Starting phenix.real_space_refine
on Sat May 10 03:30:25 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ykj_33892/05_2025/7ykj_33892.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ykj_33892/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ykj_33892/05_2025/7ykj_33892.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ykj_33892/05_2025/7ykj_33892.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ykj_33892/05_2025/7ykj_33892.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ykj_33892/05_2025/7ykj_33892.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: {'PHE:plan': 2, 'ARG:plan': 2, 'ASN:plan1': 3, 'ASP:plan': 1}
          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: {'PHE:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 2, 'ASP:plan': 2}
          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: {'GLN:plan1': 1, 'GLU:plan': 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: 3.59, per 1000 atoms: 0.75
  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: 1.18
  Conformation dependent library (CDL) restraints added in 601.2 milliseconds
  

  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: 0.62
  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: 1.22

  Time building geometry restraints manager: 1.38 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:             2.230
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.450
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.900
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.51 (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
 TRP   0.128   0.026   TRP A  36 
 HIS   0.019   0.004   HIS A  59 
 PHE   0.045   0.008   PHE A  27 
 TYR   0.175   0.020   TYR A  32 
 ARG   0.040   0.003   ARG B 403 

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

*********************** 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  : 0.582 
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: 0.2298
  time to fit residues: 35.6982
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  : 0.574 
-------------------------------------------------------------------------------
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 50 optimal weight:    5.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    0.8980
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 24 optimal weight:    0.7980
   chunk 47 optimal weight:   10.0000
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    0.5980
   chunk 35 optimal weight:    5.9990
   chunk 54 optimal weight:    0.8980
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
C 354 ASN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.175167 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.129030 restraints weight = 9562.295|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.131844 restraints weight = 5667.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.133752 restraints weight = 4077.493|
|-----------------------------------------------------------------------------|
r_work (final): 0.3776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7304
moved from start:          0.2175

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4950  Z= 0.148
  Angle     :  0.679   6.455   6756  Z= 0.356
  Chirality :  0.047   0.203    728
  Planarity :  0.006   0.063    878
  Dihedral  :  6.103  43.875    702
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  5.02 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 18.89 %
    Favored  : 77.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.34), residues: 618
  helix: -3.88 (0.49), residues: 43
  sheet: -1.14 (0.38), residues: 152
  loop : -0.76 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A  36 
 HIS   0.003   0.001   HIS C 519 
 PHE   0.012   0.001   PHE D 100 
 TYR   0.016   0.002   TYR A  95 
 ARG   0.004   0.001   ARG C 408 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04309 (  140)
  hydrogen bonds       : angle       7.34818 (  333)
  SS BOND              : bond        0.00470 (    9)
  SS BOND              : angle       1.04314 (   18)
  covalent geometry    : bond        0.00342 ( 4941)
  covalent geometry    : angle       0.67805 ( 6738)

*********************** 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
  128 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 109
  time to evaluate  : 0.523 
Fit side-chains
REVERT: B  400 PHE cc_start: 0.6202 (p90) cc_final: 0.5962 (p90)
REVERT: B  418 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6871 (mm)
REVERT: B  457 ARG cc_start: 0.4977 (ttt-90) cc_final: 0.4726 (ttt180)
REVERT: A   28 THR cc_start: 0.9115 (m) cc_final: 0.8728 (p)
REVERT: A   32 TYR cc_start: 0.7391 (m-80) cc_final: 0.7128 (m-10)
REVERT: A   57 ASP cc_start: 0.7948 (t70) cc_final: 0.7652 (t70)
REVERT: A   95 TYR cc_start: 0.8583 (m-80) cc_final: 0.8194 (m-80)
  outliers start: 19
  outliers final: 8
  residues processed: 119
  average time/residue: 0.2115
  time to fit residues: 30.7592
Evaluate side-chains
  97 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 88
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
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   20 LEU
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 10 optimal weight:    7.9990
   chunk 11 optimal weight:    4.9990
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 52 optimal weight:   20.0000
   chunk 23 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0070
   chunk 45 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   overall best weight:    1.2602

-------------------------------------------------------------------------------
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
C 506 GLN
D  38 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.177092 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.132408 restraints weight = 9460.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.134960 restraints weight = 5828.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.136829 restraints weight = 4314.552|
|-----------------------------------------------------------------------------|
r_work (final): 0.3762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7359
moved from start:          0.2914

