Starting phenix.real_space_refine
on Wed Apr 30 04:59:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yf1_39207/04_2025/8yf1_39207.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yf1_39207/04_2025/8yf1_39207.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.38
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yf1_39207/04_2025/8yf1_39207.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yf1_39207/04_2025/8yf1_39207.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yf1_39207/04_2025/8yf1_39207.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yf1_39207/04_2025/8yf1_39207.cif"
  }
  resolution = 3.38
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.090
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      70      5.16       5
     C    5998      2.51       5
     N    1520      2.21       5
     O    1599      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 9187
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4505
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 567, 4505
          Classifications: {'peptide': 567}
          Link IDs: {'PTRANS': 13, 'TRANS': 553}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 4652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 589, 4652
          Classifications: {'peptide': 589}
          Link IDs: {'PTRANS': 15, 'TRANS': 573}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'VLX': 1}
          Classifications: {'undetermined': 1}
    Chain: "A"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 15
          Unusual residues: {'VLX': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.68, per 1000 atoms: 0.62
  Number of scatterers: 9187
  At special positions: 0
  Unit cell: (118.364, 101.588, 129.548, 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      70     16.00
     O    1599      8.00
     N    1520      7.00
     C    5998      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.60
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2094

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 2 sheets defined
      70.6% alpha, 0.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.83
  Creating SS restraints...
    Processing helix  chain 'B' and resid 133 through 160
      removed outlier: 3.989A  pdb=" N   GLU B 146 " --> pdb=" O   ARG B 142 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   GLU B 147 " --> pdb=" O   LYS B 143 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   GLY B 160 " --> pdb=" O   LEU B 156 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 163 through 189
      removed outlier: 3.907A  pdb=" N   ALA B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      removed outlier: 3.902A  pdb=" N   ASP B 179 " --> pdb=" O   ALA B 175 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 202 through 226
      removed outlier: 5.667A  pdb=" N   GLY B 208 " --> pdb=" O   LYS B 204 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   LEU B 209 " --> pdb=" O   GLY B 205 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 251
      removed outlier: 3.510A  pdb=" N   LEU B 235 " --> pdb=" O   ARG B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 254 through 271
      removed outlier: 4.265A  pdb=" N   GLY B 271 " --> pdb=" O   VAL B 267 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 272 through 282
    Processing helix  chain 'B' and resid 289 through 294
    Processing helix  chain 'B' and resid 295 through 315
      removed outlier: 3.904A  pdb=" N   PHE B 299 " --> pdb=" O   TRP B 295 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 318 through 322
      removed outlier: 3.987A  pdb=" N   SER B 321 " --> pdb=" O   TYR B 318 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE B 322 " --> pdb=" O   GLY B 319 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 318 through 322'
    Processing helix  chain 'B' and resid 332 through 341
      removed outlier: 3.556A  pdb=" N   ALA B 341 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 341 through 351
    Processing helix  chain 'B' and resid 357 through 365
      removed outlier: 3.746A  pdb=" N   PHE B 361 " --> pdb=" O   SER B 357 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 382
    Processing helix  chain 'B' and resid 388 through 399
      removed outlier: 3.619A  pdb=" N   PHE B 392 " --> pdb=" O   PRO B 388 " (cutoff:3.500A)
      removed outlier: 4.835A  pdb=" N   VAL B 394 " --> pdb=" O   ARG B 390 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   THR B 395 " --> pdb=" O   VAL B 391 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   HIS B 396 " --> pdb=" O   PHE B 392 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ILE B 397 " --> pdb=" O   SER B 393 " (cutoff:3.500A)
      removed outlier: 4.068A  pdb=" N   LYS B 398 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 439
      removed outlier: 3.649A  pdb=" N   CYS B 438 " --> pdb=" O   ASN B 434 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   PHE B 439 " --> pdb=" O   PHE B 435 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 443 through 457
    Processing helix  chain 'B' and resid 458 through 484
      removed outlier: 5.419A  pdb=" N   PHE B 468 " --> pdb=" O   LEU B 464 " (cutoff:3.500A)
      Proline residue:  B 469  - end of helix
    Processing helix  chain 'B' and resid 562 through 566
      removed outlier: 3.516A  pdb=" N   LYS B 565 " --> pdb=" O   PHE B 562 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 596 through 609
      removed outlier: 4.093A  pdb=" N   LEU B 609 " --> pdb=" O   THR B 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 609 through 622
      removed outlier: 4.045A  pdb=" N   VAL B 614 " --> pdb=" O   PRO B 610 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER B 615 " --> pdb=" O   GLY B 611 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 625 through 644
    Processing helix  chain 'B' and resid 649 through 677
      removed outlier: 4.263A  pdb=" N   VAL B 661 " --> pdb=" O   LEU B 657 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU B 675 " --> pdb=" O   VAL B 671 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   LEU B 676 " --> pdb=" O   LEU B 672 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   TYR B 677 " --> pdb=" O   THR B 673 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 678 through 680
      No H-bonds generated for 'chain 'B' and resid 678 through 680'
    Processing helix  chain 'B' and resid 681 through 708
      removed outlier: 3.507A  pdb=" N   ALA B 685 " --> pdb=" O   LYS B 681 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 160
    Processing helix  chain 'A' and resid 162 through 189
    Processing helix  chain 'A' and resid 192 through 196
      removed outlier: 3.999A  pdb=" N   LYS A 195 " --> pdb=" O   SER A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 202 through 230
      removed outlier: 4.261A  pdb=" N   MET A 206 " --> pdb=" O   SER A 202 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ASP A 227 " --> pdb=" O   GLY A 223 " (cutoff:3.500A)
      removed outlier: 4.345A  pdb=" N   ARG A 228 " --> pdb=" O   GLY A 224 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 230 through 251
    Processing helix  chain 'A' and resid 254 through 271
      removed outlier: 3.586A  pdb=" N   VAL A 267 " --> pdb=" O   LEU A 263 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   GLY A 268 " --> pdb=" O   LEU A 264 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 281
      removed outlier: 3.876A  pdb=" N   SER A 278 " --> pdb=" O   PRO A 274 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   TYR A 279 " --> pdb=" O   ILE A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 284
      No H-bonds generated for 'chain 'A' and resid 282 through 284'
    Processing helix  chain 'A' and resid 285 through 294
      removed outlier: 4.450A  pdb=" N   GLY A 290 " --> pdb=" O   GLN A 286 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   GLU A 291 " --> pdb=" O   GLU A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 315
      removed outlier: 3.734A  pdb=" N   TRP A 300 " --> pdb=" O   LEU A 296 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 341
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 3.797A  pdb=" N   THR A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 357 through 364
      removed outlier: 3.534A  pdb=" N   PHE A 361 " --> pdb=" O   SER A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 386 through 391
    Processing helix  chain 'A' and resid 392 through 402
    Processing helix  chain 'A' and resid 419 through 438
    Processing helix  chain 'A' and resid 445 through 466
      removed outlier: 4.199A  pdb=" N   PHE A 459 " --> pdb=" O   PHE A 455 " (cutoff:3.500A)
      removed outlier: 5.037A  pdb=" N   SER A 460 " --> pdb=" O   THR A 456 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   GLY A 463 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 483
    Processing helix  chain 'A' and resid 591 through 593
      No H-bonds generated for 'chain 'A' and resid 591 through 593'
    Processing helix  chain 'A' and resid 594 through 620
      Proline residue:  A 610  - end of helix
      removed outlier: 3.871A  pdb=" N   ASP A 620 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 626 through 643
    Processing helix  chain 'A' and resid 648 through 677
      removed outlier: 3.808A  pdb=" N   GLY A 660 " --> pdb=" O   CYS A 656 " (cutoff:3.500A)
      removed outlier: 4.453A  pdb=" N   VAL A 661 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   ASN A 667 " --> pdb=" O   ILE A 663 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ALA A 668 " --> pdb=" O   ALA A 664 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU A 669 " --> pdb=" O   SER A 665 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   TYR A 677 " --> pdb=" O   THR A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 681 through 707
    Processing helix  chain 'A' and resid 713 through 727
    Processing sheet with id=AA1, first strand: chain 'B' and resid 535 through 536
      removed outlier: 3.722A  pdb=" N   PHE B 536 " --> pdb=" O   VAL B 555 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 521 through 522
      removed outlier: 6.574A  pdb=" N   LEU A 521 " --> pdb=" O   SER A 542 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2

