Starting phenix.real_space_refine
on Fri Mar 14 00:26:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ygs_39261/03_2025/8ygs_39261_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ygs_39261/03_2025/8ygs_39261.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ygs_39261/03_2025/8ygs_39261.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ygs_39261/03_2025/8ygs_39261.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ygs_39261/03_2025/8ygs_39261_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ygs_39261/03_2025/8ygs_39261_neut.cif"
  }
  resolution = 3.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.033
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      26      5.16       5
     C    5920      2.51       5
     N    1555      2.21       5
     O    1790      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9291
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 2158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 274, 2158
          Classifications: {'peptide': 274}
          Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 259}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2049
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 260, 2049
          Classifications: {'peptide': 260}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 246}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 1675
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 210, 1675
          Classifications: {'peptide': 210}
          Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 202}
    Chain: "H"
      Number of atoms: 884
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 114, 884
          Classifications: {'peptide': 114}
          Link IDs: {'PTRANS': 4, 'TRANS': 109}
    Chain: "L"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 818
          Classifications: {'peptide': 107}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "M"
      Number of atoms: 899
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 116, 899
          Classifications: {'peptide': 116}
          Link IDs: {'PTRANS': 4, 'TRANS': 111}
    Chain: "N"
      Number of atoms: 808
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 808
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
  Residues with excluded nonbonded symmetry interactions: 18
    residue:
      pdb=" N   SER H  17 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER H  17 " occ=0.50
    residue:
      pdb=" N   SER H  61 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER H  61 " occ=0.50
    residue:
      pdb=" N   MET L  11 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET L  11 " occ=0.50
    residue:
      pdb=" N   ARG L  18 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG L  18 " occ=0.50
    residue:
      pdb=" N   GLN L  27 " occ=0.83
      ... (7 atoms not shown)
      pdb=" NE2 GLN L  27 " occ=0.83
    residue:
      pdb=" N   SER L  43 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER L  43 " occ=0.50
    residue:
      pdb=" N   SER L  50 " occ=0.90
      ... (4 atoms not shown)
      pdb=" OG  SER L  50 " occ=0.90
    residue:
      pdb=" N   SER L  67 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER L  67 " occ=0.50
    residue:
      pdb=" N   GLU L 105 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU L 105 " occ=0.50
    residue:
      pdb=" N   SER M  17 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER M  17 " occ=0.50
    residue:
      pdb=" N   SER M  61 " occ=0.50
      ... (4 atoms not shown)
      pdb=" OG  SER M  61 " occ=0.50
    residue:
      pdb=" N   MET N  11 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CE  MET N  11 " occ=0.50
    ... (remaining 6 not shown)
  Time building chain proxies: 6.18, per 1000 atoms: 0.67
  Number of scatterers: 9291
  At special positions: 0
  Unit cell: (108, 130, 131, 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      26     16.00
     O    1790      8.00
     N    1555      7.00
     C    5920      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.28
    Simple disulfide: pdb=" SG  CYS M  22 " - pdb=" SG  CYS M  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N  23 " - pdb=" SG  CYS N  88 " distance=2.28

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 2.16
  Conformation dependent library (CDL) restraints added in 1.6 seconds
  

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2186

  Finding SS restraints...
    Secondary structure from input PDB file:
      7 helices and 22 sheets defined
      3.0% alpha, 37.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 360 through 365
      removed outlier: 3.539A  pdb=" N   VAL A 365 " --> pdb=" O   PHE A 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 359 through 364
      removed outlier: 3.880A  pdb=" N   ARG B 363 " --> pdb=" O   SER B 359 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 360 through 364
    Processing helix  chain 'H' and resid 61 through 65
      removed outlier: 4.314A  pdb=" N   SER H  65 " --> pdb=" O   ALA H  62 " (cutoff:3.500A)
    Processing helix  chain 'M' and resid 73 through 76
    Processing helix  chain 'M' and resid 86 through 90
    Processing helix  chain 'N' and resid 79 through 83
    Processing sheet with id=AA1, first strand: chain 'A' and resid 33 through 34
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 33 through 34
    current: chain 'C' and resid 290 through 296
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 290 through 296
    current: chain 'C' and resid 338 through 345
    Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 50
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 48 through 50
    current: chain 'A' and resid 311 through 321
      removed outlier: 3.556A  pdb=" N   TRP A 356 " --> pdb=" O   HIS A 315 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 350 through 357
    current: chain 'A' and resid 396 through 415
      removed outlier: 6.454A  pdb=" N   VAL A 396 " --> pdb=" O   LEU A 439 " (cutoff:3.500A)
      removed outlier: 4.443A  pdb=" N   LEU A 439 " --> pdb=" O   VAL A 396 " (cutoff:3.500A)
      removed outlier: 6.688A  pdb=" N   THR A 398 " --> pdb=" O   PHE A 437 " (cutoff:3.500A)
      removed outlier: 4.617A  pdb=" N   PHE A 437 " --> pdb=" O   THR A 398 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   GLY A 400 " --> pdb=" O   PRO A 435 " (cutoff:3.500A)
      removed outlier: 4.817A  pdb=" N   VAL A 402 " --> pdb=" O   GLU A 433 " (cutoff:3.500A)
      removed outlier: 6.113A  pdb=" N   GLU A 433 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 5.580A  pdb=" N   LEU A 404 " --> pdb=" O   ALA A 431 " (cutoff:3.500A)
      removed outlier: 6.856A  pdb=" N   ALA A 431 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   SER A 406 " --> pdb=" O   ARG A 429 " (cutoff:3.500A)
      removed outlier: 5.284A  pdb=" N   ARG A 429 " --> pdb=" O   SER A 406 " (cutoff:3.500A)
      removed outlier: 5.229A  pdb=" N   GLY A 408 " --> pdb=" O   ARG A 427 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 420 through 439
    current: chain 'B' and resid 311 through 321
  WARNING: can't find start of bonding for strands!
    previous: chain 'B' and resid 350 through 357
    current: chain 'B' and resid 401 through 415
      removed outlier: 5.233A  pdb=" N   VAL B 402 " --> pdb=" O   GLU B 433 " (cutoff:3.500A)
      removed outlier: 6.258A  pdb=" N   GLU B 433 " --> pdb=" O   VAL B 402 " (cutoff:3.500A)
      removed outlier: 5.748A  pdb=" N   LEU B 404 " --> pdb=" O   ALA B 431 " (cutoff:3.500A)
      removed outlier: 7.410A  pdb=" N   ALA B 431 " --> pdb=" O   LEU B 404 " (cutoff:3.500A)
      removed outlier: 5.308A  pdb=" N   SER B 406 " --> pdb=" O   ARG B 429 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   ARG B 429 " --> pdb=" O   SER B 406 " (cutoff:3.500A)
      removed outlier: 4.196A  pdb=" N   GLY B 408 " --> pdb=" O   ARG B 427 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 59 through 60
      removed outlier: 7.145A  pdb=" N   THR A  59 " --> pdb=" O   ASP B 325 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 275
      removed outlier: 6.825A  pdb=" N   LEU A 473 " --> pdb=" O   VAL A 368 " (cutoff:3.500A)
      removed outlier: 6.693A  pdb=" N   VAL A 368 " --> pdb=" O   LEU A 473 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 279 through 283
    Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 329
      removed outlier: 5.570A  pdb=" N   PHE A 328 " --> pdb=" O   SER A 340 " (cutoff:3.500A)
      removed outlier: 4.868A  pdb=" N   SER A 340 " --> pdb=" O   PHE A 328 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   ILE A 345 " --> pdb=" O   LEU A 450 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 262 through 275
      removed outlier: 6.709A  pdb=" N   ALA B 465 " --> pdb=" O   LEU B 375 " (cutoff:3.500A)
      removed outlier: 4.609A  pdb=" N   LEU B 375 " --> pdb=" O   ALA B 465 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   ARG B 467 " --> pdb=" O   ALA B 373 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   ALA B 373 " --> pdb=" O   ARG B 467 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   SER B 469 " --> pdb=" O   LEU B 371 " (cutoff:3.500A)
      removed outlier: 4.315A  pdb=" N   LEU B 371 " --> pdb=" O   SER B 469 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   ILE B 471 " --> pdb=" O   ARG B 369 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 279 through 283
      removed outlier: 6.434A  pdb=" N   THR B 280 " --> pdb=" O   ILE B 294 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE B 294 " --> pdb=" O   THR B 280 " (cutoff:3.500A)
      removed outlier: 6.593A  pdb=" N   ILE B 282 " --> pdb=" O   SER B 292 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 384 through 386
    Processing sheet with id=AB1, first strand: chain 'C' and resid 266 through 275
      removed outlier: 4.052A  pdb=" N   SER C 370 " --> pdb=" O   ILE C 471 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 307
      removed outlier: 6.091A  pdb=" N   ASP C 357 " --> pdb=" O   ASN C 422 " (cutoff:3.500A)
      removed outlier: 8.011A  pdb=" N   ASN C 422 " --> pdb=" O   ASP C 357 " (cutoff:3.500A)
      removed outlier: 4.681A  pdb=" N   GLY C 408 " --> pdb=" O   ARG C 427 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   ARG C 429 " --> pdb=" O   SER C 406 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   SER C 406 " --> pdb=" O   ARG C 429 " (cutoff:3.500A)
      removed outlier: 6.803A  pdb=" N   ALA C 431 " --> pdb=" O   LEU C 404 " (cutoff:3.500A)
      removed outlier: 5.462A  pdb=" N   LEU C 404 " --> pdb=" O   ALA C 431 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   VAL C 378 " --> pdb=" O   LEU C 404 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'C' and resid 384 through 386
    Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 5
    Processing sheet with id=AB5, first strand: chain 'H' and resid 34 through 39
      removed outlier: 3.714A  pdb=" N   GLY H  49 " --> pdb=" O   TRP H  36 " (cutoff:3.500A)
      removed outlier: 6.658A  pdb=" N   ARG H  38 " --> pdb=" O   TRP H  47 " (cutoff:3.500A)
      removed outlier: 5.775A  pdb=" N   TRP H  47 " --> pdb=" O   ARG H  38 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'H' and resid 57 through 59
    current: chain 'H' and resid 104 through 107
    Processing sheet with id=AB6, first strand: chain 'L' and resid 4 through 6
      removed outlier: 4.007A  pdb=" N   ASP L  70 " --> pdb=" O   SER L  67 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'L' and resid 10 through 12
    Processing sheet with id=AB8, first strand: chain 'M' and resid 11 through 12
    Processing sheet with id=AB9, first strand: chain 'M' and resid 19 through 20
      removed outlier: 3.935A  pdb=" N   GLN M  77 " --> pdb=" O   ASP M  72 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'M' and resid 33 through 39
      removed outlier: 3.730A  pdb=" N   GLY M  49 " --> pdb=" O   TRP M  36 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ARG M  38 " --> pdb=" O   TRP M  47 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   TRP M  47 " --> pdb=" O   ARG M  38 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'M' and resid 57 through 59
    current: chain 'M' and resid 104 through 107
    Processing sheet with id=AC2, first strand: chain 'N' and resid 4 through 6
      removed outlier: 4.113A  pdb=" N   ASP N  70 " --> pdb=" O   SER N  67 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'N' and resid 10 through 12
      removed outlier: 6.455A  pdb=" N   MET N  11 " --> pdb=" O   GLU N 105 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC3
    Processing sheet with id=AC4, first strand: chain 'N' and resid 45 through 48
      removed outlier: 6.420A  pdb=" N   TRP N  35 " --> pdb=" O   LEU N  47 " (cutoff:3.500A)

