Starting phenix.real_space_refine
on Fri Aug 22 15:21:04 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ykj_33892/08_2025/7ykj_33892.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ykj_33892/08_2025/7ykj_33892.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ykj_33892/08_2025/7ykj_33892.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ykj_33892/08_2025/7ykj_33892.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ykj_33892/08_2025/7ykj_33892.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ykj_33892/08_2025/7ykj_33892.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.067
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      23      5.16       5
     C    3072      2.51       5
     N     810      2.21       5
     O     906      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 28 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4811
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 1529
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1529
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 63
          Unresolved non-hydrogen angles: 77
          Unresolved non-hydrogen dihedrals: 53
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 2, 'PHE:plan': 2, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 34
    Chain: "C"
      Number of atoms: 1556
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1556
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 12, 'TRANS': 185}
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 28
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ASP:plan': 2, 'PHE:plan': 1, 'ASN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 23
    Chain: "A"
      Number of atoms: 906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 906
          Classifications: {'peptide': 121}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PTRANS': 3, 'TRANS': 117}
          Unresolved non-hydrogen bonds: 25
          Unresolved non-hydrogen angles: 31
          Unresolved non-hydrogen dihedrals: 19
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1, 'ARG:plan': 2, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 21
    Chain: "D"
      Number of atoms: 820
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 820
          Classifications: {'peptide': 109}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 7, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 7
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
  Time building chain proxies: 1.48, per 1000 atoms: 0.31
  Number of scatterers: 4811
  At special positions: 0
  Unit cell: (73.14, 112.36, 95.4, 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      23     16.00
     O     906      8.00
     N     810      7.00
     C    3072      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=9, symmetry=0
    Simple disulfide: pdb=" SG  CYS B 336 " - pdb=" SG  CYS B 361 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B 379 " - pdb=" SG  CYS B 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 391 " - pdb=" SG  CYS B 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS B 480 " - pdb=" SG  CYS B 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.01
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.06
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.02

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 221.0 milliseconds
  
  Enol-peptide restraints added in 238.4 nanoseconds
  

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1154

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 13 sheets defined
      13.6% alpha, 25.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'B' and resid 337 through 343
      removed outlier: 3.828A  pdb=" N   VAL B 341 " --> pdb=" O   PRO B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 364 through 370
      removed outlier: 4.034A  pdb=" N   LEU B 368 " --> pdb=" O   ASP B 364 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 385 through 389
      removed outlier: 3.702A  pdb=" N   ASN B 388 " --> pdb=" O   THR B 385 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 405 through 410
      removed outlier: 4.538A  pdb=" N   ARG B 408 " --> pdb=" O   ASP B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 423
    Processing helix  chain 'C' and resid 337 through 344
    Processing helix  chain 'C' and resid 365 through 371
      removed outlier: 3.802A  pdb=" N   TYR C 369 " --> pdb=" O   TYR C 365 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 3.708A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 410
      removed outlier: 4.379A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 417 through 422
      removed outlier: 4.206A  pdb=" N   TYR C 421 " --> pdb=" O   ASN C 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 28 through 32
    Processing helix  chain 'A' and resid 87 through 91
    Processing helix  chain 'D' and resid 29 through 33
      removed outlier: 4.178A  pdb=" N   SER D  32 " --> pdb=" O   VAL D  29 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 80 through 84
    Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358
      removed outlier: 3.990A  pdb=" N   ASN B 394 " --> pdb=" O   GLU B 516 " (cutoff:3.500A)
      removed outlier: 4.100A  pdb=" N   ILE B 434 " --> pdb=" O   VAL B 511 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'B' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'C' and resid 354 through 357
    Processing sheet with id=AA6, first strand: chain 'C' and resid 391 through 392
    Processing sheet with id=AA7, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA8, first strand: chain 'C' and resid 473 through 474
      removed outlier: 3.769A  pdb=" N   TYR C 473 " --> pdb=" O   TYR C 489 " (cutoff:3.500A)
      removed outlier: 3.983A  pdb=" N   TYR C 489 " --> pdb=" O   TYR C 473 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3 through 7
    Processing sheet with id=AB1, first strand: chain 'A' and resid 11 through 12
      removed outlier: 7.082A  pdb=" N   MET A  34 " --> pdb=" O   ALA A  50 " (cutoff:3.500A)
      removed outlier: 4.800A  pdb=" N   ALA A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 7.109A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12
      removed outlier: 7.017A  pdb=" N   CYS A  96 " --> pdb=" O   TRP A 111 " (cutoff:3.500A)
      removed outlier: 4.747A  pdb=" N   TRP A 111 " --> pdb=" O   CYS A  96 " (cutoff:3.500A)
      removed outlier: 7.007A  pdb=" N   LYS A  98 " --> pdb=" O   ASP A 109 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'D' and resid 19 through 24
    Processing sheet with id=AB4, first strand: chain 'D' and resid 54 through 55
      removed outlier: 6.676A  pdb=" N   TRP D  36 " --> pdb=" O   LEU D  48 " (cutoff:3.500A)

