Starting phenix.real_space_refine
on Wed Sep 17 07:12:38 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yfx_39232/09_2025/8yfx_39232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yfx_39232/09_2025/8yfx_39232.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.56
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yfx_39232/09_2025/8yfx_39232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yfx_39232/09_2025/8yfx_39232.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yfx_39232/09_2025/8yfx_39232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yfx_39232/09_2025/8yfx_39232.map"
  }
  resolution = 3.56
  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=   0.088
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     C    4414      2.51       5
     N    1054      2.21       5
     O    1088      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 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: 6588
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3294
          Classifications: {'peptide': 396}
          Link IDs: {'PTRANS': 15, 'TRANS': 380}
    Chain: "B"
      Number of atoms: 3294
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 396, 3294
          Classifications: {'peptide': 396}
          Link IDs: {'PTRANS': 15, 'TRANS': 380}
  Time building chain proxies: 1.86, per 1000 atoms: 0.28
  Number of scatterers: 6588
  At special positions: 0
  Unit cell: (79.2, 68.2, 130.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      32     16.00
     O    1088      8.00
     N    1054      7.00
     C    4414      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: 0.55
  Conformation dependent library (CDL) restraints added in 371.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1504

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 0 sheets defined
      77.4% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 230 through 258
      removed outlier: 3.711A  pdb=" N   THR A 234 " --> pdb=" O   PRO A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 265 through 296
      removed outlier: 5.052A  pdb=" N   GLY A 274 " --> pdb=" O   ARG A 270 " (cutoff:3.500A)
      removed outlier: 4.709A  pdb=" N   GLY A 275 " --> pdb=" O   ILE A 271 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 304
      removed outlier: 3.985A  pdb=" N   ILE A 302 " --> pdb=" O   ASN A 298 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 312 through 337
      removed outlier: 3.737A  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 369 through 383
    Processing helix  chain 'A' and resid 384 through 387
    Processing helix  chain 'A' and resid 390 through 402
      removed outlier: 3.603A  pdb=" N   SER A 402 " --> pdb=" O   ASP A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 419
      removed outlier: 3.969A  pdb=" N   LEU A 407 " --> pdb=" O   LEU A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 471
      removed outlier: 4.128A  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 472 through 503
      removed outlier: 4.397A  pdb=" N   HIS A 476 " --> pdb=" O   ARG A 472 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   THR A 486 " --> pdb=" O   LYS A 482 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   PHE A 487 " --> pdb=" O   TYR A 483 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   PHE A 488 " --> pdb=" O   SER A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 532
      removed outlier: 3.773A  pdb=" N   PHE A 510 " --> pdb=" O   ASP A 506 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   PHE A 511 " --> pdb=" O   THR A 507 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   LEU A 513 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
      removed outlier: 3.985A  pdb=" N   TRP A 514 " --> pdb=" O   PHE A 510 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   TYR A 524 " --> pdb=" O   ILE A 520 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ILE A 527 " --> pdb=" O   CYS A 523 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 583
      removed outlier: 3.884A  pdb=" N   TYR A 559 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   PHE A 571 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   ALA A 572 " --> pdb=" O   ILE A 568 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   THR A 574 " --> pdb=" O   ARG A 570 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 587 through 622
      removed outlier: 4.599A  pdb=" N   ILE A 591 " --> pdb=" O   HIS A 587 " (cutoff:3.500A)
      Proline residue:  A 598  - end of helix
      removed outlier: 4.241A  pdb=" N   VAL A 601 " --> pdb=" O   ALA A 597 " (cutoff:3.500A)
      removed outlier: 4.832A  pdb=" N   PHE A 602 " --> pdb=" O   PRO A 598 " (cutoff:3.500A)
      removed outlier: 4.192A  pdb=" N   PHE A 609 " --> pdb=" O   PHE A 605 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   PHE A 610 " --> pdb=" O   VAL A 606 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 230 through 258
      removed outlier: 3.678A  pdb=" N   THR B 234 " --> pdb=" O   PRO B 230 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 265 through 296
      removed outlier: 4.955A  pdb=" N   GLY B 274 " --> pdb=" O   ARG B 270 " (cutoff:3.500A)
      removed outlier: 4.656A  pdb=" N   GLY B 275 " --> pdb=" O   ILE B 271 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 304
    Processing helix  chain 'B' and resid 312 through 337
      removed outlier: 3.754A  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 390 through 403
    Processing helix  chain 'B' and resid 403 through 420
      removed outlier: 4.175A  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 472 through 503
      removed outlier: 4.063A  pdb=" N   HIS B 476 " --> pdb=" O   ARG B 472 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA B 480 " --> pdb=" O   HIS B 476 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY B 481 " --> pdb=" O   LEU B 477 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   THR B 486 " --> pdb=" O   LYS B 482 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   PHE B 487 " --> pdb=" O   TYR B 483 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 532
      removed outlier: 3.775A  pdb=" N   TYR B 512 " --> pdb=" O   MET B 508 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   LEU B 513 " --> pdb=" O   VAL B 509 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ILE B 527 " --> pdb=" O   CYS B 523 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 583
      removed outlier: 4.325A  pdb=" N   TYR B 559 " --> pdb=" O   GLN B 555 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   VAL B 567 " --> pdb=" O   ILE B 563 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE B 568 " --> pdb=" O   ILE B 564 " (cutoff:3.500A)
      removed outlier: 4.235A  pdb=" N   PHE B 571 " --> pdb=" O   VAL B 567 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   ALA B 572 " --> pdb=" O   ILE B 568 " (cutoff:3.500A)
      removed outlier: 3.630A  pdb=" N   SER B 581 " --> pdb=" O   ILE B 577 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   THR B 583 " --> pdb=" O   ILE B 579 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 588 through 622
      Proline residue:  B 598  - end of helix
      removed outlier: 4.289A  pdb=" N   VAL B 601 " --> pdb=" O   ALA B 597 " (cutoff:3.500A)
      removed outlier: 4.668A  pdb=" N   PHE B 602 " --> pdb=" O   PRO B 598 " (cutoff:3.500A)
      removed outlier: 4.144A  pdb=" N   PHE B 609 " --> pdb=" O   PHE B 605 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   PHE B 610 " --> pdb=" O   VAL B 606 " (cutoff:3.500A)