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4950  Z= 0.156
  Angle     :  0.678  11.152   6756  Z= 0.352
  Chirality :  0.047   0.192    728
  Planarity :  0.005   0.061    878
  Dihedral  :  5.704  42.838    696
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 10.62
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  6.15 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  6.56 %
    Allowed  : 18.69 %
    Favored  : 74.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.51 (0.34), residues: 618
  helix: -3.28 (0.59), residues: 43
  sheet: -0.62 (0.39), residues: 160
  loop : -0.90 (0.33), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 111 
 HIS   0.003   0.001   HIS C 505 
 PHE   0.011   0.001   PHE A  27 
 TYR   0.023   0.002   TYR A  60 
 ARG   0.004   0.001   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03654 (  140)
  hydrogen bonds       : angle       6.66249 (  333)
  SS BOND              : bond        0.00536 (    9)
  SS BOND              : angle       2.30241 (   18)
  covalent geometry    : bond        0.00370 ( 4941)
  covalent geometry    : angle       0.66873 ( 6738)

*********************** 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
  128 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 95
  time to evaluate  : 0.590 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5663 (OUTLIER) cc_final: 0.4921 (p90)
REVERT: B  400 PHE cc_start: 0.6089 (p90) cc_final: 0.5807 (p90)
REVERT: B  418 ILE cc_start: 0.7261 (OUTLIER) cc_final: 0.7017 (mm)
REVERT: C  378 LYS cc_start: 0.8095 (OUTLIER) cc_final: 0.7873 (ttpt)
REVERT: A   28 THR cc_start: 0.9114 (m) cc_final: 0.8669 (p)
REVERT: A   32 TYR cc_start: 0.7745 (m-80) cc_final: 0.7343 (m-10)
REVERT: A   57 ASP cc_start: 0.7970 (t70) cc_final: 0.7652 (t70)
REVERT: A   95 TYR cc_start: 0.8520 (m-80) cc_final: 0.8270 (m-80)
  outliers start: 33
  outliers final: 22
  residues processed: 116
  average time/residue: 0.1857
  time to fit residues: 26.9648
Evaluate side-chains
  109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 84
  time to evaluate  : 0.516 
-------------------------------------------------------------------------------
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  399 SER
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  378 LYS
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 C residue  470 THR
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue   35 ASN
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    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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 51 optimal weight:    0.0770
   chunk 52 optimal weight:    0.6980
   chunk 43 optimal weight:    0.5980
   chunk 56 optimal weight:    8.9990
   chunk 55 optimal weight:    0.1980
   chunk 20 optimal weight:    2.9990
   chunk 6 optimal weight:    0.6980
   chunk 39 optimal weight:    8.9990
   chunk 4 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   overall best weight:    0.4538

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.176082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.133923 restraints weight = 9736.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.135043 restraints weight = 5617.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.135340 restraints weight = 4228.417|
|-----------------------------------------------------------------------------|
r_work (final): 0.3785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.3327

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4950  Z= 0.111
  Angle     :  0.612   7.225   6756  Z= 0.317
  Chirality :  0.045   0.173    728
  Planarity :  0.005   0.055    878
  Dihedral  :  5.293  39.176    696
  Min Nonbonded Distance : 2.567

Molprobity Statistics.
  All-atom Clashscore : 9.33
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.69 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 21.47 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.29 (0.35), residues: 618
  helix: -2.59 (0.71), residues: 44
  sheet: -0.45 (0.40), residues: 159
  loop : -0.81 (0.33), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A  36 
 HIS   0.002   0.001   HIS C 505 
 PHE   0.009   0.001   PHE A  27 
 TYR   0.015   0.001   TYR D  37 
 ARG   0.007   0.001   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03109 (  140)
  hydrogen bonds       : angle       6.21921 (  333)
  SS BOND              : bond        0.00274 (    9)
  SS BOND              : angle       1.70715 (   18)
  covalent geometry    : bond        0.00254 ( 4941)
  covalent geometry    : angle       0.60611 ( 6738)