    230 hydrogen bonds defined for protein.
    585 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.35

  Time building geometry restraints manager: 2.58 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1496
        1.28 -     1.41: 2580
        1.41 -     1.55: 5358
        1.55 -     1.68: 53
        1.68 -     1.81: 38
  Bond restraints: 9525
  Sorted by residual:
  bond pdb=" C   ILE M  20 "
       pdb=" O   ILE M  20 "
    ideal  model  delta    sigma   weight residual
    1.235  1.144  0.091 9.90e-03 1.02e+04 8.39e+01
  bond pdb=" CA  VAL A  33 "
       pdb=" C   VAL A  33 "
    ideal  model  delta    sigma   weight residual
    1.525  1.450  0.075 1.22e-02 6.72e+03 3.76e+01
  bond pdb=" CA  LYS H  64 "
       pdb=" C   LYS H  64 "
    ideal  model  delta    sigma   weight residual
    1.523  1.444  0.079 1.30e-02 5.92e+03 3.73e+01
  bond pdb=" CA  ASN H  60 "
       pdb=" C   ASN H  60 "
    ideal  model  delta    sigma   weight residual
    1.524  1.445  0.078 1.33e-02 5.65e+03 3.46e+01
  bond pdb=" CA  VAL A  33 "
       pdb=" CB  VAL A  33 "
    ideal  model  delta    sigma   weight residual
    1.540  1.477  0.063 1.10e-02 8.26e+03 3.29e+01
  ... (remaining 9520 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.20: 12310
        3.20 -     6.41: 563
        6.41 -     9.61: 65
        9.61 -    12.81: 12
       12.81 -    16.01: 3
  Bond angle restraints: 12953
  Sorted by residual:
  angle pdb=" N   VAL L  58 "
        pdb=" CA  VAL L  58 "
        pdb=" C   VAL L  58 "
      ideal   model   delta    sigma   weight residual
     109.19   97.67   11.52 8.20e-01 1.49e+00 1.97e+02
  angle pdb=" N   SER B 445 "
        pdb=" CA  SER B 445 "
        pdb=" C   SER B 445 "
      ideal   model   delta    sigma   weight residual
     109.62  125.63  -16.01 1.50e+00 4.44e-01 1.14e+02
  angle pdb=" N   SER L   7 "
        pdb=" CA  SER L   7 "
        pdb=" C   SER L   7 "
      ideal   model   delta    sigma   weight residual
     111.07  122.41  -11.34 1.07e+00 8.73e-01 1.12e+02
  angle pdb=" N   ALA B  41 "
        pdb=" CA  ALA B  41 "
        pdb=" C   ALA B  41 "
      ideal   model   delta    sigma   weight residual
     110.53  123.67  -13.14 1.32e+00 5.74e-01 9.91e+01
  angle pdb=" CA  ASP A 354 "
        pdb=" C   ASP A 354 "
        pdb=" O   ASP A 354 "
      ideal   model   delta    sigma   weight residual
     121.87  111.81   10.06 1.16e+00 7.43e-01 7.53e+01
  ... (remaining 12948 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.08: 5151
       17.08 -    34.17: 340
       34.17 -    51.25: 47
       51.25 -    68.34: 15
       68.34 -    85.42: 6
  Dihedral angle restraints: 5559
    sinusoidal: 2133
      harmonic: 3426
  Sorted by residual:
  dihedral pdb=" C   SER H  65 "
           pdb=" N   SER H  65 "
           pdb=" CA  SER H  65 "
           pdb=" CB  SER H  65 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -151.24   28.64     0      2.50e+00 1.60e-01 1.31e+02
  dihedral pdb=" C   ALA B  41 "
           pdb=" N   ALA B  41 "
           pdb=" CA  ALA B  41 "
           pdb=" CB  ALA B  41 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -151.14   28.54     0      2.50e+00 1.60e-01 1.30e+02
  dihedral pdb=" N   ALA B  41 "
           pdb=" C   ALA B  41 "
           pdb=" CA  ALA B  41 "
           pdb=" CB  ALA B  41 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.90  151.17  -28.27     0      2.50e+00 1.60e-01 1.28e+02
  ... (remaining 5556 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.255: 1403
       0.255 -    0.510: 18
       0.510 -    0.765: 0
       0.765 -    1.020: 0
       1.020 -    1.275: 5
  Chirality restraints: 1426
  Sorted by residual:
  chirality pdb=" CA  SER H  65 "
            pdb=" N   SER H  65 "
            pdb=" C   SER H  65 "
            pdb=" CB  SER H  65 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.24    1.28 2.00e-01 2.50e+01 4.06e+01
  chirality pdb=" CA  ALA B  41 "
            pdb=" N   ALA B  41 "
            pdb=" C   ALA B  41 "
            pdb=" CB  ALA B  41 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.23    1.25 2.00e-01 2.50e+01 3.91e+01
  chirality pdb=" CB  THR A  34 "
            pdb=" CA  THR A  34 "
            pdb=" OG1 THR A  34 "
            pdb=" CG2 THR A  34 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    1.30    1.25 2.00e-01 2.50e+01 3.89e+01
  ... (remaining 1423 not shown)

