Starting phenix.real_space_refine
on Tue Mar 11 19:27:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yfx_39232/03_2025/8yfx_39232.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yfx_39232/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yfx_39232/03_2025/8yfx_39232.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yfx_39232/03_2025/8yfx_39232.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yfx_39232/03_2025/8yfx_39232.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yfx_39232/03_2025/8yfx_39232.cif"
  }
  resolution = 3.56
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.088
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 4.93, per 1000 atoms: 0.75
  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: 1.47
  Conformation dependent library (CDL) restraints added in 854.7 milliseconds
  

  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: 0.50
  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: 2.52

  Time building geometry restraints manager: 1.80 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: 0.03
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:                  0.010
  Normalize map: mean=0, sd=1:             2.090
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.840
  Find NCS groups from input model:        0.580
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:4.450
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.360
-------------------------------------------------------------------------------
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   6808  Z= 0.257
  Angle     :  0.648   7.670   9268  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.74 (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
 TRP   0.027   0.002   TRP B 266 
 HIS   0.007   0.001   HIS A 313 
 PHE   0.024   0.002   PHE B 596 
 TYR   0.043   0.002   TYR A 496 
 ARG   0.003   0.000   ARG A 448 

*********************** 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  : 0.748 
Fit side-chains
   revert: symmetry clash
  outliers start: 2
  outliers final: 2
  residues processed: 103
  average time/residue: 0.2253
  time to fit residues: 31.7618
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  : 0.791 
-------------------------------------------------------------------------------
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 65 optimal weight:    0.8980
   chunk 59 optimal weight:   10.0000
   chunk 32 optimal weight:    0.7980
   chunk 20 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 61 optimal weight:    0.0170
   chunk 23 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 45 optimal weight:    0.9980
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.6018

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

Flipped N/Q/H residues before XYZ refinement:
A 608 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 = 0.4346 r_free = 0.4346 target = 0.209873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.172173 restraints weight = 7964.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.175737 restraints weight = 5361.311|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.177773 restraints weight = 4223.129|
|-----------------------------------------------------------------------------|
r_work (final): 0.4018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.0926

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6808  Z= 0.185
  Angle     :  0.557   6.073   9268  Z= 0.303
  Chirality :  0.041   0.144   1012
  Planarity :  0.004   0.039   1134
  Dihedral  :  4.749  49.531    876
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 19.18 %
    Favored  : 77.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.22 (0.31), residues: 788
  helix:  1.92 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -2.08 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 266 
 HIS   0.006   0.001   HIS A 504 
 PHE   0.023   0.001   PHE B 596 
 TYR   0.017   0.002   TYR B 558 
 ARG   0.004   0.000   ARG A 371 

*********************** 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  : 0.719 
Fit side-chains
REVERT: A  483 TYR cc_start: 0.7505 (m-80) cc_final: 0.7191 (m-80)
REVERT: A  496 TYR cc_start: 0.5910 (t80) cc_final: 0.5590 (t80)
REVERT: A  508 MET cc_start: 0.7316 (pmm) cc_final: 0.7037 (ttt)
REVERT: B  617 LEU cc_start: 0.8618 (OUTLIER) cc_final: 0.8408 (mm)
  outliers start: 22
  outliers final: 11
  residues processed: 121
  average time/residue: 0.1666
  time to fit residues: 27.5034
Evaluate side-chains
  109 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.719 
-------------------------------------------------------------------------------
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  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  567 VAL
Chi-restraints excluded: chain B residue  587 HIS
Chi-restraints excluded: chain B residue  613 GLU
Chi-restraints excluded: chain B residue  617 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 31 optimal weight:    5.9990
   chunk 46 optimal weight:    0.5980
   chunk 24 optimal weight:    0.8980
   chunk 12 optimal weight:    2.9990
   chunk 49 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 66 optimal weight:    4.9990
   chunk 60 optimal weight:   10.0000
   chunk 7 optimal weight:    0.8980
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.8180

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4330 r_free = 0.4330 target = 0.208059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3930 r_free = 0.3930 target = 0.169145 restraints weight = 8181.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3970 r_free = 0.3970 target = 0.173090 restraints weight = 5264.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.175765 restraints weight = 4060.287|
|-----------------------------------------------------------------------------|
r_work (final): 0.4001
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
moved from start:          0.1252

