Starting phenix.real_space_refine
on Mon May 12 09:59:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fuy_50782/05_2025/9fuy_50782.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fuy_50782/05_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_50782/05_2025/9fuy_50782.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fuy_50782/05_2025/9fuy_50782.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fuy_50782/05_2025/9fuy_50782.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fuy_50782/05_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-5687/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: 5.99, per 1000 atoms: 0.68
  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: 2.55
  Conformation dependent library (CDL) restraints added in 1.1 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: 2.47

  Time building geometry restraints manager: 2.94 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:             5.090
  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:          0.400
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     23.510
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.040
  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:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.160
-------------------------------------------------------------------------------
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  : 1.027 
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: 0.1593
  time to fit residues: 52.9394
Evaluate side-chains
  208 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 204
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
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 = 0.3432 r_free = 0.3432 target = 0.075250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.056130 restraints weight = 33977.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.058368 restraints weight = 20233.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.060004 restraints weight = 13931.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3131
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
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       4.93028 ( 1653)
  covalent geometry    : bond        0.00326 ( 8950)
  covalent geometry    : angle       0.66106 (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  : 1.112 
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: 0.9161 (tpp) cc_final: 0.8860 (tpp)
REVERT: A  107 HIS cc_start: 0.8592 (t-90) cc_final: 0.7794 (t-170)
REVERT: A  109 MET cc_start: 0.9287 (mmp) cc_final: 0.8963 (mmp)
REVERT: A  216 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8926 (pt0)
REVERT: A  218 LEU cc_start: 0.9643 (mt) cc_final: 0.9355 (mt)
REVERT: A  244 MET cc_start: 0.9261 (ppp) cc_final: 0.8984 (ppp)
REVERT: A  261 LEU cc_start: 0.9624 (mm) cc_final: 0.9422 (mm)
REVERT: A  263 LEU cc_start: 0.9704 (tt) cc_final: 0.9456 (tt)
REVERT: A  312 MET cc_start: 0.7293 (ttt) cc_final: 0.6868 (tpt)
REVERT: A  382 LYS cc_start: 0.7911 (mmpt) cc_final: 0.7258 (mmtm)
REVERT: A  405 HIS cc_start: 0.8958 (m90) cc_final: 0.8699 (m90)
REVERT: A  523 LEU cc_start: 0.9043 (mt) cc_final: 0.8802 (mt)
REVERT: B   47 LEU cc_start: 0.9378 (mt) cc_final: 0.9134 (mt)
REVERT: B   62 SER cc_start: 0.8724 (t) cc_final: 0.8427 (p)
REVERT: B  111 MET cc_start: 0.9041 (ttt) cc_final: 0.8837 (ttt)
REVERT: B  131 ASP cc_start: 0.9290 (m-30) cc_final: 0.9084 (m-30)
REVERT: B  149 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8424 (mp0)
REVERT: B  196 MET cc_start: 0.9231 (mmm) cc_final: 0.8905 (mmm)
REVERT: B  210 MET cc_start: 0.8975 (tpp) cc_final: 0.8665 (tpp)
REVERT: B  244 MET cc_start: 0.9284 (ppp) cc_final: 0.8999 (ppp)
REVERT: B  456 MET cc_start: 0.9131 (pmm) cc_final: 0.8872 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 259
  average time/residue: 0.1745
  time to fit residues: 65.5049
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  : 1.025 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 62 optimal weight:    2.9990
   chunk 4 optimal weight:    4.9990
   chunk 46 optimal weight:    9.9990
   chunk 27 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 52 optimal weight:    0.0670
   chunk 16 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   chunk 82 optimal weight:    4.9990
   overall best weight:    1.9524

-------------------------------------------------------------------------------
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 = 0.3386 r_free = 0.3386 target = 0.072868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.053505 restraints weight = 35274.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.055619 restraints weight = 21118.049|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.057150 restraints weight = 14640.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3062