  Planarity restraints: 1660
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE C 342 "   -0.019 2.00e-02 2.50e+03   3.82e-02 1.46e+01
        pdb=" C   PHE C 342 "    0.066 2.00e-02 2.50e+03
        pdb=" O   PHE C 342 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   GLU C 343 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 354 "   -0.018 2.00e-02 2.50e+03   3.74e-02 1.40e+01
        pdb=" C   ASP A 354 "    0.065 2.00e-02 2.50e+03
        pdb=" O   ASP A 354 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   TYR A 355 "   -0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER C 412 "    0.017 2.00e-02 2.50e+03   3.35e-02 1.12e+01
        pdb=" C   SER C 412 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   SER C 412 "    0.022 2.00e-02 2.50e+03
        pdb=" N   THR C 413 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1657 not shown)

  Histogram of nonbonded interaction distances:
        2.32 -     2.84: 3049
        2.84 -     3.35: 7880
        3.35 -     3.87: 13950
        3.87 -     4.38: 16150
        4.38 -     4.90: 28975
  Nonbonded interactions: 70004
  Sorted by model distance:
  nonbonded pdb=" N   ASN H  60 "
            pdb=" O   ASN H  60 "
     model   vdw
     2.320 2.496
  nonbonded pdb=" N   SER L  50 "
            pdb=" O   SER L  50 "
     model   vdw
     2.329 2.496
  nonbonded pdb=" OE1 GLN B 266 "
            pdb=" OG  SER H  56 "
     model   vdw
     2.334 3.040
  nonbonded pdb=" OD1 ASP B  57 "
            pdb=" N   SER B  58 "
     model   vdw
     2.389 3.120
  nonbonded pdb=" O   ASN C 300 "
            pdb=" OD1 ASN C 300 "
     model   vdw
     2.389 3.040
  ... (remaining 69999 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 32 through 476)
  selection = chain 'B'
}
ncs_group {
  reference = chain 'H'
  selection = (chain 'M' and resid 2 through 115)
}
ncs_group {
  reference = (chain 'L' and resid 1 through 106)
  selection = chain 'N'
}

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=0.50 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.020
  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:          0.360
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     23.880
  Find NCS groups from input model:        0.270
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.870
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
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      :  0.011   0.091   9525  Z= 0.699
  Angle     :  1.471  16.013  12953  Z= 0.983
  Chirality :  0.112   1.275   1426
  Planarity :  0.007   0.084   1660
  Dihedral  : 11.765  85.422   3361
  Min Nonbonded Distance : 2.320

Molprobity Statistics.
  All-atom Clashscore : 2.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.90 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.46 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.41 (0.21), residues: 1169
  helix: -2.90 (1.13), residues: 12
  sheet: -1.68 (0.21), residues: 521
  loop : -2.81 (0.19), residues: 636

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.002   TRP B 356 
 HIS   0.013   0.003   HIS A 436 
 PHE   0.031   0.003   PHE A 437 
 TYR   0.022   0.002   TYR C 355 
 ARG   0.007   0.001   ARG L  54 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 262
  time to evaluate  : 0.964 
Fit side-chains
   revert: symmetry clash
REVERT: A   42 GLN cc_start: 0.7361 (mm110) cc_final: 0.7088 (mm-40)
REVERT: A   49 ASN cc_start: 0.6692 (t0) cc_final: 0.6435 (p0)
REVERT: A  254 ILE cc_start: 0.7512 (mm) cc_final: 0.7173 (mm)
REVERT: A  256 ILE cc_start: 0.7300 (tt) cc_final: 0.6868 (pt)
REVERT: A  267 TYR cc_start: 0.6885 (m-80) cc_final: 0.6658 (m-80)
REVERT: A  274 ARG cc_start: 0.6968 (mtt180) cc_final: 0.6351 (mtp85)
REVERT: A  326 PHE cc_start: 0.6673 (m-80) cc_final: 0.6093 (m-80)
REVERT: A  474 VAL cc_start: 0.6921 (t) cc_final: 0.6380 (m)
REVERT: B   55 ILE cc_start: 0.7041 (pt) cc_final: 0.6633 (mt)
REVERT: B  281 ILE cc_start: 0.7114 (pt) cc_final: 0.6820 (mt)
REVERT: B  282 ILE cc_start: 0.7453 (pt) cc_final: 0.7237 (pt)
REVERT: B  352 TYR cc_start: 0.7375 (m-10) cc_final: 0.7157 (m-10)
REVERT: B  378 VAL cc_start: 0.8251 (p) cc_final: 0.7757 (m)
REVERT: B  412 SER cc_start: 0.7134 (p) cc_final: 0.6823 (m)
REVERT: C  289 TYR cc_start: 0.6859 (m-80) cc_final: 0.6557 (m-80)
REVERT: C  303 TYR cc_start: 0.7909 (p90) cc_final: 0.6799 (p90)
REVERT: C  305 TYR cc_start: 0.7807 (p90) cc_final: 0.7423 (p90)
REVERT: C  329 ASN cc_start: 0.7430 (t0) cc_final: 0.7090 (t0)
REVERT: C  441 ARG cc_start: 0.7489 (ttt90) cc_final: 0.7202 (ttt90)
REVERT: C  469 SER cc_start: 0.7416 (m) cc_final: 0.7178 (t)
REVERT: H   19 SER cc_start: 0.7003 (p) cc_final: 0.6799 (m)
REVERT: H   58 ASP cc_start: 0.6753 (t70) cc_final: 0.6374 (t70)
REVERT: M   33 SER cc_start: 0.7040 (p) cc_final: 0.6448 (t)
REVERT: M   50 MET cc_start: 0.7173 (ttt) cc_final: 0.6907 (ttt)
REVERT: M   68 SER cc_start: 0.6942 (m) cc_final: 0.6276 (p)
REVERT: N   79 GLN cc_start: 0.7310 (mt0) cc_final: 0.6917 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 262
  average time/residue: 0.1696
  time to fit residues: 65.2912
Evaluate side-chains
  175 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 175
  time to evaluate  : 0.999 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 97 optimal weight:    0.5980
   chunk 87 optimal weight:    3.9990
   chunk 48 optimal weight:    0.8980
   chunk 30 optimal weight:    0.0670
   chunk 59 optimal weight:    0.7980
   chunk 46 optimal weight:    0.8980
   chunk 90 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9980
   chunk 67 optimal weight:    2.9990
   chunk 105 optimal weight:    0.5980
   overall best weight:    0.5318

