Starting phenix.real_space_refine
on Wed Sep 17 17:34:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8xw2_38728/09_2025/8xw2_38728.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8xw2_38728/09_2025/8xw2_38728.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8xw2_38728/09_2025/8xw2_38728.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8xw2_38728/09_2025/8xw2_38728.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8xw2_38728/09_2025/8xw2_38728.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8xw2_38728/09_2025/8xw2_38728.map"
  }
  resolution = 3.59
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.066
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      48      5.16       5
     C    6744      2.51       5
     N    1650      2.21       5
     O    1708      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 68 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: 10150
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 5075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 634, 5075
          Classifications: {'peptide': 634}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 34, 'TRANS': 599}
          Chain breaks: 4
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 88
          Unresolved non-hydrogen dihedrals: 61
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1}
          Unresolved non-hydrogen planarities: 39
  Restraints were copied for chains:
    B
  Time building chain proxies: 4.40, per 1000 atoms: 0.43
  Number of scatterers: 10150
  At special positions: 0
  Unit cell: (91.785, 140.315, 98.115, 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      48     16.00
     O    1708      8.00
     N    1650      7.00
     C    6744      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.99
  Conformation dependent library (CDL) restraints added in 371.8 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2432

  Finding SS restraints...
    Secondary structure from input PDB file:
      70 helices and 2 sheets defined
      77.1% alpha, 3.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 30
      removed outlier: 3.501A  pdb=" N   LEU A  30 " --> pdb=" O   ALA A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 31 through 33
      No H-bonds generated for 'chain 'A' and resid 31 through 33'
    Processing helix  chain 'A' and resid 34 through 39
    Processing helix  chain 'A' and resid 74 through 80
      removed outlier: 3.757A  pdb=" N   LEU A  80 " --> pdb=" O   MET A  76 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 83 through 92
    Processing helix  chain 'A' and resid 92 through 121
      removed outlier: 4.119A  pdb=" N   TYR A 102 " --> pdb=" O   TYR A  98 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TRP A 103 " --> pdb=" O   LEU A  99 " (cutoff:3.500A)
      Proline residue:  A 111  - end of helix
    Processing helix  chain 'A' and resid 157 through 195
    Processing helix  chain 'A' and resid 198 through 201
    Processing helix  chain 'A' and resid 216 through 229
    Processing helix  chain 'A' and resid 242 through 269
    Processing helix  chain 'A' and resid 290 through 313
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 329 through 338
    Processing helix  chain 'A' and resid 360 through 366
      removed outlier: 3.747A  pdb=" N   ALA A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE A 366 " --> pdb=" O   ASN A 363 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 369
      No H-bonds generated for 'chain 'A' and resid 367 through 369'
    Processing helix  chain 'A' and resid 370 through 389
    Processing helix  chain 'A' and resid 389 through 400
      removed outlier: 3.786A  pdb=" N   ILE A 393 " --> pdb=" O   PHE A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 422 through 438
      Proline residue:  A 430  - end of helix
    Processing helix  chain 'A' and resid 440 through 452
    Processing helix  chain 'A' and resid 456 through 475
    Processing helix  chain 'A' and resid 477 through 489
    Processing helix  chain 'A' and resid 504 through 509
    Processing helix  chain 'A' and resid 512 through 534
      removed outlier: 3.615A  pdb=" N   ALA A 526 " --> pdb=" O   VAL A 522 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLY A 527 " --> pdb=" O   ASP A 523 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   LEU A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   MET A 534 " --> pdb=" O   GLY A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 534 through 548
    Processing helix  chain 'A' and resid 554 through 559
    Processing helix  chain 'A' and resid 565 through 584
      Proline residue:  A 571  - end of helix
    Processing helix  chain 'A' and resid 587 through 589
      No H-bonds generated for 'chain 'A' and resid 587 through 589'