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.3028

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   8950  Z= 0.196
  Angle     :  0.657   7.364  12092  Z= 0.349
  Chirality :  0.043   0.168   1440
  Planarity :  0.004   0.037   1532
  Dihedral  :  4.570  21.020   1238
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.67 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.82 %
    Favored  : 96.07 %
  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:  0.55 (0.26), residues: 1134
  helix:  1.36 (0.19), residues: 694
  sheet: -1.37 (0.71), residues: 54
  loop : -1.20 (0.34), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  17 
 HIS   0.004   0.001   HIS B 568 
 PHE   0.028   0.002   PHE B  23 
 TYR   0.014   0.001   TYR B 439 
 ARG   0.006   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04478 (  553)
  hydrogen bonds       : angle       4.74832 ( 1653)
  covalent geometry    : bond        0.00395 ( 8950)
  covalent geometry    : angle       0.65684 (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
  243 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 242
  time to evaluate  : 1.077 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8648 (t-90) cc_final: 0.7769 (t-170)
REVERT: A  109 MET cc_start: 0.9387 (mmp) cc_final: 0.8902 (mmp)
REVERT: A  111 MET cc_start: 0.8908 (tmm) cc_final: 0.8676 (tmm)
REVERT: A  149 GLU cc_start: 0.9178 (mp0) cc_final: 0.8783 (mp0)
REVERT: A  214 HIS cc_start: 0.8711 (t-170) cc_final: 0.8425 (t-170)
REVERT: A  216 GLU cc_start: 0.9286 (mt-10) cc_final: 0.8990 (mt-10)
REVERT: A  244 MET cc_start: 0.9280 (ppp) cc_final: 0.8985 (ppp)
REVERT: A  263 LEU cc_start: 0.9707 (tt) cc_final: 0.9438 (tt)
REVERT: A  312 MET cc_start: 0.7459 (ttt) cc_final: 0.6943 (tpt)
REVERT: A  322 LEU cc_start: 0.9614 (tp) cc_final: 0.9308 (tp)
REVERT: A  382 LYS cc_start: 0.7696 (mmpt) cc_final: 0.7117 (mmtm)
REVERT: A  402 MET cc_start: 0.8550 (mmm) cc_final: 0.8295 (mmm)
REVERT: A  405 HIS cc_start: 0.8866 (m90) cc_final: 0.8578 (m90)
REVERT: A  517 ARG cc_start: 0.9074 (mtm110) cc_final: 0.8824 (mtm110)
REVERT: B   47 LEU cc_start: 0.9395 (mt) cc_final: 0.9135 (mt)
REVERT: B   62 SER cc_start: 0.8770 (t) cc_final: 0.8504 (p)
REVERT: B   71 VAL cc_start: 0.9249 (t) cc_final: 0.8880 (t)
REVERT: B   90 SER cc_start: 0.9320 (m) cc_final: 0.8615 (p)
REVERT: B  131 ASP cc_start: 0.9333 (m-30) cc_final: 0.9091 (m-30)
REVERT: B  149 GLU cc_start: 0.9132 (mm-30) cc_final: 0.8893 (mm-30)
REVERT: B  196 MET cc_start: 0.9291 (mmm) cc_final: 0.8995 (mmm)
REVERT: B  244 MET cc_start: 0.9323 (ppp) cc_final: 0.9005 (ppp)
REVERT: B  284 ILE cc_start: 0.9120 (tt) cc_final: 0.8849 (tp)
REVERT: B  456 MET cc_start: 0.9132 (pmm) cc_final: 0.8814 (pmm)
REVERT: B  460 MET cc_start: 0.8615 (tmm) cc_final: 0.8327 (tmm)
  outliers start: 1
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1756
  time to fit residues: 61.7625
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  : 0.968 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 98 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 16 optimal weight:    0.9990
   chunk 92 optimal weight:    0.9990
   chunk 99 optimal weight:    4.9990
   chunk 107 optimal weight:    7.9990
   chunk 2 optimal weight:    0.7980
   chunk 77 optimal weight:    0.3980
   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 = 0.3422 r_free = 0.3422 target = 0.074577 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.054996 restraints weight = 34520.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.057155 restraints weight = 20952.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.058766 restraints weight = 14620.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3298

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= 0.132
  Angle     :  0.620   7.838  12092  Z= 0.318
  Chirality :  0.042   0.154   1440
  Planarity :  0.003   0.025   1532
  Dihedral  :  4.388  22.634   1238
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.14 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.96 %
    Favored  : 97.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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 (0.26), residues: 1134
  helix:  1.43 (0.19), residues: 694
  sheet: -1.28 (0.74), residues: 54
  loop : -1.25 (0.33), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  91 
 HIS   0.004   0.001   HIS B 568 
 PHE   0.027   0.002   PHE B 230 
 TYR   0.009   0.001   TYR A 572 
 ARG   0.006   0.000   ARG B 441 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04074 (  553)
