Starting phenix.real_space_refine
on Sat May  2 21:36:25 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8rf1_19115/05_2026/8rf1_19115.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8rf1_19115/05_2026/8rf1_19115.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8rf1_19115/05_2026/8rf1_19115.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8rf1_19115/05_2026/8rf1_19115.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8rf1_19115/05_2026/8rf1_19115.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8rf1_19115/05_2026/8rf1_19115.map"
  }
  resolution = 4.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.055
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      36      5.16       5
     C    5706      2.51       5
     N    1472      2.21       5
     O    1654      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8868
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4401
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
    Chain: "B"
      Number of atoms: 4401
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4401
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 17, 'TRANS': 554}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'RHQ': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 33
          Unusual residues: {'RHQ': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.29, per 1000 atoms: 0.26
  Number of scatterers: 8868
  At special positions: 0
  Unit cell: (112.36, 79.5, 129.32, 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      36     16.00
     O    1654      8.00
     N    1472      7.00
     C    5706      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.91
  Conformation dependent library (CDL) restraints added in 350.4 milliseconds
  

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2104

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 4 sheets defined
      71.6% alpha, 5.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 20
      removed outlier: 4.182A  pdb=" N   PHE A  15 " --> pdb=" O   LYS A  11 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 24
      Proline residue:  A  24  - end of helix
      No H-bonds generated for 'chain 'A' and resid 21 through 24'
    Processing helix  chain 'A' and resid 25 through 60
      removed outlier: 3.565A  pdb=" N   ALA A  30 " --> pdb=" O   TYR A  26 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ALA A  34 " --> pdb=" O   ALA A  30 " (cutoff:3.500A)
      Proline residue:  A  47  - end of helix
    Processing helix  chain 'A' and resid 64 through 110
      removed outlier: 3.764A  pdb=" N   GLY A  68 " --> pdb=" O   GLY A  64 " (cutoff:3.500A)
      removed outlier: 4.202A  pdb=" N   TYR A  86 " --> pdb=" O   ALA A  82 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ALA A  87 " --> pdb=" O   TYR A  83 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   LEU A  88 " --> pdb=" O   ALA A  84 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 111 through 116
      removed outlier: 4.042A  pdb=" N   PHE A 115 " --> pdb=" O   PRO A 111 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 119 through 140
      removed outlier: 4.796A  pdb=" N   SER A 125 " --> pdb=" O   GLY A 121 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   THR A 128 " --> pdb=" O   VAL A 124 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   THR A 140 " --> pdb=" O   GLU A 136 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 163
    Processing helix  chain 'A' and resid 167 through 179
      Proline residue:  A 175  - end of helix
    Processing helix  chain 'A' and resid 180 through 210
      removed outlier: 4.186A  pdb=" N   ILE A 184 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 220
    Processing helix  chain 'A' and resid 221 through 272
      removed outlier: 4.215A  pdb=" N   ARG A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      Proline residue:  A 252  - end of helix
      removed outlier: 4.379A  pdb=" N   VAL A 257 " --> pdb=" O   LEU A 253 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   LEU A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 277
      removed outlier: 3.581A  pdb=" N   GLY A 276 " --> pdb=" O   GLN A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 279 through 322
      removed outlier: 3.502A  pdb=" N   ALA A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
      removed outlier: 3.881A  pdb=" N   MET A 295 " --> pdb=" O   PHE A 291 " (cutoff:3.500A)
      Proline residue:  A 296  - end of helix
      removed outlier: 4.889A  pdb=" N   GLN A 299 " --> pdb=" O   MET A 295 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   ILE A 300 " --> pdb=" O   PRO A 296 " (cutoff:3.500A)
      removed outlier: 4.355A  pdb=" N   THR A 301 " --> pdb=" O   MET A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 325 through 331
      removed outlier: 3.860A  pdb=" N   VAL A 329 " --> pdb=" O   GLU A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 388
      removed outlier: 4.147A  pdb=" N   THR A 382 " --> pdb=" O   GLY A 378 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LEU A 383 " --> pdb=" O   GLY A 379 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 408
      removed outlier: 3.660A  pdb=" N   TYR A 408 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 411 through 418
    Processing helix  chain 'A' and resid 430 through 436
    Processing helix  chain 'A' and resid 447 through 455
      removed outlier: 4.143A  pdb=" N   ALA A 451 " --> pdb=" O   GLU A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 461
    Processing helix  chain 'A' and resid 462 through 468
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.628A  pdb=" N   ASN A 496 " --> pdb=" O   ALA A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 508 through 510
      No H-bonds generated for 'chain 'A' and resid 508 through 510'
    Processing helix  chain 'A' and resid 511 through 526
      removed outlier: 4.535A  pdb=" N   ALA A 520 " --> pdb=" O   SER A 516 " (cutoff:3.500A)
      removed outlier: 4.289A  pdb=" N   VAL A 523 " --> pdb=" O   GLN A 519 " (cutoff:3.500A)
      removed outlier: 4.086A  pdb=" N   LEU A 524 " --> pdb=" O   ALA A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 560 through 571
      removed outlier: 4.565A  pdb=" N   LEU A 569 " --> pdb=" O   ALA A 565 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 571 through 578
      removed outlier: 3.540A  pdb=" N   LEU A 578 " --> pdb=" O   ALA A 574 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 20
    Processing helix  chain 'B' and resid 25 through 60
      Proline residue:  B  47  - end of helix
    Processing helix  chain 'B' and resid 64 through 108
      removed outlier: 3.518A  pdb=" N   GLY B  68 " --> pdb=" O   GLY B  64 " (cutoff:3.500A)
      removed outlier: 4.163A  pdb=" N   TYR B  86 " --> pdb=" O   ALA B  82 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   ALA B  87 " --> pdb=" O   TYR B  83 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   LEU B  88 " --> pdb=" O   ALA B  84 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 119