    145 hydrogen bonds defined for protein.
    333 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1077
        1.33 -     1.45: 1243
        1.45 -     1.58: 2596
        1.58 -     1.70: 0
        1.70 -     1.82: 25
  Bond restraints: 4941
  Sorted by residual:
  bond pdb=" N   ILE D  59 "
       pdb=" CA  ILE D  59 "
    ideal  model  delta    sigma   weight residual
    1.456  1.493 -0.036 8.70e-03 1.32e+04 1.74e+01
  bond pdb=" CE1 HIS B 505 "
       pdb=" NE2 HIS B 505 "
    ideal  model  delta    sigma   weight residual
    1.321  1.362 -0.041 1.00e-02 1.00e+04 1.70e+01
  bond pdb=" CE1 HIS C 505 "
       pdb=" NE2 HIS C 505 "
    ideal  model  delta    sigma   weight residual
    1.321  1.361 -0.040 1.00e-02 1.00e+04 1.59e+01
  bond pdb=" N   PRO C 373 "
       pdb=" CD  PRO C 373 "
    ideal  model  delta    sigma   weight residual
    1.473  1.527 -0.054 1.40e-02 5.10e+03 1.51e+01
  bond pdb=" N   SER B 446 "
       pdb=" CA  SER B 446 "
    ideal  model  delta    sigma   weight residual
    1.457  1.493 -0.036 1.16e-02 7.43e+03 9.81e+00
  ... (remaining 4936 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 5832
        2.67 -     5.35: 858
        5.35 -     8.02: 42
        8.02 -    10.70: 4
       10.70 -    13.37: 2
  Bond angle restraints: 6738
  Sorted by residual:
  angle pdb=" CA  PRO C 373 "
        pdb=" N   PRO C 373 "
        pdb=" CD  PRO C 373 "
      ideal   model   delta    sigma   weight residual
     112.00   98.63   13.37 1.40e+00 5.10e-01 9.12e+01
  angle pdb=" OD1 ASN A  74 "
        pdb=" CG  ASN A  74 "
        pdb=" ND2 ASN A  74 "
      ideal   model   delta    sigma   weight residual
     122.60  117.20    5.40 1.00e+00 1.00e+00 2.92e+01
  angle pdb=" OE1 GLN C 409 "
        pdb=" CD  GLN C 409 "
        pdb=" NE2 GLN C 409 "
      ideal   model   delta    sigma   weight residual
     122.60  117.41    5.19 1.00e+00 1.00e+00 2.70e+01
  angle pdb=" OD1 ASN C 439 "
        pdb=" CG  ASN C 439 "
        pdb=" ND2 ASN C 439 "
      ideal   model   delta    sigma   weight residual
     122.60  117.41    5.19 1.00e+00 1.00e+00 2.70e+01
  angle pdb=" OD1 ASN C 394 "
        pdb=" CG  ASN C 394 "
        pdb=" ND2 ASN C 394 "
      ideal   model   delta    sigma   weight residual
     122.60  117.49    5.11 1.00e+00 1.00e+00 2.61e+01
  ... (remaining 6733 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.52: 2552
       17.52 -    35.04: 277
       35.04 -    52.56: 54
       52.56 -    70.08: 12
       70.08 -    87.60: 6
  Dihedral angle restraints: 2901
    sinusoidal: 1082
      harmonic: 1819
  Sorted by residual:
  dihedral pdb=" CD  ARG B 466 "
           pdb=" NE  ARG B 466 "
           pdb=" CZ  ARG B 466 "
           pdb=" NH1 ARG B 466 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00   87.60  -87.60     1      1.00e+01 1.00e-02 9.20e+01
  dihedral pdb=" CA  SER D  95 "
           pdb=" C   SER D  95 "
           pdb=" N   PRO D  96 "
           pdb=" CA  PRO D  96 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -134.01  -45.99     0      5.00e+00 4.00e-02 8.46e+01
  dihedral pdb=" CD  ARG C 498 "
           pdb=" NE  ARG C 498 "
           pdb=" CZ  ARG C 498 "
           pdb=" NH1 ARG C 498 "
      ideal   model   delta sinusoidal    sigma   weight residual
       0.00  -82.34   82.34     1      1.00e+01 1.00e-02 8.32e+01
  ... (remaining 2898 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 525
       0.095 -    0.190: 167
       0.190 -    0.285: 31
       0.285 -    0.380: 4
       0.380 -    0.475: 1
  Chirality restraints: 728
  Sorted by residual:
  chirality pdb=" CA  THR D   5 "
            pdb=" N   THR D   5 "
            pdb=" C   THR D   5 "
            pdb=" CB  THR D   5 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.05    0.48 2.00e-01 2.50e+01 5.65e+00
  chirality pdb=" CA  ASN B 360 "
            pdb=" N   ASN B 360 "
            pdb=" C   ASN B 360 "
            pdb=" CB  ASN B 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.18    0.33 2.00e-01 2.50e+01 2.67e+00
  chirality pdb=" CB  THR A 115 "
            pdb=" CA  THR A 115 "
            pdb=" OG1 THR A 115 "
            pdb=" CG2 THR A 115 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.25    0.30 2.00e-01 2.50e+01 2.24e+00
  ... (remaining 725 not shown)