  hydrogen bonds       : angle       4.53361 ( 1653)
  covalent geometry    : bond        0.00272 ( 8950)
  covalent geometry    : angle       0.61952 (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
  239 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 238
  time to evaluate  : 0.965 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ARG cc_start: 0.6249 (mtm180) cc_final: 0.5802 (mtt180)
REVERT: A   98 MET cc_start: 0.9092 (tpp) cc_final: 0.8814 (tpt)
REVERT: A  107 HIS cc_start: 0.8569 (t-90) cc_final: 0.7943 (t-90)
REVERT: A  109 MET cc_start: 0.9322 (mmp) cc_final: 0.8915 (mmp)
REVERT: A  111 MET cc_start: 0.8838 (tmm) cc_final: 0.8583 (tmm)
REVERT: A  200 MET cc_start: 0.9412 (ptt) cc_final: 0.9149 (ptt)
REVERT: A  214 HIS cc_start: 0.8465 (t-170) cc_final: 0.7750 (t-170)
REVERT: A  216 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8860 (pt0)
REVERT: A  218 LEU cc_start: 0.9606 (mt) cc_final: 0.9270 (mt)
REVERT: A  224 GLU cc_start: 0.8982 (mp0) cc_final: 0.8779 (pm20)
REVERT: A  240 GLN cc_start: 0.8590 (tp40) cc_final: 0.8336 (tp40)
REVERT: A  244 MET cc_start: 0.9290 (ppp) cc_final: 0.8969 (ppp)
REVERT: A  261 LEU cc_start: 0.9640 (mm) cc_final: 0.9406 (mm)
REVERT: A  312 MET cc_start: 0.7382 (ttt) cc_final: 0.6928 (tpt)
REVERT: A  382 LYS cc_start: 0.7650 (mmpt) cc_final: 0.7102 (mmtm)
REVERT: A  402 MET cc_start: 0.8601 (mmm) cc_final: 0.8354 (mmm)
REVERT: A  405 HIS cc_start: 0.8830 (m90) cc_final: 0.8539 (m90)
REVERT: A  432 THR cc_start: 0.9121 (p) cc_final: 0.8919 (t)
REVERT: A  456 MET cc_start: 0.9147 (pmm) cc_final: 0.8875 (pmm)
REVERT: B   47 LEU cc_start: 0.9371 (mt) cc_final: 0.9103 (mt)
REVERT: B   62 SER cc_start: 0.8782 (t) cc_final: 0.8530 (p)
REVERT: B   67 MET cc_start: 0.9401 (tmm) cc_final: 0.9063 (ppp)
REVERT: B   90 SER cc_start: 0.9286 (m) cc_final: 0.8614 (p)
REVERT: B  116 PHE cc_start: 0.9337 (m-80) cc_final: 0.8952 (m-80)
REVERT: B  131 ASP cc_start: 0.9340 (m-30) cc_final: 0.9055 (m-30)
REVERT: B  149 GLU cc_start: 0.9056 (mm-30) cc_final: 0.8821 (mm-30)
REVERT: B  196 MET cc_start: 0.9316 (mmm) cc_final: 0.9005 (mmm)
REVERT: B  210 MET cc_start: 0.8823 (tpp) cc_final: 0.8433 (tpt)
REVERT: B  242 MET cc_start: 0.9506 (mmt) cc_final: 0.9244 (mmt)
REVERT: B  244 MET cc_start: 0.9303 (ppp) cc_final: 0.8987 (ppp)
REVERT: B  456 MET cc_start: 0.9150 (pmm) cc_final: 0.8800 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 238
  average time/residue: 0.1598
  time to fit residues: 56.4082
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  : 1.021 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 35 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   chunk 57 optimal weight:    4.9990
   chunk 11 optimal weight:    0.9980
   chunk 70 optimal weight:    0.9980
   chunk 65 optimal weight:    0.8980
   chunk 40 optimal weight:    7.9990
   chunk 9 optimal weight:    2.9990
   chunk 60 optimal weight:    0.0980
   chunk 66 optimal weight:    0.0010
   overall best weight:    0.5986

-------------------------------------------------------------------------------
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 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.075831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.055971 restraints weight = 34141.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.058145 restraints weight = 20995.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.059780 restraints weight = 14753.227|
|-----------------------------------------------------------------------------|
r_work (final): 0.3111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8261
moved from start:          0.3520

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= 0.121
  Angle     :  0.609   6.260  12092  Z= 0.311
  Chirality :  0.042   0.182   1440
  Planarity :  0.003   0.026   1532
  Dihedral  :  4.319  21.801   1238
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 12.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    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:  0.60 (0.26), residues: 1134
  helix:  1.46 (0.20), residues: 692
  sheet: -1.36 (0.70), residues: 54
  loop : -1.30 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  91 
 HIS   0.010   0.001   HIS B 214 
 PHE   0.022   0.001   PHE B 230 
 TYR   0.012   0.001   TYR A 439 
 ARG   0.005   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03893 (  553)
  hydrogen bonds       : angle       4.41691 ( 1653)
  covalent geometry    : bond        0.00253 ( 8950)
  covalent geometry    : angle       0.60864 (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
  243 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 243
