Starting phenix.real_space_refine
on Wed Sep 17 17:32:43 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yet_39203/09_2025/8yet_39203.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yet_39203/09_2025/8yet_39203.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.16
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yet_39203/09_2025/8yet_39203.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yet_39203/09_2025/8yet_39203.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yet_39203/09_2025/8yet_39203.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yet_39203/09_2025/8yet_39203.map"
  }
  resolution = 4.16
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.047
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: 5
    Type Number    sf(0)   Gaussians
     P      12      5.49       5
     S      42      5.16       5
     C    6618      2.51       5
     N    1652      2.21       5
     O    1778      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10102
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 5015
          Classifications: {'peptide': 603}
          Link IDs: {'PTRANS': 20, 'TRANS': 582}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 5015
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 603, 5015
          Classifications: {'peptide': 603}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 582}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 72
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 72
          Unusual residues: {'IHP': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.83, per 1000 atoms: 0.28
  Number of scatterers: 10102
  At special positions: 0
  Unit cell: (113.3, 116.6, 108.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      42     16.00
     P      12     15.00
     O    1778      8.00
     N    1652      7.00
     C    6618      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 415 " - pdb=" SG  CYS A 440 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 415 " - pdb=" SG  CYS B 440 " distance=2.03

  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: 1.08
  Conformation dependent library (CDL) restraints added in 387.2 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2320

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 0 sheets defined
      78.5% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.27
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 11
    Processing helix  chain 'A' and resid 12 through 19
      removed outlier: 6.031A  pdb=" N   LYS A  17 " --> pdb=" O   GLU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 36
      removed outlier: 3.803A  pdb=" N   ALA A  36 " --> pdb=" O   ALA A  32 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 100
    Processing helix  chain 'A' and resid 119 through 167
    Processing helix  chain 'A' and resid 170 through 180
      removed outlier: 3.613A  pdb=" N   ASP A 174 " --> pdb=" O   SER A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 189 through 206
      removed outlier: 3.649A  pdb=" N   GLN A 193 " --> pdb=" O   LYS A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 218
    Processing helix  chain 'A' and resid 230 through 258
      removed outlier: 3.654A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 4.521A  pdb=" N   ILE A 271 " --> pdb=" O   PRO A 267 " (cutoff:3.500A)
      removed outlier: 5.935A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 5.219A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   PHE A 276 " --> pdb=" O   TYR A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 303
      removed outlier: 3.542A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.860A  pdb=" N   LEU A 316 " --> pdb=" O   SER A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 346 through 360
    Processing helix  chain 'A' and resid 367 through 383
    Processing helix  chain 'A' and resid 391 through 401
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 4.214A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 3.807A  pdb=" N   ILE A 450 " --> pdb=" O   GLY A 446 " (cutoff:3.500A)
      Proline residue:  A 455  - end of helix
    Processing helix  chain 'A' and resid 476 through 483
      removed outlier: 3.848A  pdb=" N   TYR A 483 " --> pdb=" O   ASN A 479 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 503
      removed outlier: 3.610A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 529
      removed outlier: 3.750A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   PHE A 511 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TYR A 512 " --> pdb=" O   MET A 508 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   LEU A 513 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   TRP A 514 " --> pdb=" O   PHE A 510 " (cutoff:3.500A)
      removed outlier: 4.155A  pdb=" N   TYR A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ILE A 527 " --> pdb=" O   CYS A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 556 through 583
      removed outlier: 4.319A  pdb=" N   VAL A 567 " --> pdb=" O   ILE A 563 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   ILE A 568 " --> pdb=" O   ILE A 564 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR A 583 " --> pdb=" O   ILE A 579 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 588 through 618
      Proline residue:  A 598  - end of helix
      removed outlier: 4.124A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   LEU A 617 " --> pdb=" O   GLU A 613 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 2 through 10
      removed outlier: 3.589A  pdb=" N   HIS B   6 " --> pdb=" O   LYS B   2 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 36
      removed outlier: 3.643A  pdb=" N   GLN B  35 " --> pdb=" O   SER B  31 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   ALA B  36 " --> pdb=" O   ALA B  32 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 43 through 100
      removed outlier: 3.825A  pdb=" N   VAL B  47 " --> pdb=" O   ASP B  43 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 119 through 167
    Processing helix  chain 'B' and resid 170 through 180
    Processing helix  chain 'B' and resid 183 through 188
    Processing helix  chain 'B' and resid 189 through 205
      removed outlier: 3.544A  pdb=" N   GLN B 193 " --> pdb=" O   LYS B 189 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 210 through 218
    Processing helix  chain 'B' and resid 230 through 258
      removed outlier: 3.649A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 296
      removed outlier: 5.287A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.511A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 303
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.859A  pdb=" N   LEU B 316 " --> pdb=" O   SER B 312 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 346 through 360
    Processing helix  chain 'B' and resid 367 through 383
    Processing helix  chain 'B' and resid 384 through 387
    Processing helix  chain 'B' and resid 390 through 402
      removed outlier: 3.596A  pdb=" N   TRP B 395 " --> pdb=" O   PHE B 391 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   LEU B 396 " --> pdb=" O   ALA B 392 " (cutoff:3.500A)
      removed outlier: 3.826A  pdb=" N   SER B 402 " --> pdb=" O   ASP B 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 419
      removed outlier: 4.244A  pdb=" N   LEU B 407 " --> pdb=" O   LEU B 403 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 448 through 471
      Proline residue:  B 455  - end of helix
    Processing helix  chain 'B' and resid 475 through 503
      removed outlier: 4.551A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 4.884A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
      removed outlier: 3.768A  pdb=" N   PHE B 488 " --> pdb=" O   SER B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.820A  pdb=" N   PHE B 510 " --> pdb=" O   ASP B 506 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   PHE B 511 " --> pdb=" O   THR B 507 " (cutoff:3.500A)
      removed outlier: 3.685A  pdb=" N   TYR B 512 " --> pdb=" O   MET B 508 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   LEU B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   TYR B 524 " --> pdb=" O   ILE B 520 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ILE B 527 " --> pdb=" O   CYS B 523 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   MET B 532 " --> pdb=" O   TRP B 528 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 556 through 583
      removed outlier: 4.359A  pdb=" N   VAL B 567 " --> pdb=" O   ILE B 563 " (cutoff:3.500A)
      removed outlier: 4.427A  pdb=" N   ILE B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 587 through 618
      removed outlier: 4.529A  pdb=" N   ILE B 591 " --> pdb=" O   HIS B 587 " (cutoff:3.500A)
      Proline residue:  B 598  - end of helix
      removed outlier: 4.141A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 4.953A  pdb=" N   PHE B 602 " --> pdb=" O   PRO B 598 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASN B 608 " --> pdb=" O   ARG B 604 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 4.089A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   LEU B 617 " --> pdb=" O   GLU B 613 " (cutoff:3.500A)