*********************** 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
  120 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 97
  time to evaluate  : 0.496 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.5388 (OUTLIER) cc_final: 0.4648 (p90)
REVERT: B  400 PHE cc_start: 0.6122 (p90) cc_final: 0.5855 (p90)
REVERT: B  403 ARG cc_start: 0.4990 (ptm-80) cc_final: 0.4659 (ptm-80)
REVERT: A   28 THR cc_start: 0.9057 (m) cc_final: 0.8575 (p)
REVERT: A   32 TYR cc_start: 0.7591 (m-80) cc_final: 0.7167 (m-10)
REVERT: A   43 LYS cc_start: 0.8381 (mppt) cc_final: 0.8062 (mppt)
REVERT: A   44 GLU cc_start: 0.7557 (pm20) cc_final: 0.7306 (pm20)
REVERT: A   57 ASP cc_start: 0.7967 (t70) cc_final: 0.7615 (t70)
REVERT: D   55 ARG cc_start: 0.7866 (ttp-110) cc_final: 0.7587 (ttm110)
  outliers start: 23
  outliers final: 17
  residues processed: 109
  average time/residue: 0.2043
  time to fit residues: 27.4870
Evaluate side-chains
  105 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 87
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  336 CYS
Chi-restraints excluded: chain B residue  369 TYR
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  401 VAL
Chi-restraints excluded: chain C residue  405 ASP
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   20 THR
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   79 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 49 optimal weight:    4.9990
   chunk 28 optimal weight:    1.9990
   chunk 54 optimal weight:    0.0670
   chunk 9 optimal weight:    0.0070
   chunk 56 optimal weight:    7.9990
   chunk 22 optimal weight:    0.1980
   chunk 44 optimal weight:    0.0010
   chunk 27 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 53 optimal weight:    0.8980
   overall best weight:    0.2342

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

Flipped N/Q/H residues before XYZ refinement:
B 331 ASN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4337 r_free = 0.4337 target = 0.178124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.138721 restraints weight = 9689.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.138901 restraints weight = 5404.260|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.139957 restraints weight = 4120.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3862
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7204
moved from start:          0.3732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   4950  Z= 0.099
  Angle     :  0.589   8.566   6756  Z= 0.300
  Chirality :  0.044   0.149    728
  Planarity :  0.005   0.053    878
  Dihedral  :  4.878  31.883    696
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.21 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 21.47 %
    Favored  : 73.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.34), residues: 618
  helix: -2.98 (0.68), residues: 43
  sheet: -0.24 (0.40), residues: 159
  loop : -0.72 (0.32), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 111 
 HIS   0.002   0.000   HIS A  59 
 PHE   0.009   0.001   PHE D 100 
 TYR   0.011   0.001   TYR C 495 
 ARG   0.009   0.001   ARG B 457 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02873 (  140)
  hydrogen bonds       : angle       5.92417 (  333)
  SS BOND              : bond        0.00147 (    9)
  SS BOND              : angle       1.18611 (   18)
  covalent geometry    : bond        0.00223 ( 4941)
  covalent geometry    : angle       0.58708 ( 6738)

*********************** 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
  129 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 102
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.5388 (OUTLIER) cc_final: 0.4632 (p90)
REVERT: B  398 ASP cc_start: 0.6568 (m-30) cc_final: 0.5695 (p0)
REVERT: B  400 PHE cc_start: 0.6049 (p90) cc_final: 0.5639 (p90)
REVERT: B  461 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.6058 (mp)
REVERT: C  378 LYS cc_start: 0.8241 (ttpt) cc_final: 0.8001 (ttpt)
REVERT: A   28 THR cc_start: 0.9094 (m) cc_final: 0.8668 (p)
REVERT: A   32 TYR cc_start: 0.7486 (m-80) cc_final: 0.7074 (m-10)
REVERT: A   57 ASP cc_start: 0.7948 (OUTLIER) cc_final: 0.7544 (t70)
REVERT: D   55 ARG cc_start: 0.7775 (ttp-110) cc_final: 0.7519 (ttm110)
  outliers start: 27
  outliers final: 20
  residues processed: 114
  average time/residue: 0.2338
  time to fit residues: 32.2370
Evaluate side-chains
  116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.523 
-------------------------------------------------------------------------------
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  434 ILE
Chi-restraints excluded: chain B residue  461 LEU
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 C residue  441 LEU
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   20 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    5 THR
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   79 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:    0.6980
   chunk 22 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 23 optimal weight:    3.9990
   chunk 1 optimal weight:    8.9990
   chunk 40 optimal weight:    0.0870
   chunk 8 optimal weight:   20.0000
   chunk 3 optimal weight:    3.9990
   chunk 46 optimal weight:    6.9990
   chunk 0 optimal weight:    0.8980
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.5362