      removed outlier: 3.938A  pdb=" N   PHE B 115 " --> pdb=" O   PRO B 111 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   THR B 117 " --> pdb=" O   SER B 113 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 120 through 139
      removed outlier: 3.706A  pdb=" N   THR B 131 " --> pdb=" O   VAL B 127 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 140 through 163
      removed outlier: 3.669A  pdb=" N   ASN B 163 " --> pdb=" O   LEU B 159 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 210
      removed outlier: 4.133A  pdb=" N   LEU B 168 " --> pdb=" O   TRP B 164 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   VAL B 170 " --> pdb=" O   LEU B 166 " (cutoff:3.500A)
      Proline residue:  B 175  - end of helix
      removed outlier: 3.658A  pdb=" N   LEU B 179 " --> pdb=" O   PRO B 175 " (cutoff:3.500A)
      removed outlier: 4.790A  pdb=" N   ILE B 180 " --> pdb=" O   LEU B 176 " (cutoff:3.500A)
      removed outlier: 4.084A  pdb=" N   LEU B 181 " --> pdb=" O   ALA B 177 " (cutoff:3.500A)
      Proline residue:  B 183  - end of helix
    Processing helix  chain 'B' and resid 212 through 220
    Processing helix  chain 'B' and resid 221 through 276
      removed outlier: 3.723A  pdb=" N   GLU B 225 " --> pdb=" O   ALA B 221 " (cutoff:3.500A)
      removed outlier: 4.150A  pdb=" N   ARG B 242 " --> pdb=" O   LYS B 238 " (cutoff:3.500A)
      Proline residue:  B 252  - end of helix
    Processing helix  chain 'B' and resid 279 through 295
    Processing helix  chain 'B' and resid 295 through 321
      removed outlier: 4.065A  pdb=" N   GLN B 299 " --> pdb=" O   MET B 295 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   THR B 301 " --> pdb=" O   MET B 297 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   GLY B 312 " --> pdb=" O   GLN B 308 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   ALA B 313 " --> pdb=" O   LYS B 309 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 388
      removed outlier: 3.671A  pdb=" N   LEU B 383 " --> pdb=" O   GLY B 379 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 409 through 416
    Processing helix  chain 'B' and resid 430 through 436
    Processing helix  chain 'B' and resid 437 through 440
      removed outlier: 4.055A  pdb=" N   GLU B 440 " --> pdb=" O   TYR B 437 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 437 through 440'
    Processing helix  chain 'B' and resid 448 through 452
      removed outlier: 4.269A  pdb=" N   ALA B 451 " --> pdb=" O   ILE B 448 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 458 through 463
      removed outlier: 3.851A  pdb=" N   GLU B 463 " --> pdb=" O   ASN B 459 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 496
      removed outlier: 3.805A  pdb=" N   ARG B 486 " --> pdb=" O   GLY B 482 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 508 through 512
      removed outlier: 4.051A  pdb=" N   GLN B 512 " --> pdb=" O   LEU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 513 through 525
      removed outlier: 4.901A  pdb=" N   ALA B 520 " --> pdb=" O   SER B 516 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   VAL B 523 " --> pdb=" O   GLN B 519 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 536 through 541
    Processing helix  chain 'B' and resid 560 through 568
    Processing helix  chain 'B' and resid 571 through 580
    Processing sheet with id=AA1, first strand: chain 'A' and resid 357 through 364
      removed outlier: 5.325A  pdb=" N   VAL A 346 " --> pdb=" O   GLU A 359 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   SER A 361 " --> pdb=" O   ASP A 344 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ASP A 344 " --> pdb=" O   SER A 361 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   VAL A 363 " --> pdb=" O   GLN A 342 " (cutoff:3.500A)
      removed outlier: 6.634A  pdb=" N   GLN A 342 " --> pdb=" O   VAL A 363 " (cutoff:3.500A)
      removed outlier: 5.546A  pdb=" N   LEU A 343 " --> pdb=" O   ARG A 399 " (cutoff:3.500A)
      removed outlier: 6.017A  pdb=" N   ARG A 399 " --> pdb=" O   LEU A 343 " (cutoff:3.500A)
      removed outlier: 5.159A  pdb=" N   ARG A 345 " --> pdb=" O   THR A 397 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   THR A 397 " --> pdb=" O   ARG A 345 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ALA A 395 " --> pdb=" O   SER A 347 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 500 through 502
      removed outlier: 6.594A  pdb=" N   LEU A 500 " --> pdb=" O   ILE A 531 " (cutoff:3.500A)
      removed outlier: 8.551A  pdb=" N   ILE A 533 " --> pdb=" O   LEU A 500 " (cutoff:3.500A)
      removed outlier: 6.878A  pdb=" N   LEU A 502 " --> pdb=" O   ILE A 533 " (cutoff:3.500A)
      removed outlier: 6.845A  pdb=" N   VAL A 369 " --> pdb=" O   GLN A 545 " (cutoff:3.500A)
      removed outlier: 8.247A  pdb=" N   LEU A 547 " --> pdb=" O   VAL A 369 " (cutoff:3.500A)
      removed outlier: 6.867A  pdb=" N   ALA A 371 " --> pdb=" O   LEU A 547 " (cutoff:3.500A)
      removed outlier: 7.769A  pdb=" N   VAL A 549 " --> pdb=" O   ALA A 371 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   VAL A 373 " --> pdb=" O   VAL A 549 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 360 through 364
      removed outlier: 7.301A  pdb=" N   ALA B 362 " --> pdb=" O   ASP B 344 " (cutoff:3.500A)
      removed outlier: 5.336A  pdb=" N   ASP B 344 " --> pdb=" O   ALA B 362 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ILE B 364 " --> pdb=" O   GLN B 342 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   GLN B 342 " --> pdb=" O   ILE B 364 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 418 through 421
      removed outlier: 6.223A  pdb=" N   GLY B 418 " --> pdb=" O   MET B 501 " (cutoff:3.500A)
      removed outlier: 7.890A  pdb=" N   ASP B 503 " --> pdb=" O   GLY B 418 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   VAL B 420 " --> pdb=" O   ASP B 503 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   VAL B 532 " --> pdb=" O   THR B 370 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   VAL B 369 " --> pdb=" O   GLN B 545 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   LEU B 547 " --> pdb=" O   VAL B 369 " (cutoff:3.500A)
      removed outlier: 6.855A  pdb=" N   ALA B 371 " --> pdb=" O   LEU B 547 " (cutoff:3.500A)
      removed outlier: 7.857A  pdb=" N   VAL B 549 " --> pdb=" O   ALA B 371 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL B 373 " --> pdb=" O   VAL B 549 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   GLY B 558 " --> pdb=" O   LEU B 546 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   PHE B 548 " --> pdb=" O   GLY B 556 " (cutoff:3.500A)
      removed outlier: 4.372A  pdb=" N   GLY B 556 " --> pdb=" O   PHE B 548 " (cutoff:3.500A)