    693 hydrogen bonds defined for protein.
    2064 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: 1.60

  Time building geometry restraints manager: 1.37 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: 3086
        1.34 -     1.46: 2286
        1.46 -     1.58: 4946
        1.58 -     1.69: 14
        1.69 -     1.81: 60
  Bond restraints: 10392
  Sorted by residual:
  bond pdb=" O16 IHP A 701 "
       pdb=" P6  IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.672  1.617  0.055 2.00e-02 2.50e+03 7.57e+00
  bond pdb=" C3  IHP A 701 "
       pdb=" O13 IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.393  1.343  0.050 2.00e-02 2.50e+03 6.32e+00
  bond pdb=" C3  IHP A 701 "
       pdb=" C4  IHP A 701 "
    ideal  model  delta    sigma   weight residual
    1.535  1.585 -0.050 2.00e-02 2.50e+03 6.24e+00
  bond pdb=" C3  IHP A 702 "
       pdb=" C4  IHP A 702 "
    ideal  model  delta    sigma   weight residual
    1.535  1.584 -0.049 2.00e-02 2.50e+03 6.01e+00
  bond pdb=" O16 IHP A 702 "
       pdb=" P6  IHP A 702 "
    ideal  model  delta    sigma   weight residual
    1.672  1.624  0.048 2.00e-02 2.50e+03 5.64e+00
  ... (remaining 10387 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.35: 13865
        2.35 -     4.70: 174
        4.70 -     7.04: 57
        7.04 -     9.39: 11
        9.39 -    11.74: 5
  Bond angle restraints: 14112
  Sorted by residual:
  angle pdb=" O12 IHP A 702 "
        pdb=" P2  IHP A 702 "
        pdb=" O32 IHP A 702 "
      ideal   model   delta    sigma   weight residual
     100.47  111.70  -11.23 3.00e+00 1.11e-01 1.40e+01
  angle pdb=" O12 IHP A 701 "
        pdb=" P2  IHP A 701 "
        pdb=" O32 IHP A 701 "
      ideal   model   delta    sigma   weight residual
     100.47  111.61  -11.14 3.00e+00 1.11e-01 1.38e+01
  angle pdb=" C   ALA B  78 "
        pdb=" N   GLU B  79 "
        pdb=" CA  GLU B  79 "
      ideal   model   delta    sigma   weight residual
     120.72  114.65    6.07 1.67e+00 3.59e-01 1.32e+01
  angle pdb=" N   GLU B  79 "
        pdb=" CA  GLU B  79 "
        pdb=" CB  GLU B  79 "
      ideal   model   delta    sigma   weight residual
     110.39  116.39   -6.00 1.66e+00 3.63e-01 1.31e+01
  angle pdb=" O13 IHP A 702 "
        pdb=" P3  IHP A 702 "
        pdb=" O43 IHP A 702 "
      ideal   model   delta    sigma   weight residual
     101.78  112.04  -10.26 3.00e+00 1.11e-01 1.17e+01
  ... (remaining 14107 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    26.32: 5704
       26.32 -    52.64: 342
       52.64 -    78.96: 32
       78.96 -   105.29: 12
      105.29 -   131.61: 16
  Dihedral angle restraints: 6106
    sinusoidal: 2526
      harmonic: 3580
  Sorted by residual:
  dihedral pdb=" CB  CYS A 415 "
           pdb=" SG  CYS A 415 "
           pdb=" SG  CYS A 440 "
           pdb=" CB  CYS A 440 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  167.09  -74.09     1      1.00e+01 1.00e-02 6.97e+01
  dihedral pdb=" CA  CYS B 440 "
           pdb=" C   CYS B 440 "
           pdb=" N   HIS B 441 "
           pdb=" CA  HIS B 441 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.18   26.82     0      5.00e+00 4.00e-02 2.88e+01
  dihedral pdb=" CA  ILE B 342 "
           pdb=" C   ILE B 342 "
           pdb=" N   PRO B 343 "
           pdb=" CA  PRO B 343 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.51  -22.49     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 6103 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 1411
       0.073 -    0.146: 110
       0.146 -    0.219: 8
       0.219 -    0.293: 1
       0.293 -    0.366: 2
  Chirality restraints: 1532
  Sorted by residual:
  chirality pdb=" C2  IHP A 701 "
            pdb=" C1  IHP A 701 "
            pdb=" C3  IHP A 701 "
            pdb=" O12 IHP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.15   -0.37 2.00e-01 2.50e+01 3.34e+00
  chirality pdb=" C2  IHP A 702 "
            pdb=" C1  IHP A 702 "
            pdb=" C3  IHP A 702 "
            pdb=" O12 IHP A 702 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.22   -0.29 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" C3  IHP A 701 "
            pdb=" C2  IHP A 701 "
            pdb=" C4  IHP A 701 "
            pdb=" O13 IHP A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.34   -2.11   -0.23 2.00e-01 2.50e+01 1.29e+00
  ... (remaining 1529 not shown)