  Planarity restraints: 878
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  32 "    0.175 2.00e-02 2.50e+03   9.32e-02 1.74e+02
        pdb=" CG  TYR A  32 "   -0.060 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  32 "   -0.076 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  32 "   -0.094 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  32 "   -0.049 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  32 "   -0.038 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  32 "    0.011 2.00e-02 2.50e+03
        pdb=" OH  TYR A  32 "    0.130 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASP A 109 "    0.061 2.00e-02 2.50e+03   1.26e-01 1.59e+02
        pdb=" CG  ASP A 109 "   -0.218 2.00e-02 2.50e+03
        pdb=" OD1 ASP A 109 "    0.079 2.00e-02 2.50e+03
        pdb=" OD2 ASP A 109 "    0.079 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  36 "    0.128 2.00e-02 2.50e+03   7.75e-02 1.50e+02
        pdb=" CG  TRP A  36 "    0.009 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  36 "   -0.084 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  36 "   -0.017 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  36 "   -0.065 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  36 "    0.020 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  36 "   -0.082 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  36 "    0.107 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  36 "   -0.089 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  36 "    0.073 2.00e-02 2.50e+03
  ... (remaining 875 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 5
        2.39 -     3.02: 2646
        3.02 -     3.64: 6997
        3.64 -     4.27: 10751
        4.27 -     4.90: 17483
  Nonbonded interactions: 37882
  Sorted by model distance:
  nonbonded pdb=" O   TYR C 495 "
            pdb=" OG  SER C 496 "
     model   vdw
     1.761 3.040
  nonbonded pdb=" OG  SER A 101 "
            pdb=" O   TYR A 103 "
     model   vdw
     2.026 3.040
  nonbonded pdb=" OG1 THR A  54 "
            pdb=" OD1 ASP A  56 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   PRO D  96 "
            pdb=" N   LEU D  98 "
     model   vdw
     2.286 3.120
  nonbonded pdb=" NH1 ARG D  55 "
            pdb=" O   PHE D  63 "
     model   vdw
     2.356 3.120
  ... (remaining 37877 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 'B' and (resid 331 through 374 or (resid 375 through 377 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 378 through 426 or (resid 427  \ 
and (name N or name CA or name C or name O or name CB )) or resid 428 through 49 \ 
2 or (resid 493 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 494 through 516 or (resid 517 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 518 through 528))
  selection = (chain 'C' and (resid 331 through 345 or (resid 346 through 348 and (name N or n \ 
ame CA or name C or name O or name CB )) or resid 349 through 357 or (resid 358  \ 
and (name N or name CA or name C or name O or name CB )) or resid 359 through 37 \ 
5 or (resid 376 through 377 and (name N or name CA or name C or name O or name C \ 
B )) or resid 378 through 423 or (resid 424 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 425 through 439 or (resid 440 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 441 through 445 or (resid 446 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 447 through 451 or \ 
 (resid 452 and (name N or name CA or name C or name O or name CB )) or resid 45 \ 
3 through 480 or (resid 481 and (name N or name CA or name C or name O or name C \ 
B )) or resid 482 through 495 or (resid 496 and (name N or name CA or name C or  \ 
name O or name CB )) or resid 497 or (resid 498 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 499 through 528))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.000
  Set scattering table:                    0.010
  Process input model:                     6.540
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.150
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7085
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      :  0.013   0.058   4950  Z= 0.783
  Angle     :  1.781  13.371   6756  Z= 1.181
  Chirality :  0.095   0.475    728
  Planarity :  0.040   0.488    878
  Dihedral  : 15.542  87.598   1720
  Min Nonbonded Distance : 1.761

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  1.13 %
    Allowed  :  6.63 %
    Favored  : 92.23 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 16.70 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.17 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    Twisted General : 0.17 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -2.51 (0.31), residues: 618
  helix: -4.60 (0.38), residues: 42
  sheet: -1.24 (0.41), residues: 148
  loop : -1.57 (0.28), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.040   0.003   ARG B 403 
 TYR   0.175   0.020   TYR A  32 
 PHE   0.045   0.008   PHE A  27 
 TRP   0.128   0.026   TRP A  36 
 HIS   0.019   0.004   HIS A  59 