    567 hydrogen bonds defined for protein.
    1674 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.32

  Time building geometry restraints manager: 1.17 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2841
        1.34 -     1.46: 1293
        1.46 -     1.58: 4804
        1.58 -     1.69: 0
        1.69 -     1.81: 70
  Bond restraints: 9008
  Sorted by residual:
  bond pdb=" C11 RHQ B 601 "
       pdb=" N1  RHQ B 601 "
    ideal  model  delta    sigma   weight residual
    1.437  1.344  0.093 2.00e-02 2.50e+03 2.18e+01
  bond pdb=" C26 RHQ A 601 "
       pdb=" O2  RHQ A 601 "
    ideal  model  delta    sigma   weight residual
    1.360  1.453 -0.093 2.00e-02 2.50e+03 2.15e+01
  bond pdb=" C26 RHQ B 601 "
       pdb=" O2  RHQ B 601 "
    ideal  model  delta    sigma   weight residual
    1.360  1.450 -0.090 2.00e-02 2.50e+03 2.03e+01
  bond pdb=" C11 RHQ A 601 "
       pdb=" N1  RHQ A 601 "
    ideal  model  delta    sigma   weight residual
    1.437  1.347  0.090 2.00e-02 2.50e+03 2.01e+01
  bond pdb=" C5  RHQ B 601 "
       pdb=" N2  RHQ B 601 "
    ideal  model  delta    sigma   weight residual
    1.436  1.349  0.087 2.00e-02 2.50e+03 1.88e+01
  ... (remaining 9003 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.78: 12160
        5.78 -    11.56: 32
       11.56 -    17.34: 3
       17.34 -    23.13: 0
       23.13 -    28.91: 1
  Bond angle restraints: 12196
  Sorted by residual:
  angle pdb=" N   GLY B 276 "
        pdb=" CA  GLY B 276 "
        pdb=" C   GLY B 276 "
      ideal   model   delta    sigma   weight residual
     113.18  142.09  -28.91 2.37e+00 1.78e-01 1.49e+02
  angle pdb=" N   GLU B 277 "
        pdb=" CA  GLU B 277 "
        pdb=" CB  GLU B 277 "
      ideal   model   delta    sigma   weight residual
     110.19  125.19  -15.00 1.55e+00 4.16e-01 9.37e+01
  angle pdb=" C   SER B 275 "
        pdb=" CA  SER B 275 "
        pdb=" CB  SER B 275 "
      ideal   model   delta    sigma   weight residual
     109.29   94.74   14.55 1.82e+00 3.02e-01 6.40e+01
  angle pdb=" N   VAL B 273 "
        pdb=" CA  VAL B 273 "
        pdb=" C   VAL B 273 "
      ideal   model   delta    sigma   weight residual
     110.42  103.59    6.83 9.40e-01 1.13e+00 5.28e+01
  angle pdb=" N   SER B 120 "
        pdb=" CA  SER B 120 "
        pdb=" C   SER B 120 "
      ideal   model   delta    sigma   weight residual
     113.55  104.45    9.10 1.26e+00 6.30e-01 5.21e+01
  ... (remaining 12191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.76: 4902
       17.76 -    35.51: 422
       35.51 -    53.27: 79
       53.27 -    71.03: 13
       71.03 -    88.79: 10
  Dihedral angle restraints: 5426
    sinusoidal: 2150
      harmonic: 3276
  Sorted by residual:
  dihedral pdb=" C   SER B 274 "
           pdb=" N   SER B 274 "
           pdb=" CA  SER B 274 "
           pdb=" CB  SER B 274 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.38   17.78     0      2.50e+00 1.60e-01 5.06e+01
  dihedral pdb=" C   SER B 275 "
           pdb=" N   SER B 275 "
           pdb=" CA  SER B 275 "
           pdb=" CB  SER B 275 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -109.56  -13.04     0      2.50e+00 1.60e-01 2.72e+01
  dihedral pdb=" CA  ASN A  23 "
           pdb=" C   ASN A  23 "
           pdb=" N   PRO A  24 "
           pdb=" CA  PRO A  24 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -155.65  -24.35     0      5.00e+00 4.00e-02 2.37e+01
  ... (remaining 5423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.127: 1444
       0.127 -    0.254: 18
       0.254 -    0.381: 1
       0.381 -    0.508: 0
       0.508 -    0.635: 1
  Chirality restraints: 1464
  Sorted by residual:
  chirality pdb=" CA  SER B 274 "
            pdb=" N   SER B 274 "
            pdb=" C   SER B 274 "
            pdb=" CB  SER B 274 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.88    0.63 2.00e-01 2.50e+01 1.01e+01
  chirality pdb=" CA  ALA B 119 "
            pdb=" N   ALA B 119 "
            pdb=" C   ALA B 119 "
            pdb=" CB  ALA B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.17    0.31 2.00e-01 2.50e+01 2.42e+00
  chirality pdb=" CA  THR B 123 "
            pdb=" N   THR B 123 "
            pdb=" C   THR B 123 "
            pdb=" CB  THR B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.31    0.22 2.00e-01 2.50e+01 1.16e+00
  ... (remaining 1461 not shown)

  Planarity restraints: 1526
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN B  23 "    0.041 5.00e-02 4.00e+02   6.11e-02 5.97e+00
        pdb=" N   PRO B  24 "   -0.106 5.00e-02 4.00e+02
        pdb=" CA  PRO B  24 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO B  24 "    0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN B 272 "    0.012 2.00e-02 2.50e+03   2.43e-02 5.92e+00
        pdb=" C   GLN B 272 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   GLN B 272 "    0.016 2.00e-02 2.50e+03
        pdb=" N   VAL B 273 "    0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 464 "    0.033 5.00e-02 4.00e+02   4.98e-02 3.97e+00
        pdb=" N   PRO A 465 "   -0.086 5.00e-02 4.00e+02
        pdb=" CA  PRO A 465 "    0.025 5.00e-02 4.00e+02
        pdb=" CD  PRO A 465 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1523 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 302
        2.71 -     3.26: 10316
        3.26 -     3.80: 14783
        3.80 -     4.35: 17202
        4.35 -     4.90: 27507
  Nonbonded interactions: 70110
  Sorted by model distance:
  nonbonded pdb=" O   SER B  36 "
            pdb=" OG1 THR B  39 "
     model   vdw
     2.161 3.040
  nonbonded pdb=" OE2 GLU A 550 "
            pdb=" OG1 THR A 555 "
     model   vdw
     2.163 3.040
  nonbonded pdb=" O   GLY B 377 "
            pdb=" NZ  LYS B 551 "
     model   vdw
     2.193 3.120
  nonbonded pdb=" O   ALA B  82 "
            pdb=" OG1 THR B  85 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" O   VAL A  37 "
            pdb=" OG1 THR A  40 "
     model   vdw
     2.236 3.040
  ... (remaining 70105 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.920
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.560
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.340
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.170
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
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   0.093   9008  Z= 0.264
  Angle     :  0.929  28.907  12196  Z= 0.506
  Chirality :  0.048   0.635   1464
  Planarity :  0.005   0.061   1526
  Dihedral  : 14.308  88.787   3322
  Min Nonbonded Distance : 2.161