  Planarity restraints: 1744
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 292 "   -0.024 2.00e-02 2.50e+03   1.64e-02 6.74e+00
        pdb=" CG  TRP A 292 "    0.043 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 292 "   -0.015 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 292 "    0.002 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 292 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 292 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 292 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 292 "   -0.006 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 292 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 292 "   -0.005 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 292 "   -0.015 2.00e-02 2.50e+03   1.01e-02 2.54e+00
        pdb=" CG  TRP B 292 "    0.026 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 292 "   -0.009 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 292 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 292 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 292 "    0.004 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 292 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 292 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 292 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 292 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE B 335 "   -0.013 2.00e-02 2.50e+03   1.17e-02 2.41e+00
        pdb=" CG  PHE B 335 "    0.027 2.00e-02 2.50e+03
        pdb=" CD1 PHE B 335 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 PHE B 335 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE B 335 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE B 335 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ  PHE B 335 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1741 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1257
        2.75 -     3.29: 10680
        3.29 -     3.83: 17326
        3.83 -     4.36: 18001
        4.36 -     4.90: 30967
  Nonbonded interactions: 78231
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG B 176 "
            pdb=" OE2 GLU B 181 "
     model   vdw
     2.213 3.120
  nonbonded pdb=" O   HIS A   6 "
            pdb=" ND1 HIS A  10 "
     model   vdw
     2.224 3.120
  nonbonded pdb=" OH  TYR A 345 "
            pdb=" O   TRP A 423 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" NH2 ARG A 273 "
            pdb=" OG1 THR A 594 "
     model   vdw
     2.233 3.120
  nonbonded pdb=" O   TRP B 175 "
            pdb=" ND1 HIS B 179 "
     model   vdw
     2.266 3.120
  ... (remaining 78226 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 1 through 620)
  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:             2.880
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     11.380
  Find NCS groups from input model:        0.160
  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:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7400
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      :  0.003   0.055  10394  Z= 0.161
  Angle     :  0.742  11.741  14116  Z= 0.343
  Chirality :  0.042   0.366   1532
  Planarity :  0.003   0.029   1744
  Dihedral  : 17.601 131.608   3780
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.84 %
    Favored  : 94.07 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  0.28 %
    Favored  : 99.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.25), residues: 1198
  helix:  1.65 (0.17), residues: 900
  sheet:  None (None), residues: 0
  loop : -1.51 (0.39), residues: 298