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6808  Z= 0.200
  Angle     :  0.548   5.990   9268  Z= 0.296
  Chirality :  0.042   0.157   1012
  Planarity :  0.004   0.033   1134
  Dihedral  :  4.651  52.151    874
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 8.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.84 %
    Allowed  : 19.89 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.37 (0.30), residues: 788
  helix:  2.06 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -2.08 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 266 
 HIS   0.005   0.001   HIS A 313 
 PHE   0.027   0.001   PHE B 596 
 TYR   0.019   0.002   TYR B 558 
 ARG   0.003   0.000   ARG A 371 

*********************** 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: 27
    poor density    : 111
  time to evaluate  : 0.702 
Fit side-chains
REVERT: A  394 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7084 (p90)
REVERT: A  483 TYR cc_start: 0.7594 (m-80) cc_final: 0.7147 (m-80)
REVERT: A  570 ARG cc_start: 0.7294 (OUTLIER) cc_final: 0.6964 (mmt-90)
  outliers start: 27
  outliers final: 16
  residues processed: 131
  average time/residue: 0.1762
  time to fit residues: 31.5326
Evaluate side-chains
  116 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 0.759 
-------------------------------------------------------------------------------
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  423 TRP
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  269 ILE
Chi-restraints excluded: chain B residue  300 VAL
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  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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 53 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0170
   chunk 32 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0040
   chunk 77 optimal weight:    0.9980
   chunk 45 optimal weight:    0.8980
   chunk 70 optimal weight:    0.0470
   overall best weight:    0.2128

-------------------------------------------------------------------------------
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**
B 452 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4361 r_free = 0.4361 target = 0.211385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3963 r_free = 0.3963 target = 0.172367 restraints weight = 8313.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.176464 restraints weight = 5410.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.179091 restraints weight = 4142.370|
|-----------------------------------------------------------------------------|
r_work (final): 0.4038
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6907
moved from start:          0.1535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6808  Z= 0.154
  Angle     :  0.530   9.327   9268  Z= 0.283
  Chirality :  0.041   0.181   1012
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.540  52.846    874
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.33 %
    Favored  : 94.67 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 22.02 %
    Favored  : 75.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.69 (0.31), residues: 788
  helix:  2.31 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.99 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 504 
 PHE   0.029   0.001   PHE B 596 
 TYR   0.017   0.001   TYR B 345 
 ARG   0.003   0.000   ARG B 270 

*********************** 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
  137 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 116
  time to evaluate  : 0.700 
Fit side-chains
REVERT: A  394 PHE cc_start: 0.7642 (OUTLIER) cc_final: 0.6751 (p90)
REVERT: A  483 TYR cc_start: 0.7682 (m-80) cc_final: 0.7185 (m-80)
REVERT: A  570 ARG cc_start: 0.7112 (OUTLIER) cc_final: 0.6861 (mmt-90)
  outliers start: 21
  outliers final: 11
  residues processed: 132
  average time/residue: 0.1549
  time to fit residues: 28.4022
Evaluate side-chains
  119 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 106
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
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  394 PHE
Chi-restraints excluded: chain A residue  423 TRP
Chi-restraints excluded: chain A residue  570 ARG
Chi-restraints excluded: chain B residue  253 LEU
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
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 12 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 52 optimal weight:    0.0020
   chunk 2 optimal weight:    0.9990
   chunk 3 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 48 optimal weight:    0.9990
   chunk 21 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   overall best weight:    0.7390

-------------------------------------------------------------------------------
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 = 0.4340 r_free = 0.4340 target = 0.209197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3939 r_free = 0.3939 target = 0.170062 restraints weight = 8100.146|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.174052 restraints weight = 5259.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.176662 restraints weight = 4057.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3984
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6936
moved from start:          0.1599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6808  Z= 0.191
  Angle     :  0.544   7.518   9268  Z= 0.294
  Chirality :  0.042   0.165   1012
  Planarity :  0.004   0.036   1134
  Dihedral  :  4.570  55.040    874
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 7.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  4.40 %
    Allowed  : 21.73 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.60 (0.31), residues: 788
  helix:  2.21 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.98 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 504 
 PHE   0.025   0.001   PHE B 596 
 TYR   0.017   0.001   TYR B 558 
 ARG   0.002   0.000   ARG B 270 