  time to evaluate  : 0.966 
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: 0.9072 (tpp) cc_final: 0.8733 (tpt)
REVERT: A  107 HIS cc_start: 0.8524 (t-90) cc_final: 0.7820 (t-90)
REVERT: A  111 MET cc_start: 0.8882 (tmm) cc_final: 0.8640 (tmm)
REVERT: A  200 MET cc_start: 0.9418 (ptt) cc_final: 0.9112 (ptt)
REVERT: A  210 MET cc_start: 0.9320 (tpp) cc_final: 0.9072 (tpt)
REVERT: A  214 HIS cc_start: 0.8415 (t-170) cc_final: 0.7779 (t-170)
REVERT: A  216 GLU cc_start: 0.9299 (mt-10) cc_final: 0.8875 (pt0)
REVERT: A  218 LEU cc_start: 0.9595 (mt) cc_final: 0.9223 (mt)
REVERT: A  229 ARG cc_start: 0.9322 (mtp180) cc_final: 0.9046 (mtp180)
REVERT: A  240 GLN cc_start: 0.8553 (tp40) cc_final: 0.8309 (tp40)
REVERT: A  244 MET cc_start: 0.9316 (ppp) cc_final: 0.9060 (ppp)
REVERT: A  261 LEU cc_start: 0.9633 (mm) cc_final: 0.9391 (mm)
REVERT: A  312 MET cc_start: 0.7210 (ttt) cc_final: 0.6737 (tpt)
REVERT: A  402 MET cc_start: 0.8676 (mmm) cc_final: 0.8432 (mmm)
REVERT: A  405 HIS cc_start: 0.8797 (m90) cc_final: 0.8494 (m90)
REVERT: A  456 MET cc_start: 0.9155 (pmm) cc_final: 0.8868 (pmm)
REVERT: B   47 LEU cc_start: 0.9361 (mt) cc_final: 0.9088 (mt)
REVERT: B   62 SER cc_start: 0.8759 (t) cc_final: 0.8541 (p)
REVERT: B   64 LEU cc_start: 0.9365 (pp) cc_final: 0.9134 (pp)
REVERT: B   67 MET cc_start: 0.9398 (tmm) cc_final: 0.9122 (ppp)
REVERT: B   90 SER cc_start: 0.9254 (m) cc_final: 0.8587 (p)
REVERT: B  111 MET cc_start: 0.9047 (ttt) cc_final: 0.8801 (ttt)
REVERT: B  116 PHE cc_start: 0.9332 (m-80) cc_final: 0.8917 (m-80)
REVERT: B  131 ASP cc_start: 0.9319 (m-30) cc_final: 0.9019 (m-30)
REVERT: B  149 GLU cc_start: 0.9039 (mm-30) cc_final: 0.8801 (mm-30)
REVERT: B  196 MET cc_start: 0.9307 (mmm) cc_final: 0.9009 (mmm)
REVERT: B  218 LEU cc_start: 0.9203 (mm) cc_final: 0.8967 (tp)
REVERT: B  244 MET cc_start: 0.9313 (ppp) cc_final: 0.8974 (ppp)
REVERT: B  432 THR cc_start: 0.9369 (p) cc_final: 0.9113 (t)
REVERT: B  456 MET cc_start: 0.9127 (pmm) cc_final: 0.8865 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 243
  average time/residue: 0.1556
  time to fit residues: 56.1979
Evaluate side-chains
  198 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 86 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0170
   chunk 55 optimal weight:   20.0000
   chunk 33 optimal weight:    4.9990
   chunk 21 optimal weight:    6.9990
   chunk 101 optimal weight:    0.0370
   chunk 106 optimal weight:    0.0770
   chunk 7 optimal weight:    0.8980
   chunk 29 optimal weight:    0.6980
   overall best weight:    0.3454

-------------------------------------------------------------------------------
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 = 0.3464 r_free = 0.3464 target = 0.076791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3070 r_free = 0.3070 target = 0.057153 restraints weight = 33587.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.059329 restraints weight = 20730.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.061003 restraints weight = 14614.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.3781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8950  Z= 0.115
  Angle     :  0.613   7.960  12092  Z= 0.310
  Chirality :  0.042   0.175   1440
  Planarity :  0.003   0.027   1532
  Dihedral  :  4.197  22.030   1238
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.55 %
    Favored  : 98.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.39 (0.70), residues: 54
  loop : -1.29 (0.33), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  91 
 HIS   0.007   0.001   HIS B 214 
 PHE   0.040   0.002   PHE B 319 
 TYR   0.010   0.001   TYR B 393 
 ARG   0.005   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03773 (  553)
  hydrogen bonds       : angle       4.33249 ( 1653)
  covalent geometry    : bond        0.00236 ( 8950)
  covalent geometry    : angle       0.61275 (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
  237 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 236
  time to evaluate  : 1.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   98 MET cc_start: 0.9088 (tpp) cc_final: 0.8723 (tpt)
REVERT: A  107 HIS cc_start: 0.8412 (t-90) cc_final: 0.7688 (t-90)
REVERT: A  111 MET cc_start: 0.8829 (tmm) cc_final: 0.8595 (tmm)
REVERT: A  214 HIS cc_start: 0.8468 (t-170) cc_final: 0.7823 (t-170)
REVERT: A  216 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8894 (pt0)
REVERT: A  218 LEU cc_start: 0.9571 (mt) cc_final: 0.9229 (mt)
REVERT: A  224 GLU cc_start: 0.8961 (mp0) cc_final: 0.8710 (pm20)
REVERT: A  229 ARG cc_start: 0.9341 (mtp180) cc_final: 0.9009 (mtp180)
REVERT: A  244 MET cc_start: 0.9368 (ppp) cc_final: 0.9034 (ppp)