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 308 
 TYR   0.022   0.001   TYR A  30 
 PHE   0.027   0.001   PHE B 335 
 TRP   0.043   0.001   TRP A 292 
 HIS   0.003   0.001   HIS B 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (10392)
  covalent geometry    : angle       0.74129 (14112)
  SS BOND              : bond        0.00053 (    2)
  SS BOND              : angle       1.40445 (    4)
  hydrogen bonds       : bond        0.10982 (  693)
  hydrogen bonds       : angle       4.66064 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.406 
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: symmetry clash
REVERT: A   27 ASP cc_start: 0.8976 (m-30) cc_final: 0.8691 (p0)
REVERT: A  288 ASN cc_start: 0.8231 (m110) cc_final: 0.7674 (m110)
REVERT: B   25 PHE cc_start: 0.7196 (m-80) cc_final: 0.6947 (m-80)
REVERT: B  145 LEU cc_start: 0.9365 (mt) cc_final: 0.9096 (mt)
REVERT: B  383 THR cc_start: 0.7313 (p) cc_final: 0.7056 (p)
REVERT: B  575 ILE cc_start: 0.8744 (tp) cc_final: 0.8440 (tt)
  outliers start: 1
  outliers final: 0
  residues processed: 172
  average time/residue: 0.0985
  time to fit residues: 24.5133
Evaluate side-chains
  130 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    1.9990
   chunk 113 optimal weight:    5.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    4.9990
   chunk 62 optimal weight:    0.9980
   chunk 51 optimal weight:    1.9990
   chunk 117 optimal weight:    2.9990
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
A 149 GLN
** A 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 499 HIS
A 614 ASN
A 618 ASN
B 149 GLN
B 387 HIS
B 401 ASN
** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.154621 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.123884 restraints weight = 17879.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.126408 restraints weight = 21538.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.127624 restraints weight = 12903.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.127806 restraints weight = 9337.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.128351 restraints weight = 9183.020|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7489
moved from start:          0.1027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  10394  Z= 0.180
  Angle     :  0.617   8.825  14116  Z= 0.319
  Chirality :  0.041   0.195   1532
  Planarity :  0.004   0.031   1744
  Dihedral  : 16.151 125.001   1408
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.26 %
    Favored  : 94.57 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  7.26 %
    Favored  : 92.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.35 (0.25), residues: 1198
  helix:  1.65 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.51 (0.39), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 371 
 TYR   0.024   0.002   TYR B 148 
 PHE   0.016   0.002   PHE A 537 
 TRP   0.025   0.001   TRP A 292 
 HIS   0.006   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (10392)
  covalent geometry    : angle       0.61717 (14112)
  SS BOND              : bond        0.00244 (    2)
  SS BOND              : angle       1.00109 (    4)
  hydrogen bonds       : bond        0.05086 (  693)
  hydrogen bonds       : angle       3.84089 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.375 
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: symmetry clash
REVERT: A  489 MET cc_start: 0.8326 (mmm) cc_final: 0.7955 (ttm)
REVERT: B   25 PHE cc_start: 0.7146 (m-80) cc_final: 0.6683 (m-80)
REVERT: B  195 ILE cc_start: 0.7084 (pt) cc_final: 0.6791 (pt)
REVERT: B  215 MET cc_start: 0.4893 (mtm) cc_final: 0.4652 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 176
  average time/residue: 0.0930
  time to fit residues: 23.9512
Evaluate side-chains
  128 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 127
  time to evaluate  : 0.557 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 42 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 67 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 12 optimal weight:    0.9980
   chunk 68 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0000
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.9586

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
A 149 GLN
A 452 GLN
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 149 GLN
B 387 HIS
B 452 GLN
** B 476 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 618 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.155930 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.125216 restraints weight = 17912.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.127007 restraints weight = 20602.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.128085 restraints weight = 12973.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.128677 restraints weight = 9932.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.129158 restraints weight = 9977.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.3701
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.1304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10394  Z= 0.148
  Angle     :  0.599   9.347  14116  Z= 0.307
  Chirality :  0.041   0.213   1532
  Planarity :  0.003   0.025   1744
  Dihedral  : 15.714 121.964   1408
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 8.51
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.92 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.25), residues: 1198
  helix:  1.56 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.68 (0.38), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 465 
 TYR   0.015   0.001   TYR B 483 
 PHE   0.022   0.001   PHE A  51 
 TRP   0.019   0.001   TRP B 607 
 HIS   0.004   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (10392)
  covalent geometry    : angle       0.59879 (14112)
  SS BOND              : bond        0.00173 (    2)
  SS BOND              : angle       1.79984 (    4)
  hydrogen bonds       : bond        0.04865 (  693)
  hydrogen bonds       : angle       3.73709 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 179
  time to evaluate  : 0.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8168 (m-40) cc_final: 0.7921 (m-40)
REVERT: A  195 ILE cc_start: 0.7253 (pt) cc_final: 0.7025 (pt)
REVERT: A  215 MET cc_start: 0.4583 (ptt) cc_final: 0.4329 (ptt)
REVERT: A  408 MET cc_start: 0.7911 (tpt) cc_final: 0.7697 (tpt)
REVERT: A  489 MET cc_start: 0.8383 (mmm) cc_final: 0.7979 (ttm)
REVERT: B   26 LYS cc_start: 0.8199 (tptt) cc_final: 0.6391 (tttt)
REVERT: B   30 TYR cc_start: 0.7875 (m-80) cc_final: 0.7581 (m-80)
REVERT: B  195 ILE cc_start: 0.7002 (pt) cc_final: 0.6718 (pt)
REVERT: B  383 THR cc_start: 0.7163 (p) cc_final: 0.6876 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 179
  average time/residue: 0.0926
  time to fit residues: 24.4179
Evaluate side-chains
  124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 45 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0020
   chunk 13 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 35 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0870
   chunk 46 optimal weight:    1.9990
   chunk 113 optimal weight:    2.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.5766