Details of bonding type rmsd
  covalent geometry    : bond        0.01301 ( 4941)
  covalent geometry    : angle       1.78074 ( 6738)
  SS BOND              : bond        0.01631 (    9)
  SS BOND              : angle       1.87069 (   18)
  hydrogen bonds       : bond        0.22438 (  140)
  hydrogen bonds       : angle      10.09743 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 123
  time to evaluate  : 0.113 
Fit side-chains
REVERT: B  400 PHE cc_start: 0.6246 (p90) cc_final: 0.5878 (p90)
REVERT: A   28 THR cc_start: 0.9157 (m) cc_final: 0.8909 (p)
  outliers start: 15
  outliers final: 4
  residues processed: 129
  average time/residue: 0.1043
  time to fit residues: 16.0890
Evaluate side-chains
  89 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  362 VAL
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  501 TYR
Chi-restraints excluded: chain D residue   98 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 56 optimal weight:    5.9990
   chunk 26 optimal weight:    0.1980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    8.9990
   chunk 32 optimal weight:    0.9980
   chunk 31 optimal weight:    0.9990
   chunk 25 optimal weight:    0.9980
   chunk 58 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
C 354 ASN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 506 GLN
D  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4316 r_free = 0.4316 target = 0.176271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.129780 restraints weight = 9719.262|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.132663 restraints weight = 5511.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.134775 restraints weight = 3894.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.135921 restraints weight = 3148.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3847 r_free = 0.3847 target = 0.136815 restraints weight = 2778.989|
|-----------------------------------------------------------------------------|
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7242
moved from start:          0.2250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4950  Z= 0.138
  Angle     :  0.671   6.572   6756  Z= 0.351
  Chirality :  0.047   0.189    728
  Planarity :  0.006   0.064    878
  Dihedral  :  6.064  43.158    702
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 8.80
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  4.85 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 18.29 %
    Favored  : 77.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.64 (0.34), residues: 618
  helix: -3.84 (0.50), residues: 43
  sheet: -1.17 (0.38), residues: 150
  loop : -0.73 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 408 
 TYR   0.016   0.002   TYR A 103 
 PHE   0.012   0.001   PHE D 100 
 TRP   0.015   0.002   TRP A  36 
 HIS   0.003   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4941)
  covalent geometry    : angle       0.66979 ( 6738)
  SS BOND              : bond        0.00460 (    9)
  SS BOND              : angle       0.96266 (   18)
  hydrogen bonds       : bond        0.04044 (  140)
  hydrogen bonds       : angle       7.25892 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 113
  time to evaluate  : 0.192 
Fit side-chains
REVERT: B  418 ILE cc_start: 0.7133 (OUTLIER) cc_final: 0.6858 (mm)
REVERT: B  457 ARG cc_start: 0.5060 (ttt-90) cc_final: 0.4841 (ttt180)
REVERT: A    3 GLN cc_start: 0.7083 (OUTLIER) cc_final: 0.6816 (pp30)
REVERT: A   28 THR cc_start: 0.9025 (m) cc_final: 0.8681 (p)
REVERT: A   57 ASP cc_start: 0.7920 (t70) cc_final: 0.7598 (t70)
REVERT: A   91 THR cc_start: 0.8353 (m) cc_final: 0.8086 (t)
REVERT: A   95 TYR cc_start: 0.8534 (m-80) cc_final: 0.8142 (m-80)
  outliers start: 21
  outliers final: 9
  residues processed: 125
  average time/residue: 0.0968
  time to fit residues: 14.7655
Evaluate side-chains
  99 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.187 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  335 LEU
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 9 optimal weight:    0.4980
   chunk 49 optimal weight:    5.9990
   chunk 12 optimal weight:    8.9990
   chunk 4 optimal weight:    0.8980
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 59 optimal weight:    5.9990
   chunk 58 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 505 HIS
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 505 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.176189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.134271 restraints weight = 9643.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.134906 restraints weight = 6348.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.134998 restraints weight = 4270.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.135806 restraints weight = 3930.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3822 r_free = 0.3822 target = 0.135820 restraints weight = 3800.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3779
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7308
moved from start:          0.2896

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4950  Z= 0.124
  Angle     :  0.647  10.729   6756  Z= 0.335
  Chirality :  0.046   0.196    728
  Planarity :  0.005   0.058    878
  Dihedral  :  5.484  41.254    696
  Min Nonbonded Distance : 2.536