REVERT: A  261 LEU cc_start: 0.9620 (mm) cc_final: 0.9387 (mm)
REVERT: A  312 MET cc_start: 0.7004 (ttt) cc_final: 0.6628 (tpt)
REVERT: A  382 LYS cc_start: 0.7583 (mmpt) cc_final: 0.7181 (mmtm)
REVERT: A  402 MET cc_start: 0.8714 (mmm) cc_final: 0.8471 (mmm)
REVERT: A  405 HIS cc_start: 0.8753 (m90) cc_final: 0.8446 (m90)
REVERT: B   47 LEU cc_start: 0.9330 (mt) cc_final: 0.9077 (mt)
REVERT: B   62 SER cc_start: 0.8748 (t) cc_final: 0.8479 (p)
REVERT: B   98 MET cc_start: 0.9133 (tpp) cc_final: 0.7942 (tpp)
REVERT: B  102 ARG cc_start: 0.9231 (ttm110) cc_final: 0.8992 (mtm-85)
REVERT: B  109 MET cc_start: 0.8688 (tmm) cc_final: 0.8228 (tmm)
REVERT: B  116 PHE cc_start: 0.9302 (m-80) cc_final: 0.8941 (m-80)
REVERT: B  131 ASP cc_start: 0.9318 (m-30) cc_final: 0.9009 (m-30)
REVERT: B  196 MET cc_start: 0.9302 (mmm) cc_final: 0.9047 (mmm)
REVERT: B  218 LEU cc_start: 0.9220 (mm) cc_final: 0.8848 (tp)
REVERT: B  244 MET cc_start: 0.9324 (ppp) cc_final: 0.8977 (ppp)
REVERT: B  432 THR cc_start: 0.9356 (p) cc_final: 0.9109 (t)
REVERT: B  456 MET cc_start: 0.9120 (pmm) cc_final: 0.8899 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 236
  average time/residue: 0.1618
  time to fit residues: 55.9546
Evaluate side-chains
  200 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.949 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 100 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   chunk 104 optimal weight:    0.7980
   chunk 40 optimal weight:    7.9990
   chunk 70 optimal weight:    0.8980
   chunk 74 optimal weight:    4.9990
   chunk 71 optimal weight:    0.9990
   chunk 59 optimal weight:    2.9990
   chunk 30 optimal weight:    3.9990
   chunk 67 optimal weight:    4.9990
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3440 r_free = 0.3440 target = 0.075413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.055751 restraints weight = 34554.879|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.057840 restraints weight = 21329.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.059445 restraints weight = 15128.782|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8280
moved from start:          0.3858

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= 0.133
  Angle     :  0.627   7.644  12092  Z= 0.321
  Chirality :  0.042   0.165   1440
  Planarity :  0.003   0.027   1532
  Dihedral  :  4.174  20.444   1238
  Min Nonbonded Distance : 2.597

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.41 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.93 %
    Favored  : 99.07 %
  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:  0.69 (0.26), residues: 1134
  helix:  1.53 (0.20), residues: 694
  sheet: -1.48 (0.68), residues: 54
  loop : -1.23 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  17 
 HIS   0.006   0.001   HIS B 214 
 PHE   0.029   0.002   PHE B 319 
 TYR   0.008   0.001   TYR B 393 
 ARG   0.005   0.000   ARG A 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03795 (  553)
  hydrogen bonds       : angle       4.33614 ( 1653)
  covalent geometry    : bond        0.00280 ( 8950)
  covalent geometry    : angle       0.62743 (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
  233 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 1.060 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8438 (t-90) cc_final: 0.7685 (t-90)
REVERT: A  149 GLU cc_start: 0.9208 (mp0) cc_final: 0.8831 (mp0)
REVERT: A  210 MET cc_start: 0.9330 (tpp) cc_final: 0.8750 (tpt)
REVERT: A  214 HIS cc_start: 0.8549 (t-170) cc_final: 0.8049 (t-170)
REVERT: A  218 LEU cc_start: 0.9595 (mt) cc_final: 0.9239 (mt)
REVERT: A  224 GLU cc_start: 0.8996 (mp0) cc_final: 0.8729 (pm20)
REVERT: A  229 ARG cc_start: 0.9345 (mtp180) cc_final: 0.9058 (mtp180)
REVERT: A  244 MET cc_start: 0.9376 (ppp) cc_final: 0.9060 (ppp)
REVERT: A  261 LEU cc_start: 0.9634 (mm) cc_final: 0.9380 (mm)
REVERT: A  312 MET cc_start: 0.7119 (ttt) cc_final: 0.6775 (tpt)
REVERT: A  382 LYS cc_start: 0.7739 (mmpt) cc_final: 0.7326 (mmtm)
REVERT: A  402 MET cc_start: 0.8727 (mmm) cc_final: 0.8471 (mmm)
REVERT: A  405 HIS cc_start: 0.8698 (m90) cc_final: 0.8381 (m90)
REVERT: A  456 MET cc_start: 0.9207 (pmm) cc_final: 0.8758 (pmm)
REVERT: B   47 LEU cc_start: 0.9372 (mt) cc_final: 0.9079 (mt)
REVERT: B   62 SER cc_start: 0.8761 (t) cc_final: 0.8539 (p)
REVERT: B   64 LEU cc_start: 0.9334 (pp) cc_final: 0.9109 (pp)
REVERT: B   67 MET cc_start: 0.9490 (ppp) cc_final: 0.9246 (ppp)
REVERT: B   98 MET cc_start: 0.9116 (tpp) cc_final: 0.8797 (tpp)
REVERT: B  116 PHE cc_start: 0.9321 (m-80) cc_final: 0.8980 (m-80)
REVERT: B  131 ASP cc_start: 0.9325 (m-30) cc_final: 0.8993 (m-30)