    566 hydrogen bonds defined for protein.
    1683 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.51

  Time building geometry restraints manager: 3.01 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1413
        1.31 -     1.43: 2875
        1.43 -     1.56: 5042
        1.56 -     1.69: 0
        1.69 -     1.82: 112
  Bond restraints: 9442
  Sorted by residual:
  bond pdb=" C6  VLX A 801 "
       pdb=" N1  VLX A 801 "
    ideal  model  delta    sigma   weight residual
    1.351  1.518 -0.167 2.00e-02 2.50e+03 6.95e+01
  bond pdb=" C6  VLX B 801 "
       pdb=" N1  VLX B 801 "
    ideal  model  delta    sigma   weight residual
    1.351  1.507 -0.156 2.00e-02 2.50e+03 6.06e+01
  bond pdb=" C9  VLX A 801 "
       pdb=" N2  VLX A 801 "
    ideal  model  delta    sigma   weight residual
    1.339  1.461 -0.122 2.00e-02 2.50e+03 3.70e+01
  bond pdb=" C9  VLX B 801 "
       pdb=" N2  VLX B 801 "
    ideal  model  delta    sigma   weight residual
    1.339  1.457 -0.118 2.00e-02 2.50e+03 3.51e+01
  bond pdb=" CA  GLU B 282 "
       pdb=" C   GLU B 282 "
    ideal  model  delta    sigma   weight residual
    1.523  1.450  0.073 1.41e-02 5.03e+03 2.67e+01
  ... (remaining 9437 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.85: 12516
        1.85 -     3.70: 174
        3.70 -     5.55: 64
        5.55 -     7.40: 13
        7.40 -     9.25: 4
  Bond angle restraints: 12771
  Sorted by residual:
  angle pdb=" N   GLU B 282 "
        pdb=" CA  GLU B 282 "
        pdb=" C   GLU B 282 "
      ideal   model   delta    sigma   weight residual
     113.16  107.70    5.46 1.24e+00 6.50e-01 1.94e+01
  angle pdb=" N   THR A 684 "
        pdb=" CA  THR A 684 "
        pdb=" CB  THR A 684 "
      ideal   model   delta    sigma   weight residual
     109.82  115.87   -6.05 1.52e+00 4.33e-01 1.58e+01
  angle pdb=" N   HIS A 378 "
        pdb=" CA  HIS A 378 "
        pdb=" CB  HIS A 378 "
      ideal   model   delta    sigma   weight residual
     110.16  115.06   -4.90 1.48e+00 4.57e-01 1.10e+01
  angle pdb=" O   THR A 683 "
        pdb=" C   THR A 683 "
        pdb=" N   THR A 684 "
      ideal   model   delta    sigma   weight residual
     122.15  118.38    3.77 1.14e+00 7.69e-01 1.10e+01
  angle pdb=" CA  THR A 683 "
        pdb=" C   THR A 683 "
        pdb=" N   THR A 684 "
      ideal   model   delta    sigma   weight residual
     117.39  121.36   -3.97 1.24e+00 6.50e-01 1.03e+01
  ... (remaining 12766 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.85: 5008
       23.85 -    47.71: 354
       47.71 -    71.56: 26
       71.56 -    95.41: 10
       95.41 -   119.27: 4
  Dihedral angle restraints: 5402
    sinusoidal: 2116
      harmonic: 3286
  Sorted by residual:
  dihedral pdb=" C6  VLX B 801 "
           pdb=" C5  VLX B 801 "
           pdb=" N1  VLX B 801 "
           pdb=" C8  VLX B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -168.88  -49.61 -119.27     1      3.00e+01 1.11e-03 1.59e+01
  dihedral pdb=" C6  VLX B 801 "
           pdb=" C5  VLX B 801 "
           pdb=" N1  VLX B 801 "
           pdb=" C9  VLX B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      68.19 -177.87 -113.94     1      3.00e+01 1.11e-03 1.50e+01
  dihedral pdb=" C2  VLX B 801 "
           pdb=" C5  VLX B 801 "
           pdb=" N1  VLX B 801 "
           pdb=" C8  VLX B 801 "
      ideal   model   delta sinusoidal    sigma   weight residual
      26.74  132.70 -105.96     1      3.00e+01 1.11e-03 1.36e+01
  ... (remaining 5399 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.065: 1217
       0.065 -    0.130: 146
       0.130 -    0.194: 4
       0.194 -    0.259: 2
       0.259 -    0.324: 2
  Chirality restraints: 1371
  Sorted by residual:
  chirality pdb=" C5  VLX B 801 "
            pdb=" C8  VLX B 801 "
            pdb=" C9  VLX B 801 "
            pdb=" N1  VLX B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.16   -0.32 2.00e-01 2.50e+01 2.62e+00
  chirality pdb=" C1  VLX A 801 "
            pdb=" C2  VLX A 801 "
            pdb=" C3  VLX A 801 "
            pdb=" C4  VLX A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.61   -2.88    0.27 2.00e-01 2.50e+01 1.79e+00
  chirality pdb=" C1  VLX B 801 "
            pdb=" C2  VLX B 801 "
            pdb=" C3  VLX B 801 "
            pdb=" C4  VLX B 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.61   -2.86    0.25 2.00e-01 2.50e+01 1.53e+00
  ... (remaining 1368 not shown)

  Planarity restraints: 1605
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B 281 "   -0.019 2.00e-02 2.50e+03   3.84e-02 1.47e+01