*********************** 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: 31
    poor density    : 111
  time to evaluate  : 0.653 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7582 (tpp) cc_final: 0.7350 (tpp)
REVERT: A  457 TRP cc_start: 0.7961 (t-100) cc_final: 0.7529 (t-100)
REVERT: A  483 TYR cc_start: 0.7655 (m-80) cc_final: 0.7152 (m-80)
REVERT: A  570 ARG cc_start: 0.7202 (OUTLIER) cc_final: 0.6884 (mmt-90)
  outliers start: 31
  outliers final: 16
  residues processed: 135
  average time/residue: 0.1643
  time to fit residues: 30.3261
Evaluate side-chains
  120 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 103
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
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  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  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 9 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 52 optimal weight:    0.0570
   chunk 62 optimal weight:    0.8980
   chunk 2 optimal weight:    0.9990
   chunk 64 optimal weight:    0.5980
   chunk 19 optimal weight:    0.4980
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   overall best weight:    0.5098

-------------------------------------------------------------------------------
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 = 0.4356 r_free = 0.4356 target = 0.210900 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3962 r_free = 0.3962 target = 0.172190 restraints weight = 7981.584|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.176174 restraints weight = 5164.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.178690 restraints weight = 3980.303|
|-----------------------------------------------------------------------------|
r_work (final): 0.4029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.1781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6808  Z= 0.170
  Angle     :  0.542   7.702   9268  Z= 0.291
  Chirality :  0.042   0.190   1012
  Planarity :  0.004   0.041   1134
  Dihedral  :  4.579  57.696    874
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 7.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 21.88 %
    Favored  : 74.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.70 (0.31), residues: 788
  helix:  2.31 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.99 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 504 
 PHE   0.019   0.001   PHE B 596 
 TYR   0.021   0.001   TYR B 518 
 ARG   0.002   0.000   ARG B 270 

*********************** 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
  142 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 114
  time to evaluate  : 0.786 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7680 (tpp) cc_final: 0.7363 (tpp)
REVERT: A  483 TYR cc_start: 0.7676 (m-80) cc_final: 0.7194 (m-80)
REVERT: A  570 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6849 (mmt-90)
REVERT: B  293 ARG cc_start: 0.6364 (tpm170) cc_final: 0.5434 (tpp-160)
REVERT: B  607 TRP cc_start: 0.6820 (t60) cc_final: 0.6079 (t60)
  outliers start: 28
  outliers final: 18
  residues processed: 135
  average time/residue: 0.1532
  time to fit residues: 28.7691
Evaluate side-chains
  126 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 107
  time to evaluate  : 0.658 
-------------------------------------------------------------------------------
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  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  342 ILE
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0030
   chunk 42 optimal weight:    2.9990
   chunk 57 optimal weight:    0.7980
   chunk 62 optimal weight:    0.6980
   chunk 52 optimal weight:    0.0470
   chunk 51 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 75 optimal weight:    0.7980
   chunk 2 optimal weight:    0.8980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.4688

-------------------------------------------------------------------------------
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 = 0.4351 r_free = 0.4351 target = 0.210090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3951 r_free = 0.3951 target = 0.171046 restraints weight = 8108.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.174897 restraints weight = 5238.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.177493 restraints weight = 4048.813|
|-----------------------------------------------------------------------------|
r_work (final): 0.4022
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.1911

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6808  Z= 0.168
  Angle     :  0.543   8.042   9268  Z= 0.290
  Chirality :  0.041   0.191   1012
  Planarity :  0.004   0.036   1134
  Dihedral  :  4.595  59.617    874
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.70 %
    Favored  : 95.30 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 23.01 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.78 (0.31), residues: 788
  helix:  2.34 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.88 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 504 
 PHE   0.016   0.001   PHE B 596 
 TYR   0.020   0.001   TYR B 518 
 ARG   0.004   0.000   ARG A 611 