REVERT: B  196 MET cc_start: 0.9317 (mmm) cc_final: 0.9035 (mmm)
REVERT: B  218 LEU cc_start: 0.9262 (mm) cc_final: 0.8856 (tp)
REVERT: B  244 MET cc_start: 0.9337 (ppp) cc_final: 0.8982 (ppp)
REVERT: B  432 THR cc_start: 0.9363 (p) cc_final: 0.9109 (t)
REVERT: B  456 MET cc_start: 0.9147 (pmm) cc_final: 0.8941 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 233
  average time/residue: 0.1613
  time to fit residues: 55.6389
Evaluate side-chains
  195 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 195
  time to evaluate  : 1.089 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 96 optimal weight:    2.9990
   chunk 51 optimal weight:    3.9990
   chunk 85 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 102 optimal weight:    0.0170
   chunk 99 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 86 optimal weight:    2.9990
   chunk 41 optimal weight:    9.9990
   chunk 49 optimal weight:    4.9990
   overall best weight:    1.5822

-------------------------------------------------------------------------------
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 = 0.3410 r_free = 0.3410 target = 0.074116 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.054283 restraints weight = 35787.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.056424 restraints weight = 22112.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.058020 restraints weight = 15613.731|
|-----------------------------------------------------------------------------|
r_work (final): 0.3066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8320
moved from start:          0.3933

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   8950  Z= 0.158
  Angle     :  0.647   7.114  12092  Z= 0.334
  Chirality :  0.043   0.170   1440
  Planarity :  0.003   0.032   1532
  Dihedral  :  4.225  19.253   1238
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 14.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.50 %
    Favored  : 95.50 %
  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:  0.64 (0.25), residues: 1134
  helix:  1.53 (0.20), residues: 692
  sheet: -1.67 (0.65), residues: 54
  loop : -1.30 (0.32), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP B  17 
 HIS   0.007   0.001   HIS B 214 
 PHE   0.040   0.002   PHE B 230 
 TYR   0.016   0.001   TYR A 439 
 ARG   0.007   0.001   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03966 (  553)
  hydrogen bonds       : angle       4.38880 ( 1653)
  covalent geometry    : bond        0.00327 ( 8950)
  covalent geometry    : angle       0.64673 (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
  234 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  107 HIS cc_start: 0.8488 (t-90) cc_final: 0.7703 (t-90)
REVERT: A  111 MET cc_start: 0.8687 (tmm) cc_final: 0.8302 (tmm)
REVERT: A  210 MET cc_start: 0.9347 (tpp) cc_final: 0.8937 (tpp)
REVERT: A  214 HIS cc_start: 0.8654 (t-170) cc_final: 0.8325 (t-170)
REVERT: A  216 GLU cc_start: 0.9367 (mt-10) cc_final: 0.8939 (pt0)
REVERT: A  218 LEU cc_start: 0.9614 (mt) cc_final: 0.9274 (mt)
REVERT: A  224 GLU cc_start: 0.9030 (mp0) cc_final: 0.8759 (pm20)
REVERT: A  244 MET cc_start: 0.9368 (ppp) cc_final: 0.9060 (ppp)
REVERT: A  261 LEU cc_start: 0.9645 (mm) cc_final: 0.9436 (mm)
REVERT: A  291 MET cc_start: 0.9487 (mmp) cc_final: 0.9245 (mmm)
REVERT: A  312 MET cc_start: 0.7139 (ttt) cc_final: 0.6901 (tpt)
REVERT: A  382 LYS cc_start: 0.7659 (mmpt) cc_final: 0.7394 (mptt)
REVERT: A  402 MET cc_start: 0.8678 (mmm) cc_final: 0.8474 (mmm)
REVERT: A  405 HIS cc_start: 0.8779 (m90) cc_final: 0.8471 (m90)
REVERT: A  456 MET cc_start: 0.9155 (pmm) cc_final: 0.8874 (pmm)
REVERT: B   47 LEU cc_start: 0.9393 (mt) cc_final: 0.9122 (mt)
REVERT: B   62 SER cc_start: 0.8828 (t) cc_final: 0.8620 (p)
REVERT: B   98 MET cc_start: 0.9098 (tpp) cc_final: 0.8758 (tpp)
REVERT: B  109 MET cc_start: 0.8594 (tmm) cc_final: 0.8234 (tmm)
REVERT: B  111 MET cc_start: 0.8918 (ttt) cc_final: 0.8441 (tmm)
REVERT: B  131 ASP cc_start: 0.9323 (m-30) cc_final: 0.9000 (m-30)
REVERT: B  196 MET cc_start: 0.9343 (mmm) cc_final: 0.9054 (mmm)
REVERT: B  244 MET cc_start: 0.9370 (ppp) cc_final: 0.8987 (ppp)
REVERT: B  456 MET cc_start: 0.9224 (pmm) cc_final: 0.8976 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.1586
  time to fit residues: 54.6356
Evaluate side-chains
  189 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 189
  time to evaluate  : 0.980 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 3 optimal weight:    2.9990
   chunk 78 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 79 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 87 optimal weight:    4.9990
   chunk 77 optimal weight:    0.8980