        pdb=" C   SER B 281 "    0.066 2.00e-02 2.50e+03
        pdb=" O   SER B 281 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   GLU B 282 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 354 "   -0.036 5.00e-02 4.00e+02   5.45e-02 4.75e+00
        pdb=" N   PRO A 355 "    0.094 5.00e-02 4.00e+02
        pdb=" CA  PRO A 355 "   -0.029 5.00e-02 4.00e+02
        pdb=" CD  PRO A 355 "   -0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 315 "   -0.034 5.00e-02 4.00e+02   5.17e-02 4.28e+00
        pdb=" N   PRO A 316 "    0.089 5.00e-02 4.00e+02
        pdb=" CA  PRO A 316 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 316 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1602 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1048
        2.75 -     3.29: 9430
        3.29 -     3.82: 15768
        3.82 -     4.36: 17142
        4.36 -     4.90: 29901
  Nonbonded interactions: 73289
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 279 "
            pdb=" O   PRO B 355 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OG  SER A 238 "
            pdb=" O   GLY A 268 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" OG  SER A 542 "
            pdb=" OG1 THR A 588 "
     model   vdw
     2.255 3.040
  nonbonded pdb=" O   MET B 619 "
            pdb=" NH1 ARG B 626 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   CYS A 549 "
            pdb=" OG  SER A 569 "
     model   vdw
     2.279 3.040
  ... (remaining 73284 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 133 through 709 or resid 801))
  selection = (chain 'B' and (resid 133 through 402 or resid 416 through 709 or resid 801))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.380
  Check model and map are aligned:         0.070
  Set scattering table:                    0.080
  Process input model:                     23.660
  Find NCS groups from input model:        0.380
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.470
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6061
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   0.167   9442  Z= 0.237
  Angle     :  0.641   9.246  12771  Z= 0.330
  Chirality :  0.043   0.324   1371
  Planarity :  0.004   0.054   1605
  Dihedral  : 15.672 119.268   3308
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 12.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.96 %
    Favored  : 97.04 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1148
  helix:  0.98 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.02 (0.34), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 666 
 HIS   0.013   0.001   HIS A 396 
 PHE   0.032   0.001   PHE B 640 
 TYR   0.017   0.001   TYR B 595 
 ARG   0.007   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.10403 (  566)
  hydrogen bonds       : angle       4.91092 ( 1683)
  covalent geometry    : bond        0.00466 ( 9442)
  covalent geometry    : angle       0.64110 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 139
  time to evaluate  : 0.950 
Fit side-chains
REVERT: B  450 MET cc_start: 0.6702 (tpp) cc_final: 0.6298 (tpp)
REVERT: A  206 MET cc_start: 0.7032 (tmm) cc_final: 0.6580 (tmm)
REVERT: A  344 SER cc_start: 0.9049 (p) cc_final: 0.8840 (p)
REVERT: A  382 MET cc_start: 0.6213 (ttm) cc_final: 0.5867 (ttm)
REVERT: A  420 TRP cc_start: 0.7028 (m100) cc_final: 0.6704 (m100)
REVERT: A  596 MET cc_start: 0.6916 (tpt) cc_final: 0.6461 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 139
  average time/residue: 0.1871
  time to fit residues: 37.6764
Evaluate side-chains
  124 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.945 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 96 optimal weight:   30.0000
   chunk 86 optimal weight:    0.6980
   chunk 47 optimal weight:    0.1980
   chunk 29 optimal weight:   10.0000
   chunk 58 optimal weight:    0.2980
   chunk 46 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   chunk 34 optimal weight:   20.0000
   chunk 54 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 612 ASN
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4804 r_free = 0.4804 target = 0.262888 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4241 r_free = 0.4241 target = 0.193375 restraints weight = 10108.747|
|-----------------------------------------------------------------------------|
r_work (start): 0.4198 rms_B_bonded: 2.70
r_work: 0.4060 rms_B_bonded: 3.68 restraints_weight: 0.5000
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6120
moved from start:          0.0783