    Processing helix  chain 'A' and resid 590 through 612
      removed outlier: 3.724A  pdb=" N   ILE A 594 " --> pdb=" O   LEU A 590 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 646
    Processing helix  chain 'A' and resid 647 through 649
      No H-bonds generated for 'chain 'A' and resid 647 through 649'
    Processing helix  chain 'A' and resid 654 through 659
    Processing helix  chain 'A' and resid 659 through 677
      removed outlier: 4.024A  pdb=" N   VAL A 663 " --> pdb=" O   ILE A 659 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 677 through 682
    Processing helix  chain 'A' and resid 684 through 699
    Processing helix  chain 'A' and resid 703 through 710
      removed outlier: 4.109A  pdb=" N   ASN A 710 " --> pdb=" O   GLY A 706 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 30
      removed outlier: 3.501A  pdb=" N   LEU B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 33
      No H-bonds generated for 'chain 'B' and resid 31 through 33'
    Processing helix  chain 'B' and resid 34 through 39
    Processing helix  chain 'B' and resid 74 through 80
      removed outlier: 3.756A  pdb=" N   LEU B  80 " --> pdb=" O   MET B  76 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 83 through 92
    Processing helix  chain 'B' and resid 92 through 121
      removed outlier: 4.118A  pdb=" N   TYR B 102 " --> pdb=" O   TYR B  98 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   TRP B 103 " --> pdb=" O   LEU B  99 " (cutoff:3.500A)
      Proline residue:  B 111  - end of helix
    Processing helix  chain 'B' and resid 157 through 195
    Processing helix  chain 'B' and resid 198 through 201
    Processing helix  chain 'B' and resid 216 through 229
    Processing helix  chain 'B' and resid 242 through 269
    Processing helix  chain 'B' and resid 290 through 313
    Processing helix  chain 'B' and resid 315 through 317
      No H-bonds generated for 'chain 'B' and resid 315 through 317'
    Processing helix  chain 'B' and resid 329 through 338
    Processing helix  chain 'B' and resid 360 through 366
      removed outlier: 3.746A  pdb=" N   ALA B 365 " --> pdb=" O   SER B 362 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   ILE B 366 " --> pdb=" O   ASN B 363 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 367 through 369
      No H-bonds generated for 'chain 'B' and resid 367 through 369'
    Processing helix  chain 'B' and resid 370 through 389
    Processing helix  chain 'B' and resid 389 through 400
      removed outlier: 3.786A  pdb=" N   ILE B 393 " --> pdb=" O   PHE B 389 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 422 through 438
      Proline residue:  B 430  - end of helix
    Processing helix  chain 'B' and resid 440 through 452
    Processing helix  chain 'B' and resid 456 through 475
    Processing helix  chain 'B' and resid 477 through 489
    Processing helix  chain 'B' and resid 504 through 509
    Processing helix  chain 'B' and resid 512 through 534
      removed outlier: 3.617A  pdb=" N   ALA B 526 " --> pdb=" O   VAL B 522 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   GLY B 527 " --> pdb=" O   ASP B 523 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   LEU B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   MET B 534 " --> pdb=" O   GLY B 530 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 534 through 548
    Processing helix  chain 'B' and resid 554 through 559
    Processing helix  chain 'B' and resid 565 through 584
      Proline residue:  B 571  - end of helix
    Processing helix  chain 'B' and resid 587 through 589
      No H-bonds generated for 'chain 'B' and resid 587 through 589'
    Processing helix  chain 'B' and resid 590 through 612
      removed outlier: 3.724A  pdb=" N   ILE B 594 " --> pdb=" O   LEU B 590 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 623 through 646
    Processing helix  chain 'B' and resid 647 through 649
      No H-bonds generated for 'chain 'B' and resid 647 through 649'
    Processing helix  chain 'B' and resid 654 through 659
    Processing helix  chain 'B' and resid 659 through 677
      removed outlier: 4.024A  pdb=" N   VAL B 663 " --> pdb=" O   ILE B 659 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 677 through 682
    Processing helix  chain 'B' and resid 684 through 699
    Processing helix  chain 'B' and resid 703 through 710
      removed outlier: 4.108A  pdb=" N   ASN B 710 " --> pdb=" O   GLY B 706 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 240
      removed outlier: 5.660A  pdb=" N   ALA A 322 " --> pdb=" O   VAL A 239 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 240
      removed outlier: 5.660A  pdb=" N   ALA B 322 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)