-------------------------------------------------------------------------------
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  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.172025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.127053 restraints weight = 9616.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.129881 restraints weight = 5631.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.131809 restraints weight = 4035.975|
|-----------------------------------------------------------------------------|
r_work (final): 0.3745
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7399
moved from start:          0.3884

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.070   4950  Z= 0.174
  Angle     :  0.644   7.987   6756  Z= 0.332
  Chirality :  0.046   0.165    728
  Planarity :  0.005   0.055    878
  Dihedral  :  5.286  36.412    696
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 11.16
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.83 %
    Favored  : 93.69 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 19.88 %
    Favored  : 74.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.34), residues: 618
  helix: -2.52 (0.79), residues: 37
  sheet: -0.18 (0.40), residues: 159
  loop : -0.80 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 111 
 HIS   0.002   0.001   HIS B 505 
 PHE   0.009   0.001   PHE C 377 
 TYR   0.023   0.002   TYR D  50 
 ARG   0.006   0.001   ARG C 346 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03287 (  140)
  hydrogen bonds       : angle       5.97947 (  333)
  SS BOND              : bond        0.00533 (    9)
  SS BOND              : angle       1.80373 (   18)
  covalent geometry    : bond        0.00416 ( 4941)
  covalent geometry    : angle       0.63768 ( 6738)

*********************** 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
  124 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 94
  time to evaluate  : 0.515 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5519 (OUTLIER) cc_final: 0.4677 (p90)
REVERT: B  461 LEU cc_start: 0.6344 (OUTLIER) cc_final: 0.5921 (mp)
REVERT: A   32 TYR cc_start: 0.7846 (m-80) cc_final: 0.7457 (m-10)
REVERT: A   57 ASP cc_start: 0.7917 (OUTLIER) cc_final: 0.7510 (t70)
REVERT: D   43 GLN cc_start: 0.8082 (mt0) cc_final: 0.7711 (mt0)
  outliers start: 30
  outliers final: 19
  residues processed: 111
  average time/residue: 0.1771
  time to fit residues: 24.7887
Evaluate side-chains
  109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 87
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
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  461 LEU
Chi-restraints excluded: chain C residue  338 PHE
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 C residue  441 LEU
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   12 VAL
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   23 CYS
Chi-restraints excluded: chain D residue   29 VAL
Chi-restraints excluded: chain D residue   64 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 1 optimal weight:    0.0030
   chunk 52 optimal weight:    9.9990
   chunk 2 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    0.5980
   chunk 7 optimal weight:    0.6980
   chunk 43 optimal weight:    0.7980
   chunk 8 optimal weight:    9.9990
   chunk 45 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 29 optimal weight:    2.9990
   overall best weight:    0.4590

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4299 r_free = 0.4299 target = 0.175537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.134811 restraints weight = 9396.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.135733 restraints weight = 5361.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.135822 restraints weight = 4193.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.4142

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4950  Z= 0.111
  Angle     :  0.604   8.115   6756  Z= 0.312
  Chirality :  0.045   0.155    728
  Planarity :  0.005   0.052    878
  Dihedral  :  4.994  32.906    696
  Min Nonbonded Distance : 2.522

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.53 %
    Favored  : 95.15 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 21.47 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.34), residues: 618
  helix: -2.72 (0.69), residues: 43
  sheet: -0.10 (0.41), residues: 161
  loop : -0.72 (0.32), residues: 414

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B 505 
 PHE   0.007   0.001   PHE C 374 
 TYR   0.023   0.001   TYR D  50 
 ARG   0.009   0.001   ARG A  19 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02935 (  140)
  hydrogen bonds       : angle       5.78197 (  333)
  SS BOND              : bond        0.00220 (    9)
  SS BOND              : angle       1.10777 (   18)
  covalent geometry    : bond        0.00258 ( 4941)
  covalent geometry    : angle       0.60211 ( 6738)