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

Flipped N/Q/H residues before XYZ refinement:
A  70 ASN
A 212 GLN
A 387 HIS
A 452 GLN
** A 608 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 387 HIS
B 452 GLN
B 476 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.157906 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.127508 restraints weight = 17773.377|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.129513 restraints weight = 20861.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.131226 restraints weight = 13074.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.131219 restraints weight = 9853.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.131674 restraints weight = 9681.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3744
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7423
moved from start:          0.1444

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025  10394  Z= 0.124
  Angle     :  0.584   9.853  14116  Z= 0.296
  Chirality :  0.040   0.185   1532
  Planarity :  0.003   0.034   1744
  Dihedral  : 15.209 118.904   1408
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.84 %
    Favored  : 95.08 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.05 %
    Favored  : 97.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.39 (0.25), residues: 1198
  helix:  1.69 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.55 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 465 
 TYR   0.022   0.001   TYR A  22 
 PHE   0.027   0.001   PHE B  54 
 TRP   0.017   0.001   TRP B 607 
 HIS   0.007   0.001   HIS A 387 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10392)
  covalent geometry    : angle       0.58362 (14112)
  SS BOND              : bond        0.00087 (    2)
  SS BOND              : angle       1.12935 (    4)
  hydrogen bonds       : bond        0.04441 (  693)
  hydrogen bonds       : angle       3.58933 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.402 
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   26 LYS cc_start: 0.9182 (mttt) cc_final: 0.8681 (mttp)
REVERT: A  195 ILE cc_start: 0.7231 (pt) cc_final: 0.6969 (pt)
REVERT: A  215 MET cc_start: 0.4580 (ptt) cc_final: 0.4250 (ptt)
REVERT: A  489 MET cc_start: 0.8378 (mmm) cc_final: 0.7771 (ttm)
REVERT: B  131 LEU cc_start: 0.9004 (tt) cc_final: 0.8745 (tt)
REVERT: B  195 ILE cc_start: 0.6940 (pt) cc_final: 0.6689 (pt)
REVERT: B  383 THR cc_start: 0.7076 (p) cc_final: 0.6748 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0935
  time to fit residues: 24.9448
Evaluate side-chains
  124 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 8 optimal weight:    7.9990
   chunk 105 optimal weight:    0.5980
   chunk 51 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 109 optimal weight:    0.0570
   chunk 47 optimal weight:    1.9990
   chunk 72 optimal weight:    1.9990
   chunk 56 optimal weight:    0.4980
   overall best weight:    0.8300

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

Flipped N/Q/H residues before XYZ refinement:
A 152 ASN
A 452 GLN
A 499 HIS
B 387 HIS
B 452 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.156648 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.128133 restraints weight = 17945.559|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.127440 restraints weight = 16625.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.129031 restraints weight = 15302.958|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.129238 restraints weight = 9753.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.129735 restraints weight = 9182.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.1634

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10394  Z= 0.136
  Angle     :  0.586  10.252  14116  Z= 0.299
  Chirality :  0.041   0.281   1532
  Planarity :  0.003   0.024   1744
  Dihedral  : 14.659 115.253   1408
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  4.84 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  3.07 %
    Favored  : 96.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.25), residues: 1198
  helix:  1.72 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.50 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 570 
 TYR   0.025   0.002   TYR A 483 
 PHE   0.025   0.001   PHE A  25 
 TRP   0.016   0.001   TRP B 607 
 HIS   0.002   0.001   HIS B 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 (10392)
  covalent geometry    : angle       0.58634 (14112)
  SS BOND              : bond        0.00075 (    2)
  SS BOND              : angle       0.89273 (    4)
  hydrogen bonds       : bond        0.04490 (  693)
  hydrogen bonds       : angle       3.58817 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  184 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 182
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   26 LYS cc_start: 0.9209 (mttt) cc_final: 0.8961 (mttp)
REVERT: A  195 ILE cc_start: 0.7304 (pt) cc_final: 0.7070 (pt)
REVERT: A  215 MET cc_start: 0.4778 (ptt) cc_final: 0.4430 (ptt)
REVERT: A  408 MET cc_start: 0.8010 (tpt) cc_final: 0.7739 (tpt)
REVERT: A  489 MET cc_start: 0.8381 (mmm) cc_final: 0.7784 (ttm)
REVERT: B   25 PHE cc_start: 0.7292 (m-80) cc_final: 0.6880 (m-80)
REVERT: B   27 ASP cc_start: 0.8334 (m-30) cc_final: 0.7921 (m-30)
REVERT: B  195 ILE cc_start: 0.7049 (pt) cc_final: 0.6783 (pt)
  outliers start: 2
  outliers final: 0
  residues processed: 184
  average time/residue: 0.0850
  time to fit residues: 23.2724
Evaluate side-chains
  133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 16 optimal weight:    6.9990
   chunk 48 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 67 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 65 optimal weight:    3.9990
   chunk 71 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 96 optimal weight:    2.9990
   chunk 3 optimal weight:    5.9990
   overall best weight:    1.6784