    443 hydrogen bonds defined for protein.
    1326 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: 0.92

  Time building geometry restraints manager: 0.76 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: 1922
        1.34 -     1.46: 1431
        1.46 -     1.58: 3411
        1.58 -     1.69: 0
        1.69 -     1.81: 44
  Bond restraints: 6808
  Sorted by residual:
  bond pdb=" CA  TYR A 368 "
       pdb=" C   TYR A 368 "
    ideal  model  delta    sigma   weight residual
    1.523  1.502  0.021 1.34e-02 5.57e+03 2.56e+00
  bond pdb=" CB  LYS A 369 "
       pdb=" CG  LYS A 369 "
    ideal  model  delta    sigma   weight residual
    1.520  1.560 -0.040 3.00e-02 1.11e+03 1.82e+00
  bond pdb=" C   ALA A 384 "
       pdb=" N   PRO A 385 "
    ideal  model  delta    sigma   weight residual
    1.337  1.347 -0.011 9.80e-03 1.04e+04 1.16e+00
  bond pdb=" CB  TYR A 496 "
       pdb=" CG  TYR A 496 "
    ideal  model  delta    sigma   weight residual
    1.512  1.535 -0.023 2.20e-02 2.07e+03 1.08e+00
  bond pdb=" CB  ASN A 288 "
       pdb=" CG  ASN A 288 "
    ideal  model  delta    sigma   weight residual
    1.516  1.491  0.025 2.50e-02 1.60e+03 9.96e-01
  ... (remaining 6803 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.53: 8944
        1.53 -     3.07: 269
        3.07 -     4.60: 34
        4.60 -     6.14: 16
        6.14 -     7.67: 5
  Bond angle restraints: 9268
  Sorted by residual:
  angle pdb=" CA  LYS A 471 "
        pdb=" CB  LYS A 471 "
        pdb=" CG  LYS A 471 "
      ideal   model   delta    sigma   weight residual
     114.10  121.74   -7.64 2.00e+00 2.50e-01 1.46e+01
  angle pdb=" N   VAL A 341 "
        pdb=" CA  VAL A 341 "
        pdb=" C   VAL A 341 "
      ideal   model   delta    sigma   weight residual
     111.58  107.91    3.67 1.06e+00 8.90e-01 1.20e+01
  angle pdb=" CA  GLU A 304 "
        pdb=" CB  GLU A 304 "
        pdb=" CG  GLU A 304 "
      ideal   model   delta    sigma   weight residual
     114.10  121.00   -6.90 2.00e+00 2.50e-01 1.19e+01
  angle pdb=" N   ALA B 473 "
        pdb=" CA  ALA B 473 "
        pdb=" C   ALA B 473 "
      ideal   model   delta    sigma   weight residual
     110.97  114.53   -3.56 1.09e+00 8.42e-01 1.07e+01
  angle pdb=" C   VAL B 595 "
        pdb=" N   PHE B 596 "
        pdb=" CA  PHE B 596 "
      ideal   model   delta    sigma   weight residual
     122.65  117.84    4.81 1.60e+00 3.91e-01 9.02e+00
  ... (remaining 9263 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.03: 3275
       17.03 -    34.07: 444
       34.07 -    51.10: 131
       51.10 -    68.14: 10
       68.14 -    85.17: 8
  Dihedral angle restraints: 3868
    sinusoidal: 1532
      harmonic: 2336
  Sorted by residual:
  dihedral pdb=" CA  ALA B 473 "
           pdb=" C   ALA B 473 "
           pdb=" N   PHE B 474 "
           pdb=" CA  PHE B 474 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.99  -21.01     0      5.00e+00 4.00e-02 1.77e+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 -159.97  -20.03     0      5.00e+00 4.00e-02 1.60e+01
  dihedral pdb=" CA  PHE A 511 "
           pdb=" C   PHE A 511 "
           pdb=" N   TYR A 512 "
           pdb=" CA  TYR A 512 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.85  -17.15     0      5.00e+00 4.00e-02 1.18e+01
  ... (remaining 3865 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 666
       0.039 -    0.078: 267
       0.078 -    0.117: 66
       0.117 -    0.156: 9
       0.156 -    0.195: 4
  Chirality restraints: 1012
  Sorted by residual:
  chirality pdb=" CG  LEU B 617 "
            pdb=" CB  LEU B 617 "
            pdb=" CD1 LEU B 617 "
            pdb=" CD2 LEU B 617 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.39   -0.20 2.00e-01 2.50e+01 9.52e-01
  chirality pdb=" CB  VAL B 595 "
            pdb=" CA  VAL B 595 "
            pdb=" CG1 VAL B 595 "
            pdb=" CG2 VAL B 595 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.45   -0.18 2.00e-01 2.50e+01 8.31e-01
  chirality pdb=" CA  PHE B 596 "
            pdb=" N   PHE B 596 "
            pdb=" C   PHE B 596 "
            pdb=" CB  PHE B 596 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.07e-01
  ... (remaining 1009 not shown)