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  5.66 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 19.68 %
    Favored  : 75.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.34), residues: 618
  helix: -3.05 (0.63), residues: 43
  sheet: -0.90 (0.39), residues: 151
  loop : -0.75 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.023   0.001   TYR A  60 
 PHE   0.015   0.001   PHE A  27 
 TRP   0.010   0.001   TRP A 111 
 HIS   0.004   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 4941)
  covalent geometry    : angle       0.63858 ( 6738)
  SS BOND              : bond        0.00531 (    9)
  SS BOND              : angle       2.16058 (   18)
  hydrogen bonds       : bond        0.03500 (  140)
  hydrogen bonds       : angle       6.57407 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.187 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5538 (OUTLIER) cc_final: 0.4697 (p90)
REVERT: B  418 ILE cc_start: 0.7342 (OUTLIER) cc_final: 0.7115 (mm)
REVERT: B  455 LEU cc_start: 0.6932 (OUTLIER) cc_final: 0.6725 (mt)
REVERT: B  457 ARG cc_start: 0.4970 (ttt-90) cc_final: 0.4658 (ttt-90)
REVERT: B  519 HIS cc_start: 0.3621 (OUTLIER) cc_final: 0.3343 (p90)
REVERT: A   28 THR cc_start: 0.9156 (m) cc_final: 0.8792 (p)
REVERT: A   32 TYR cc_start: 0.7439 (m-80) cc_final: 0.7027 (m-10)
REVERT: A   57 ASP cc_start: 0.7864 (t70) cc_final: 0.7565 (t70)
REVERT: A   95 TYR cc_start: 0.8539 (m-80) cc_final: 0.8273 (m-80)
REVERT: A  103 TYR cc_start: 0.8201 (m-80) cc_final: 0.7999 (m-10)
  outliers start: 24
  outliers final: 15
  residues processed: 117
  average time/residue: 0.0839
  time to fit residues: 12.1782
Evaluate side-chains
  111 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  455 LEU
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   79 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 15 optimal weight:    9.9990
   chunk 55 optimal weight:    0.0570
   chunk 51 optimal weight:    0.1980
   chunk 25 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   chunk 34 optimal weight:    0.0370
   chunk 24 optimal weight:    0.7980
   chunk 20 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 42 optimal weight:    8.9990
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
B 505 HIS
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.177421 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3794 r_free = 0.3794 target = 0.132836 restraints weight = 9582.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.135654 restraints weight = 5642.478|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.137401 restraints weight = 4023.063|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.138758 restraints weight = 3261.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.139685 restraints weight = 2847.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3859
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7211
moved from start:          0.3420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4950  Z= 0.111
  Angle     :  0.606   7.391   6756  Z= 0.313
  Chirality :  0.045   0.152    728
  Planarity :  0.005   0.056    878
  Dihedral  :  5.141  36.669    696
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.85 %
    Favored  : 94.66 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.67 %
    Favored  : 73.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.20 (0.35), residues: 618
  helix: -2.66 (0.66), residues: 50
  sheet: -0.35 (0.40), residues: 161
  loop : -0.72 (0.33), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 457 
 TYR   0.014   0.001   TYR D  37 
 PHE   0.012   0.001   PHE A  27 
 TRP   0.012   0.001   TRP A  36 
 HIS   0.004   0.001   HIS C 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 4941)
  covalent geometry    : angle       0.60076 ( 6738)
  SS BOND              : bond        0.00209 (    9)
  SS BOND              : angle       1.58611 (   18)
  hydrogen bonds       : bond        0.02959 (  140)
  hydrogen bonds       : angle       6.15399 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 0.197 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.5381 (OUTLIER) cc_final: 0.4667 (p90)
REVERT: B  457 ARG cc_start: 0.5013 (ttt-90) cc_final: 0.4686 (ttt-90)
REVERT: B  519 HIS cc_start: 0.3665 (OUTLIER) cc_final: 0.3408 (p90)
REVERT: C  378 LYS cc_start: 0.8136 (ttpt) cc_final: 0.7907 (ttpt)
REVERT: A   18 LEU cc_start: 0.8044 (tp) cc_final: 0.7834 (tp)
REVERT: A   28 THR cc_start: 0.9089 (m) cc_final: 0.8711 (p)
REVERT: A   32 TYR cc_start: 0.7457 (m-80) cc_final: 0.7058 (m-10)
REVERT: A   57 ASP cc_start: 0.7835 (t70) cc_final: 0.7514 (t70)
REVERT: A   95 TYR cc_start: 0.8431 (m-80) cc_final: 0.8209 (m-80)
  outliers start: 24
  outliers final: 14
  residues processed: 114
  average time/residue: 0.0838
  time to fit residues: 11.8071
Evaluate side-chains
  104 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 88
  time to evaluate  : 0.191 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   89 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 35 optimal weight:    0.9990
   chunk 28 optimal weight:    0.7980
   chunk 9 optimal weight:    8.9990
   chunk 53 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 51 optimal weight:    6.9990
   chunk 25 optimal weight:    3.9990
   chunk 7 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   chunk 14 optimal weight:   10.0000
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.170724 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3686 r_free = 0.3686 target = 0.125799 restraints weight = 9601.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.128337 restraints weight = 5881.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.130049 restraints weight = 4367.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.131042 restraints weight = 3592.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.131472 restraints weight = 3185.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7401
moved from start:          0.3803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.082   4950  Z= 0.196
  Angle     :  0.696   9.286   6756  Z= 0.354
  Chirality :  0.047   0.174    728
  Planarity :  0.006   0.057    878
  Dihedral  :  5.621  40.027    696
  Min Nonbonded Distance : 2.516