Molprobity Statistics.
  All-atom Clashscore : 14.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.38 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.25), residues: 1140
  helix:  0.64 (0.19), residues: 715
  sheet: -0.60 (0.58), residues: 74
  loop : -2.21 (0.31), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 214 
 TYR   0.016   0.002   TYR A 114 
 PHE   0.021   0.002   PHE B 202 
 TRP   0.017   0.002   TRP B 104 
 HIS   0.006   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00531 ( 9008)
  covalent geometry    : angle       0.92948 (12196)
  hydrogen bonds       : bond        0.14739 (  567)
  hydrogen bonds       : angle       6.44229 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 201
  time to evaluate  : 0.363 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   59 MET cc_start: 0.8690 (mmp) cc_final: 0.7703 (ptt)
REVERT: A   91 ASN cc_start: 0.7965 (t0) cc_final: 0.7619 (t0)
REVERT: A  206 LEU cc_start: 0.9192 (tp) cc_final: 0.8877 (tp)
REVERT: A  358 LYS cc_start: 0.8881 (tptt) cc_final: 0.8575 (tptp)
REVERT: A  421 SER cc_start: 0.8512 (p) cc_final: 0.8266 (p)
REVERT: A  548 PHE cc_start: 0.8432 (t80) cc_final: 0.7752 (t80)
REVERT: B  208 GLN cc_start: 0.8928 (tm-30) cc_final: 0.8582 (tm-30)
REVERT: B  478 MET cc_start: 0.6839 (mtp) cc_final: 0.6630 (mtp)
REVERT: B  501 MET cc_start: 0.8990 (mpp) cc_final: 0.8728 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0786
  time to fit residues: 23.0979
Evaluate side-chains
  166 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    6.9990
   chunk 100 optimal weight:    2.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.126549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.095928 restraints weight = 25778.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.098671 restraints weight = 17072.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.100623 restraints weight = 12757.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.101956 restraints weight = 10314.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.102973 restraints weight = 8875.107|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.0990

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   9008  Z= 0.174
  Angle     :  0.677   8.249  12196  Z= 0.359
  Chirality :  0.043   0.173   1464
  Planarity :  0.005   0.062   1526
  Dihedral  :  6.977  59.329   1242
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 11.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  4.77 %
    Favored  : 95.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.25), residues: 1140
  helix:  1.00 (0.19), residues: 729
  sheet: -0.76 (0.55), residues: 74
  loop : -1.99 (0.33), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 486 
 TYR   0.013   0.002   TYR A 570 
 PHE   0.015   0.002   PHE A  57 
 TRP   0.008   0.001   TRP A 164 
 HIS   0.005   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 9008)
  covalent geometry    : angle       0.67700 (12196)
  hydrogen bonds       : bond        0.05249 (  567)
  hydrogen bonds       : angle       5.18768 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 199
  time to evaluate  : 0.358 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 SER cc_start: 0.8595 (m) cc_final: 0.8120 (p)
REVERT: A  114 TYR cc_start: 0.8393 (t80) cc_final: 0.8133 (t80)
REVERT: A  130 ASP cc_start: 0.8058 (m-30) cc_final: 0.7760 (m-30)
REVERT: A  195 THR cc_start: 0.8520 (p) cc_final: 0.8315 (p)
REVERT: A  231 MET cc_start: 0.8391 (tpp) cc_final: 0.8130 (tmm)
REVERT: A  387 LEU cc_start: 0.9405 (mm) cc_final: 0.8981 (mm)
REVERT: A  421 SER cc_start: 0.8544 (p) cc_final: 0.8266 (p)
REVERT: A  454 MET cc_start: 0.8388 (mtm) cc_final: 0.8180 (mtt)
REVERT: A  548 PHE cc_start: 0.8311 (t80) cc_final: 0.7551 (t80)
REVERT: B  110 LEU cc_start: 0.9342 (mt) cc_final: 0.9120 (mt)
REVERT: B  478 MET cc_start: 0.6839 (mtp) cc_final: 0.6520 (mtp)
  outliers start: 2
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0736
  time to fit residues: 22.3026
Evaluate side-chains
  163 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 43 optimal weight:    0.9980
   chunk 80 optimal weight:    0.7980
   chunk 28 optimal weight:    7.9990
   chunk 42 optimal weight:    3.9990
   chunk 90 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   chunk 18 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 32 optimal weight:    6.9990
   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 163 ASN
A 518 GLN
B 434 ASN
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.128024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.097544 restraints weight = 25482.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.100371 restraints weight = 16738.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.102335 restraints weight = 12438.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.103709 restraints weight = 10037.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.104691 restraints weight = 8608.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.3614
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7697
moved from start:          0.1389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9008  Z= 0.151
  Angle     :  0.658   8.840  12196  Z= 0.340
  Chirality :  0.042   0.166   1464
  Planarity :  0.005   0.059   1526
  Dihedral  :  6.722  55.450   1242
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 11.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  0.31 %
    Allowed  :  3.22 %
    Favored  : 96.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.25), residues: 1140
  helix:  1.09 (0.19), residues: 733
  sheet: -0.84 (0.55), residues: 68
  loop : -1.89 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG B 486 
 TYR   0.011   0.001   TYR A 570 
 PHE   0.013   0.001   PHE B 202 
 TRP   0.008   0.001   TRP B 104 
 HIS   0.006   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 9008)
  covalent geometry    : angle       0.65770 (12196)
  hydrogen bonds       : bond        0.04980 (  567)
  hydrogen bonds       : angle       4.91454 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 205
  time to evaluate  : 0.339 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 SER cc_start: 0.8498 (m) cc_final: 0.8039 (p)
REVERT: A  130 ASP cc_start: 0.8084 (m-30) cc_final: 0.7793 (m-30)
REVERT: A  195 THR cc_start: 0.8502 (p) cc_final: 0.8266 (p)
REVERT: A  231 MET cc_start: 0.8383 (tpp) cc_final: 0.8072 (tmm)
REVERT: A  387 LEU cc_start: 0.9350 (mm) cc_final: 0.8948 (mm)
REVERT: A  421 SER cc_start: 0.8554 (p) cc_final: 0.8260 (p)
REVERT: A  454 MET cc_start: 0.8372 (mtm) cc_final: 0.8133 (mtt)
REVERT: A  478 MET cc_start: 0.6904 (tpp) cc_final: 0.6206 (tpp)
REVERT: A  518 GLN cc_start: 0.8322 (OUTLIER) cc_final: 0.7954 (pp30)
REVERT: A  548 PHE cc_start: 0.8227 (t80) cc_final: 0.7429 (t80)
REVERT: B  110 LEU cc_start: 0.9249 (mt) cc_final: 0.9010 (mt)
REVERT: B  118 ASN cc_start: 0.8646 (m-40) cc_final: 0.8221 (m-40)
REVERT: B  139 THR cc_start: 0.9322 (p) cc_final: 0.9041 (t)
REVERT: B  326 GLU cc_start: 0.6204 (tm-30) cc_final: 0.5980 (tm-30)
REVERT: B  385 LYS cc_start: 0.9044 (mppt) cc_final: 0.8703 (mttp)
REVERT: B  478 MET cc_start: 0.6883 (mtp) cc_final: 0.6506 (mtp)
  outliers start: 3
  outliers final: 0
  residues processed: 208
  average time/residue: 0.0763
  time to fit residues: 23.2402
Evaluate side-chains
  174 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.322 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 3 optimal weight:    6.9990
   chunk 5 optimal weight:    6.9990
   chunk 38 optimal weight:    8.9990
   chunk 100 optimal weight:    8.9990
   chunk 24 optimal weight:    0.0060
   chunk 92 optimal weight:    8.9990
   chunk 90 optimal weight:    7.9990
   chunk 14 optimal weight:    0.8980
   chunk 48 optimal weight:    4.9990
   chunk 37 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9990
   overall best weight:    1.9802