  Planarity restraints: 1134
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 496 "    0.007 2.00e-02 2.50e+03   1.98e-02 7.82e+00
        pdb=" CG  TYR A 496 "   -0.043 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 496 "    0.017 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 496 "    0.029 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 496 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 496 "   -0.011 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 496 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR A 496 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 304 "   -0.009 2.00e-02 2.50e+03   1.80e-02 3.25e+00
        pdb=" C   GLU A 304 "    0.031 2.00e-02 2.50e+03
        pdb=" O   GLU A 304 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LEU A 305 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 430 "   -0.026 5.00e-02 4.00e+02   4.00e-02 2.56e+00
        pdb=" N   PRO A 431 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 431 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 431 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1131 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 63
        2.64 -     3.20: 6282
        3.20 -     3.77: 10327
        3.77 -     4.33: 12774
        4.33 -     4.90: 21442
  Nonbonded interactions: 50888
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 271 "
            pdb=" OH  TYR A 352 "
     model   vdw
     2.071 3.040
  nonbonded pdb=" O   ARG A 466 "
            pdb=" OG1 THR A 470 "
     model   vdw
     2.149 3.040
  nonbonded pdb=" OD1 ASP A 533 "
            pdb=" NH1 ARG A 611 "
     model   vdw
     2.151 3.120
  nonbonded pdb=" NH2 ARG B 548 "
            pdb=" OE2 GLU B 613 "
     model   vdw
     2.164 3.120
  nonbonded pdb=" O   SER A 578 "
            pdb=" OG1 THR A 582 "
     model   vdw
     2.181 3.040
  ... (remaining 50883 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.240
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     7.710
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.010
  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:             0.010
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6985
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      :  0.004   0.040   6810  Z= 0.180
  Angle     :  0.648   7.670   9272  Z= 0.364
  Chirality :  0.045   0.195   1012
  Planarity :  0.005   0.040   1134
  Dihedral  : 16.588  85.173   2358
  Min Nonbonded Distance : 2.071