    691 hydrogen bonds defined for protein.
    2049 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.24

  Time building geometry restraints manager: 1.28 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: 3094
        1.34 -     1.46: 2463
        1.46 -     1.58: 4795
        1.58 -     1.70: 0
        1.70 -     1.82: 88
  Bond restraints: 10440
  Sorted by residual:
  bond pdb=" CG  LEU A 441 "
       pdb=" CD2 LEU A 441 "
    ideal  model  delta    sigma   weight residual
    1.521  1.459  0.062 3.30e-02 9.18e+02 3.58e+00
  bond pdb=" CG  LEU B 441 "
       pdb=" CD2 LEU B 441 "
    ideal  model  delta    sigma   weight residual
    1.521  1.460  0.061 3.30e-02 9.18e+02 3.46e+00
  bond pdb=" C   ASN A 344 "
       pdb=" N   PRO A 345 "
    ideal  model  delta    sigma   weight residual
    1.334  1.319  0.014 8.40e-03 1.42e+04 2.95e+00
  bond pdb=" C   ASN B 344 "
       pdb=" N   PRO B 345 "
    ideal  model  delta    sigma   weight residual
    1.334  1.319  0.014 8.40e-03 1.42e+04 2.89e+00
  bond pdb=" CD  GLU B 297 "
       pdb=" OE1 GLU B 297 "
    ideal  model  delta    sigma   weight residual
    1.249  1.222  0.027 1.90e-02 2.77e+03 2.06e+00
  ... (remaining 10435 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.59: 13606
        1.59 -     3.18: 455
        3.18 -     4.77: 95
        4.77 -     6.36: 30
        6.36 -     7.95: 14
  Bond angle restraints: 14200
  Sorted by residual:
  angle pdb=" C   ALA B 296 "
        pdb=" N   GLU B 297 "
        pdb=" CA  GLU B 297 "
      ideal   model   delta    sigma   weight residual
     121.14  113.19    7.95 1.75e+00 3.27e-01 2.07e+01
  angle pdb=" C   ALA A 296 "
        pdb=" N   GLU A 297 "
        pdb=" CA  GLU A 297 "
      ideal   model   delta    sigma   weight residual
     121.14  113.20    7.94 1.75e+00 3.27e-01 2.06e+01
  angle pdb=" N   GLU A 297 "
        pdb=" CA  GLU A 297 "
        pdb=" CB  GLU A 297 "
      ideal   model   delta    sigma   weight residual
     110.40  115.85   -5.45 1.63e+00 3.76e-01 1.12e+01
  angle pdb=" N   GLU B 297 "
        pdb=" CA  GLU B 297 "
        pdb=" CB  GLU B 297 "
      ideal   model   delta    sigma   weight residual
     110.40  115.84   -5.44 1.63e+00 3.76e-01 1.12e+01
  angle pdb=" N   PRO B 345 "
        pdb=" CA  PRO B 345 "
        pdb=" C   PRO B 345 "
      ideal   model   delta    sigma   weight residual
     114.68  111.35    3.33 1.04e+00 9.25e-01 1.03e+01
  ... (remaining 14195 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 5597
       17.96 -    35.92: 426
       35.92 -    53.87: 83
       53.87 -    71.83: 12
       71.83 -    89.79: 10
  Dihedral angle restraints: 6128
    sinusoidal: 2386
      harmonic: 3742
  Sorted by residual:
  dihedral pdb=" CA  ILE A 108 "
           pdb=" C   ILE A 108 "
           pdb=" N   PHE A 109 "
           pdb=" CA  PHE A 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.30  -19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ILE B 108 "
           pdb=" C   ILE B 108 "
           pdb=" N   PHE B 109 "
           pdb=" CA  PHE B 109 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.30  -19.70     0      5.00e+00 4.00e-02 1.55e+01
  dihedral pdb=" CA  ASN B 475 "
           pdb=" C   ASN B 475 "
           pdb=" N   VAL B 476 "
           pdb=" CA  VAL B 476 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.44  -17.56     0      5.00e+00 4.00e-02 1.23e+01
  ... (remaining 6125 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.088: 1491
       0.088 -    0.176: 109
       0.176 -    0.264: 2
       0.264 -    0.351: 0
       0.351 -    0.439: 2
  Chirality restraints: 1604
  Sorted by residual:
  chirality pdb=" CB  ILE A 112 "
            pdb=" CA  ILE A 112 "
            pdb=" CG1 ILE A 112 "
            pdb=" CG2 ILE A 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.82e+00
  chirality pdb=" CB  ILE B 112 "
            pdb=" CA  ILE B 112 "
            pdb=" CG1 ILE B 112 "
            pdb=" CG2 ILE B 112 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.21    0.44 2.00e-01 2.50e+01 4.77e+00
  chirality pdb=" CA  GLU A 297 "
            pdb=" N   GLU A 297 "
            pdb=" C   GLU A 297 "
            pdb=" CB  GLU A 297 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.33    0.18 2.00e-01 2.50e+01 7.90e-01
  ... (remaining 1601 not shown)

  Planarity restraints: 1762
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 391 "   -0.045 5.00e-02 4.00e+02   6.70e-02 7.19e+00
        pdb=" N   PRO B 392 "    0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO B 392 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO B 392 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 391 "    0.045 5.00e-02 4.00e+02   6.69e-02 7.16e+00
        pdb=" N   PRO A 392 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO A 392 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 392 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU B 677 "    0.036 5.00e-02 4.00e+02   5.47e-02 4.78e+00
        pdb=" N   PRO B 678 "   -0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO B 678 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 678 "    0.031 5.00e-02 4.00e+02
  ... (remaining 1759 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 379
        2.71 -     3.26: 10994
        3.26 -     3.81: 17007
        3.81 -     4.35: 19419
        4.35 -     4.90: 33328
  Nonbonded interactions: 81127
  Sorted by model distance:
  nonbonded pdb=" O   PRO A 354 "
            pdb=" OH  TYR A 712 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" O   PRO B 354 "
            pdb=" OH  TYR B 712 "
     model   vdw
     2.169 3.040
  nonbonded pdb=" OG  SER A 216 "
            pdb=" OE1 GLU A 219 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" OG  SER B 216 "
            pdb=" OE1 GLU B 219 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NE  ARG A 343 "
            pdb=" OE2 GLU B 687 "
     model   vdw
     2.236 3.120
  ... (remaining 81122 not shown)