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
** A 518 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3916 r_free = 0.3916 target = 0.125883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.095633 restraints weight = 24123.039|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.098439 restraints weight = 15691.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.100496 restraints weight = 11521.611|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.101921 restraints weight = 9164.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.102867 restraints weight = 7764.635|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9008  Z= 0.170
  Angle     :  0.665   7.653  12196  Z= 0.346
  Chirality :  0.043   0.176   1464
  Planarity :  0.005   0.084   1526
  Dihedral  :  6.498  55.286   1242
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 11.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.73 %
    Favored  : 96.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.25), residues: 1140
  helix:  1.15 (0.19), residues: 735
  sheet: -0.85 (0.54), residues: 68
  loop : -1.85 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 486 
 TYR   0.021   0.002   TYR A 114 
 PHE   0.012   0.001   PHE B 237 
 TRP   0.006   0.001   TRP B 104 
 HIS   0.007   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00357 ( 9008)
  covalent geometry    : angle       0.66511 (12196)
  hydrogen bonds       : bond        0.04846 (  567)
  hydrogen bonds       : angle       4.88043 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 210
  time to evaluate  : 0.309 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 SER cc_start: 0.8615 (m) cc_final: 0.8167 (p)
REVERT: A  231 MET cc_start: 0.8449 (tpp) cc_final: 0.8111 (tmm)
REVERT: A  387 LEU cc_start: 0.9377 (mm) cc_final: 0.8990 (mm)
REVERT: A  421 SER cc_start: 0.8601 (p) cc_final: 0.8303 (p)
REVERT: A  454 MET cc_start: 0.8418 (mtm) cc_final: 0.8160 (mtt)
REVERT: A  548 PHE cc_start: 0.8245 (t80) cc_final: 0.7342 (t80)
REVERT: A  569 LEU cc_start: 0.8986 (tp) cc_final: 0.8782 (mp)
REVERT: B  110 LEU cc_start: 0.9252 (mt) cc_final: 0.9003 (mt)
REVERT: B  130 ASP cc_start: 0.7581 (m-30) cc_final: 0.7378 (m-30)
REVERT: B  385 LYS cc_start: 0.9244 (mppt) cc_final: 0.8871 (mttp)
REVERT: B  478 MET cc_start: 0.6811 (mtp) cc_final: 0.6351 (mtp)
REVERT: B  571 ARG cc_start: 0.8657 (mtm110) cc_final: 0.8405 (mtm110)
  outliers start: 1
  outliers final: 0
  residues processed: 211
  average time/residue: 0.0817
  time to fit residues: 25.2617
Evaluate side-chains
  162 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 58 optimal weight:    0.2980
   chunk 43 optimal weight:    0.9980
   chunk 101 optimal weight:    8.9990
   chunk 85 optimal weight:    7.9990
   chunk 107 optimal weight:    2.9990
   chunk 82 optimal weight:    3.9990
   chunk 90 optimal weight:    5.9990
   chunk 62 optimal weight:    9.9990
   chunk 6 optimal weight:    0.8980
   chunk 51 optimal weight:    1.9990
   chunk 53 optimal weight:    0.0060
   overall best weight:    0.8398

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
B 141 HIS
** B 560 HIS ** 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 = 0.3938 r_free = 0.3938 target = 0.127615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.097098 restraints weight = 24276.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.100079 restraints weight = 15661.600|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.102150 restraints weight = 11434.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.103599 restraints weight = 9128.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.104616 restraints weight = 7758.488|
|-----------------------------------------------------------------------------|
r_work (final): 0.3569
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.1831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   9008  Z= 0.136
  Angle     :  0.656   7.795  12196  Z= 0.338
  Chirality :  0.042   0.164   1464
  Planarity :  0.005   0.071   1526
  Dihedral  :  6.400  56.739   1242
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 11.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.49 %
    Favored  : 97.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.25), residues: 1140
  helix:  1.17 (0.19), residues: 735
  sheet: -0.71 (0.54), residues: 68
  loop : -1.86 (0.34), residues: 337