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9442  Z= 0.126
  Angle     :  0.546   6.961  12771  Z= 0.282
  Chirality :  0.040   0.325   1371
  Planarity :  0.004   0.044   1605
  Dihedral  :  7.857 101.631   1292
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  :  8.16 %
    Favored  : 90.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.25), residues: 1148
  helix:  1.25 (0.19), residues: 744
  sheet:  None (None), residues: 0
  loop : -0.13 (0.34), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 333 
 HIS   0.014   0.001   HIS A 378 
 PHE   0.030   0.001   PHE B 640 
 TYR   0.009   0.001   TYR A 212 
 ARG   0.004   0.000   ARG B 626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04036 (  566)
  hydrogen bonds       : angle       4.22128 ( 1683)
  covalent geometry    : bond        0.00274 ( 9442)
  covalent geometry    : angle       0.54611 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 0.976 
Fit side-chains
REVERT: B  163 ARG cc_start: 0.4412 (tpp-160) cc_final: 0.3816 (tpp-160)
REVERT: B  657 LEU cc_start: 0.7649 (mp) cc_final: 0.7405 (mp)
REVERT: A  382 MET cc_start: 0.5235 (ttm) cc_final: 0.4703 (ttm)
REVERT: A  420 TRP cc_start: 0.6947 (m100) cc_final: 0.6544 (m100)
REVERT: A  596 MET cc_start: 0.6975 (tpt) cc_final: 0.6594 (tpt)
  outliers start: 9
  outliers final: 6
  residues processed: 127
  average time/residue: 0.1904
  time to fit residues: 35.5297
Evaluate side-chains
  126 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 120
  time to evaluate  : 0.877 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  711 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 31 optimal weight:    0.4980
   chunk 82 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 2 optimal weight:    3.9990
   chunk 90 optimal weight:    4.9990
   chunk 54 optimal weight:    0.8980
   chunk 78 optimal weight:    3.9990
   chunk 110 optimal weight:    0.5980
   chunk 25 optimal weight:    9.9990
   chunk 81 optimal weight:    0.4980
   chunk 42 optimal weight:    6.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 242 ASN
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4798 r_free = 0.4798 target = 0.261478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.189464 restraints weight = 10291.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.4177 rms_B_bonded: 2.80
r_work: 0.4051 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.0991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   9442  Z= 0.136
  Angle     :  0.538   6.767  12771  Z= 0.278
  Chirality :  0.039   0.147   1371
  Planarity :  0.003   0.038   1605
  Dihedral  :  6.483  69.560   1292
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 11.78 %
    Favored  : 86.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.20 (0.25), residues: 1148
  helix:  1.34 (0.19), residues: 747
  sheet:  None (None), residues: 0
  loop : -0.11 (0.34), residues: 401