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

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.870
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     11.840
  Find NCS groups from input model:        0.060
  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:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7978
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.062  10440  Z= 0.207
  Angle     :  0.756   7.955  14200  Z= 0.418
  Chirality :  0.047   0.439   1604
  Planarity :  0.005   0.067   1762
  Dihedral  : 13.677  89.790   3696
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 11.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.69 (0.24), residues: 1248
  helix:  1.62 (0.18), residues: 866
  sheet: -1.63 (0.86), residues: 34
  loop : -2.42 (0.31), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  36 
 TYR   0.025   0.002   TYR A 294 
 PHE   0.023   0.002   PHE A 471 
 TRP   0.022   0.002   TRP A 624 
 HIS   0.005   0.001   HIS B 542 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (10440)
  covalent geometry    : angle       0.75562 (14200)
  hydrogen bonds       : bond        0.08065 (  691)
  hydrogen bonds       : angle       4.88464 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8340 (p) cc_final: 0.8039 (m)
REVERT: A   74 ASN cc_start: 0.8548 (p0) cc_final: 0.7948 (p0)
REVERT: A  165 MET cc_start: 0.8227 (tpt) cc_final: 0.7867 (tpp)
REVERT: A  167 TYR cc_start: 0.7771 (m-80) cc_final: 0.7267 (m-10)
REVERT: A  256 GLN cc_start: 0.8376 (tm-30) cc_final: 0.8031 (tm-30)
REVERT: A  440 PHE cc_start: 0.7389 (m-80) cc_final: 0.7174 (m-80)
REVERT: B   40 SER cc_start: 0.8420 (p) cc_final: 0.8163 (m)
REVERT: B  165 MET cc_start: 0.8360 (tpt) cc_final: 0.7896 (tpp)
REVERT: B  256 GLN cc_start: 0.8181 (tm-30) cc_final: 0.7835 (tm-30)
REVERT: B  437 PHE cc_start: 0.8638 (m-80) cc_final: 0.8428 (m-10)
REVERT: B  615 GLN cc_start: 0.6946 (mt0) cc_final: 0.6601 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 225
  average time/residue: 0.0775
  time to fit residues: 26.9259
Evaluate side-chains
  173 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.402 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    0.8980
   chunk 53 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 123 optimal weight:    0.7980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 338 GLN
A 472 ASN
A 639 GLN
B 338 GLN
B 639 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.136534 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.102690 restraints weight = 17417.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.105613 restraints weight = 9829.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.107492 restraints weight = 7019.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108609 restraints weight = 5775.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.108913 restraints weight = 5176.903|
|-----------------------------------------------------------------------------|
r_work (final): 0.3311
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.1243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10440  Z= 0.145
  Angle     :  0.661  13.610  14200  Z= 0.328
  Chirality :  0.044   0.152   1604
  Planarity :  0.005   0.057   1762
  Dihedral  :  4.427  19.106   1360
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.33 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  :  8.51 %
    Favored  : 90.26 %
  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:  0.67 (0.24), residues: 1248
  helix:  1.77 (0.17), residues: 856
  sheet: -1.79 (0.73), residues: 46
  loop : -2.77 (0.29), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  36 
 TYR   0.014   0.001   TYR A 468 
 PHE   0.025   0.002   PHE B 169 
 TRP   0.018   0.002   TRP A 624 
 HIS   0.005   0.001   HIS A 293 

Details of bonding type rmsd
  covalent geometry    : bond        0.00337 (10440)
  covalent geometry    : angle       0.66097 (14200)
  hydrogen bonds       : bond        0.04111 (  691)
  hydrogen bonds       : angle       4.47095 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 194
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8130 (p) cc_final: 0.7730 (m)
REVERT: A   74 ASN cc_start: 0.8446 (p0) cc_final: 0.7826 (p0)
REVERT: A  102 TYR cc_start: 0.8709 (m-10) cc_final: 0.8466 (m-80)
REVERT: A  165 MET cc_start: 0.8078 (tpt) cc_final: 0.7668 (ttt)
REVERT: A  256 GLN cc_start: 0.8422 (tm-30) cc_final: 0.8178 (tm-30)
REVERT: A  559 MET cc_start: 0.8148 (tpt) cc_final: 0.7539 (tpt)
REVERT: B   40 SER cc_start: 0.8172 (p) cc_final: 0.7945 (m)
REVERT: B  256 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8033 (tm-30)
  outliers start: 13
  outliers final: 8
  residues processed: 200
  average time/residue: 0.0755
  time to fit residues: 23.4634
Evaluate side-chains
  177 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 169
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 ILE
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue  297 GLU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  578 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 125 optimal weight:    4.9990
   chunk 101 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 39 optimal weight:    4.9990
   chunk 21 optimal weight:   40.0000
   chunk 3 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 100 optimal weight:    1.9990
   chunk 103 optimal weight:    0.0980
   chunk 78 optimal weight:    0.6980
   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 243 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 = 0.3721 r_free = 0.3721 target = 0.137395 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3261 r_free = 0.3261 target = 0.103728 restraints weight = 17459.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.106650 restraints weight = 9797.948|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.108548 restraints weight = 6989.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.109673 restraints weight = 5739.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.109954 restraints weight = 5137.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.1635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10440  Z= 0.130
  Angle     :  0.629  14.178  14200  Z= 0.311
  Chirality :  0.043   0.152   1604
  Planarity :  0.005   0.056   1762
  Dihedral  :  4.246  19.075   1360
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 7.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 12.19 %
    Favored  : 86.39 %
  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:  0.82 (0.24), residues: 1248
  helix:  1.89 (0.18), residues: 848
  sheet: -2.15 (0.71), residues: 46
  loop : -2.59 (0.30), residues: 354