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG B 486 
 TYR   0.014   0.002   TYR B 570 
 PHE   0.013   0.001   PHE B 202 
 TRP   0.008   0.001   TRP B 104 
 HIS   0.003   0.001   HIS A 338 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 9008)
  covalent geometry    : angle       0.65630 (12196)
  hydrogen bonds       : bond        0.04693 (  567)
  hydrogen bonds       : angle       4.70592 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  213 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 SER cc_start: 0.8472 (m) cc_final: 0.7953 (p)
REVERT: A  114 TYR cc_start: 0.8470 (t80) cc_final: 0.8207 (t80)
REVERT: A  130 ASP cc_start: 0.8163 (m-30) cc_final: 0.7917 (m-30)
REVERT: A  231 MET cc_start: 0.8468 (tpp) cc_final: 0.8113 (tmm)
REVERT: A  387 LEU cc_start: 0.9340 (mm) cc_final: 0.8955 (mm)
REVERT: A  421 SER cc_start: 0.8548 (p) cc_final: 0.8315 (p)
REVERT: A  454 MET cc_start: 0.8414 (mtm) cc_final: 0.8187 (mtt)
REVERT: A  478 MET cc_start: 0.6903 (tpp) cc_final: 0.6198 (tpp)
REVERT: A  548 PHE cc_start: 0.8313 (t80) cc_final: 0.7567 (t80)
REVERT: A  569 LEU cc_start: 0.9006 (tp) cc_final: 0.8787 (mp)
REVERT: B  110 LEU cc_start: 0.9196 (mt) cc_final: 0.8904 (mt)
REVERT: B  139 THR cc_start: 0.9398 (p) cc_final: 0.9110 (t)
REVERT: B  208 GLN cc_start: 0.9071 (tm-30) cc_final: 0.8715 (tm-30)
REVERT: B  478 MET cc_start: 0.6835 (mtp) cc_final: 0.6301 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 213
  average time/residue: 0.0778
  time to fit residues: 24.3736
Evaluate side-chains
  172 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 172
  time to evaluate  : 0.260 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 2 optimal weight:    3.9990
   chunk 94 optimal weight:    2.9990
   chunk 90 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 25 optimal weight:    0.7980
   chunk 108 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 112 optimal weight:   10.0000
   chunk 75 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
B 220 ASN
** B 560 HIS ** 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 = 0.3925 r_free = 0.3925 target = 0.126632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.095473 restraints weight = 24687.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3501 r_free = 0.3501 target = 0.098532 restraints weight = 15973.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.100663 restraints weight = 11631.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.102165 restraints weight = 9230.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.103167 restraints weight = 7819.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.3556
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7665
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9008  Z= 0.148
  Angle     :  0.661   8.205  12196  Z= 0.339
  Chirality :  0.043   0.160   1464
  Planarity :  0.005   0.061   1526
  Dihedral  :  6.310  56.486   1242
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.40 %
    Favored  : 93.60 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.80 %
    Favored  : 96.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.25), residues: 1140
  helix:  1.17 (0.19), residues: 736
  sheet: -0.64 (0.53), residues: 76
  loop : -1.86 (0.35), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 486 
 TYR   0.012   0.001   TYR A 570 
 PHE   0.013   0.001   PHE B 202 
 TRP   0.007   0.001   TRP B 104 
 HIS   0.004   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 9008)
  covalent geometry    : angle       0.66104 (12196)
  hydrogen bonds       : bond        0.04621 (  567)
  hydrogen bonds       : angle       4.70244 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  202 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 200
  time to evaluate  : 0.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  113 SER cc_start: 0.8501 (m) cc_final: 0.7998 (p)
REVERT: A  114 TYR cc_start: 0.8445 (t80) cc_final: 0.8149 (t80)
REVERT: A  130 ASP cc_start: 0.8188 (m-30) cc_final: 0.7955 (m-30)
REVERT: A  231 MET cc_start: 0.8475 (tpp) cc_final: 0.8121 (tmm)
REVERT: A  387 LEU cc_start: 0.9287 (mm) cc_final: 0.8956 (mm)
REVERT: A  421 SER cc_start: 0.8544 (p) cc_final: 0.8218 (p)
REVERT: A  437 TYR cc_start: 0.8714 (t80) cc_final: 0.8375 (t80)
REVERT: A  454 MET cc_start: 0.8361 (mtm) cc_final: 0.8123 (mtt)
REVERT: A  478 MET cc_start: 0.6809 (tpp) cc_final: 0.6125 (tpp)
REVERT: A  548 PHE cc_start: 0.8321 (t80) cc_final: 0.7577 (t80)
REVERT: B   59 MET cc_start: 0.7882 (mmp) cc_final: 0.7366 (tmm)
REVERT: B  110 LEU cc_start: 0.9242 (mt) cc_final: 0.8956 (mt)
REVERT: B  139 THR cc_start: 0.9410 (p) cc_final: 0.9079 (t)
REVERT: B  208 GLN cc_start: 0.9093 (tm-30) cc_final: 0.8771 (tm-30)
REVERT: B  385 LYS cc_start: 0.9187 (mppt) cc_final: 0.8979 (mmtp)
REVERT: B  478 MET cc_start: 0.6865 (mtp) cc_final: 0.6307 (mtp)
REVERT: B  501 MET cc_start: 0.8948 (mpp) cc_final: 0.8721 (mmp)
  outliers start: 2
  outliers final: 0
  residues processed: 202
  average time/residue: 0.0772
  time to fit residues: 22.7905
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.345 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 73 optimal weight:    0.0000
   chunk 76 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9980
   chunk 31 optimal weight:    8.9990
   chunk 7 optimal weight:    1.9990
   chunk 94 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9990
   chunk 42 optimal weight:    0.8980
   chunk 102 optimal weight:    0.4980
   chunk 71 optimal weight:    5.9990
   overall best weight:    0.6786