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  5.50 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 21.27 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.27 (0.34), residues: 618
  helix: -2.71 (0.76), residues: 37
  sheet: -0.26 (0.40), residues: 158
  loop : -0.92 (0.31), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  46 
 TYR   0.020   0.002   TYR D  50 
 PHE   0.014   0.002   PHE D 100 
 TRP   0.011   0.001   TRP A 111 
 HIS   0.004   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00475 ( 4941)
  covalent geometry    : angle       0.68866 ( 6738)
  SS BOND              : bond        0.00627 (    9)
  SS BOND              : angle       2.11852 (   18)
  hydrogen bonds       : bond        0.03440 (  140)
  hydrogen bonds       : angle       6.28415 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 92
  time to evaluate  : 0.179 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.5653 (OUTLIER) cc_final: 0.4791 (p90)
REVERT: C  420 ASP cc_start: 0.7799 (OUTLIER) cc_final: 0.7590 (m-30)
REVERT: A   32 TYR cc_start: 0.7852 (m-80) cc_final: 0.7386 (m-10)
REVERT: A   57 ASP cc_start: 0.8012 (OUTLIER) cc_final: 0.7613 (t70)
REVERT: D   88 TYR cc_start: 0.8280 (m-80) cc_final: 0.7957 (m-80)
  outliers start: 29
  outliers final: 19
  residues processed: 108
  average time/residue: 0.0893
  time to fit residues: 11.9832
Evaluate side-chains
  107 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 85
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  420 ASP
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   89 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 10 optimal weight:    6.9990
   chunk 50 optimal weight:    0.0470
   chunk 9 optimal weight:    5.9990
   chunk 56 optimal weight:   10.0000
   chunk 55 optimal weight:    6.9990
   chunk 0 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    5.9990
   chunk 58 optimal weight:    6.9990
   chunk 4 optimal weight:    5.9990
   overall best weight:    3.5684

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
B 448 ASN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A   3 GLN
D  38 GLN
** D  91 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 = 0.4173 r_free = 0.4173 target = 0.165095 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.120214 restraints weight = 9724.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.122528 restraints weight = 6119.610|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.124253 restraints weight = 4560.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.125062 restraints weight = 3761.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.125695 restraints weight = 3375.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7525
moved from start:          0.4468

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.125   4950  Z= 0.341
  Angle     :  0.814   8.871   6756  Z= 0.423
  Chirality :  0.051   0.203    728
  Planarity :  0.006   0.068    878
  Dihedral  :  6.427  44.740    696
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 15.34
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  7.28 %
    Favored  : 92.07 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 21.67 %
    Favored  : 71.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.61 (0.34), residues: 618
  helix: -2.73 (0.77), residues: 37
  sheet: -0.32 (0.39), residues: 169
  loop : -1.28 (0.31), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG D  78 
 TYR   0.020   0.002   TYR C 473 
 PHE   0.018   0.003   PHE C 377 
 TRP   0.008   0.002   TRP C 436 
 HIS   0.004   0.002   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00809 ( 4941)
  covalent geometry    : angle       0.80415 ( 6738)
  SS BOND              : bond        0.00937 (    9)
  SS BOND              : angle       2.61565 (   18)
  hydrogen bonds       : bond        0.04042 (  140)
  hydrogen bonds       : angle       6.68823 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 85
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.6313 (OUTLIER) cc_final: 0.5473 (p90)
REVERT: B  468 ILE cc_start: 0.7313 (OUTLIER) cc_final: 0.7070 (mt)
REVERT: C  467 ASP cc_start: 0.6932 (t0) cc_final: 0.6627 (t0)
REVERT: C  489 TYR cc_start: 0.7300 (m-80) cc_final: 0.7038 (m-80)
REVERT: A   32 TYR cc_start: 0.7981 (m-80) cc_final: 0.7429 (m-10)
REVERT: A   57 ASP cc_start: 0.7970 (OUTLIER) cc_final: 0.7609 (t70)
  outliers start: 33
  outliers final: 26
  residues processed: 108
  average time/residue: 0.0733
  time to fit residues: 10.2368
Evaluate side-chains
  105 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 76
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  331 ASN
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  468 ILE
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue    5 THR
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain D residue   89 CYS
Chi-restraints excluded: chain D residue   98 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 15 optimal weight:   20.0000
   chunk 49 optimal weight:    4.9990
   chunk 40 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 1 optimal weight:    9.9990
   chunk 5 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 53 optimal weight:    0.8980
   chunk 3 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.169296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.125639 restraints weight = 9834.101|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.128191 restraints weight = 6140.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.129654 restraints weight = 4511.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.130929 restraints weight = 3754.298|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.131185 restraints weight = 3310.538|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7428
moved from start:          0.4586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4950  Z= 0.162
  Angle     :  0.663   7.030   6756  Z= 0.345
  Chirality :  0.047   0.193    728
  Planarity :  0.006   0.064    878
  Dihedral  :  5.703  42.673    696
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.66 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 23.66 %
    Favored  : 71.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.53 (0.34), residues: 618
  helix: -2.69 (0.76), residues: 37
  sheet: -0.35 (0.41), residues: 155
  loop : -1.15 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 454 
 TYR   0.016   0.001   TYR A  95 
 PHE   0.011   0.001   PHE D 100 
 TRP   0.008   0.001   TRP B 436 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00385 ( 4941)
  covalent geometry    : angle       0.65859 ( 6738)
  SS BOND              : bond        0.00433 (    9)
  SS BOND              : angle       1.59685 (   18)
  hydrogen bonds       : bond        0.03359 (  140)
  hydrogen bonds       : angle       6.27747 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.6227 (OUTLIER) cc_final: 0.5481 (p90)
REVERT: C  467 ASP cc_start: 0.6936 (t0) cc_final: 0.6596 (t0)
REVERT: A   32 TYR cc_start: 0.7830 (m-80) cc_final: 0.7427 (m-10)
REVERT: A   57 ASP cc_start: 0.7980 (t70) cc_final: 0.7670 (t70)
  outliers start: 25
  outliers final: 22
  residues processed: 105
  average time/residue: 0.0788
  time to fit residues: 10.4970
Evaluate side-chains
  108 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 85
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   73 THR
Chi-restraints excluded: chain D residue   98 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 53 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 25 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0770
   chunk 21 optimal weight:    0.6980
   chunk 8 optimal weight:    6.9990
   chunk 6 optimal weight:    9.9990
   overall best weight:    0.6942