Molprobity Statistics.
  All-atom Clashscore : 9.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  : 21.31 %
    Favored  : 78.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.74 (0.31), residues: 788
  helix:  1.56 (0.22), residues: 546
  sheet:  None (None), residues: 0
  loop : -2.08 (0.41), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 448 
 TYR   0.043   0.002   TYR A 496 
 PHE   0.024   0.002   PHE B 596 
 TRP   0.027   0.002   TRP B 266 
 HIS   0.007   0.001   HIS A 313 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 ( 6808)
  covalent geometry    : angle       0.64785 ( 9268)
  SS BOND              : bond        0.00092 (    2)
  SS BOND              : angle       0.62461 (    4)
  hydrogen bonds       : bond        0.14646 (  443)
  hydrogen bonds       : angle       6.05659 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 103
  average time/residue: 0.0878
  time to fit residues: 12.2388
Evaluate side-chains
  98 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 96
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain B residue  495 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.8980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    0.0050
   chunk 45 optimal weight:    0.9980
   chunk 74 optimal weight:    1.9990
   overall best weight:    0.7594

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

Flipped N/Q/H residues before XYZ refinement:
A 401 ASN
A 608 ASN
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 587 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.208719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.169597 restraints weight = 8145.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.173660 restraints weight = 5277.466|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.175853 restraints weight = 4056.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4020 r_free = 0.4020 target = 0.177829 restraints weight = 3485.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.178629 restraints weight = 3153.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6930
moved from start:          0.0932

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6810  Z= 0.144
  Angle     :  0.566   6.067   9272  Z= 0.307
  Chirality :  0.042   0.142   1012
  Planarity :  0.004   0.039   1134
  Dihedral  :  4.768  50.333    876
  Min Nonbonded Distance : 2.505

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.32 %
    Favored  : 77.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.14 (0.30), residues: 788
  helix:  1.85 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -2.08 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 371 
 TYR   0.018   0.002   TYR B 558 
 PHE   0.023   0.001   PHE B 596 
 TRP   0.014   0.002   TRP B 266 
 HIS   0.005   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 6808)
  covalent geometry    : angle       0.56626 ( 9268)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       0.53799 (    4)
  hydrogen bonds       : bond        0.05238 (  443)
  hydrogen bonds       : angle       4.29548 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 107
  time to evaluate  : 0.255 
Fit side-chains
   revert: symmetry clash
REVERT: A  483 TYR cc_start: 0.7503 (m-80) cc_final: 0.7179 (m-80)
REVERT: A  496 TYR cc_start: 0.5860 (t80) cc_final: 0.5575 (t80)
REVERT: A  508 MET cc_start: 0.7288 (pmm) cc_final: 0.7034 (ttt)
  outliers start: 22
  outliers final: 11
  residues processed: 121
  average time/residue: 0.0845
  time to fit residues: 14.0359
Evaluate side-chains
  107 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 96
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  545 THR
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  613 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    3.9990
   chunk 1 optimal weight:    0.5980
   chunk 66 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 14 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 58 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 12 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   overall best weight:    0.9182

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.207364 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.168400 restraints weight = 8128.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.172296 restraints weight = 5344.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.174892 restraints weight = 4140.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.176132 restraints weight = 3540.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.177051 restraints weight = 3243.524|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.1182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6810  Z= 0.147
  Angle     :  0.560   6.003   9272  Z= 0.302
  Chirality :  0.042   0.159   1012
  Planarity :  0.004   0.033   1134
  Dihedral  :  4.675  53.151    874
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 19.74 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.30), residues: 788
  helix:  2.00 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -2.09 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 371 
 TYR   0.019   0.002   TYR B 558 
 PHE   0.028   0.001   PHE B 596 
 TRP   0.012   0.001   TRP B 266 
 HIS   0.006   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 6808)
  covalent geometry    : angle       0.55988 ( 9268)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       0.61548 (    4)
  hydrogen bonds       : bond        0.05060 (  443)
  hydrogen bonds       : angle       4.16424 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 108
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A  394 PHE cc_start: 0.7800 (OUTLIER) cc_final: 0.7073 (p90)
REVERT: A  483 TYR cc_start: 0.7563 (m-80) cc_final: 0.7170 (m-80)
REVERT: A  570 ARG cc_start: 0.7299 (OUTLIER) cc_final: 0.6893 (mmt-90)
  outliers start: 30
  outliers final: 19
  residues processed: 129
  average time/residue: 0.0813
  time to fit residues: 14.2392
Evaluate side-chains
  118 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 97
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  300 VAL
Chi-restraints excluded: chain B residue  306 ASN
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  613 GLU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 7 optimal weight:    0.8980
   chunk 24 optimal weight:    3.9990
   chunk 27 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0470
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:    0.8980
   chunk 38 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.207264 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.168042 restraints weight = 8188.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.171960 restraints weight = 5334.097|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.174485 restraints weight = 4131.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.175634 restraints weight = 3560.956|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.176666 restraints weight = 3270.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.4002
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6919
moved from start:          0.1426