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
A 567 HIS
** B 560 HIS ** 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 = 0.3942 r_free = 0.3942 target = 0.127667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.096330 restraints weight = 24802.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3515 r_free = 0.3515 target = 0.099410 restraints weight = 15944.748|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.101489 restraints weight = 11666.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.102963 restraints weight = 9329.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.104013 restraints weight = 7941.300|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9008  Z= 0.134
  Angle     :  0.672   7.664  12196  Z= 0.340
  Chirality :  0.043   0.210   1464
  Planarity :  0.005   0.059   1526
  Dihedral  :  6.374  57.556   1242
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 11.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.05 %
    Favored  : 93.95 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.24 %
    Favored  : 98.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.25), residues: 1140
  helix:  1.21 (0.19), residues: 738
  sheet: -0.74 (0.57), residues: 64
  loop : -1.95 (0.33), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 486 
 TYR   0.013   0.001   TYR B 437 
 PHE   0.015   0.001   PHE B 202 
 TRP   0.012   0.001   TRP B 104 
 HIS   0.005   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 9008)
  covalent geometry    : angle       0.67243 (12196)
  hydrogen bonds       : bond        0.04528 (  567)
  hydrogen bonds       : angle       4.59279 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 200
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8324 (t80) cc_final: 0.7668 (m-10)
REVERT: A  113 SER cc_start: 0.8456 (m) cc_final: 0.7868 (p)
REVERT: A  114 TYR cc_start: 0.8288 (t80) cc_final: 0.8024 (t80)
REVERT: A  130 ASP cc_start: 0.8130 (m-30) cc_final: 0.7909 (m-30)
REVERT: A  231 MET cc_start: 0.8466 (tpp) cc_final: 0.8112 (tmm)
REVERT: A  387 LEU cc_start: 0.9274 (mm) cc_final: 0.8897 (mm)
REVERT: A  421 SER cc_start: 0.8534 (p) cc_final: 0.8319 (p)
REVERT: A  454 MET cc_start: 0.8407 (mtm) cc_final: 0.8187 (mtt)
REVERT: A  478 MET cc_start: 0.6790 (tpp) cc_final: 0.6110 (tpp)
REVERT: A  548 PHE cc_start: 0.8367 (t80) cc_final: 0.7462 (t80)
REVERT: B  110 LEU cc_start: 0.9161 (mt) cc_final: 0.8893 (mt)
REVERT: B  382 THR cc_start: 0.8833 (m) cc_final: 0.8622 (t)
REVERT: B  478 MET cc_start: 0.6909 (mtp) cc_final: 0.6366 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 201
  average time/residue: 0.0775
  time to fit residues: 23.0226
Evaluate side-chains
  161 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 161
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 55 optimal weight:   30.0000
   chunk 82 optimal weight:    0.7980
   chunk 45 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 16 optimal weight:    2.9990
   chunk 66 optimal weight:    0.5980
   chunk 53 optimal weight:    9.9990
   chunk 38 optimal weight:    5.9990
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
A  91 ASN
A 163 ASN
A 567 HIS
** B 560 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.126722 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.094817 restraints weight = 25575.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.097921 restraints weight = 16232.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.100185 restraints weight = 11846.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.101715 restraints weight = 9413.348|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.102764 restraints weight = 7993.640|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   9008  Z= 0.141
  Angle     :  0.680   7.343  12196  Z= 0.346
  Chirality :  0.043   0.198   1464
  Planarity :  0.005   0.056   1526
  Dihedral  :  6.264  57.485   1242
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.45 %
    Favored  : 98.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.25), residues: 1140
  helix:  1.20 (0.19), residues: 742
  sheet: -0.64 (0.57), residues: 64
  loop : -1.86 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG B 486 
 TYR   0.013   0.001   TYR A 570 
 PHE   0.013   0.001   PHE B 202 
 TRP   0.009   0.001   TRP B 104 
 HIS   0.006   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 9008)
  covalent geometry    : angle       0.68014 (12196)
  hydrogen bonds       : bond        0.04455 (  567)
  hydrogen bonds       : angle       4.59641 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 203
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8330 (t80) cc_final: 0.7714 (m-10)
REVERT: A  113 SER cc_start: 0.8488 (m) cc_final: 0.7909 (p)
REVERT: A  114 TYR cc_start: 0.8239 (t80) cc_final: 0.7953 (t80)
REVERT: A  130 ASP cc_start: 0.8149 (m-30) cc_final: 0.7929 (m-30)
REVERT: A  231 MET cc_start: 0.8477 (tpp) cc_final: 0.8115 (tmm)
REVERT: A  358 LYS cc_start: 0.8525 (tptp) cc_final: 0.8294 (tptp)
REVERT: A  387 LEU cc_start: 0.9290 (mm) cc_final: 0.8905 (mm)
REVERT: A  421 SER cc_start: 0.8543 (p) cc_final: 0.8326 (p)
REVERT: A  436 CYS cc_start: 0.8873 (m) cc_final: 0.7746 (p)
REVERT: A  454 MET cc_start: 0.8328 (mtm) cc_final: 0.8063 (mtt)
REVERT: A  478 MET cc_start: 0.6847 (tpp) cc_final: 0.6176 (tpp)
REVERT: A  548 PHE cc_start: 0.8475 (t80) cc_final: 0.7507 (t80)
REVERT: B   59 MET cc_start: 0.7980 (mmp) cc_final: 0.7474 (tmm)
REVERT: B  139 THR cc_start: 0.9376 (p) cc_final: 0.9029 (t)
REVERT: B  478 MET cc_start: 0.6851 (mtp) cc_final: 0.6363 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 204
  average time/residue: 0.0822
  time to fit residues: 24.5534
Evaluate side-chains
  159 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.284 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 87 optimal weight:    0.5980
   chunk 110 optimal weight:    0.0060
   chunk 26 optimal weight:    0.2980
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    0.7980
   chunk 77 optimal weight:    0.1980
   chunk 91 optimal weight:    1.9990
   chunk 57 optimal weight:   10.0000
   chunk 16 optimal weight:    0.2980
   chunk 12 optimal weight:    0.5980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.2796