*********************** 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
  120 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 95
  time to evaluate  : 0.578 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.5447 (OUTLIER) cc_final: 0.4580 (p90)
REVERT: B  398 ASP cc_start: 0.6715 (m-30) cc_final: 0.5793 (p0)
REVERT: A   18 LEU cc_start: 0.8171 (tp) cc_final: 0.7827 (mp)
REVERT: A   32 TYR cc_start: 0.7531 (m-80) cc_final: 0.7143 (m-10)
REVERT: A   57 ASP cc_start: 0.7815 (t70) cc_final: 0.7497 (t70)
  outliers start: 25
  outliers final: 19
  residues processed: 108
  average time/residue: 0.1919
  time to fit residues: 25.7318
Evaluate side-chains
  107 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 87
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
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 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 A residue    3 GLN
Chi-restraints excluded: chain A residue   12 VAL
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    5 THR
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 23 optimal weight:    0.7980
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 46 optimal weight:   10.0000
   chunk 59 optimal weight:    0.4980
   chunk 45 optimal weight:    0.8980
   chunk 12 optimal weight:   10.0000
   chunk 6 optimal weight:   10.0000
   chunk 40 optimal weight:    0.4980
   overall best weight:    0.7382

-------------------------------------------------------------------------------
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  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.174808 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.130923 restraints weight = 9477.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.133777 restraints weight = 5516.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3826 r_free = 0.3826 target = 0.135779 restraints weight = 3916.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7332
moved from start:          0.4380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4950  Z= 0.121
  Angle     :  0.616   8.359   6756  Z= 0.316
  Chirality :  0.045   0.156    728
  Planarity :  0.005   0.054    878
  Dihedral  :  4.948  33.324    696
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  4.53 %
    Favored  : 94.98 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.91 (0.35), residues: 618
  helix: -2.70 (0.74), residues: 37
  sheet:  0.12 (0.41), residues: 157
  loop : -0.69 (0.32), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  47 
 HIS   0.003   0.001   HIS B 505 
 PHE   0.007   0.001   PHE C 377 
 TYR   0.021   0.001   TYR D  50 
 ARG   0.004   0.001   ARG B 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02949 (  140)
  hydrogen bonds       : angle       5.74942 (  333)
  SS BOND              : bond        0.00283 (    9)
  SS BOND              : angle       1.19564 (   18)
  covalent geometry    : bond        0.00287 ( 4941)
  covalent geometry    : angle       0.61337 ( 6738)

*********************** 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: 24
    poor density    : 88
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.5545 (OUTLIER) cc_final: 0.4640 (p90)
REVERT: A   18 LEU cc_start: 0.8157 (tp) cc_final: 0.7799 (mp)
REVERT: A   32 TYR cc_start: 0.7634 (m-80) cc_final: 0.7223 (m-10)
REVERT: A   57 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7489 (t70)
REVERT: D   43 GLN cc_start: 0.8045 (mt0) cc_final: 0.7681 (pm20)
REVERT: D  108 ILE cc_start: 0.4285 (OUTLIER) cc_final: 0.3619 (tp)
  outliers start: 24
  outliers final: 19
  residues processed: 100
  average time/residue: 0.1942
  time to fit residues: 24.2910
Evaluate side-chains
  106 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 84
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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 C residue  335 LEU
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 A residue   12 VAL
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    5 THR
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   94 THR
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 27 optimal weight:    0.0670
   chunk 4 optimal weight:   10.0000
   chunk 12 optimal weight:    9.9990
   chunk 8 optimal weight:    0.0570
   chunk 16 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 5 optimal weight:    0.2980
   chunk 9 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 10 optimal weight:    5.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.4236