*********************** 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
  138 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 114
  time to evaluate  : 0.691 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7710 (tpp) cc_final: 0.7393 (tpp)
REVERT: A  483 TYR cc_start: 0.7634 (m-80) cc_final: 0.7163 (m-80)
REVERT: A  570 ARG cc_start: 0.7073 (OUTLIER) cc_final: 0.6867 (mmt-90)
REVERT: B  607 TRP cc_start: 0.6785 (t60) cc_final: 0.6107 (t60)
  outliers start: 24
  outliers final: 18
  residues processed: 132
  average time/residue: 0.1602
  time to fit residues: 29.2532
Evaluate side-chains
  128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
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  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  342 ILE
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 57 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 32 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9980
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 11 optimal weight:    0.7980
   overall best weight:    0.8980

-------------------------------------------------------------------------------
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 294 GLN
** B 306 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.206046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3905 r_free = 0.3905 target = 0.166474 restraints weight = 8208.511|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.170285 restraints weight = 5293.768|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.172816 restraints weight = 4110.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3957
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6955
moved from start:          0.1897

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6808  Z= 0.213
  Angle     :  0.571   7.820   9268  Z= 0.307
  Chirality :  0.043   0.201   1012
  Planarity :  0.004   0.036   1134
  Dihedral  :  4.610  56.472    874
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 7.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  3.41 %
    Allowed  : 23.15 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.57 (0.31), residues: 788
  helix:  2.18 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.96 (0.41), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 313 
 PHE   0.017   0.001   PHE B 394 
 TYR   0.018   0.002   TYR B 558 
 ARG   0.003   0.000   ARG B 465 

*********************** 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: 24
    poor density    : 113
  time to evaluate  : 0.664 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7722 (tpp) cc_final: 0.7392 (tpp)
REVERT: A  457 TRP cc_start: 0.7933 (t-100) cc_final: 0.7442 (t-100)
REVERT: A  483 TYR cc_start: 0.7628 (m-80) cc_final: 0.7095 (m-80)
REVERT: A  570 ARG cc_start: 0.7219 (OUTLIER) cc_final: 0.6945 (mmt-90)
REVERT: A  611 ARG cc_start: 0.7994 (tpt-90) cc_final: 0.7385 (tpt170)
REVERT: B  292 TRP cc_start: 0.7535 (m-90) cc_final: 0.6538 (m-90)
REVERT: B  607 TRP cc_start: 0.6778 (t60) cc_final: 0.6355 (t60)
  outliers start: 24
  outliers final: 18
  residues processed: 129
  average time/residue: 0.1727
  time to fit residues: 31.0042
Evaluate side-chains
  123 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 1.391 
-------------------------------------------------------------------------------
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  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  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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 22 optimal weight:    0.0770
   chunk 50 optimal weight:    0.4980
   chunk 1 optimal weight:    1.9990
   chunk 20 optimal weight:    8.9990
   chunk 0 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 35 optimal weight:    6.9990
   chunk 36 optimal weight:    0.6980
   chunk 64 optimal weight:    0.8980
   chunk 15 optimal weight:    0.8980
   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 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 = 0.4333 r_free = 0.4333 target = 0.208189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.168902 restraints weight = 8184.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.172873 restraints weight = 5304.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.175484 restraints weight = 4101.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.3998
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6931
moved from start:          0.2016

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   6808  Z= 0.186
  Angle     :  0.562   8.361   9268  Z= 0.303
  Chirality :  0.042   0.194   1012
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.567  54.572    874
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 23.44 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.31), residues: 788
  helix:  2.24 (0.21), residues: 556
  sheet:  None (None), residues: 0
  loop : -1.88 (0.42), residues: 232

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.030   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 504 
 PHE   0.018   0.001   PHE B 596 
 TYR   0.017   0.001   TYR B 558 
 ARG   0.003   0.000   ARG A 611 