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
** B 452 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 = 0.3990 r_free = 0.3990 target = 0.149815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.120939 restraints weight = 18218.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.120699 restraints weight = 15018.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.121762 restraints weight = 14571.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.121885 restraints weight = 9832.176|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.122381 restraints weight = 9307.360|
|-----------------------------------------------------------------------------|
r_work (final): 0.3623
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7601
moved from start:          0.2093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.054  10394  Z= 0.212
  Angle     :  0.683  10.945  14116  Z= 0.357
  Chirality :  0.044   0.214   1532
  Planarity :  0.004   0.052   1744
  Dihedral  : 14.448 112.644   1408
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.59 %
    Favored  : 94.24 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.25), residues: 1198
  helix:  1.37 (0.17), residues: 904
  sheet:  None (None), residues: 0
  loop : -1.72 (0.38), residues: 294

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 548 
 TYR   0.024   0.002   TYR A 483 
 PHE   0.017   0.002   PHE A 537 
 TRP   0.017   0.002   TRP B 607 
 HIS   0.003   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00488 (10392)
  covalent geometry    : angle       0.68155 (14112)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       2.39491 (    4)
  hydrogen bonds       : bond        0.05604 (  693)
  hydrogen bonds       : angle       3.94173 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.325 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8256 (m-40) cc_final: 0.7899 (m-40)
REVERT: A  195 ILE cc_start: 0.7290 (pt) cc_final: 0.7064 (pt)
REVERT: A  215 MET cc_start: 0.5219 (ptt) cc_final: 0.4907 (ptt)
REVERT: A  398 ASP cc_start: 0.8579 (m-30) cc_final: 0.7903 (t0)
REVERT: A  489 MET cc_start: 0.8392 (mmm) cc_final: 0.7835 (ttm)
REVERT: B   25 PHE cc_start: 0.7430 (m-80) cc_final: 0.6985 (m-80)
REVERT: B   27 ASP cc_start: 0.8281 (m-30) cc_final: 0.7888 (m-30)
REVERT: B   79 GLU cc_start: 0.8147 (pm20) cc_final: 0.7872 (pm20)
REVERT: B  195 ILE cc_start: 0.7109 (pt) cc_final: 0.6878 (pt)
REVERT: B  216 LYS cc_start: 0.8618 (tmtt) cc_final: 0.8159 (tttm)
REVERT: B  219 ARG cc_start: 0.7803 (mmp-170) cc_final: 0.6714 (mmm160)
REVERT: B  383 THR cc_start: 0.7107 (p) cc_final: 0.6862 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0915
  time to fit residues: 24.5032
Evaluate side-chains
  136 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 136
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 74 optimal weight:    7.9990
   chunk 49 optimal weight:    0.6980
   chunk 9 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 117 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 70 optimal weight:    7.9990
   chunk 60 optimal weight:    7.9990
   chunk 118 optimal weight:    0.0470
   chunk 113 optimal weight:    0.6980
   overall best weight:    0.6080

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
B 452 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.154780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.126670 restraints weight = 17716.331|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.124988 restraints weight = 15812.644|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.126319 restraints weight = 14265.999|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.126912 restraints weight = 10195.796|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.127336 restraints weight = 8969.022|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
moved from start:          0.2055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10394  Z= 0.131
  Angle     :  0.614  11.316  14116  Z= 0.313
  Chirality :  0.042   0.233   1532
  Planarity :  0.003   0.035   1744
  Dihedral  : 14.039 111.288   1408
  Min Nonbonded Distance : 2.367