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

Flipped N/Q/H residues before XYZ refinement:
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.173079 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.131187 restraints weight = 9777.697|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.133731 restraints weight = 6085.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.135252 restraints weight = 4453.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3830 r_free = 0.3830 target = 0.136594 restraints weight = 3660.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.137155 restraints weight = 3198.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.3823
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7382
moved from start:          0.4752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4950  Z= 0.123
  Angle     :  0.629   6.752   6756  Z= 0.327
  Chirality :  0.046   0.179    728
  Planarity :  0.005   0.058    878
  Dihedral  :  5.248  38.410    696
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.34 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 22.66 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.42 (0.34), residues: 618
  helix: -2.82 (0.77), residues: 37
  sheet: -0.25 (0.42), residues: 156
  loop : -1.07 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B 357 
 TYR   0.017   0.001   TYR A  95 
 PHE   0.008   0.001   PHE A  27 
 TRP   0.007   0.001   TRP B 436 
 HIS   0.004   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00288 ( 4941)
  covalent geometry    : angle       0.62648 ( 6738)
  SS BOND              : bond        0.00265 (    9)
  SS BOND              : angle       1.21885 (   18)
  hydrogen bonds       : bond        0.03091 (  140)
  hydrogen bonds       : angle       6.02884 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.145 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.6006 (OUTLIER) cc_final: 0.5212 (p90)
REVERT: C  467 ASP cc_start: 0.6780 (t0) cc_final: 0.6565 (t0)
REVERT: A   32 TYR cc_start: 0.7444 (m-80) cc_final: 0.7201 (m-10)
REVERT: A   57 ASP cc_start: 0.7812 (OUTLIER) cc_final: 0.7602 (t70)
REVERT: D  108 ILE cc_start: 0.3781 (OUTLIER) cc_final: 0.3166 (tp)
  outliers start: 23
  outliers final: 18
  residues processed: 100
  average time/residue: 0.0825
  time to fit residues: 10.4852
Evaluate side-chains
  106 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 85
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  472 ILE
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 55 optimal weight:    8.9990
   chunk 32 optimal weight:    0.0870
   chunk 14 optimal weight:    3.9990
   chunk 50 optimal weight:    0.0170
   chunk 36 optimal weight:    0.9990
   chunk 21 optimal weight:    0.9990
   chunk 28 optimal weight:    0.3980
   chunk 51 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 46 optimal weight:   10.0000
   overall best weight:    0.5000