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6810  Z= 0.133
  Angle     :  0.552   9.998   9272  Z= 0.295
  Chirality :  0.041   0.163   1012
  Planarity :  0.004   0.032   1134
  Dihedral  :  4.678  55.374    874
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  4.69 %
    Allowed  : 21.02 %
    Favored  : 74.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.31), residues: 788
  helix:  2.15 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -2.02 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 611 
 TYR   0.019   0.002   TYR B 558 
 PHE   0.029   0.001   PHE B 596 
 TRP   0.012   0.001   TRP B 292 
 HIS   0.006   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6808)
  covalent geometry    : angle       0.55162 ( 9268)
  SS BOND              : bond        0.00185 (    2)
  SS BOND              : angle       0.71772 (    4)
  hydrogen bonds       : bond        0.04684 (  443)
  hydrogen bonds       : angle       4.03096 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 113
  time to evaluate  : 0.245 
Fit side-chains
REVERT: A  394 PHE cc_start: 0.7789 (OUTLIER) cc_final: 0.7067 (p90)
REVERT: A  483 TYR cc_start: 0.7514 (m-80) cc_final: 0.7066 (m-80)
REVERT: A  515 ILE cc_start: 0.8421 (OUTLIER) cc_final: 0.7939 (mm)
REVERT: A  570 ARG cc_start: 0.7279 (OUTLIER) cc_final: 0.6879 (mmt-90)
  outliers start: 33
  outliers final: 19
  residues processed: 136
  average time/residue: 0.0744
  time to fit residues: 14.1053
Evaluate side-chains
  127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.286 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  394 PHE
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  590 ASP
Chi-restraints excluded: chain B residue  613 GLU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 5 optimal weight:    1.9990
   chunk 57 optimal weight:    2.9990
   chunk 74 optimal weight:    0.0870
   chunk 18 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9980
   chunk 73 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 69 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   overall best weight:    0.7358

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 401 ASN
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4326 r_free = 0.4326 target = 0.207658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.168564 restraints weight = 8267.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.172517 restraints weight = 5361.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.175052 restraints weight = 4134.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.176030 restraints weight = 3545.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.177088 restraints weight = 3279.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6924
moved from start:          0.1576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6810  Z= 0.134
  Angle     :  0.545   7.332   9272  Z= 0.294
  Chirality :  0.042   0.168   1012
  Planarity :  0.004   0.041   1134
  Dihedral  :  4.694  58.027    874
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 8.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 21.88 %
    Favored  : 73.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.54 (0.30), residues: 788
  helix:  2.18 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.98 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 270 
 TYR   0.019   0.002   TYR B 558 
 PHE   0.027   0.001   PHE B 596 
 TRP   0.019   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 ( 6808)
  covalent geometry    : angle       0.54479 ( 9268)
  SS BOND              : bond        0.00147 (    2)
  SS BOND              : angle       0.74448 (    4)
  hydrogen bonds       : bond        0.04628 (  443)
  hydrogen bonds       : angle       3.99775 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.270 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7519 (tpp) cc_final: 0.7276 (tpp)
REVERT: A  419 LEU cc_start: 0.8227 (tt) cc_final: 0.8010 (mm)
REVERT: A  483 TYR cc_start: 0.7624 (m-80) cc_final: 0.7185 (m-80)
REVERT: A  570 ARG cc_start: 0.7251 (OUTLIER) cc_final: 0.6892 (mmt-90)
REVERT: B  270 ARG cc_start: 0.7713 (tpp80) cc_final: 0.7499 (ttm-80)
  outliers start: 30
  outliers final: 18
  residues processed: 134
  average time/residue: 0.0814
  time to fit residues: 14.9707
Evaluate side-chains
  120 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.230 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  312 SER
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 43 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 51 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 14 optimal weight:    0.4980
   chunk 70 optimal weight:    0.0070
   chunk 54 optimal weight:    0.0020
   chunk 74 optimal weight:    3.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    0.4406