Molprobity Statistics.
  All-atom Clashscore : 7.62
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.09 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.25), residues: 1198
  helix:  1.54 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.59 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 459 
 TYR   0.042   0.002   TYR A 483 
 PHE   0.020   0.001   PHE B  54 
 TRP   0.018   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 (10392)
  covalent geometry    : angle       0.61391 (14112)
  SS BOND              : bond        0.00104 (    2)
  SS BOND              : angle       1.63891 (    4)
  hydrogen bonds       : bond        0.04648 (  693)
  hydrogen bonds       : angle       3.73987 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 182
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  152 ASN cc_start: 0.8218 (m-40) cc_final: 0.7990 (m-40)
REVERT: A  195 ILE cc_start: 0.7272 (pt) cc_final: 0.7047 (pt)
REVERT: A  489 MET cc_start: 0.8422 (mmm) cc_final: 0.7798 (ttm)
REVERT: B  195 ILE cc_start: 0.7081 (pt) cc_final: 0.6809 (pt)
REVERT: B  216 LYS cc_start: 0.8662 (tmtt) cc_final: 0.8451 (tttm)
REVERT: B  383 THR cc_start: 0.6923 (p) cc_final: 0.6594 (p)
REVERT: B  548 ARG cc_start: 0.8307 (ttt180) cc_final: 0.8058 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 182
  average time/residue: 0.0853
  time to fit residues: 23.2853
Evaluate side-chains
  130 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.422 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 80 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0270
   chunk 5 optimal weight:    0.7980
   chunk 110 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 17 optimal weight:    0.0770
   chunk 117 optimal weight:    3.9990
   chunk 21 optimal weight:    0.8980
   chunk 0 optimal weight:    9.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 452 GLN
B 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4077 r_free = 0.4077 target = 0.157972 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.130599 restraints weight = 17317.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.131696 restraints weight = 13879.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.132768 restraints weight = 11062.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.132892 restraints weight = 7385.849|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.133579 restraints weight = 7030.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7408
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10394  Z= 0.125
  Angle     :  0.615  11.539  14116  Z= 0.309
  Chirality :  0.042   0.231   1532
  Planarity :  0.003   0.030   1744
  Dihedral  : 13.761 109.792   1408
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.01 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.21 %
    Favored  : 98.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.25), residues: 1198
  helix:  1.56 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.54 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG B 459 
 TYR   0.031   0.002   TYR A 483 
 PHE   0.019   0.001   PHE B  54 
 TRP   0.017   0.001   TRP B 607 
 HIS   0.002   0.001   HIS B 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10392)
  covalent geometry    : angle       0.61465 (14112)
  SS BOND              : bond        0.00040 (    2)
  SS BOND              : angle       1.36015 (    4)
  hydrogen bonds       : bond        0.04406 (  693)
  hydrogen bonds       : angle       3.66592 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 180
  time to evaluate  : 0.409 
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  152 ASN cc_start: 0.8144 (m-40) cc_final: 0.7937 (m-40)
REVERT: A  195 ILE cc_start: 0.7259 (pt) cc_final: 0.7025 (pt)
REVERT: B  195 ILE cc_start: 0.7082 (pt) cc_final: 0.6800 (pt)
REVERT: B  383 THR cc_start: 0.6907 (p) cc_final: 0.6560 (p)
REVERT: B  548 ARG cc_start: 0.8290 (ttt180) cc_final: 0.8068 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 180
  average time/residue: 0.0849
  time to fit residues: 22.9360
Evaluate side-chains
  131 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 66 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 119 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 43 optimal weight:    0.0670
   chunk 58 optimal weight:    1.9990
   chunk 71 optimal weight:    6.9990
   chunk 88 optimal weight:    0.1980
   chunk 93 optimal weight:    0.8980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A 288 ASN
A 452 GLN
B 452 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4082 r_free = 0.4082 target = 0.158440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.131133 restraints weight = 17842.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130526 restraints weight = 14963.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.132176 restraints weight = 13723.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.132401 restraints weight = 8626.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.132865 restraints weight = 8124.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.3750
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2137

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10394  Z= 0.124
  Angle     :  0.622  11.704  14116  Z= 0.311
  Chirality :  0.042   0.229   1532
  Planarity :  0.003   0.033   1744
  Dihedral  : 13.526 108.644   1408
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.09 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.25), residues: 1198
  helix:  1.59 (0.17), residues: 906
  sheet:  None (None), residues: 0
  loop : -1.52 (0.39), residues: 292