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 374 
 TYR   0.012   0.001   TYR A 468 
 PHE   0.026   0.001   PHE A 159 
 TRP   0.017   0.001   TRP A 624 
 HIS   0.002   0.001   HIS B 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10440)
  covalent geometry    : angle       0.62876 (14200)
  hydrogen bonds       : bond        0.03800 (  691)
  hydrogen bonds       : angle       4.41597 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  205 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 190
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8143 (p) cc_final: 0.7735 (m)
REVERT: A   74 ASN cc_start: 0.8447 (p0) cc_final: 0.7851 (p0)
REVERT: A  102 TYR cc_start: 0.8642 (m-10) cc_final: 0.8433 (m-80)
REVERT: A  256 GLN cc_start: 0.8443 (tm-30) cc_final: 0.8225 (tm-30)
REVERT: A  559 MET cc_start: 0.8268 (tpt) cc_final: 0.7840 (tpt)
REVERT: A  643 MET cc_start: 0.7958 (tmm) cc_final: 0.7716 (tmm)
REVERT: B  165 MET cc_start: 0.8009 (tpp) cc_final: 0.7557 (ttp)
REVERT: B  256 GLN cc_start: 0.8380 (tm-30) cc_final: 0.8005 (tm-30)
REVERT: B  559 MET cc_start: 0.8267 (tpp) cc_final: 0.6959 (ppp)
REVERT: B  661 LEU cc_start: 0.8499 (tp) cc_final: 0.7942 (tp)
  outliers start: 15
  outliers final: 10
  residues processed: 198
  average time/residue: 0.0767
  time to fit residues: 23.8084
Evaluate side-chains
  190 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 180
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  157 MET
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  548 LEU
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  672 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 101 optimal weight:    0.6980
   chunk 51 optimal weight:    0.6980
   chunk 110 optimal weight:    3.9990
   chunk 35 optimal weight:    8.9990
   chunk 15 optimal weight:    0.0470
   chunk 108 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 103 optimal weight:    3.9990
   chunk 75 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 47 optimal weight:    3.9990
   overall best weight:    0.8680

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

Flipped N/Q/H residues before XYZ refinement:
A 639 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.137421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.103600 restraints weight = 17466.901|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.106543 restraints weight = 9823.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108428 restraints weight = 6990.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.109569 restraints weight = 5755.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.109785 restraints weight = 5147.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3344
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.1843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10440  Z= 0.132
  Angle     :  0.624  13.414  14200  Z= 0.308
  Chirality :  0.043   0.152   1604
  Planarity :  0.005   0.055   1762
  Dihedral  :  4.148  19.319   1360
  Min Nonbonded Distance : 2.415

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 13.99 %
    Favored  : 84.03 %
  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:  1.01 (0.24), residues: 1248
  helix:  1.86 (0.18), residues: 872
  sheet: -2.50 (0.74), residues: 36
  loop : -2.24 (0.32), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 188 
 TYR   0.012   0.001   TYR A 468 
 PHE   0.026   0.001   PHE B 159 
 TRP   0.017   0.001   TRP A 624 
 HIS   0.002   0.001   HIS B 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10440)
  covalent geometry    : angle       0.62360 (14200)
  hydrogen bonds       : bond        0.03653 (  691)
  hydrogen bonds       : angle       4.39780 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  210 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 189
  time to evaluate  : 0.383 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8172 (p) cc_final: 0.7815 (m)
REVERT: A   74 ASN cc_start: 0.8424 (p0) cc_final: 0.7851 (p0)
REVERT: A  165 MET cc_start: 0.8287 (tpp) cc_final: 0.8014 (tpp)
REVERT: A  256 GLN cc_start: 0.8453 (tm-30) cc_final: 0.8219 (tm-30)
REVERT: A  523 ASP cc_start: 0.8103 (t70) cc_final: 0.7771 (t70)
REVERT: A  559 MET cc_start: 0.8171 (tpt) cc_final: 0.7851 (tpt)
REVERT: B  165 MET cc_start: 0.8307 (tpp) cc_final: 0.8025 (tpp)
REVERT: B  256 GLN cc_start: 0.8419 (tm-30) cc_final: 0.8045 (tm-30)
REVERT: B  389 PHE cc_start: 0.8160 (OUTLIER) cc_final: 0.7156 (t80)
  outliers start: 21
  outliers final: 14
  residues processed: 199
  average time/residue: 0.0734
  time to fit residues: 22.8998
Evaluate side-chains
  187 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 172
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  572 ARG
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  297 GLU
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  472 ASN
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  646 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 125 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 120 optimal weight:    0.0570
   chunk 31 optimal weight:    0.0980
   chunk 59 optimal weight:    2.9990
   chunk 108 optimal weight:    7.9990
   chunk 43 optimal weight:    0.5980
   chunk 121 optimal weight:    1.9990
   chunk 45 optimal weight:    6.9990
   chunk 98 optimal weight:    0.9990
   chunk 93 optimal weight:    0.4980
   overall best weight:    0.4500