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.206708 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.167168 restraints weight = 8312.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.170742 restraints weight = 5346.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.173751 restraints weight = 4151.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3993 r_free = 0.3993 target = 0.175103 restraints weight = 3521.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.176115 restraints weight = 3207.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6899
moved from start:          0.1741

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6810  Z= 0.120
  Angle     :  0.532   7.933   9272  Z= 0.287
  Chirality :  0.041   0.195   1012
  Planarity :  0.004   0.036   1134
  Dihedral  :  4.650  59.160    874
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  4.26 %
    Allowed  : 22.30 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.72 (0.31), residues: 788
  helix:  2.30 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.87 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 270 
 TYR   0.022   0.001   TYR B 518 
 PHE   0.018   0.001   PHE B 596 
 TRP   0.025   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 ( 6808)
  covalent geometry    : angle       0.53153 ( 9268)
  SS BOND              : bond        0.00159 (    2)
  SS BOND              : angle       0.58830 (    4)
  hydrogen bonds       : bond        0.04285 (  443)
  hydrogen bonds       : angle       3.95318 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 116
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7641 (tpp) cc_final: 0.7307 (tpp)
REVERT: A  419 LEU cc_start: 0.8183 (tt) cc_final: 0.7979 (mm)
REVERT: A  448 ARG cc_start: 0.7041 (mpp-170) cc_final: 0.6804 (mtm-85)
REVERT: A  483 TYR cc_start: 0.7625 (m-80) cc_final: 0.7208 (m-80)
REVERT: A  570 ARG cc_start: 0.7109 (OUTLIER) cc_final: 0.6871 (mmt-90)
REVERT: B  607 TRP cc_start: 0.6857 (t60) cc_final: 0.6429 (t60)
  outliers start: 30
  outliers final: 14
  residues processed: 137
  average time/residue: 0.0791
  time to fit residues: 14.9328
Evaluate side-chains
  121 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.242 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  590 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.0060
   chunk 60 optimal weight:    0.8980
   chunk 66 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 6 optimal weight:    0.9990
   chunk 47 optimal weight:    0.0870
   overall best weight:    0.5174

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.208300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.169452 restraints weight = 8127.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.173542 restraints weight = 5240.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4000 r_free = 0.4000 target = 0.175688 restraints weight = 4000.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.177595 restraints weight = 3434.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.178423 restraints weight = 3116.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.4015
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6876
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6810  Z= 0.126
  Angle     :  0.548   7.903   9272  Z= 0.293
  Chirality :  0.041   0.190   1012
  Planarity :  0.004   0.046   1134
  Dihedral  :  4.597  56.690    874
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.58 %
    Favored  : 73.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.31), residues: 788
  helix:  2.32 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.87 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 611 
 TYR   0.017   0.001   TYR B 345 
 PHE   0.015   0.001   PHE B 596 
 TRP   0.031   0.001   TRP B 292 
 HIS   0.006   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 6808)
  covalent geometry    : angle       0.54800 ( 9268)
  SS BOND              : bond        0.00150 (    2)
  SS BOND              : angle       0.59613 (    4)
  hydrogen bonds       : bond        0.04262 (  443)
  hydrogen bonds       : angle       3.97601 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.237 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7652 (tpp) cc_final: 0.7307 (tpp)
REVERT: A  419 LEU cc_start: 0.8215 (tt) cc_final: 0.8010 (mm)
REVERT: A  448 ARG cc_start: 0.7060 (mpp-170) cc_final: 0.6849 (mtm-85)
REVERT: A  483 TYR cc_start: 0.7622 (m-80) cc_final: 0.7105 (m-80)
REVERT: A  570 ARG cc_start: 0.7138 (OUTLIER) cc_final: 0.6834 (mmt-90)
REVERT: A  611 ARG cc_start: 0.7829 (tpt-90) cc_final: 0.7403 (tpt170)
REVERT: B  607 TRP cc_start: 0.6784 (t60) cc_final: 0.6353 (t60)
  outliers start: 21
  outliers final: 17
  residues processed: 127
  average time/residue: 0.0789
  time to fit residues: 13.7123
Evaluate side-chains
  128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 110
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  590 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 75 optimal weight:    3.9990
   chunk 60 optimal weight:    0.0770
   chunk 32 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9980
   chunk 47 optimal weight:    0.9990
   chunk 16 optimal weight:    0.6980
   chunk 74 optimal weight:    8.9990
   chunk 62 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   overall best weight:    0.6138