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
B 300 ASN
B 376 ASN
B 454 ASN
C 324 ASN
H  53 ASN
H  98 ASN
L   6 GLN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.116479 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3228 r_free = 0.3228 target = 0.102215 restraints weight = 15125.547|
|-----------------------------------------------------------------------------|
r_work (start): 0.3261 rms_B_bonded: 2.13
r_work: 0.3157 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.3018 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3016
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3016 r_free = 0.3016    target_work(ls_wunit_k1) = 0.089         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3001 r_free = 0.3001    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3001
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7501
moved from start:          0.2289

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9525  Z= 0.193
  Angle     :  0.624   7.436  12953  Z= 0.332
  Chirality :  0.046   0.167   1426
  Planarity :  0.004   0.045   1660
  Dihedral  :  5.214  21.308   1291
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 4.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  :  6.91 %
    Favored  : 90.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.52 (0.22), residues: 1169
  helix: -4.10 (0.72), residues: 12
  sheet: -0.99 (0.22), residues: 530
  loop : -2.27 (0.20), residues: 627

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 356 
 HIS   0.005   0.002   HIS B 436 
 PHE   0.023   0.002   PHE M  27 
 TYR   0.021   0.001   TYR L  92 
 ARG   0.008   0.001   ARG B 363 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 216
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
REVERT: A   49 ASN cc_start: 0.7969 (t0) cc_final: 0.7753 (t0)
REVERT: A  254 ILE cc_start: 0.8458 (mm) cc_final: 0.8248 (mm)
REVERT: A  256 ILE cc_start: 0.8226 (tt) cc_final: 0.8011 (pt)
REVERT: A  316 THR cc_start: 0.8405 (p) cc_final: 0.8049 (m)
REVERT: A  323 VAL cc_start: 0.8726 (p) cc_final: 0.8427 (m)
REVERT: A  369 ARG cc_start: 0.7998 (ttp80) cc_final: 0.7664 (ttt90)
REVERT: A  474 VAL cc_start: 0.7667 (t) cc_final: 0.7292 (m)
REVERT: B   55 ILE cc_start: 0.7778 (pt) cc_final: 0.7356 (mm)
REVERT: B  257 SER cc_start: 0.8188 (m) cc_final: 0.7590 (p)
REVERT: B  265 MET cc_start: 0.8265 (mtp) cc_final: 0.7986 (mtp)
REVERT: B  282 ILE cc_start: 0.8417 (pt) cc_final: 0.8044 (mt)
REVERT: B  326 PHE cc_start: 0.8236 (m-80) cc_final: 0.7883 (m-80)
REVERT: B  338 VAL cc_start: 0.8599 (t) cc_final: 0.8251 (p)
REVERT: B  378 VAL cc_start: 0.8779 (p) cc_final: 0.8392 (m)
REVERT: B  421 LEU cc_start: 0.7617 (tt) cc_final: 0.7405 (tp)
REVERT: C  303 TYR cc_start: 0.8341 (p90) cc_final: 0.7887 (p90)
REVERT: C  305 TYR cc_start: 0.8476 (p90) cc_final: 0.8155 (p90)
REVERT: C  307 ARG cc_start: 0.8207 (ttp-170) cc_final: 0.7875 (tmm160)
REVERT: C  344 VAL cc_start: 0.8261 (OUTLIER) cc_final: 0.7691 (m)
REVERT: C  355 TYR cc_start: 0.8205 (t80) cc_final: 0.7606 (t80)
REVERT: C  376 ASN cc_start: 0.7815 (m110) cc_final: 0.7514 (m-40)
REVERT: C  391 VAL cc_start: 0.7820 (t) cc_final: 0.7609 (p)
REVERT: C  432 VAL cc_start: 0.8044 (p) cc_final: 0.7695 (m)
REVERT: L   52 SER cc_start: 0.8230 (p) cc_final: 0.7933 (m)
REVERT: M   33 SER cc_start: 0.8119 (p) cc_final: 0.7713 (t)
  outliers start: 26
  outliers final: 22
  residues processed: 230
  average time/residue: 0.2110
  time to fit residues: 67.2397
Evaluate side-chains
  205 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 182
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  340 SER
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain A residue  489 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  317 THR
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   56 SER
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain M residue   61 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   76 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 50 optimal weight:    1.9990
   chunk 67 optimal weight:    0.2980
   chunk 59 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 112 optimal weight:    8.9990
   chunk 2 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   chunk 81 optimal weight:    5.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    1.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 454 ASN
C 456 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  79 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.108697 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.094331 restraints weight = 15193.637|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.07
r_work: 0.2990 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2850 rms_B_bonded: 4.33 restraints_weight: 0.2500
r_work (final): 0.2850
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2852
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.37   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2852 r_free = 0.2852    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2852
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7637
moved from start:          0.3831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.076   9525  Z= 0.417
  Angle     :  0.744   8.118  12953  Z= 0.396
  Chirality :  0.050   0.188   1426
  Planarity :  0.005   0.044   1660
  Dihedral  :  5.917  21.146   1291
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.36 %
    Favored  : 95.64 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 10.12 %
    Favored  : 85.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.33 (0.22), residues: 1169
  helix: -3.53 (1.16), residues: 12
  sheet: -0.76 (0.21), residues: 539
  loop : -2.28 (0.20), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 356 
 HIS   0.011   0.003   HIS N  91 
 PHE   0.023   0.003   PHE B 428 
 TYR   0.028   0.002   TYR M  94 
 ARG   0.005   0.001   ARG B 363 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 162
  time to evaluate  : 1.007 
Fit side-chains
REVERT: B  257 SER cc_start: 0.8331 (m) cc_final: 0.7745 (p)
REVERT: B  282 ILE cc_start: 0.8420 (pt) cc_final: 0.8103 (mt)
REVERT: B  338 VAL cc_start: 0.8641 (t) cc_final: 0.8396 (p)
REVERT: B  378 VAL cc_start: 0.8785 (p) cc_final: 0.8440 (m)
REVERT: B  424 LEU cc_start: 0.7922 (tt) cc_final: 0.7618 (tp)
REVERT: C  274 ARG cc_start: 0.8269 (mtt180) cc_final: 0.7920 (mtt180)
REVERT: C  280 THR cc_start: 0.8026 (OUTLIER) cc_final: 0.7755 (p)
REVERT: C  305 TYR cc_start: 0.8512 (p90) cc_final: 0.8194 (p90)
REVERT: C  344 VAL cc_start: 0.8296 (OUTLIER) cc_final: 0.7723 (m)
REVERT: C  349 SER cc_start: 0.8164 (OUTLIER) cc_final: 0.7939 (p)
REVERT: C  440 THR cc_start: 0.8455 (m) cc_final: 0.7918 (p)
REVERT: M   50 MET cc_start: 0.8006 (ttp) cc_final: 0.7196 (ttp)
REVERT: M   68 SER cc_start: 0.7940 (OUTLIER) cc_final: 0.7480 (p)
REVERT: N    5 THR cc_start: 0.7837 (OUTLIER) cc_final: 0.7469 (m)
  outliers start: 46
  outliers final: 34
  residues processed: 191
  average time/residue: 0.2152
  time to fit residues: 57.2269
Evaluate side-chains
  187 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 148
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  406 SER
Chi-restraints excluded: chain A residue  421 LEU
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  280 THR
Chi-restraints excluded: chain B residue  311 GLU
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  338 VAL
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  469 SER
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   58 ASP
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain M residue   61 SER
Chi-restraints excluded: chain M residue   68 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   79 PHE
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 88 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   chunk 2 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 56 optimal weight:    1.9990
   chunk 100 optimal weight:    1.9990
   chunk 94 optimal weight:    0.8980
   chunk 33 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9980
   chunk 97 optimal weight:    4.9990
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
C 324 ASN
** L  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  79 GLN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.109538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.094931 restraints weight = 15107.522|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.13
r_work: 0.2998 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.2855 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2855 r_free = 0.2855    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2856 r_free = 0.2856    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2856
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.4208