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

Flipped N/Q/H residues before XYZ refinement:
A 639 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105570 restraints weight = 17225.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.108531 restraints weight = 9703.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.110406 restraints weight = 6904.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.111381 restraints weight = 5686.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 43)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.112156 restraints weight = 5122.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3373
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.2134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10440  Z= 0.118
  Angle     :  0.610  13.203  14200  Z= 0.297
  Chirality :  0.041   0.152   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.053  19.873   1360
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 7.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 15.41 %
    Favored  : 83.27 %
  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:  1.11 (0.25), residues: 1248
  helix:  1.93 (0.18), residues: 872
  sheet: -2.46 (0.76), residues: 36
  loop : -2.19 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 374 
 TYR   0.010   0.001   TYR A 468 
 PHE   0.026   0.001   PHE B 428 
 TRP   0.016   0.001   TRP A 624 
 HIS   0.001   0.000   HIS B 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00254 (10440)
  covalent geometry    : angle       0.61017 (14200)
  hydrogen bonds       : bond        0.03425 (  691)
  hydrogen bonds       : angle       4.33384 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 198
  time to evaluate  : 0.425 
Fit side-chains
   revert: symmetry clash
REVERT: A   40 SER cc_start: 0.8074 (p) cc_final: 0.7869 (m)
REVERT: A   74 ASN cc_start: 0.8406 (p0) cc_final: 0.7887 (p0)
REVERT: A  165 MET cc_start: 0.8318 (tpp) cc_final: 0.8041 (tpp)
REVERT: A  256 GLN cc_start: 0.8517 (tm-30) cc_final: 0.8268 (tm-30)
REVERT: A  523 ASP cc_start: 0.8026 (t70) cc_final: 0.7666 (t70)
REVERT: A  643 MET cc_start: 0.7941 (tmm) cc_final: 0.7737 (tmm)
REVERT: B  165 MET cc_start: 0.8441 (tpp) cc_final: 0.8162 (tpp)
REVERT: B  256 GLN cc_start: 0.8396 (tm-30) cc_final: 0.8041 (tm-30)
REVERT: B  389 PHE cc_start: 0.8085 (OUTLIER) cc_final: 0.6562 (t80)
REVERT: B  559 MET cc_start: 0.8095 (tpp) cc_final: 0.7891 (tpp)
  outliers start: 14
  outliers final: 9
  residues processed: 202
  average time/residue: 0.0702
  time to fit residues: 22.0066
Evaluate side-chains
  187 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 177
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  646 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 74 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 80 optimal weight:    0.0470
   chunk 35 optimal weight:    1.9990
   chunk 5 optimal weight:    0.7980
   chunk 122 optimal weight:    0.7980
   chunk 52 optimal weight:    0.8980
   chunk 109 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
A 344 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.139107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.105305 restraints weight = 17520.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.108335 restraints weight = 9876.102|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.110225 restraints weight = 6982.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.110755 restraints weight = 5723.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.111556 restraints weight = 5284.636|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7953
moved from start:          0.2267

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10440  Z= 0.122
  Angle     :  0.620  13.293  14200  Z= 0.303
  Chirality :  0.042   0.151   1604
  Planarity :  0.005   0.053   1762
  Dihedral  :  4.010  19.803   1360
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 7.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 16.45 %
    Favored  : 82.14 %
  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:  1.17 (0.25), residues: 1248
  helix:  1.98 (0.17), residues: 872
  sheet: -2.47 (0.77), residues: 36
  loop : -2.16 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 374 
 TYR   0.010   0.001   TYR A 468 
 PHE   0.025   0.001   PHE B 159 
 TRP   0.015   0.001   TRP B 624 
 HIS   0.002   0.000   HIS B 628 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10440)
  covalent geometry    : angle       0.61988 (14200)
  hydrogen bonds       : bond        0.03421 (  691)
  hydrogen bonds       : angle       4.32157 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 181
  time to evaluate  : 0.438 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8448 (p0) cc_final: 0.7963 (p0)
REVERT: A  165 MET cc_start: 0.8403 (tpp) cc_final: 0.8142 (tpp)
REVERT: A  256 GLN cc_start: 0.8470 (tm-30) cc_final: 0.8224 (tm-30)
REVERT: A  523 ASP cc_start: 0.8081 (t70) cc_final: 0.7717 (t70)
REVERT: A  643 MET cc_start: 0.8010 (tmm) cc_final: 0.7727 (tmm)
REVERT: B  165 MET cc_start: 0.8462 (tpp) cc_final: 0.8179 (tpp)
REVERT: B  256 GLN cc_start: 0.8356 (tm-30) cc_final: 0.7988 (tm-30)
REVERT: B  389 PHE cc_start: 0.8106 (OUTLIER) cc_final: 0.6566 (t80)
REVERT: B  559 MET cc_start: 0.8127 (tpp) cc_final: 0.7909 (tpp)
  outliers start: 15
  outliers final: 11
  residues processed: 186
  average time/residue: 0.0729
  time to fit residues: 21.4493
Evaluate side-chains
  183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 171
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain A residue  690 MET
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  646 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 115 optimal weight:    2.9990
   chunk 82 optimal weight:    5.9990
   chunk 20 optimal weight:    1.9990
   chunk 5 optimal weight:    0.0980
   chunk 7 optimal weight:    0.0970
   chunk 2 optimal weight:    7.9990
   chunk 47 optimal weight:    0.5980
   chunk 79 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 12 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9990
   overall best weight:    0.3978