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

Flipped N/Q/H residues before XYZ refinement:
A 387 HIS
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.206138 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.166177 restraints weight = 8201.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.170103 restraints weight = 5446.021|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.172586 restraints weight = 4258.779|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.173818 restraints weight = 3670.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3994 r_free = 0.3994 target = 0.174817 restraints weight = 3371.280|
|-----------------------------------------------------------------------------|
r_work (final): 0.3997
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6911
moved from start:          0.1934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6810  Z= 0.127
  Angle     :  0.546   8.129   9272  Z= 0.293
  Chirality :  0.042   0.201   1012
  Planarity :  0.004   0.037   1134
  Dihedral  :  4.582  54.442    874
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 23.58 %
    Favored  : 73.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.74 (0.31), residues: 788
  helix:  2.29 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.83 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 465 
 TYR   0.017   0.001   TYR B 345 
 PHE   0.016   0.001   PHE B 596 
 TRP   0.035   0.001   TRP B 292 
 HIS   0.006   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6808)
  covalent geometry    : angle       0.54618 ( 9268)
  SS BOND              : bond        0.00145 (    2)
  SS BOND              : angle       0.61225 (    4)
  hydrogen bonds       : bond        0.04294 (  443)
  hydrogen bonds       : angle       3.99210 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 114
  time to evaluate  : 0.250 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7656 (tpp) cc_final: 0.7306 (tpp)
REVERT: A  483 TYR cc_start: 0.7595 (m-80) cc_final: 0.7106 (m-80)
REVERT: A  570 ARG cc_start: 0.7177 (OUTLIER) cc_final: 0.6902 (mmt-90)
REVERT: B  292 TRP cc_start: 0.7420 (m-90) cc_final: 0.6534 (m-90)
REVERT: B  607 TRP cc_start: 0.6772 (t60) cc_final: 0.6319 (t60)
  outliers start: 23
  outliers final: 20
  residues processed: 130
  average time/residue: 0.0725
  time to fit residues: 13.0807
Evaluate side-chains
  128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  447 VAL
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  306 ASN
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  590 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 72 optimal weight:    0.8980
   chunk 45 optimal weight:    0.7980
   chunk 21 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9990
   chunk 3 optimal weight:    0.0070
   chunk 60 optimal weight:    0.5980
   chunk 24 optimal weight:    0.7980
   chunk 64 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
** A 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.208452 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.169495 restraints weight = 8269.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.173330 restraints weight = 5358.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.175488 restraints weight = 4137.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.177334 restraints weight = 3569.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.178062 restraints weight = 3250.288|
|-----------------------------------------------------------------------------|
r_work (final): 0.4006
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6894
moved from start:          0.2045

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6810  Z= 0.127
  Angle     :  0.550   8.407   9272  Z= 0.296
  Chirality :  0.042   0.192   1012
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.543  53.227    874
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.01 %
    Favored  : 72.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.73 (0.31), residues: 788
  helix:  2.30 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.87 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 611 
 TYR   0.022   0.001   TYR B 518 
 PHE   0.017   0.001   PHE B 596 
 TRP   0.034   0.001   TRP B 292 
 HIS   0.006   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6808)
  covalent geometry    : angle       0.54996 ( 9268)
  SS BOND              : bond        0.00152 (    2)
  SS BOND              : angle       0.59349 (    4)
  hydrogen bonds       : bond        0.04245 (  443)
  hydrogen bonds       : angle       3.98320 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  135 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 112
  time to evaluate  : 0.268 
Fit side-chains
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.7663 (tpp) cc_final: 0.7325 (tpp)
REVERT: A  483 TYR cc_start: 0.7560 (m-80) cc_final: 0.7058 (m-80)
REVERT: A  570 ARG cc_start: 0.7175 (OUTLIER) cc_final: 0.6943 (mmt-90)
REVERT: A  611 ARG cc_start: 0.7915 (tpt-90) cc_final: 0.7347 (tpt170)
REVERT: B  292 TRP cc_start: 0.7453 (m-90) cc_final: 0.6505 (m-90)
REVERT: B  607 TRP cc_start: 0.6781 (t60) cc_final: 0.6338 (t60)
  outliers start: 23
  outliers final: 21
  residues processed: 130
  average time/residue: 0.0783
  time to fit residues: 14.1399
Evaluate side-chains
  131 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 109
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  342 ILE
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  306 ASN
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  590 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 75 optimal weight:    0.8980
   chunk 5 optimal weight:    0.8980
   chunk 76 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   chunk 45 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 28 optimal weight:    0.6980
   chunk 56 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 67 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4329 r_free = 0.4329 target = 0.207608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.168195 restraints weight = 8199.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.172133 restraints weight = 5371.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.174716 restraints weight = 4147.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.175975 restraints weight = 3555.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.177101 restraints weight = 3261.725|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.2062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6810  Z= 0.136
  Angle     :  0.569   8.595   9272  Z= 0.306
  Chirality :  0.042   0.189   1012
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.539  51.571    874
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.27 %
    Allowed  : 24.15 %
    Favored  : 72.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.31), residues: 788
  helix:  2.26 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.86 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 611 
 TYR   0.017   0.002   TYR B 345 
 PHE   0.018   0.001   PHE B 596 
 TRP   0.031   0.001   TRP B 292 
 HIS   0.006   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6808)
  covalent geometry    : angle       0.56914 ( 9268)
  SS BOND              : bond        0.00141 (    2)
  SS BOND              : angle       0.60683 (    4)
  hydrogen bonds       : bond        0.04376 (  443)
  hydrogen bonds       : angle       4.04526 ( 1326)