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   9525  Z= 0.295
  Angle     :  0.637   8.583  12953  Z= 0.339
  Chirality :  0.046   0.155   1426
  Planarity :  0.004   0.050   1660
  Dihedral  :  5.504  19.504   1291
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 11.96 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.90 (0.22), residues: 1169
  helix: -3.55 (1.03), residues: 12
  sheet: -0.46 (0.22), residues: 535
  loop : -1.98 (0.21), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 356 
 HIS   0.006   0.002   HIS N  91 
 PHE   0.018   0.002   PHE A 342 
 TYR   0.017   0.002   TYR B 355 
 ARG   0.006   0.001   ARG C 446 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  208 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 160
  time to evaluate  : 1.045 
Fit side-chains
   revert: symmetry clash
REVERT: B  257 SER cc_start: 0.8307 (m) cc_final: 0.7763 (p)
REVERT: B  265 MET cc_start: 0.8090 (mmm) cc_final: 0.7862 (mmm)
REVERT: B  268 ASN cc_start: 0.7793 (t0) cc_final: 0.7520 (m-40)
REVERT: B  282 ILE cc_start: 0.8463 (pt) cc_final: 0.8117 (mt)
REVERT: B  338 VAL cc_start: 0.8618 (t) cc_final: 0.8345 (p)
REVERT: B  378 VAL cc_start: 0.8737 (p) cc_final: 0.8422 (m)
REVERT: B  424 LEU cc_start: 0.7920 (tt) cc_final: 0.7617 (tp)
REVERT: C  274 ARG cc_start: 0.8256 (mtt180) cc_final: 0.7942 (mtt180)
REVERT: C  280 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7797 (p)
REVERT: C  305 TYR cc_start: 0.8475 (p90) cc_final: 0.8131 (p90)
REVERT: C  344 VAL cc_start: 0.8339 (OUTLIER) cc_final: 0.7773 (m)
REVERT: C  349 SER cc_start: 0.8140 (OUTLIER) cc_final: 0.7882 (p)
REVERT: C  440 THR cc_start: 0.8451 (m) cc_final: 0.7929 (p)
REVERT: M   50 MET cc_start: 0.8056 (ttp) cc_final: 0.7310 (ttp)
REVERT: M   68 SER cc_start: 0.7926 (m) cc_final: 0.7473 (p)
REVERT: N   11 MET cc_start: 0.6722 (mmm) cc_final: 0.5697 (mtt)
REVERT: N   98 PHE cc_start: 0.8395 (m-10) cc_final: 0.8174 (m-80)
  outliers start: 48
  outliers final: 37
  residues processed: 189
  average time/residue: 0.2122
  time to fit residues: 55.9087
Evaluate side-chains
  186 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 146
  time to evaluate  : 1.038 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue  260 SER
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  358 ASP
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  311 GLU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  348 ASN
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain C residue  434 GLU
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   61 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   79 PHE
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 1 optimal weight:    0.9990
   chunk 109 optimal weight:    0.6980
   chunk 23 optimal weight:    0.0770
   chunk 78 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 74 optimal weight:    3.9990
   chunk 42 optimal weight:    0.7980
   chunk 11 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.6738

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

Flipped N/Q/H residues before XYZ refinement:
A 315 HIS
B 300 ASN
B 364 ASN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.110856 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.096133 restraints weight = 15056.477|
|-----------------------------------------------------------------------------|
r_work (start): 0.3124 rms_B_bonded: 2.15
r_work: 0.3015 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2862
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2862 r_free = 0.2862    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2862
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7613
moved from start:          0.4418

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9525  Z= 0.187
  Angle     :  0.565   7.716  12953  Z= 0.300
  Chirality :  0.044   0.283   1426
  Planarity :  0.004   0.055   1660
  Dihedral  :  5.107  20.662   1291
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 4.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 13.33 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.62 (0.23), residues: 1169
  helix: -2.96 (1.15), residues: 12
  sheet: -0.30 (0.22), residues: 533
  loop : -1.77 (0.21), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 356 
 HIS   0.005   0.001   HIS N  91 
 PHE   0.018   0.002   PHE H  27 
 TYR   0.018   0.001   TYR A 305 
 ARG   0.011   0.001   ARG C 441 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  196 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 154
  time to evaluate  : 0.984 
Fit side-chains
REVERT: A  457 ASN cc_start: 0.8336 (t0) cc_final: 0.8098 (t0)
REVERT: B   42 GLN cc_start: 0.8527 (mm-40) cc_final: 0.8272 (mm-40)
REVERT: B  257 SER cc_start: 0.8324 (m) cc_final: 0.7774 (p)
REVERT: B  265 MET cc_start: 0.7997 (OUTLIER) cc_final: 0.7768 (mmm)
REVERT: B  282 ILE cc_start: 0.8468 (pt) cc_final: 0.8126 (mt)
REVERT: B  338 VAL cc_start: 0.8619 (t) cc_final: 0.8337 (p)
REVERT: B  378 VAL cc_start: 0.8735 (p) cc_final: 0.8423 (m)
REVERT: B  424 LEU cc_start: 0.7898 (tt) cc_final: 0.7596 (tp)
REVERT: C  274 ARG cc_start: 0.8254 (mtt180) cc_final: 0.7927 (mtt180)
REVERT: C  280 THR cc_start: 0.8017 (OUTLIER) cc_final: 0.7807 (p)
REVERT: C  300 ASN cc_start: 0.8202 (OUTLIER) cc_final: 0.7899 (m-40)
REVERT: C  305 TYR cc_start: 0.8421 (p90) cc_final: 0.8073 (p90)
REVERT: C  344 VAL cc_start: 0.8344 (OUTLIER) cc_final: 0.7766 (m)
REVERT: C  349 SER cc_start: 0.8153 (OUTLIER) cc_final: 0.7933 (p)
REVERT: C  440 THR cc_start: 0.8429 (m) cc_final: 0.7906 (p)
REVERT: H   27 PHE cc_start: 0.8087 (p90) cc_final: 0.7826 (p90)
REVERT: M   50 MET cc_start: 0.8024 (ttp) cc_final: 0.7580 (ttp)
REVERT: M   68 SER cc_start: 0.7906 (m) cc_final: 0.7473 (p)
REVERT: N   11 MET cc_start: 0.6624 (mmm) cc_final: 0.5902 (mtt)
  outliers start: 42
  outliers final: 34
  residues processed: 181
  average time/residue: 0.2209
  time to fit residues: 55.1554
Evaluate side-chains
  193 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 154
  time to evaluate  : 1.080 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  311 GLU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  300 ASN
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  348 ASN
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   61 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   79 PHE
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 106 optimal weight:    4.9990
   chunk 66 optimal weight:    3.9990
   chunk 2 optimal weight:    0.5980
   chunk 99 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9980
   chunk 107 optimal weight:    0.0980
   chunk 64 optimal weight:    2.9990
   chunk 79 optimal weight:    1.9990
   chunk 101 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9990
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
B 300 ASN
B 364 ASN
C 324 ASN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.110312 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.095637 restraints weight = 15008.078|
|-----------------------------------------------------------------------------|
r_work (start): 0.3123 rms_B_bonded: 2.13
r_work: 0.3014 rms_B_bonded: 2.51 restraints_weight: 0.5000
r_work: 0.2872 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2859
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.56   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2859 r_free = 0.2859    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2859
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.4601