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG B 459 
 TYR   0.026   0.001   TYR A 483 
 PHE   0.021   0.001   PHE B 335 
 TRP   0.016   0.001   TRP B 607 
 HIS   0.002   0.001   HIS B 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (10392)
  covalent geometry    : angle       0.62154 (14112)
  SS BOND              : bond        0.00077 (    2)
  SS BOND              : angle       1.21073 (    4)
  hydrogen bonds       : bond        0.04297 (  693)
  hydrogen bonds       : angle       3.62520 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 183
  time to evaluate  : 0.412 
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  152 ASN cc_start: 0.8158 (m-40) cc_final: 0.7920 (m-40)
REVERT: A  195 ILE cc_start: 0.7188 (pt) cc_final: 0.6948 (pt)
REVERT: A  489 MET cc_start: 0.8240 (mmm) cc_final: 0.7963 (ttm)
REVERT: B  195 ILE cc_start: 0.7118 (pt) cc_final: 0.6833 (pt)
REVERT: B  383 THR cc_start: 0.6891 (p) cc_final: 0.6602 (p)
REVERT: B  548 ARG cc_start: 0.8244 (ttt180) cc_final: 0.8036 (ttt180)
  outliers start: 0
  outliers final: 0
  residues processed: 183
  average time/residue: 0.0871
  time to fit residues: 23.8924
Evaluate side-chains
  133 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 90 optimal weight:    2.9990
   chunk 115 optimal weight:    1.9990
   chunk 119 optimal weight:    0.6980
   chunk 60 optimal weight:    8.9990
   chunk 103 optimal weight:    2.9990
   chunk 42 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 82 optimal weight:    0.5980
   chunk 16 optimal weight:    1.9990
   chunk 86 optimal weight:    0.5980
   chunk 92 optimal weight:    0.0040
   overall best weight:    0.4392

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
B 452 GLN
B 479 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.159573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.133020 restraints weight = 17098.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.131678 restraints weight = 14750.568|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.133925 restraints weight = 13605.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.133943 restraints weight = 8527.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.134421 restraints weight = 8166.785|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.2248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  10394  Z= 0.119
  Angle     :  0.616  11.853  14116  Z= 0.307
  Chirality :  0.042   0.228   1532
  Planarity :  0.003   0.032   1744
  Dihedral  : 13.268 108.391   1408
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.01 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.47 %
    Favored  : 99.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.25), residues: 1198
  helix:  1.64 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.45 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 459 
 TYR   0.023   0.001   TYR A 483 
 PHE   0.020   0.001   PHE B 335 
 TRP   0.016   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10392)
  covalent geometry    : angle       0.61560 (14112)
  SS BOND              : bond        0.00099 (    2)
  SS BOND              : angle       1.43660 (    4)
  hydrogen bonds       : bond        0.04134 (  693)
  hydrogen bonds       : angle       3.58867 ( 2064)

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

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

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2396 Ramachandran restraints generated.
    1198 Oldfield, 0 Emsley, 1198 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  188 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 188
  time to evaluate  : 0.380 
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  137 GLU cc_start: 0.8036 (pp20) cc_final: 0.7554 (tm-30)
REVERT: A  152 ASN cc_start: 0.8122 (m-40) cc_final: 0.7908 (m-40)
REVERT: A  195 ILE cc_start: 0.7228 (pt) cc_final: 0.7010 (pt)
REVERT: A  489 MET cc_start: 0.8156 (mmm) cc_final: 0.7880 (ttm)
REVERT: A  575 ILE cc_start: 0.8751 (tp) cc_final: 0.8349 (tt)
REVERT: B  195 ILE cc_start: 0.7084 (pt) cc_final: 0.6816 (pt)
REVERT: B  408 MET cc_start: 0.8432 (tpt) cc_final: 0.8174 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 188
  average time/residue: 0.0875
  time to fit residues: 24.5475
Evaluate side-chains
  134 residues out of total 1074 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 120
   random chunks:
   chunk 106 optimal weight:    0.9980
   chunk 104 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 23 optimal weight:    0.6980
   chunk 61 optimal weight:    4.9990
   chunk 1 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 85 optimal weight:    0.6980
   chunk 107 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 452 GLN
B 452 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.156437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.128218 restraints weight = 17773.925|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.128543 restraints weight = 15811.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.129428 restraints weight = 14778.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.130162 restraints weight = 9381.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.131466 restraints weight = 8363.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3734
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7425
moved from start:          0.2346

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10394  Z= 0.134
  Angle     :  0.619  11.912  14116  Z= 0.313
  Chirality :  0.042   0.220   1532
  Planarity :  0.003   0.032   1744
  Dihedral  : 13.125 108.146   1408
  Min Nonbonded Distance : 2.382

Molprobity Statistics.
  All-atom Clashscore : 7.96
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  5.18 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.28 %
    Favored  : 99.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.25), residues: 1198
  helix:  1.62 (0.17), residues: 908
  sheet:  None (None), residues: 0
  loop : -1.41 (0.40), residues: 290

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 459 
 TYR   0.024   0.002   TYR A 483 
 PHE   0.026   0.001   PHE A  25 
 TRP   0.016   0.001   TRP B 607 
 HIS   0.003   0.001   HIS B 163 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10392)
  covalent geometry    : angle       0.61870 (14112)
  SS BOND              : bond        0.00056 (    2)
  SS BOND              : angle       1.35189 (    4)
  hydrogen bonds       : bond        0.04363 (  693)
  hydrogen bonds       : angle       3.66723 ( 2064)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1529.24 seconds
wall clock time: 27 minutes 28.24 seconds (1648.24 seconds total)