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 166 
 HIS   0.012   0.001   HIS A 378 
 PHE   0.031   0.001   PHE B 640 
 TYR   0.014   0.001   TYR A 212 
 ARG   0.004   0.000   ARG B 445 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03985 (  566)
  hydrogen bonds       : angle       4.15353 ( 1683)
  covalent geometry    : bond        0.00309 ( 9442)
  covalent geometry    : angle       0.53848 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 1.257 
Fit side-chains
REVERT: B  324 MET cc_start: 0.2546 (pmm) cc_final: 0.2309 (pmm)
REVERT: B  675 GLU cc_start: 0.7327 (pt0) cc_final: 0.6755 (tp30)
REVERT: A  275 ILE cc_start: 0.8308 (OUTLIER) cc_final: 0.8070 (mt)
REVERT: A  382 MET cc_start: 0.5295 (ttm) cc_final: 0.4682 (ttm)
REVERT: A  420 TRP cc_start: 0.7063 (m100) cc_final: 0.6570 (m100)
REVERT: A  596 MET cc_start: 0.7021 (tpt) cc_final: 0.6646 (tpt)
  outliers start: 14
  outliers final: 12
  residues processed: 137
  average time/residue: 0.1900
  time to fit residues: 38.1124
Evaluate side-chains
  132 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 119
  time to evaluate  : 0.931 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  600 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  298 MET
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  720 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 35 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 38 optimal weight:   20.0000
   chunk 104 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 113 optimal weight:    4.9990
   chunk 87 optimal weight:    0.8980
   chunk 110 optimal weight:    0.5980
   chunk 84 optimal weight:    0.7980
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4854 r_free = 0.4854 target = 0.269272 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.199686 restraints weight = 9996.329|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 2.76
r_work: 0.3936 rms_B_bonded: 3.69 restraints_weight: 0.5000
r_work (final): 0.3936
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6065
moved from start:          0.1167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9442  Z= 0.126
  Angle     :  0.536   9.238  12771  Z= 0.272
  Chirality :  0.038   0.132   1371
  Planarity :  0.003   0.038   1605
  Dihedral  :  6.163  58.939   1292
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 13.53 %
    Favored  : 84.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.25), residues: 1148
  helix:  1.40 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -0.16 (0.34), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 300 
 HIS   0.012   0.001   HIS A 378 
 PHE   0.030   0.001   PHE B 640 
 TYR   0.010   0.001   TYR A 279 
 ARG   0.003   0.000   ARG B 626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03772 (  566)
  hydrogen bonds       : angle       4.07995 ( 1683)
  covalent geometry    : bond        0.00288 ( 9442)
  covalent geometry    : angle       0.53626 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 129
  time to evaluate  : 1.029 
Fit side-chains
REVERT: B  324 MET cc_start: 0.2632 (pmm) cc_final: 0.2391 (pmm)
REVERT: B  657 LEU cc_start: 0.7612 (mp) cc_final: 0.7399 (mp)
REVERT: B  675 GLU cc_start: 0.7247 (pt0) cc_final: 0.6714 (tp30)
REVERT: A  142 ARG cc_start: 0.5482 (ppt170) cc_final: 0.5173 (ppt170)
REVERT: A  275 ILE cc_start: 0.8331 (OUTLIER) cc_final: 0.8088 (mt)
REVERT: A  382 MET cc_start: 0.5183 (ttm) cc_final: 0.4418 (ttm)
REVERT: A  420 TRP cc_start: 0.7187 (m100) cc_final: 0.6637 (m100)
REVERT: A  596 MET cc_start: 0.6971 (tpt) cc_final: 0.6640 (tpt)
  outliers start: 18
  outliers final: 16
  residues processed: 138
  average time/residue: 0.1968
  time to fit residues: 40.5413
Evaluate side-chains
  139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 122
  time to evaluate  : 1.039 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  600 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  720 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 95 optimal weight:   20.0000
   chunk 67 optimal weight:    0.1980
   chunk 41 optimal weight:    9.9990
   chunk 73 optimal weight:    0.6980
   chunk 15 optimal weight:    0.9990
   chunk 72 optimal weight:    0.9990
   chunk 63 optimal weight:    0.9980
   chunk 14 optimal weight:    0.7980
   chunk 89 optimal weight:    4.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4836 r_free = 0.4836 target = 0.267029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.199463 restraints weight = 9972.194|
|-----------------------------------------------------------------------------|
r_work (start): 0.4082 rms_B_bonded: 2.64
r_work: 0.3933 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6135
moved from start:          0.1280

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9442  Z= 0.123
  Angle     :  0.527   9.220  12771  Z= 0.268
  Chirality :  0.038   0.131   1371
  Planarity :  0.003   0.038   1605
  Dihedral  :  5.871  58.744   1292
  Min Nonbonded Distance : 2.600

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 14.98 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.33 (0.26), residues: 1148
  helix:  1.47 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -0.15 (0.34), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 333 
 HIS   0.011   0.001   HIS A 378 
 PHE   0.030   0.001   PHE B 640 
 TYR   0.010   0.001   TYR A 279 
 ARG   0.003   0.000   ARG B 626 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03713 (  566)
  hydrogen bonds       : angle       4.03551 ( 1683)
  covalent geometry    : bond        0.00278 ( 9442)
  covalent geometry    : angle       0.52744 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 131
  time to evaluate  : 1.035 
Fit side-chains
REVERT: B  324 MET cc_start: 0.2697 (pmm) cc_final: 0.2446 (pmm)
REVERT: B  613 ILE cc_start: 0.8206 (mp) cc_final: 0.7892 (mt)
REVERT: B  657 LEU cc_start: 0.7613 (mp) cc_final: 0.7352 (mp)
REVERT: B  675 GLU cc_start: 0.7314 (pt0) cc_final: 0.6811 (tp30)
REVERT: A  275 ILE cc_start: 0.8359 (OUTLIER) cc_final: 0.8107 (mt)
REVERT: A  382 MET cc_start: 0.5370 (ttm) cc_final: 0.4479 (ttm)
REVERT: A  420 TRP cc_start: 0.7239 (m100) cc_final: 0.6628 (m100)
REVERT: A  596 MET cc_start: 0.6999 (tpt) cc_final: 0.6711 (tpt)
  outliers start: 18
  outliers final: 14
  residues processed: 141
  average time/residue: 0.1843
  time to fit residues: 38.9871
Evaluate side-chains
  140 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 125
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  600 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  711 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 13 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0270
   chunk 90 optimal weight:    0.0980
   chunk 100 optimal weight:   20.0000
   chunk 103 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 11 optimal weight:    0.9990
   chunk 75 optimal weight:    9.9990
   chunk 81 optimal weight:    3.9990
   chunk 59 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.5640