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   9525  Z= 0.200
  Angle     :  0.565   7.958  12953  Z= 0.300
  Chirality :  0.044   0.186   1426
  Planarity :  0.004   0.044   1660
  Dihedral  :  5.005  19.513   1291
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.67 %
    Allowed  : 13.42 %
    Favored  : 81.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.49 (0.23), residues: 1169
  helix: -2.73 (1.24), residues: 12
  sheet: -0.27 (0.22), residues: 537
  loop : -1.63 (0.21), residues: 620

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 356 
 HIS   0.006   0.002   HIS N  91 
 PHE   0.015   0.002   PHE B 468 
 TYR   0.015   0.001   TYR M  94 
 ARG   0.009   0.001   ARG A 441 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 150
  time to evaluate  : 1.054 
Fit side-chains
REVERT: A   61 VAL cc_start: 0.8356 (t) cc_final: 0.8133 (m)
REVERT: A  457 ASN cc_start: 0.8379 (t0) cc_final: 0.8124 (t0)
REVERT: B   42 GLN cc_start: 0.8533 (mm-40) cc_final: 0.8277 (mm-40)
REVERT: B   55 ILE cc_start: 0.7852 (pt) cc_final: 0.7600 (mm)
REVERT: B  257 SER cc_start: 0.8336 (m) cc_final: 0.7814 (p)
REVERT: B  265 MET cc_start: 0.7987 (OUTLIER) cc_final: 0.7751 (mmm)
REVERT: B  274 ARG cc_start: 0.8614 (OUTLIER) cc_final: 0.8359 (mtt180)
REVERT: B  282 ILE cc_start: 0.8466 (pt) cc_final: 0.8143 (mt)
REVERT: B  338 VAL cc_start: 0.8620 (t) cc_final: 0.8341 (p)
REVERT: B  378 VAL cc_start: 0.8719 (p) cc_final: 0.8413 (m)
REVERT: B  424 LEU cc_start: 0.7934 (tt) cc_final: 0.7622 (tp)
REVERT: C  274 ARG cc_start: 0.8277 (mtt180) cc_final: 0.7964 (mtt180)
REVERT: C  280 THR cc_start: 0.8067 (OUTLIER) cc_final: 0.7829 (p)
REVERT: C  305 TYR cc_start: 0.8418 (p90) cc_final: 0.8079 (p90)
REVERT: C  344 VAL cc_start: 0.8364 (OUTLIER) cc_final: 0.7808 (m)
REVERT: C  349 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7851 (p)
REVERT: H   27 PHE cc_start: 0.8111 (p90) cc_final: 0.7911 (p90)
REVERT: M   50 MET cc_start: 0.8017 (ttp) cc_final: 0.7594 (ttp)
REVERT: M   68 SER cc_start: 0.7896 (m) cc_final: 0.7465 (p)
REVERT: N   11 MET cc_start: 0.6599 (mmm) cc_final: 0.5995 (mtt)
  outliers start: 48
  outliers final: 39
  residues processed: 181
  average time/residue: 0.2172
  time to fit residues: 54.2382
Evaluate side-chains
  191 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 147
  time to evaluate  : 1.077 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  311 GLU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  348 ASN
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain M residue   61 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   79 PHE
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 35 optimal weight:    0.5980
   chunk 87 optimal weight:    2.9990
   chunk 94 optimal weight:    1.9990
   chunk 59 optimal weight:    0.9980
   chunk 33 optimal weight:    0.7980
   chunk 12 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 107 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0060
   chunk 82 optimal weight:    3.9990
   chunk 68 optimal weight:    4.9990
   overall best weight:    0.8798

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
B 364 ASN
C 324 ASN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.110007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.095328 restraints weight = 15093.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.3110 rms_B_bonded: 2.14
r_work: 0.3001 rms_B_bonded: 2.53 restraints_weight: 0.5000
r_work: 0.2858 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.2858
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2850
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.54   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2850 r_free = 0.2850    target_work(ls_wunit_k1) = 0.080         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2850
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.4771

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   9525  Z= 0.226
  Angle     :  0.585   9.249  12953  Z= 0.310
  Chirality :  0.044   0.156   1426
  Planarity :  0.004   0.042   1660
  Dihedral  :  5.069  18.318   1291
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  4.96 %
    Allowed  : 13.42 %
    Favored  : 81.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.23), residues: 1169
  helix: -2.93 (1.14), residues: 12
  sheet: -0.20 (0.22), residues: 560
  loop : -1.70 (0.22), residues: 597

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 356 
 HIS   0.006   0.002   HIS N  91 
 PHE   0.017   0.002   PHE B 468 
 TYR   0.015   0.002   TYR A 301 
 ARG   0.008   0.001   ARG A 441 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  198 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 147
  time to evaluate  : 0.972 
Fit side-chains
REVERT: A   61 VAL cc_start: 0.8406 (t) cc_final: 0.8198 (m)
REVERT: A  290 LYS cc_start: 0.8503 (ptpt) cc_final: 0.8282 (ptmt)
REVERT: A  447 LEU cc_start: 0.7680 (mt) cc_final: 0.7456 (mt)
REVERT: A  457 ASN cc_start: 0.8389 (t0) cc_final: 0.8133 (t0)
REVERT: B   34 THR cc_start: 0.8172 (m) cc_final: 0.7770 (p)
REVERT: B   42 GLN cc_start: 0.8509 (mm-40) cc_final: 0.8261 (mm-40)
REVERT: B   55 ILE cc_start: 0.7814 (pt) cc_final: 0.7612 (mm)
REVERT: B  257 SER cc_start: 0.8333 (m) cc_final: 0.7810 (p)
REVERT: B  265 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7790 (mmm)
REVERT: B  274 ARG cc_start: 0.8587 (OUTLIER) cc_final: 0.8328 (mtt180)
REVERT: B  282 ILE cc_start: 0.8475 (pt) cc_final: 0.8164 (mt)
REVERT: B  338 VAL cc_start: 0.8616 (t) cc_final: 0.8338 (p)
REVERT: B  378 VAL cc_start: 0.8757 (p) cc_final: 0.8441 (m)
REVERT: B  424 LEU cc_start: 0.7988 (tt) cc_final: 0.7674 (tp)
REVERT: C  274 ARG cc_start: 0.8296 (mtt180) cc_final: 0.7975 (mtt180)
REVERT: C  280 THR cc_start: 0.8088 (OUTLIER) cc_final: 0.7841 (p)
REVERT: C  300 ASN cc_start: 0.8152 (OUTLIER) cc_final: 0.7870 (m-40)
REVERT: C  305 TYR cc_start: 0.8413 (p90) cc_final: 0.8054 (p90)
REVERT: C  344 VAL cc_start: 0.8374 (OUTLIER) cc_final: 0.7852 (m)
REVERT: C  349 SER cc_start: 0.8096 (OUTLIER) cc_final: 0.7845 (p)
REVERT: C  440 THR cc_start: 0.8519 (m) cc_final: 0.7893 (p)
REVERT: C  441 ARG cc_start: 0.8168 (mtt180) cc_final: 0.7779 (mtt180)
REVERT: H   27 PHE cc_start: 0.8134 (p90) cc_final: 0.7913 (p90)
REVERT: M   68 SER cc_start: 0.7888 (m) cc_final: 0.7463 (p)
REVERT: N   11 MET cc_start: 0.6467 (mmm) cc_final: 0.6125 (mtt)
  outliers start: 51
  outliers final: 42
  residues processed: 181
  average time/residue: 0.2148
  time to fit residues: 53.6535
Evaluate side-chains
  188 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 140
  time to evaluate  : 0.957 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue   58 SER
Chi-restraints excluded: chain A residue   59 THR
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  338 VAL
Chi-restraints excluded: chain A residue  349 SER
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  265 MET
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  311 GLU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  300 ASN
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  348 ASN
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   49 SER
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain M residue   45 LEU
Chi-restraints excluded: chain M residue   61 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   79 PHE
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 112 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 35 optimal weight:    0.5980
   chunk 102 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 106 optimal weight:    5.9990
   chunk 7 optimal weight:    3.9990
   chunk 27 optimal weight:    3.9990
   chunk 30 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   overall best weight:    2.7188