   chunk 49 optimal weight:   10.0000
   chunk 32 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 240 GLN
** A 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 568 HIS
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.075030 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3027 r_free = 0.3027 target = 0.055492 restraints weight = 34360.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.057642 restraints weight = 20967.602|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.059300 restraints weight = 14721.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.4060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   8950  Z= 0.131
  Angle     :  0.663   7.891  12092  Z= 0.335
  Chirality :  0.043   0.165   1440
  Planarity :  0.004   0.061   1532
  Dihedral  :  4.249  19.949   1238
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 13.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  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:  0.52 (0.25), residues: 1134
  helix:  1.44 (0.19), residues: 692
  sheet: -1.31 (0.62), residues: 64
  loop : -1.42 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B  17 
 HIS   0.010   0.002   HIS A 568 
 PHE   0.036   0.002   PHE B 230 
 TYR   0.028   0.001   TYR B 439 
 ARG   0.008   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03875 (  553)
  hydrogen bonds       : angle       4.38757 ( 1653)
  covalent geometry    : bond        0.00281 ( 8950)
  covalent geometry    : angle       0.66253 (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
  233 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 232
  time to evaluate  : 0.975 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.9432 (mt) cc_final: 0.9231 (mt)
REVERT: A  111 MET cc_start: 0.8682 (tmm) cc_final: 0.8321 (tmm)
REVERT: A  149 GLU cc_start: 0.9174 (mp0) cc_final: 0.8768 (mp0)
REVERT: A  210 MET cc_start: 0.9365 (tpp) cc_final: 0.8778 (tpt)
REVERT: A  214 HIS cc_start: 0.8554 (t-170) cc_final: 0.8190 (t-170)
REVERT: A  218 LEU cc_start: 0.9582 (mt) cc_final: 0.9231 (mt)
REVERT: A  224 GLU cc_start: 0.9031 (mp0) cc_final: 0.8814 (pm20)
REVERT: A  226 GLU cc_start: 0.8221 (mp0) cc_final: 0.7985 (mp0)
REVERT: A  244 MET cc_start: 0.9372 (ppp) cc_final: 0.9053 (ppp)
REVERT: A  261 LEU cc_start: 0.9629 (mm) cc_final: 0.9384 (mm)
REVERT: A  382 LYS cc_start: 0.7650 (mmpt) cc_final: 0.7400 (mptt)
REVERT: A  402 MET cc_start: 0.8689 (mmm) cc_final: 0.8448 (mmm)
REVERT: A  405 HIS cc_start: 0.8731 (m90) cc_final: 0.8417 (m90)
REVERT: A  456 MET cc_start: 0.9170 (pmm) cc_final: 0.8883 (pmm)
REVERT: B   47 LEU cc_start: 0.9360 (mt) cc_final: 0.9076 (mt)
REVERT: B   62 SER cc_start: 0.8802 (t) cc_final: 0.8596 (p)
REVERT: B   67 MET cc_start: 0.9381 (ppp) cc_final: 0.9090 (ppp)
REVERT: B   98 MET cc_start: 0.9103 (tpp) cc_final: 0.8770 (tpp)
REVERT: B  109 MET cc_start: 0.8607 (tmm) cc_final: 0.8257 (tmm)
REVERT: B  111 MET cc_start: 0.8941 (ttt) cc_final: 0.8450 (tmm)
REVERT: B  131 ASP cc_start: 0.9324 (m-30) cc_final: 0.8999 (m-30)
REVERT: B  196 MET cc_start: 0.9330 (mmm) cc_final: 0.9069 (mmm)
REVERT: B  244 MET cc_start: 0.9341 (ppp) cc_final: 0.8974 (ppp)
REVERT: B  432 THR cc_start: 0.9378 (p) cc_final: 0.9115 (t)
REVERT: B  456 MET cc_start: 0.9194 (pmm) cc_final: 0.8953 (pmm)
  outliers start: 1
  outliers final: 0
  residues processed: 232
  average time/residue: 0.1518
  time to fit residues: 52.8463
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  : 0.952 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 95 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9980
   chunk 70 optimal weight:    0.8980
   chunk 87 optimal weight:    3.9990
   chunk 15 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 8 optimal weight:    0.3980
   chunk 88 optimal weight:   10.0000
   chunk 100 optimal weight:    5.9990
   chunk 68 optimal weight:    0.9990
   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 436 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 427 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.075492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.055963 restraints weight = 34087.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.058173 restraints weight = 20778.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.059806 restraints weight = 14550.823|
|-----------------------------------------------------------------------------|
r_work (final): 0.3113
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.4202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   8950  Z= 0.128
  Angle     :  0.662   8.658  12092  Z= 0.335
  Chirality :  0.043   0.169   1440
  Planarity :  0.004   0.100   1532