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

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

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1576 Ramachandran restraints generated.
    788 Oldfield, 0 Emsley, 788 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 108
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.7674 (tpp) cc_final: 0.7329 (tpp)
REVERT: A  483 TYR cc_start: 0.7565 (m-80) cc_final: 0.7007 (m-80)
REVERT: A  570 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6950 (mmt-90)
REVERT: A  611 ARG cc_start: 0.7899 (tpt-90) cc_final: 0.7413 (tpt170)
REVERT: B  292 TRP cc_start: 0.7413 (m-90) cc_final: 0.6453 (m-90)
REVERT: B  607 TRP cc_start: 0.6832 (t60) cc_final: 0.6391 (t60)
  outliers start: 23
  outliers final: 21
  residues processed: 124
  average time/residue: 0.0790
  time to fit residues: 13.4898
Evaluate side-chains
  127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  381 VAL
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  429 LEU
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  566 ASP
Chi-restraints excluded: chain A residue  567 VAL
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain A residue  608 ASN
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  269 ILE
Chi-restraints excluded: chain B residue  306 ASN
Chi-restraints excluded: chain B residue  335 PHE
Chi-restraints excluded: chain B residue  355 MET
Chi-restraints excluded: chain B residue  396 LEU
Chi-restraints excluded: chain B residue  486 THR
Chi-restraints excluded: chain B residue  495 LEU
Chi-restraints excluded: chain B residue  530 LEU
Chi-restraints excluded: chain B residue  551 ILE
Chi-restraints excluded: chain B residue  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  590 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 20 optimal weight:   10.0000
   chunk 69 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9990
   chunk 46 optimal weight:    0.0970
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    0.6980
   chunk 75 optimal weight:    3.9990
   chunk 7 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.6578

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

Flipped N/Q/H residues before XYZ refinement:
** A 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.207113 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.168041 restraints weight = 8197.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3964 r_free = 0.3964 target = 0.172022 restraints weight = 5283.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.174628 restraints weight = 4071.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.175867 restraints weight = 3478.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4009 r_free = 0.4009 target = 0.176413 restraints weight = 3186.483|
|-----------------------------------------------------------------------------|
r_work (final): 0.4017
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6909
moved from start:          0.2183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6810  Z= 0.133
  Angle     :  0.567   8.453   9272  Z= 0.304
  Chirality :  0.042   0.182   1012
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.548  51.669    874
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 23.72 %
    Favored  : 72.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.31), residues: 788
  helix:  2.25 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.85 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 548 
 TYR   0.022   0.002   TYR B 518 
 PHE   0.019   0.001   PHE B 322 
 TRP   0.028   0.001   TRP B 292 
 HIS   0.006   0.001   HIS A 504 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 6808)
  covalent geometry    : angle       0.56739 ( 9268)
  SS BOND              : bond        0.00149 (    2)
  SS BOND              : angle       0.57510 (    4)
  hydrogen bonds       : bond        0.04332 (  443)
  hydrogen bonds       : angle       4.02327 ( 1326)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1206.55 seconds
wall clock time: 21 minutes 33.76 seconds (1293.76 seconds total)