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
B 300 ASN
B 364 ASN
** C 315 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 324 ASN
** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   8 HIS
N  79 GLN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3256 r_free = 0.3256 target = 0.104603 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.089796 restraints weight = 15606.127|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 2.22
r_work: 0.2920 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2772 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2772
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2776
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2776 r_free = 0.2776    target_work(ls_wunit_k1) = 0.076         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2776
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.5091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.010   0.072   9525  Z= 0.639
  Angle     :  0.842  17.162  12953  Z= 0.441
  Chirality :  0.053   0.185   1426
  Planarity :  0.005   0.039   1660
  Dihedral  :  6.369  22.348   1291
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.33 %
    Favored  : 93.67 %
  Rotamer:
    Outliers :  5.06 %
    Allowed  : 14.20 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.23), residues: 1169
  helix: -4.46 (0.74), residues: 6
  sheet: -0.58 (0.21), residues: 590
  loop : -2.07 (0.22), residues: 573

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.003   TRP A 262 
 HIS   0.012   0.003   HIS N  91 
 PHE   0.034   0.004   PHE A 342 
 TYR   0.026   0.003   TYR C 355 
 ARG   0.007   0.001   ARG B 274 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 151
  time to evaluate  : 0.983 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 VAL cc_start: 0.8507 (t) cc_final: 0.8184 (m)
REVERT: A  290 LYS cc_start: 0.8566 (ptpt) cc_final: 0.8326 (ptmt)
REVERT: A  337 PHE cc_start: 0.8317 (t80) cc_final: 0.8054 (t80)
REVERT: A  443 ARG cc_start: 0.5589 (mmp-170) cc_final: 0.4772 (mmm160)
REVERT: A  457 ASN cc_start: 0.8477 (t0) cc_final: 0.8223 (t0)
REVERT: B  257 SER cc_start: 0.8349 (m) cc_final: 0.7760 (p)
REVERT: B  274 ARG cc_start: 0.8628 (OUTLIER) cc_final: 0.8412 (mtt180)
REVERT: B  282 ILE cc_start: 0.8482 (pt) cc_final: 0.8200 (mt)
REVERT: B  370 SER cc_start: 0.8354 (t) cc_final: 0.8093 (m)
REVERT: B  378 VAL cc_start: 0.8807 (p) cc_final: 0.8456 (m)
REVERT: B  424 LEU cc_start: 0.8037 (tt) cc_final: 0.7712 (tp)
REVERT: B  456 ASN cc_start: 0.8011 (OUTLIER) cc_final: 0.7760 (p0)
REVERT: C  274 ARG cc_start: 0.8289 (mtt180) cc_final: 0.8073 (mtt180)
REVERT: C  300 ASN cc_start: 0.8220 (OUTLIER) cc_final: 0.7960 (m-40)
REVERT: C  344 VAL cc_start: 0.8395 (OUTLIER) cc_final: 0.7928 (m)
REVERT: C  440 THR cc_start: 0.8443 (m) cc_final: 0.7882 (p)
REVERT: C  470 LEU cc_start: 0.8271 (tt) cc_final: 0.7994 (tp)
REVERT: L   90 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7818 (tm-30)
REVERT: M   68 SER cc_start: 0.7930 (m) cc_final: 0.7502 (p)
  outliers start: 52
  outliers final: 41
  residues processed: 186
  average time/residue: 0.2147
  time to fit residues: 55.7636
Evaluate side-chains
  195 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 149
  time to evaluate  : 1.046 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  313 THR
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  364 ASN
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  320 VAL
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  371 LEU
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  280 THR
Chi-restraints excluded: chain C residue  300 ASN
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  348 ASN
Chi-restraints excluded: chain C residue  371 LEU
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   22 THR
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain M residue   61 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   79 PHE
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue   93 SER
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 21 optimal weight:    0.9990
   chunk 109 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0970
   chunk 86 optimal weight:    0.7980
   chunk 59 optimal weight:    1.9990
   chunk 79 optimal weight:    0.6980
   chunk 32 optimal weight:    0.9980
   chunk 93 optimal weight:    0.9980
   chunk 95 optimal weight:    0.9990
   chunk 62 optimal weight:    0.0040
   chunk 68 optimal weight:    2.9990
   overall best weight:    0.4790

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
B 300 ASN
B 364 ASN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.109090 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3099 r_free = 0.3099 target = 0.094373 restraints weight = 15076.900|
|-----------------------------------------------------------------------------|
r_work (start): 0.3115 rms_B_bonded: 2.18
r_work: 0.3005 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2860 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2860
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2866
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.53   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2866 r_free = 0.2866    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2866
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7629
moved from start:          0.5040

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   9525  Z= 0.160
  Angle     :  0.574   8.867  12953  Z= 0.304
  Chirality :  0.044   0.350   1426
  Planarity :  0.004   0.034   1660
  Dihedral  :  5.146  18.465   1291
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 5.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.42 %
    Favored  : 96.58 %
  Rotamer:
    Outliers :  3.99 %
    Allowed  : 15.76 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.23), residues: 1169
  helix: -3.22 (1.55), residues: 6
  sheet: -0.41 (0.22), residues: 568
  loop : -1.86 (0.21), residues: 595

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 356 
 HIS   0.005   0.001   HIS M  35 
 PHE   0.015   0.002   PHE B 468 
 TYR   0.017   0.001   TYR A 301 
 ARG   0.008   0.001   ARG A 441 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 145
  time to evaluate  : 1.079 
Fit side-chains
   revert: symmetry clash
REVERT: A   61 VAL cc_start: 0.8450 (t) cc_final: 0.8217 (m)
REVERT: A  337 PHE cc_start: 0.8285 (t80) cc_final: 0.8004 (t80)
REVERT: A  457 ASN cc_start: 0.8507 (t0) cc_final: 0.8186 (t0)
REVERT: B   42 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8239 (mm-40)
REVERT: B  257 SER cc_start: 0.8329 (m) cc_final: 0.7716 (p)
REVERT: B  274 ARG cc_start: 0.8574 (OUTLIER) cc_final: 0.8327 (mtt180)
REVERT: B  282 ILE cc_start: 0.8488 (pt) cc_final: 0.8147 (mt)
REVERT: B  338 VAL cc_start: 0.8616 (t) cc_final: 0.8291 (p)
REVERT: B  378 VAL cc_start: 0.8729 (p) cc_final: 0.8414 (m)
REVERT: B  424 LEU cc_start: 0.8000 (tt) cc_final: 0.7676 (tp)
REVERT: C  274 ARG cc_start: 0.8247 (mtt180) cc_final: 0.7991 (mtt180)
REVERT: C  300 ASN cc_start: 0.8153 (OUTLIER) cc_final: 0.7864 (m-40)
REVERT: C  335 THR cc_start: 0.8450 (OUTLIER) cc_final: 0.7933 (t)
REVERT: C  344 VAL cc_start: 0.8432 (OUTLIER) cc_final: 0.7923 (m)
REVERT: C  440 THR cc_start: 0.8433 (m) cc_final: 0.7829 (p)
REVERT: H   27 PHE cc_start: 0.8070 (p90) cc_final: 0.7733 (p90)
REVERT: M   68 SER cc_start: 0.7954 (m) cc_final: 0.7523 (p)
  outliers start: 41
  outliers final: 35
  residues processed: 173
  average time/residue: 0.2724
  time to fit residues: 67.5611
Evaluate side-chains
  178 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 139
  time to evaluate  : 1.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue   64 LEU
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  311 GLU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  300 ASN
Chi-restraints excluded: chain C residue  316 THR
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  348 ASN
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain H residue  112 THR
Chi-restraints excluded: chain L residue   49 SER
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain L residue   93 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   79 PHE
Chi-restraints excluded: chain N residue    5 THR
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 70 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   chunk 47 optimal weight:    3.9990
   chunk 26 optimal weight:    5.9990
   chunk 20 optimal weight:    2.9990
   chunk 44 optimal weight:    0.0270
   chunk 109 optimal weight:    0.1980
   chunk 89 optimal weight:    0.5980
   overall best weight:    0.5038