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4835 r_free = 0.4835 target = 0.266988 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4294 r_free = 0.4294 target = 0.199487 restraints weight = 9938.366|
|-----------------------------------------------------------------------------|
r_work (start): 0.4093 rms_B_bonded: 2.65
r_work: 0.3945 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3945
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6106
moved from start:          0.1404

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9442  Z= 0.114
  Angle     :  0.525   9.657  12771  Z= 0.265
  Chirality :  0.037   0.124   1371
  Planarity :  0.003   0.037   1605
  Dihedral  :  5.511  53.907   1292
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.09 %
    Favored  : 97.91 %
  Rotamer:
    Outliers :  2.48 %
    Allowed  : 15.50 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.39 (0.26), residues: 1148
  helix:  1.52 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -0.15 (0.34), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 333 
 HIS   0.011   0.001   HIS A 378 
 PHE   0.029   0.001   PHE B 640 
 TYR   0.009   0.001   TYR A 279 
 ARG   0.004   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03568 (  566)
  hydrogen bonds       : angle       3.98270 ( 1683)
  covalent geometry    : bond        0.00250 ( 9442)
  covalent geometry    : angle       0.52463 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 128
  time to evaluate  : 1.093 
Fit side-chains
REVERT: B  161 HIS cc_start: 0.7156 (t70) cc_final: 0.6776 (t70)
REVERT: B  324 MET cc_start: 0.2707 (pmm) cc_final: 0.2457 (pmm)
REVERT: B  382 MET cc_start: 0.4543 (ttt) cc_final: 0.3697 (ptt)
REVERT: B  450 MET cc_start: 0.6828 (tpp) cc_final: 0.6344 (tpp)
REVERT: B  657 LEU cc_start: 0.7573 (mp) cc_final: 0.7262 (mp)
REVERT: B  675 GLU cc_start: 0.7264 (pt0) cc_final: 0.6783 (tp30)
REVERT: A  275 ILE cc_start: 0.8344 (OUTLIER) cc_final: 0.8089 (mt)
REVERT: A  382 MET cc_start: 0.5408 (ttm) cc_final: 0.4438 (ttm)
REVERT: A  420 TRP cc_start: 0.7249 (m100) cc_final: 0.6643 (m100)
REVERT: A  596 MET cc_start: 0.6881 (tpt) cc_final: 0.6591 (tpt)
  outliers start: 24
  outliers final: 18
  residues processed: 140
  average time/residue: 0.2058
  time to fit residues: 42.7967
Evaluate side-chains
  142 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 123
  time to evaluate  : 1.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  600 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  644 PHE
Chi-restraints excluded: chain A residue  651 MET
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  720 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 28 optimal weight:    0.8980
   chunk 82 optimal weight:    0.8980
   chunk 112 optimal weight:    3.9990
   chunk 99 optimal weight:   20.0000
   chunk 0 optimal weight:   30.0000
   chunk 34 optimal weight:   20.0000
   chunk 12 optimal weight:    4.9990
   chunk 43 optimal weight:   20.0000
   chunk 46 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    1.4982

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

Flipped N/Q/H residues before XYZ refinement:
** B 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 151 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4838 r_free = 0.4838 target = 0.267271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.198262 restraints weight = 10374.982|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 2.79
r_work: 0.3868 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3868
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6184
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   9442  Z= 0.177
  Angle     :  0.602  10.142  12771  Z= 0.305
  Chirality :  0.040   0.151   1371
  Planarity :  0.004   0.043   1605
  Dihedral  :  5.322  46.350   1292
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 10.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 16.43 %
    Favored  : 81.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.26), residues: 1148
  helix:  1.35 (0.19), residues: 748
  sheet:  None (None), residues: 0
  loop : -0.17 (0.34), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 467 
 HIS   0.012   0.001   HIS A 378 
 PHE   0.034   0.002   PHE B 640 
 TYR   0.015   0.001   TYR A 279 
 ARG   0.004   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04208 (  566)
  hydrogen bonds       : angle       4.21583 ( 1683)
  covalent geometry    : bond        0.00413 ( 9442)
  covalent geometry    : angle       0.60173 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 124
  time to evaluate  : 0.903 
Fit side-chains
REVERT: B  613 ILE cc_start: 0.8191 (mp) cc_final: 0.7887 (mt)
REVERT: A  142 ARG cc_start: 0.5455 (ppt170) cc_final: 0.5187 (ppt170)
REVERT: A  275 ILE cc_start: 0.8346 (OUTLIER) cc_final: 0.8123 (mt)
REVERT: A  382 MET cc_start: 0.5308 (ttm) cc_final: 0.4279 (ttm)
REVERT: A  420 TRP cc_start: 0.7203 (m100) cc_final: 0.6986 (m-90)
REVERT: A  596 MET cc_start: 0.7062 (tpt) cc_final: 0.6751 (tpt)
  outliers start: 22
  outliers final: 19
  residues processed: 137
  average time/residue: 0.2078
  time to fit residues: 41.7018
Evaluate side-chains
  139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 119
  time to evaluate  : 0.917 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  600 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  315 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  720 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 110 optimal weight:    0.5980
   chunk 66 optimal weight:    2.9990
   chunk 57 optimal weight:    7.9990
   chunk 24 optimal weight:    5.9990
   chunk 77 optimal weight:    0.3980
   chunk 84 optimal weight:    1.9990
   chunk 31 optimal weight:    0.8980
   chunk 90 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 93 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4878 r_free = 0.4878 target = 0.272302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.201654 restraints weight = 10550.481|
|-----------------------------------------------------------------------------|
r_work (start): 0.4168 rms_B_bonded: 2.93
r_work: 0.4041 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6164
moved from start:          0.1515

