 0.9097 (ptm-80)
REVERT: A  382 LYS cc_start: 0.7642 (mmpt) cc_final: 0.7376 (mmtm)
REVERT: A  402 MET cc_start: 0.8546 (mmm) cc_final: 0.8289 (mmm)
REVERT: A  405 HIS cc_start: 0.8689 (m90) cc_final: 0.8376 (m90)
REVERT: B   47 LEU cc_start: 0.9345 (mt) cc_final: 0.9061 (mt)
REVERT: B   67 MET cc_start: 0.9340 (ppp) cc_final: 0.9095 (ppp)
REVERT: B  109 MET cc_start: 0.8495 (tmm) cc_final: 0.8108 (tmm)
REVERT: B  111 MET cc_start: 0.8889 (ttt) cc_final: 0.8250 (tmm)
REVERT: B  131 ASP cc_start: 0.9296 (m-30) cc_final: 0.8929 (m-30)
REVERT: B  196 MET cc_start: 0.9298 (mmm) cc_final: 0.9048 (mmm)
REVERT: B  242 MET cc_start: 0.9457 (mmt) cc_final: 0.9236 (mmt)
REVERT: B  244 MET cc_start: 0.9353 (ppp) cc_final: 0.8974 (ppp)
REVERT: B  432 THR cc_start: 0.9384 (p) cc_final: 0.9124 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.1759
  time to fit residues: 61.5847
Evaluate side-chains
  193 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 193
  time to evaluate  : 1.062 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 78 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 40 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 86 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 111 optimal weight:    9.9990
   chunk 102 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 87 optimal weight:    0.9990
   overall best weight:    0.8384

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.076810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.056795 restraints weight = 34854.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.058983 restraints weight = 21567.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.060653 restraints weight = 15312.043|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.4304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   8950  Z= 0.130
  Angle     :  0.682   9.321  12092  Z= 0.343
  Chirality :  0.043   0.183   1440
  Planarity :  0.004   0.096   1532
  Dihedral  :  4.198  19.276   1238
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 13.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.54 (0.25), residues: 1134
  helix:  1.45 (0.20), residues: 692
  sheet: -1.39 (0.61), residues: 64
  loop : -1.38 (0.33), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B  17 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.034   0.002   PHE B 230 
 TYR   0.012   0.001   TYR B 393 
 ARG   0.007   0.000   ARG B 102 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03789 (  553)
  hydrogen bonds       : angle       4.36994 ( 1653)
  covalent geometry    : bond        0.00285 ( 8950)
  covalent geometry    : angle       0.68244 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3554.58 seconds
wall clock time: 63 minutes 38.80 seconds (3818.80 seconds total)