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

Flipped N/Q/H residues before XYZ refinement:
A 386 ASN
C 324 ASN
M  77 GLN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.109468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.094675 restraints weight = 15265.777|
|-----------------------------------------------------------------------------|
r_work (start): 0.3106 rms_B_bonded: 2.20
r_work: 0.2994 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2849 rms_B_bonded: 4.53 restraints_weight: 0.2500
r_work (final): 0.2849
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2878
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.51   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2878 r_free = 0.2878    target_work(ls_wunit_k1) = 0.081         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2878
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.5115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   9525  Z= 0.161
  Angle     :  0.555   7.491  12953  Z= 0.293
  Chirality :  0.043   0.244   1426
  Planarity :  0.004   0.035   1660
  Dihedral  :  4.847  17.891   1291
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.62 %
    Favored  : 95.38 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 16.34 %
    Favored  : 80.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.41 (0.23), residues: 1169
  helix: -2.97 (1.11), residues: 12
  sheet: -0.19 (0.22), residues: 576
  loop : -1.67 (0.23), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 356 
 HIS   0.005   0.001   HIS M  35 
 PHE   0.014   0.001   PHE B 468 
 TYR   0.019   0.001   TYR A 305 
 ARG   0.009   0.001   ARG A 441 

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

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

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2338 Ramachandran restraints generated.
    1169 Oldfield, 0 Emsley, 1169 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 141
  time to evaluate  : 0.958 
Fit side-chains
REVERT: A  457 ASN cc_start: 0.8501 (t0) cc_final: 0.8192 (t0)
REVERT: B   34 THR cc_start: 0.8163 (m) cc_final: 0.7787 (p)
REVERT: B   42 GLN cc_start: 0.8507 (mm-40) cc_final: 0.8261 (mm-40)
REVERT: B  257 SER cc_start: 0.8382 (m) cc_final: 0.7842 (p)
REVERT: B  274 ARG cc_start: 0.8520 (OUTLIER) cc_final: 0.8261 (mtt180)
REVERT: B  282 ILE cc_start: 0.8482 (pt) cc_final: 0.8154 (mt)
REVERT: B  338 VAL cc_start: 0.8602 (t) cc_final: 0.8310 (p)
REVERT: B  378 VAL cc_start: 0.8719 (p) cc_final: 0.8415 (m)
REVERT: B  424 LEU cc_start: 0.7998 (tt) cc_final: 0.7675 (tp)
REVERT: C  344 VAL cc_start: 0.8419 (OUTLIER) cc_final: 0.7899 (m)
REVERT: C  355 TYR cc_start: 0.8174 (t80) cc_final: 0.7543 (t80)
REVERT: C  440 THR cc_start: 0.8392 (m) cc_final: 0.7777 (p)
REVERT: C  441 ARG cc_start: 0.8080 (mtt180) cc_final: 0.7600 (mtt180)
REVERT: H   27 PHE cc_start: 0.8036 (p90) cc_final: 0.7619 (p90)
REVERT: M   68 SER cc_start: 0.7862 (m) cc_final: 0.7481 (p)
REVERT: M   77 GLN cc_start: 0.8218 (OUTLIER) cc_final: 0.8013 (pt0)
  outliers start: 35
  outliers final: 30
  residues processed: 166
  average time/residue: 0.2204
  time to fit residues: 50.3021
Evaluate side-chains
  172 residues out of total 1028 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 139
  time to evaluate  : 0.944 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  396 VAL
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  440 THR
Chi-restraints excluded: chain B residue   61 VAL
Chi-restraints excluded: chain B residue  274 ARG
Chi-restraints excluded: chain B residue  304 THR
Chi-restraints excluded: chain B residue  311 GLU
Chi-restraints excluded: chain B residue  323 VAL
Chi-restraints excluded: chain B residue  365 VAL
Chi-restraints excluded: chain B residue  366 VAL
Chi-restraints excluded: chain B residue  398 THR
Chi-restraints excluded: chain B residue  432 VAL
Chi-restraints excluded: chain B residue  447 LEU
Chi-restraints excluded: chain B residue  456 ASN
Chi-restraints excluded: chain C residue  335 THR
Chi-restraints excluded: chain C residue  339 VAL
Chi-restraints excluded: chain C residue  344 VAL
Chi-restraints excluded: chain C residue  348 ASN
Chi-restraints excluded: chain C residue  423 SER
Chi-restraints excluded: chain H residue    7 SER
Chi-restraints excluded: chain H residue   19 SER
Chi-restraints excluded: chain H residue   33 SER
Chi-restraints excluded: chain H residue   80 LEU
Chi-restraints excluded: chain L residue   49 SER
Chi-restraints excluded: chain L residue   52 SER
Chi-restraints excluded: chain M residue   70 SER
Chi-restraints excluded: chain M residue   77 GLN
Chi-restraints excluded: chain M residue   79 PHE
Chi-restraints excluded: chain N residue   49 SER
Chi-restraints excluded: chain N residue   72 THR
Chi-restraints excluded: chain N residue  102 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 116
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 85 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 76 optimal weight:    5.9990
   chunk 51 optimal weight:    0.9980
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 27 optimal weight:    0.5980
   chunk 43 optimal weight:    3.9990
   chunk 73 optimal weight:    0.7980
   overall best weight:    1.4784

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

Flipped N/Q/H residues before XYZ refinement:
** B 321 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 364 ASN
C 324 ASN
** N  90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.106954 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.092169 restraints weight = 15229.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3082 rms_B_bonded: 2.19
r_work: 0.2970 rms_B_bonded: 2.57 restraints_weight: 0.5000
r_work: 0.2823 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2823
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2834
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2834 r_free = 0.2834    target_work(ls_wunit_k1) = 0.079         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.2834
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7659
moved from start:          0.5185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.059   9525  Z= 0.360
  Angle     :  0.670  10.936  12953  Z= 0.355
  Chirality :  0.046   0.276   1426
  Planarity :  0.004   0.034   1660
  Dihedral  :  5.502  21.442   1291
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.22 %
    Favored  : 94.78 %
  Rotamer:
    Outliers :  3.79 %
    Allowed  : 16.83 %
    Favored  : 79.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.77 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.60 (0.23), residues: 1169
  helix: -3.73 (1.17), residues: 6
  sheet: -0.34 (0.21), residues: 582
  loop : -1.81 (0.23), residues: 581

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 356 
 HIS   0.008   0.002   HIS N  91 
 PHE   0.023   0.002   PHE A 342 
 TYR   0.021   0.002   TYR A 305 
 ARG   0.007   0.001   ARG A 441 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5607.48 seconds
wall clock time: 98 minutes 17.97 seconds (5897.97 seconds total)