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9442  Z= 0.125
  Angle     :  0.557  10.427  12771  Z= 0.279
  Chirality :  0.038   0.138   1371
  Planarity :  0.003   0.037   1605
  Dihedral  :  5.003  40.474   1292
  Min Nonbonded Distance : 2.554

Molprobity Statistics.
  All-atom Clashscore : 9.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.22 %
    Favored  : 80.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.26), residues: 1148
  helix:  1.46 (0.19), residues: 752
  sheet:  None (None), residues: 0
  loop : -0.12 (0.35), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 333 
 HIS   0.011   0.001   HIS A 378 
 PHE   0.030   0.001   PHE B 640 
 TYR   0.011   0.001   TYR A 279 
 ARG   0.004   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03749 (  566)
  hydrogen bonds       : angle       4.09211 ( 1683)
  covalent geometry    : bond        0.00282 ( 9442)
  covalent geometry    : angle       0.55656 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 126
  time to evaluate  : 0.993 
Fit side-chains
REVERT: B  288 LYS cc_start: 0.6392 (mmmm) cc_final: 0.6167 (mmmm)
REVERT: B  382 MET cc_start: 0.4551 (ttt) cc_final: 0.3703 (ptt)
REVERT: B  450 MET cc_start: 0.6737 (tpp) cc_final: 0.6339 (tpp)
REVERT: B  613 ILE cc_start: 0.8149 (mp) cc_final: 0.7853 (mt)
REVERT: A  275 ILE cc_start: 0.8353 (OUTLIER) cc_final: 0.8097 (mt)
REVERT: A  382 MET cc_start: 0.5342 (ttm) cc_final: 0.4283 (ttm)
REVERT: A  420 TRP cc_start: 0.7281 (m100) cc_final: 0.6635 (m100)
REVERT: A  596 MET cc_start: 0.7062 (tpt) cc_final: 0.6743 (tpt)
  outliers start: 27
  outliers final: 23
  residues processed: 142
  average time/residue: 0.1850
  time to fit residues: 38.9104
Evaluate side-chains
  148 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 124
  time to evaluate  : 0.925 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  292 HIS
Chi-restraints excluded: chain B residue  331 HIS
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  600 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  644 PHE
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  720 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 27 optimal weight:    9.9990
   chunk 101 optimal weight:    1.9990
   chunk 6 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 20 optimal weight:    0.0470
   chunk 86 optimal weight:    1.9990
   chunk 85 optimal weight:    3.9990
   chunk 54 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 78 optimal weight:    0.5980
   chunk 15 optimal weight:    0.9990
   overall best weight:    0.6680

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

Flipped N/Q/H residues before XYZ refinement:
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4861 r_free = 0.4861 target = 0.270011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.203106 restraints weight = 9975.589|
|-----------------------------------------------------------------------------|
r_work (start): 0.4076 rms_B_bonded: 2.66
r_work: 0.3926 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6141
moved from start:          0.1574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9442  Z= 0.123
  Angle     :  0.561  10.657  12771  Z= 0.279
  Chirality :  0.039   0.160   1371
  Planarity :  0.003   0.036   1605
  Dihedral  :  4.729  36.021   1292
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 9.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 16.32 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.42 (0.26), residues: 1148
  helix:  1.53 (0.19), residues: 753
  sheet:  None (None), residues: 0
  loop : -0.09 (0.35), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 333 
 HIS   0.011   0.001   HIS A 378 
 PHE   0.029   0.001   PHE B 640 
 TYR   0.010   0.001   TYR A 279 
 ARG   0.004   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03675 (  566)
  hydrogen bonds       : angle       4.06538 ( 1683)
  covalent geometry    : bond        0.00275 ( 9442)
  covalent geometry    : angle       0.56122 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  150 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 123
  time to evaluate  : 0.916 
Fit side-chains
REVERT: B  288 LYS cc_start: 0.6393 (mmmm) cc_final: 0.6160 (mmmm)
REVERT: B  382 MET cc_start: 0.4591 (ttt) cc_final: 0.3752 (ptt)
REVERT: B  450 MET cc_start: 0.6804 (tpp) cc_final: 0.6415 (tpp)
REVERT: A  275 ILE cc_start: 0.8361 (OUTLIER) cc_final: 0.8108 (mt)
REVERT: A  420 TRP cc_start: 0.7290 (m100) cc_final: 0.7024 (m-90)
REVERT: A  596 MET cc_start: 0.6849 (tpt) cc_final: 0.6570 (tpt)
  outliers start: 27
  outliers final: 22
  residues processed: 139
  average time/residue: 0.1790
  time to fit residues: 36.5863
Evaluate side-chains
  143 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 120
  time to evaluate  : 0.856 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  292 HIS
Chi-restraints excluded: chain B residue  331 HIS
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  495 VAL
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  600 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  720 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 108 optimal weight:    1.9990
   chunk 38 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9980
   chunk 90 optimal weight:   20.0000
   chunk 5 optimal weight:    0.8980
   chunk 10 optimal weight:    3.9990
   chunk 25 optimal weight:    0.1980
   chunk 112 optimal weight:    5.9990
   chunk 102 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 19 optimal weight:    1.9990
   overall best weight:    1.0182