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

Flipped N/Q/H residues before XYZ refinement:
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.176992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.133704 restraints weight = 9913.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.136581 restraints weight = 5798.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.138320 restraints weight = 4048.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.139726 restraints weight = 3262.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.140092 restraints weight = 2826.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.4958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4950  Z= 0.113
  Angle     :  0.625  10.516   6756  Z= 0.318
  Chirality :  0.046   0.170    728
  Planarity :  0.005   0.052    878
  Dihedral  :  4.953  34.341    696
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.53 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 24.25 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.15 (0.35), residues: 618
  helix: -2.41 (0.87), residues: 31
  sheet: -0.19 (0.42), residues: 156
  loop : -0.88 (0.32), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 357 
 TYR   0.014   0.001   TYR B 495 
 PHE   0.008   0.001   PHE C 374 
 TRP   0.007   0.001   TRP C 436 
 HIS   0.001   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 4941)
  covalent geometry    : angle       0.62334 ( 6738)
  SS BOND              : bond        0.00215 (    9)
  SS BOND              : angle       1.03711 (   18)
  hydrogen bonds       : bond        0.02920 (  140)
  hydrogen bonds       : angle       5.85556 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.192 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5944 (OUTLIER) cc_final: 0.5201 (p90)
REVERT: C  467 ASP cc_start: 0.6839 (t0) cc_final: 0.6532 (t0)
REVERT: A   32 TYR cc_start: 0.7448 (m-80) cc_final: 0.7180 (m-10)
REVERT: A   57 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7673 (t70)
REVERT: D  108 ILE cc_start: 0.3653 (OUTLIER) cc_final: 0.3015 (tp)
  outliers start: 19
  outliers final: 16
  residues processed: 99
  average time/residue: 0.0855
  time to fit residues: 10.4943
Evaluate side-chains
  98 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 49 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 3 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 40 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 52 optimal weight:    8.9990
   chunk 0 optimal weight:    0.7980
   chunk 16 optimal weight:    5.9990
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.170481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 83)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.127967 restraints weight = 9619.374|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.130452 restraints weight = 6043.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.131972 restraints weight = 4467.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.133256 restraints weight = 3677.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3790 r_free = 0.3790 target = 0.133540 restraints weight = 3232.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7452
moved from start:          0.5084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.095   4950  Z= 0.207
  Angle     :  0.695   6.737   6756  Z= 0.359
  Chirality :  0.048   0.183    728
  Planarity :  0.006   0.054    878
  Dihedral  :  5.366  38.255    696
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  7.12 %
    Favored  : 92.39 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 23.86 %
    Favored  : 71.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.23 (0.34), residues: 618
  helix: -2.52 (0.84), residues: 31
  sheet: -0.21 (0.41), residues: 160
  loop : -0.95 (0.31), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 346 
 TYR   0.017   0.002   TYR A  95 
 PHE   0.014   0.002   PHE C 377 
 TRP   0.009   0.002   TRP A 111 
 HIS   0.002   0.001   HIS B 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00504 ( 4941)
  covalent geometry    : angle       0.69002 ( 6738)
  SS BOND              : bond        0.00533 (    9)
  SS BOND              : angle       1.71578 (   18)
  hydrogen bonds       : bond        0.03368 (  140)
  hydrogen bonds       : angle       6.05916 (  333)

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 88
  time to evaluate  : 0.200 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.6108 (OUTLIER) cc_final: 0.5291 (p90)
REVERT: C  467 ASP cc_start: 0.6978 (t0) cc_final: 0.6574 (t0)
REVERT: A   32 TYR cc_start: 0.7669 (m-80) cc_final: 0.7273 (m-10)
REVERT: A   57 ASP cc_start: 0.7885 (OUTLIER) cc_final: 0.7592 (t70)
  outliers start: 21
  outliers final: 16
  residues processed: 100
  average time/residue: 0.0845
  time to fit residues: 10.8026
Evaluate side-chains
  103 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   98 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 3 optimal weight:    6.9990
   chunk 48 optimal weight:    0.5980
   chunk 40 optimal weight:    1.9990
   chunk 5 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    2.9990
   chunk 42 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    2.1188

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

Flipped N/Q/H residues before XYZ refinement:
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  43 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.168889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.126512 restraints weight = 9708.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.128847 restraints weight = 6048.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.130606 restraints weight = 4460.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 60)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.131746 restraints weight = 3660.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.132110 restraints weight = 3228.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3756
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7481
moved from start:          0.5284

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.088   4950  Z= 0.220
  Angle     :  0.717   6.681   6756  Z= 0.372
  Chirality :  0.048   0.194    728
  Planarity :  0.007   0.075    878
  Dihedral  :  5.691  41.279    696
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  6.96 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 22.86 %
    Favored  : 72.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.38 (0.34), residues: 618
  helix: -2.63 (0.79), residues: 32
  sheet: -0.34 (0.41), residues: 160
  loop : -1.03 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 346 
 TYR   0.019   0.002   TYR A  95 
 PHE   0.014   0.002   PHE C 377 
 TRP   0.009   0.002   TRP B 436 
 HIS   0.004   0.001   HIS B 505 

Details of bonding type rmsd
  covalent geometry    : bond        0.00528 ( 4941)
  covalent geometry    : angle       0.71284 ( 6738)
  SS BOND              : bond        0.00566 (    9)
  SS BOND              : angle       1.62007 (   18)
  hydrogen bonds       : bond        0.03518 (  140)
  hydrogen bonds       : angle       6.18308 (  333)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1255.23 seconds
wall clock time: 22 minutes 11.34 seconds (1331.34 seconds total)