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

Flipped N/Q/H residues before XYZ refinement:
B 344 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.140610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.107073 restraints weight = 17230.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.110046 restraints weight = 9790.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.111931 restraints weight = 6962.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.112739 restraints weight = 5711.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.113365 restraints weight = 5182.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  10440  Z= 0.115
  Angle     :  0.621  13.503  14200  Z= 0.300
  Chirality :  0.041   0.149   1604
  Planarity :  0.005   0.052   1762
  Dihedral  :  3.950  20.026   1360
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  1.32 %
    Allowed  : 17.01 %
    Favored  : 81.66 %
  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:  1.24 (0.25), residues: 1248
  helix:  2.02 (0.17), residues: 872
  sheet: -2.45 (0.77), residues: 36
  loop : -2.12 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A  36 
 TYR   0.009   0.001   TYR A 468 
 PHE   0.029   0.001   PHE B 428 
 TRP   0.015   0.001   TRP B 624 
 HIS   0.002   0.000   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 (10440)
  covalent geometry    : angle       0.62140 (14200)
  hydrogen bonds       : bond        0.03319 (  691)
  hydrogen bonds       : angle       4.30499 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 192
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8426 (p0) cc_final: 0.7932 (p0)
REVERT: A  165 MET cc_start: 0.8461 (tpp) cc_final: 0.8164 (tpp)
REVERT: A  256 GLN cc_start: 0.8457 (tm-30) cc_final: 0.8221 (tm-30)
REVERT: A  523 ASP cc_start: 0.8070 (t70) cc_final: 0.7283 (t0)
REVERT: B  165 MET cc_start: 0.8442 (tpp) cc_final: 0.8153 (tpp)
REVERT: B  256 GLN cc_start: 0.8334 (tm-30) cc_final: 0.7964 (tm-30)
REVERT: B  389 PHE cc_start: 0.8096 (OUTLIER) cc_final: 0.6584 (t80)
  outliers start: 14
  outliers final: 8
  residues processed: 199
  average time/residue: 0.0703
  time to fit residues: 22.3163
Evaluate side-chains
  184 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 175
  time to evaluate  : 0.408 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  344 ASN
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  478 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 3 optimal weight:    0.9980
   chunk 122 optimal weight:    0.0970
   chunk 71 optimal weight:    0.5980
   chunk 84 optimal weight:   30.0000
   chunk 52 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 75 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 77 optimal weight:    3.9990
   chunk 112 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9990
   overall best weight:    0.6178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.139791 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.105625 restraints weight = 17514.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.108667 restraints weight = 9840.431|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.110594 restraints weight = 6984.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.111502 restraints weight = 5723.871|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.112418 restraints weight = 5172.389|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2536

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10440  Z= 0.120
  Angle     :  0.622  13.469  14200  Z= 0.300
  Chirality :  0.042   0.148   1604
  Planarity :  0.005   0.052   1762
  Dihedral  :  3.906  20.122   1360
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 16.82 %
    Favored  : 81.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.33 (0.25), residues: 1248
  helix:  2.08 (0.17), residues: 872
  sheet: -2.43 (0.78), residues: 36
  loop : -2.06 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 682 
 TYR   0.010   0.001   TYR A 468 
 PHE   0.031   0.001   PHE B 428 
 TRP   0.024   0.001   TRP B 525 
 HIS   0.005   0.000   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 (10440)
  covalent geometry    : angle       0.62242 (14200)
  hydrogen bonds       : bond        0.03368 (  691)
  hydrogen bonds       : angle       4.26002 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 188
  time to evaluate  : 0.392 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8434 (p0) cc_final: 0.7943 (p0)
REVERT: A  165 MET cc_start: 0.8435 (tpp) cc_final: 0.8133 (tpp)
REVERT: A  256 GLN cc_start: 0.8460 (tm-30) cc_final: 0.8192 (tm-30)
REVERT: A  523 ASP cc_start: 0.8106 (t70) cc_final: 0.7285 (t0)
REVERT: B  165 MET cc_start: 0.8470 (tpp) cc_final: 0.8141 (tpp)
REVERT: B  256 GLN cc_start: 0.8323 (tm-30) cc_final: 0.7944 (tm-30)
REVERT: B  389 PHE cc_start: 0.8212 (OUTLIER) cc_final: 0.6680 (t80)
  outliers start: 23
  outliers final: 12
  residues processed: 199
  average time/residue: 0.0644
  time to fit residues: 20.5509
Evaluate side-chains
  194 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 181
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  440 PHE
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue  344 ASN
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Chi-restraints excluded: chain B residue  681 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    0.9980
   chunk 116 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 109 optimal weight:    8.9990
   chunk 7 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 115 optimal weight:    1.9990
   chunk 59 optimal weight:    0.4980
   chunk 73 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.139169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.105255 restraints weight = 17299.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.108206 restraints weight = 9844.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.110039 restraints weight = 6988.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.111038 restraints weight = 5746.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.111434 restraints weight = 5195.210|
|-----------------------------------------------------------------------------|
r_work (final): 0.3366
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7959
moved from start:          0.2582

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10440  Z= 0.132
  Angle     :  0.661  16.183  14200  Z= 0.316
  Chirality :  0.043   0.244   1604
  Planarity :  0.005   0.052   1762
  Dihedral  :  3.935  20.514   1360
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 17.86 %
    Favored  : 80.72 %
  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:  1.34 (0.25), residues: 1248
  helix:  2.05 (0.17), residues: 874
  sheet: -2.43 (0.79), residues: 36
  loop : -1.98 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 374 
 TYR   0.011   0.001   TYR A 468 
 PHE   0.035   0.001   PHE B 451 
 TRP   0.032   0.001   TRP B 525 
 HIS   0.002   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (10440)
  covalent geometry    : angle       0.66067 (14200)
  hydrogen bonds       : bond        0.03420 (  691)
  hydrogen bonds       : angle       4.27056 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 185
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8388 (p0) cc_final: 0.7891 (p0)
REVERT: A  165 MET cc_start: 0.8394 (tpp) cc_final: 0.8086 (tpp)
REVERT: A  256 GLN cc_start: 0.8481 (tm-30) cc_final: 0.8204 (tm-30)
REVERT: A  523 ASP cc_start: 0.8142 (t70) cc_final: 0.7721 (t70)
REVERT: A  559 MET cc_start: 0.7844 (tpp) cc_final: 0.7393 (tpp)
REVERT: B  165 MET cc_start: 0.8471 (tpp) cc_final: 0.8133 (tpp)
REVERT: B  256 GLN cc_start: 0.8352 (tm-30) cc_final: 0.7957 (tm-30)
REVERT: B  389 PHE cc_start: 0.8178 (OUTLIER) cc_final: 0.6680 (t80)
REVERT: B  525 TRP cc_start: 0.8017 (m-10) cc_final: 0.7765 (m-10)
  outliers start: 15
  outliers final: 11
  residues processed: 193
  average time/residue: 0.0687
  time to fit residues: 21.0493
Evaluate side-chains
  186 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 174
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 21 optimal weight:   30.0000
   chunk 86 optimal weight:   10.0000
   chunk 49 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 104 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 87 optimal weight:    0.7980
   chunk 92 optimal weight:    1.9990
   chunk 120 optimal weight:    0.3980
   chunk 76 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.7984