*********************** 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
  128 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.722 
Fit side-chains
REVERT: A  408 MET cc_start: 0.7732 (tpp) cc_final: 0.7397 (tpp)
REVERT: A  457 TRP cc_start: 0.7829 (t-100) cc_final: 0.7380 (t-100)
REVERT: A  483 TYR cc_start: 0.7607 (m-80) cc_final: 0.7033 (m-80)
REVERT: A  570 ARG cc_start: 0.7189 (OUTLIER) cc_final: 0.6934 (mmt-90)
REVERT: A  611 ARG cc_start: 0.7950 (tpt-90) cc_final: 0.7422 (tpt170)
REVERT: B  292 TRP cc_start: 0.7508 (m-90) cc_final: 0.6525 (m-90)
REVERT: B  607 TRP cc_start: 0.6845 (t60) cc_final: 0.6418 (t60)
  outliers start: 22
  outliers final: 20
  residues processed: 123
  average time/residue: 0.1643
  time to fit residues: 27.7477
Evaluate side-chains
  125 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 34 optimal weight:    3.9990
   chunk 44 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   chunk 30 optimal weight:    0.8980
   chunk 71 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4309 r_free = 0.4309 target = 0.205609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3896 r_free = 0.3896 target = 0.165763 restraints weight = 8190.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.169631 restraints weight = 5346.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.172214 restraints weight = 4143.263|
|-----------------------------------------------------------------------------|
r_work (final): 0.3980
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6966
moved from start:          0.2067

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   6808  Z= 0.216
  Angle     :  0.584   8.451   9268  Z= 0.313
  Chirality :  0.043   0.230   1012
  Planarity :  0.004   0.036   1134
  Dihedral  :  4.560  52.247    874
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 7.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.20 %
    Favored  : 94.80 %
  Rotamer:
    Outliers :  3.12 %
    Allowed  : 23.72 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.55 (0.31), residues: 788
  helix:  2.15 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.86 (0.42), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP B 292 
 HIS   0.005   0.001   HIS A 313 
 PHE   0.019   0.001   PHE B 596 
 TYR   0.020   0.002   TYR B 518 
 ARG   0.005   0.000   ARG A 448 

********************** 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
  127 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 105
  time to evaluate  : 0.742 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  408 MET cc_start: 0.7741 (tpp) cc_final: 0.7397 (tpp)
REVERT: A  457 TRP cc_start: 0.7976 (t-100) cc_final: 0.7499 (t-100)
REVERT: A  483 TYR cc_start: 0.7660 (m-80) cc_final: 0.7191 (m-80)
REVERT: A  570 ARG cc_start: 0.7187 (OUTLIER) cc_final: 0.6895 (mmt-90)
REVERT: B  607 TRP cc_start: 0.6835 (t60) cc_final: 0.6417 (t60)
  outliers start: 22
  outliers final: 20
  residues processed: 121
  average time/residue: 0.1654
  time to fit residues: 27.4238
Evaluate side-chains
  120 residues out of total 704 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 99
  time to evaluate  : 0.743 
-------------------------------------------------------------------------------
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 78
   random chunks:
   chunk 11 optimal weight:    0.0060
   chunk 6 optimal weight:    0.9980
   chunk 8 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 74 optimal weight:    0.7980
   chunk 64 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   overall best weight:    0.6196

-------------------------------------------------------------------------------
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 = 0.4327 r_free = 0.4327 target = 0.207506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.168020 restraints weight = 8271.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.171859 restraints weight = 5357.986|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.174335 restraints weight = 4155.229|
|-----------------------------------------------------------------------------|
r_work (final): 0.3990
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6937
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6808  Z= 0.190
  Angle     :  0.574   8.441   9268  Z= 0.309
  Chirality :  0.042   0.219   1012
  Planarity :  0.004   0.035   1134
  Dihedral  :  4.538  51.243    874
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 8.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 24.29 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.63 (0.31), residues: 788
  helix:  2.22 (0.21), residues: 554
  sheet:  None (None), residues: 0
  loop : -1.88 (0.41), residues: 234

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.001   TRP B 292 
 HIS   0.008   0.001   HIS A 504 
 PHE   0.031   0.001   PHE B 322 
 TYR   0.016   0.001   TYR B 558 
 ARG   0.005   0.000   ARG A 611 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2106.88 seconds
wall clock time: 37 minutes 23.04 seconds (2243.04 seconds total)