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
A 567 HIS
** B 560 HIS ** 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 = 0.3955 r_free = 0.3955 target = 0.128944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.097072 restraints weight = 25509.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.100305 restraints weight = 16157.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.102576 restraints weight = 11751.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.104123 restraints weight = 9320.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.105227 restraints weight = 7902.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9008  Z= 0.134
  Angle     :  0.681   8.315  12196  Z= 0.340
  Chirality :  0.043   0.179   1464
  Planarity :  0.004   0.055   1526
  Dihedral  :  6.156  58.865   1242
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 12.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.52 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.25), residues: 1140
  helix:  1.16 (0.19), residues: 744
  sheet: -0.53 (0.58), residues: 64
  loop : -1.93 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 486 
 TYR   0.032   0.001   TYR A 408 
 PHE   0.017   0.001   PHE B 202 
 TRP   0.012   0.001   TRP B 104 
 HIS   0.006   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 9008)
  covalent geometry    : angle       0.68124 (12196)
  hydrogen bonds       : bond        0.04343 (  567)
  hydrogen bonds       : angle       4.48442 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 204
  time to evaluate  : 0.347 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8252 (t80) cc_final: 0.7733 (m-10)
REVERT: A  113 SER cc_start: 0.8433 (m) cc_final: 0.7870 (p)
REVERT: A  226 TYR cc_start: 0.8899 (t80) cc_final: 0.8626 (t80)
REVERT: A  231 MET cc_start: 0.8438 (tpp) cc_final: 0.8110 (tmm)
REVERT: A  283 LEU cc_start: 0.9089 (pp) cc_final: 0.8862 (tp)
REVERT: A  387 LEU cc_start: 0.9257 (mm) cc_final: 0.9044 (mm)
REVERT: A  478 MET cc_start: 0.6766 (tpp) cc_final: 0.6146 (tpp)
REVERT: A  548 PHE cc_start: 0.8229 (t80) cc_final: 0.7212 (t80)
REVERT: B   59 MET cc_start: 0.7857 (mmp) cc_final: 0.7379 (tmm)
REVERT: B  478 MET cc_start: 0.6892 (mtp) cc_final: 0.6405 (mtp)
  outliers start: 1
  outliers final: 0
  residues processed: 205
  average time/residue: 0.0776
  time to fit residues: 23.5928
Evaluate side-chains
  164 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.274 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 95 optimal weight:    0.9980
   chunk 23 optimal weight:    2.9990
   chunk 92 optimal weight:   20.0000
   chunk 102 optimal weight:    0.9990
   chunk 11 optimal weight:    2.9990
   chunk 12 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 93 optimal weight:    8.9990
   chunk 103 optimal weight:    6.9990
   chunk 0 optimal weight:    9.9990
   chunk 54 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
** A  91 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 163 ASN
A 567 HIS
** B 560 HIS ** 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 = 0.3917 r_free = 0.3917 target = 0.126184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.093758 restraints weight = 25794.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3471 r_free = 0.3471 target = 0.096850 restraints weight = 16613.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.099010 restraints weight = 12196.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.100438 restraints weight = 9780.342|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.101491 restraints weight = 8377.410|
|-----------------------------------------------------------------------------|
r_work (final): 0.3528
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7684
moved from start:          0.2728

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   9008  Z= 0.160
  Angle     :  0.712   9.215  12196  Z= 0.357
  Chirality :  0.043   0.185   1464
  Planarity :  0.005   0.052   1526
  Dihedral  :  6.140  58.130   1242
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.32 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.31 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.25), residues: 1140
  helix:  1.14 (0.19), residues: 747
  sheet: -0.41 (0.53), residues: 74
  loop : -2.00 (0.34), residues: 319

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 484 
 TYR   0.029   0.001   TYR A 408 
 PHE   0.012   0.001   PHE A 468 
 TRP   0.017   0.002   TRP B 104 
 HIS   0.007   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 ( 9008)
  covalent geometry    : angle       0.71228 (12196)
  hydrogen bonds       : bond        0.04442 (  567)
  hydrogen bonds       : angle       4.56269 ( 1674)

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

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

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2280 Ramachandran restraints generated.
    1140 Oldfield, 0 Emsley, 1140 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 195
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   57 PHE cc_start: 0.8248 (t80) cc_final: 0.7741 (m-10)
REVERT: A  113 SER cc_start: 0.8565 (m) cc_final: 0.7982 (p)
REVERT: A  130 ASP cc_start: 0.8118 (m-30) cc_final: 0.7893 (m-30)
REVERT: A  226 TYR cc_start: 0.8952 (t80) cc_final: 0.8708 (t80)
REVERT: A  231 MET cc_start: 0.8424 (tpp) cc_final: 0.8096 (tmm)
REVERT: A  283 LEU cc_start: 0.9179 (pp) cc_final: 0.8899 (tt)
REVERT: A  387 LEU cc_start: 0.9274 (mm) cc_final: 0.9004 (mm)
REVERT: A  436 CYS cc_start: 0.8837 (m) cc_final: 0.7704 (p)
REVERT: A  478 MET cc_start: 0.6828 (tpp) cc_final: 0.6215 (tpp)
REVERT: A  548 PHE cc_start: 0.8323 (t80) cc_final: 0.7293 (t80)
REVERT: B   86 TYR cc_start: 0.7965 (t80) cc_final: 0.7751 (t80)
REVERT: B  283 LEU cc_start: 0.9165 (pp) cc_final: 0.8862 (tt)
REVERT: B  478 MET cc_start: 0.6873 (mtp) cc_final: 0.6338 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 196
  average time/residue: 0.0770
  time to fit residues: 22.5191
Evaluate side-chains
  157 residues out of total 964 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 26 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0030
   chunk 2 optimal weight:    0.7980
   chunk 98 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 81 optimal weight:    0.9990
   chunk 55 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 163 ASN
A 567 HIS
** B 560 HIS ** 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 = 0.3941 r_free = 0.3941 target = 0.127686 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.096243 restraints weight = 25184.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.099121 restraints weight = 16702.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.101206 restraints weight = 12484.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.102592 restraints weight = 10074.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.103617 restraints weight = 8672.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3574
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7636
moved from start:          0.2924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9008  Z= 0.133
  Angle     :  0.698   9.580  12196  Z= 0.345
  Chirality :  0.043   0.174   1464
  Planarity :  0.004   0.053   1526
  Dihedral  :  6.088  59.519   1242
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 12.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.23 %
    Favored  : 93.77 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.52 %
    Favored  : 99.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.25), residues: 1140
  helix:  1.15 (0.19), residues: 745
  sheet: -0.29 (0.58), residues: 64
  loop : -2.07 (0.33), residues: 331

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 214 
 TYR   0.029   0.001   TYR A 408 
 PHE   0.014   0.001   PHE B 202 
 TRP   0.018   0.001   TRP B 104 
 HIS   0.006   0.001   HIS B 560 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 9008)
  covalent geometry    : angle       0.69804 (12196)
  hydrogen bonds       : bond        0.04301 (  567)
  hydrogen bonds       : angle       4.46476 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1531.19 seconds
wall clock time: 27 minutes 17.94 seconds (1637.94 seconds total)