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.139366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.105596 restraints weight = 17140.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.108525 restraints weight = 9748.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.110348 restraints weight = 6944.533|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.111279 restraints weight = 5732.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.111462 restraints weight = 5185.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3363
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7969
moved from start:          0.2678

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035  10440  Z= 0.129
  Angle     :  0.659  15.936  14200  Z= 0.315
  Chirality :  0.043   0.219   1604
  Planarity :  0.005   0.051   1762
  Dihedral  :  3.940  22.017   1360
  Min Nonbonded Distance : 2.533

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.61 %
    Allowed  : 17.49 %
    Favored  : 80.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.30 (0.25), residues: 1248
  helix:  2.02 (0.17), residues: 874
  sheet: -2.44 (0.79), residues: 36
  loop : -1.96 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 374 
 TYR   0.010   0.001   TYR A 468 
 PHE   0.033   0.002   PHE B 428 
 TRP   0.032   0.001   TRP B 525 
 HIS   0.003   0.001   HIS A 379 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (10440)
  covalent geometry    : angle       0.65878 (14200)
  hydrogen bonds       : bond        0.03415 (  691)
  hydrogen bonds       : angle       4.25407 ( 2049)

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

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

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2496 Ramachandran restraints generated.
    1248 Oldfield, 0 Emsley, 1248 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 174
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
REVERT: A   74 ASN cc_start: 0.8390 (p0) cc_final: 0.7889 (p0)
REVERT: A  165 MET cc_start: 0.8466 (tpp) cc_final: 0.8106 (tpp)
REVERT: A  256 GLN cc_start: 0.8484 (tm-30) cc_final: 0.8194 (tm-30)
REVERT: A  523 ASP cc_start: 0.8258 (t70) cc_final: 0.7949 (t70)
REVERT: B  165 MET cc_start: 0.8431 (tpp) cc_final: 0.8200 (tpp)
REVERT: B  256 GLN cc_start: 0.8329 (tm-30) cc_final: 0.7916 (tm-30)
REVERT: B  389 PHE cc_start: 0.8190 (OUTLIER) cc_final: 0.6675 (t80)
  outliers start: 17
  outliers final: 12
  residues processed: 182
  average time/residue: 0.0746
  time to fit residues: 21.6855
Evaluate side-chains
  183 residues out of total 1092 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 170
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   17 SER
Chi-restraints excluded: chain A residue   37 VAL
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  311 GLU
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  586 VAL
Chi-restraints excluded: chain A residue  646 LEU
Chi-restraints excluded: chain B residue   27 VAL
Chi-restraints excluded: chain B residue   94 ASP
Chi-restraints excluded: chain B residue  167 TYR
Chi-restraints excluded: chain B residue  389 PHE
Chi-restraints excluded: chain B residue  578 LEU
Chi-restraints excluded: chain B residue  586 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 126
   random chunks:
   chunk 122 optimal weight:    0.9990
   chunk 79 optimal weight:    0.6980
   chunk 59 optimal weight:    0.5980
   chunk 76 optimal weight:    0.8980
   chunk 87 optimal weight:    0.5980
   chunk 27 optimal weight:    0.6980
   chunk 81 optimal weight:    0.1980
   chunk 25 optimal weight:    7.9990
   chunk 83 optimal weight:    4.9990
   chunk 117 optimal weight:    0.6980
   chunk 16 optimal weight:    3.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.140170 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.105953 restraints weight = 17325.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.109053 restraints weight = 9549.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.110980 restraints weight = 6690.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.112003 restraints weight = 5456.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.112762 restraints weight = 4900.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3392
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7918
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10440  Z= 0.124
  Angle     :  0.669  16.003  14200  Z= 0.318
  Chirality :  0.042   0.201   1604
  Planarity :  0.005   0.051   1762
  Dihedral  :  3.928  19.342   1360
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 17.96 %
    Favored  : 80.62 %
  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:  1.30 (0.25), residues: 1248
  helix:  2.02 (0.17), residues: 874
  sheet: -2.43 (0.78), residues: 36
  loop : -1.97 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 682 
 TYR   0.016   0.001   TYR B 576 
 PHE   0.032   0.001   PHE B 451 
 TRP   0.044   0.001   TRP B 525 
 HIS   0.006   0.001   HIS B 232 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (10440)
  covalent geometry    : angle       0.66907 (14200)
  hydrogen bonds       : bond        0.03393 (  691)
  hydrogen bonds       : angle       4.24780 ( 2049)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1668.91 seconds
wall clock time: 29 minutes 34.47 seconds (1774.47 seconds total)