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

Flipped N/Q/H residues before XYZ refinement:
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4831 r_free = 0.4831 target = 0.266377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.4276 r_free = 0.4276 target = 0.197867 restraints weight = 10489.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.4047 rms_B_bonded: 2.77
r_work: 0.3899 rms_B_bonded: 3.73 restraints_weight: 0.5000
r_work (final): 0.3899
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6185
moved from start:          0.1622

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046   9442  Z= 0.143
  Angle     :  0.587  10.659  12771  Z= 0.293
  Chirality :  0.039   0.149   1371
  Planarity :  0.003   0.039   1605
  Dihedral  :  4.617  34.438   1292
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  2.27 %
    Allowed  : 17.25 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.35 (0.26), residues: 1148
  helix:  1.45 (0.19), residues: 754
  sheet:  None (None), residues: 0
  loop : -0.07 (0.35), residues: 394

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 467 
 HIS   0.011   0.001   HIS A 378 
 PHE   0.032   0.001   PHE B 640 
 TYR   0.012   0.001   TYR A 279 
 ARG   0.004   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03880 (  566)
  hydrogen bonds       : angle       4.14130 ( 1683)
  covalent geometry    : bond        0.00332 ( 9442)
  covalent geometry    : angle       0.58703 (12771)

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

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

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2296 Ramachandran restraints generated.
    1148 Oldfield, 0 Emsley, 1148 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  139 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 117
  time to evaluate  : 0.994 
Fit side-chains
   revert: symmetry clash
REVERT: B  288 LYS cc_start: 0.6462 (mmmm) cc_final: 0.6197 (mmmm)
REVERT: B  382 MET cc_start: 0.4611 (ttt) cc_final: 0.3779 (ptt)
REVERT: B  450 MET cc_start: 0.6662 (tpp) cc_final: 0.6236 (tpp)
REVERT: B  613 ILE cc_start: 0.8136 (mp) cc_final: 0.7791 (mt)
REVERT: A  275 ILE cc_start: 0.8343 (OUTLIER) cc_final: 0.8096 (mt)
REVERT: A  382 MET cc_start: 0.4732 (ttm) cc_final: 0.3812 (ttm)
REVERT: A  420 TRP cc_start: 0.7293 (m100) cc_final: 0.6562 (m100)
REVERT: A  596 MET cc_start: 0.6961 (tpt) cc_final: 0.6670 (tpt)
  outliers start: 22
  outliers final: 20
  residues processed: 131
  average time/residue: 0.2079
  time to fit residues: 40.3160
Evaluate side-chains
  137 residues out of total 968 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.966 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  273 ILE
Chi-restraints excluded: chain B residue  292 HIS
Chi-restraints excluded: chain B residue  372 MET
Chi-restraints excluded: chain B residue  455 PHE
Chi-restraints excluded: chain B residue  464 LEU
Chi-restraints excluded: chain B residue  596 MET
Chi-restraints excluded: chain B residue  600 VAL
Chi-restraints excluded: chain B residue  603 LEU
Chi-restraints excluded: chain B residue  617 LEU
Chi-restraints excluded: chain A residue  182 GLU
Chi-restraints excluded: chain A residue  216 MET
Chi-restraints excluded: chain A residue  269 ILE
Chi-restraints excluded: chain A residue  275 ILE
Chi-restraints excluded: chain A residue  345 VAL
Chi-restraints excluded: chain A residue  378 HIS
Chi-restraints excluded: chain A residue  466 VAL
Chi-restraints excluded: chain A residue  478 VAL
Chi-restraints excluded: chain A residue  654 LEU
Chi-restraints excluded: chain A residue  684 THR
Chi-restraints excluded: chain A residue  711 THR
Chi-restraints excluded: chain A residue  720 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 114
   random chunks:
   chunk 78 optimal weight:    1.9990
   chunk 72 optimal weight:    0.8980
   chunk 68 optimal weight:    0.3980
   chunk 21 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 113 optimal weight:    2.9990
   chunk 53 optimal weight:    0.6980
   chunk 87 optimal weight:    0.6980
   chunk 0 optimal weight:   30.0000
   chunk 6 optimal weight:    0.5980
   chunk 60 optimal weight:    0.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 690 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4838 r_free = 0.4838 target = 0.267388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4285 r_free = 0.4285 target = 0.199035 restraints weight = 10485.844|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 2.77
r_work: 0.3926 rms_B_bonded: 3.76 restraints_weight: 0.5000
r_work (final): 0.3926
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6121
moved from start:          0.1669

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9442  Z= 0.119
  Angle     :  0.555  10.764  12771  Z= 0.276
  Chirality :  0.038   0.146   1371
  Planarity :  0.003   0.036   1605
  Dihedral  :  4.412  29.792   1292
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 17.46 %
    Favored  : 80.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.54 (0.26), residues: 1148
  helix:  1.65 (0.19), residues: 750
  sheet:  None (None), residues: 0
  loop : -0.09 (0.35), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 333 
 HIS   0.010   0.001   HIS A 378 
 PHE   0.029   0.001   PHE B 640 
 TYR   0.009   0.001   TYR A 279 
 ARG   0.004   0.000   ARG B 473 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03614 (  566)
  hydrogen bonds       : angle       4.06564 ( 1683)
  covalent geometry    : bond        0.00266 ( 9442)
  covalent geometry    : angle       0.55455 (12771)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5832.64 seconds
wall clock time: 102 minutes 33.43 seconds (6153.43 seconds total)