  Dihedral  :  4.244  19.601   1238
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.23 %
    Favored  : 95.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  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:  0.50 (0.25), residues: 1134
  helix:  1.43 (0.20), residues: 692
  sheet: -1.38 (0.61), residues: 64
  loop : -1.43 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B  17 
 HIS   0.005   0.001   HIS B 214 
 PHE   0.039   0.002   PHE B 230 
 TYR   0.014   0.001   TYR A 439 
 ARG   0.008   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03867 (  553)
  hydrogen bonds       : angle       4.35186 ( 1653)
  covalent geometry    : bond        0.00275 ( 8950)
  covalent geometry    : angle       0.66196 (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
  230 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.056 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 LEU cc_start: 0.9439 (mt) cc_final: 0.9234 (mt)
REVERT: A  111 MET cc_start: 0.8699 (tmm) cc_final: 0.8368 (tmm)
REVERT: A  149 GLU cc_start: 0.9164 (mp0) cc_final: 0.8734 (mp0)
REVERT: A  200 MET cc_start: 0.9439 (ptt) cc_final: 0.8991 (ppp)
REVERT: A  210 MET cc_start: 0.9327 (tpp) cc_final: 0.8742 (tpt)
REVERT: A  214 HIS cc_start: 0.8620 (t-170) cc_final: 0.8242 (t-170)
REVERT: A  218 LEU cc_start: 0.9580 (mt) cc_final: 0.9248 (mt)
REVERT: A  244 MET cc_start: 0.9345 (ppp) cc_final: 0.8989 (ppp)
REVERT: A  261 LEU cc_start: 0.9625 (mm) cc_final: 0.9385 (mm)
REVERT: A  382 LYS cc_start: 0.7645 (mmpt) cc_final: 0.7292 (mmmt)
REVERT: A  402 MET cc_start: 0.8656 (mmm) cc_final: 0.8415 (mmm)
REVERT: A  405 HIS cc_start: 0.8679 (m90) cc_final: 0.8356 (m90)
REVERT: A  456 MET cc_start: 0.9163 (pmm) cc_final: 0.8882 (pmm)
REVERT: B   47 LEU cc_start: 0.9361 (mt) cc_final: 0.9079 (mt)
REVERT: B   62 SER cc_start: 0.8801 (t) cc_final: 0.8586 (p)
REVERT: B   67 MET cc_start: 0.9391 (ppp) cc_final: 0.9096 (ppp)
REVERT: B   98 MET cc_start: 0.9102 (tpp) cc_final: 0.7653 (tpp)
REVERT: B  102 ARG cc_start: 0.9247 (ttm110) cc_final: 0.8951 (mtm-85)
REVERT: B  109 MET cc_start: 0.8598 (tmm) cc_final: 0.8241 (tmm)
REVERT: B  111 MET cc_start: 0.8895 (ttt) cc_final: 0.8427 (tmm)
REVERT: B  131 ASP cc_start: 0.9326 (m-30) cc_final: 0.8996 (m-30)
REVERT: B  196 MET cc_start: 0.9328 (mmm) cc_final: 0.9070 (mmm)
REVERT: B  244 MET cc_start: 0.9328 (ppp) cc_final: 0.8964 (ppp)
REVERT: B  432 THR cc_start: 0.9364 (p) cc_final: 0.9114 (t)
REVERT: B  456 MET cc_start: 0.9160 (pmm) cc_final: 0.8954 (pmm)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.1596
  time to fit residues: 54.6996
Evaluate side-chains
  190 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 190
  time to evaluate  : 0.943 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 40 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 86 optimal weight:    0.9980
   chunk 54 optimal weight:    8.9990
   chunk 111 optimal weight:    5.9990
   chunk 102 optimal weight:    0.0970
   chunk 84 optimal weight:    0.0170
   chunk 87 optimal weight:    1.9990
   overall best weight:    0.5616

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

Flipped N/Q/H residues before XYZ refinement:
A 436 ASN
A 468 ASN
** B 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.076615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.057045 restraints weight = 33877.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.059290 restraints weight = 20906.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.060958 restraints weight = 14678.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3138
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   8950  Z= 0.124
  Angle     :  0.656   9.015  12092  Z= 0.332
  Chirality :  0.042   0.179   1440
  Planarity :  0.004   0.071   1532
  Dihedral  :  4.175  19.811   1238
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 12.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.06 %
    Favored  : 95.94 %
  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:  0.48 (0.25), residues: 1134
  helix:  1.42 (0.20), residues: 692
  sheet: -1.40 (0.61), residues: 64
  loop : -1.44 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B  17 
 HIS   0.004   0.001   HIS B 214 
 PHE   0.038   0.002   PHE B 230 
 TYR   0.014   0.001   TYR B 439 
 ARG   0.007   0.000   ARG B 101 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03748 (  553)
  hydrogen bonds       : angle       4.32301 ( 1653)
  covalent geometry    : bond        0.00268 ( 8950)
  covalent geometry    : angle       0.65626 (12092)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3153.37 seconds
wall clock time: 56 minutes 19.52 seconds (3379.52 seconds total)