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

Flipped N/Q/H residues before XYZ refinement:
B 448 ASN
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  84 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4310 r_free = 0.4310 target = 0.176527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.133492 restraints weight = 9489.275|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.136119 restraints weight = 5745.198|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.137835 restraints weight = 4150.125|
|-----------------------------------------------------------------------------|
r_work (final): 0.3829
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7277
moved from start:          0.4685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   4950  Z= 0.107
  Angle     :  0.615  10.098   6756  Z= 0.311
  Chirality :  0.045   0.153    728
  Planarity :  0.005   0.053    878
  Dihedral  :  4.774  29.963    696
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.37 %
    Favored  : 95.31 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.27 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.35), residues: 618
  helix: -2.63 (0.75), residues: 37
  sheet:  0.27 (0.42), residues: 155
  loop : -0.67 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 HIS   0.001   0.000   HIS C 519 
 PHE   0.008   0.001   PHE C 374 
 TYR   0.022   0.001   TYR D  50 
 ARG   0.005   0.001   ARG B 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02858 (  140)
  hydrogen bonds       : angle       5.62747 (  333)
  SS BOND              : bond        0.00189 (    9)
  SS BOND              : angle       0.96374 (   18)
  covalent geometry    : bond        0.00249 ( 4941)
  covalent geometry    : angle       0.61375 ( 6738)

*********************** 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
  117 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 93
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.5452 (OUTLIER) cc_final: 0.4640 (p90)
REVERT: B  398 ASP cc_start: 0.6542 (m-30) cc_final: 0.5642 (p0)
REVERT: A   18 LEU cc_start: 0.8083 (tp) cc_final: 0.7750 (mp)
REVERT: A   32 TYR cc_start: 0.7557 (m-80) cc_final: 0.7124 (m-10)
REVERT: A   57 ASP cc_start: 0.7793 (OUTLIER) cc_final: 0.7448 (t70)
REVERT: D  108 ILE cc_start: 0.3942 (OUTLIER) cc_final: 0.3340 (tp)
  outliers start: 24
  outliers final: 16
  residues processed: 105
  average time/residue: 0.1915
  time to fit residues: 25.0077
Evaluate side-chains
  102 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.569 
-------------------------------------------------------------------------------
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 C residue  335 LEU
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 A residue   12 VAL
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  108 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 22 optimal weight:    0.3980
   chunk 12 optimal weight:    9.9990
   chunk 36 optimal weight:    0.3980
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 46 optimal weight:    9.9990
   chunk 56 optimal weight:    0.0170
   chunk 58 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:    5.9990
   overall best weight:    0.4218

-------------------------------------------------------------------------------
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  84 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4321 r_free = 0.4321 target = 0.176919 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.133580 restraints weight = 9793.642|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.136443 restraints weight = 5596.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3866 r_free = 0.3866 target = 0.138730 restraints weight = 3931.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.3834
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7255
moved from start:          0.4903

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4950  Z= 0.107
  Angle     :  0.608   7.292   6756  Z= 0.311
  Chirality :  0.045   0.156    728
  Planarity :  0.005   0.053    878
  Dihedral  :  4.678  26.789    696
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.05 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  4.17 %
    Allowed  : 21.87 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.86 (0.35), residues: 618
  helix: -2.60 (0.76), residues: 37
  sheet:  0.27 (0.43), residues: 151
  loop : -0.71 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 436 
 HIS   0.002   0.001   HIS B 505 
 PHE   0.007   0.001   PHE C 374 
 TYR   0.022   0.001   TYR D  50 
 ARG   0.005   0.001   ARG B 357 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02825 (  140)
  hydrogen bonds       : angle       5.50884 (  333)
  SS BOND              : bond        0.00186 (    9)
  SS BOND              : angle       1.00359 (   18)
  covalent geometry    : bond        0.00253 ( 4941)
  covalent geometry    : angle       0.60612 ( 6738)

********************** 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
  110 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 89
  time to evaluate  : 0.524 
Fit side-chains
   revert: symmetry clash
REVERT: B  369 TYR cc_start: 0.5506 (OUTLIER) cc_final: 0.4783 (p90)
REVERT: B  398 ASP cc_start: 0.6468 (m-30) cc_final: 0.5634 (p0)
REVERT: A   32 TYR cc_start: 0.7596 (m-80) cc_final: 0.7219 (m-10)
REVERT: A   57 ASP cc_start: 0.7844 (OUTLIER) cc_final: 0.7480 (t70)
REVERT: D  108 ILE cc_start: 0.4053 (OUTLIER) cc_final: 0.3459 (tp)
  outliers start: 21
  outliers final: 18
  residues processed: 101
  average time/residue: 0.1774
  time to fit residues: 22.9852
Evaluate side-chains
  103 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 82
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
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  503 VAL
Chi-restraints excluded: chain C residue  335 LEU
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 A residue   12 VAL
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  108 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    0.8980
   chunk 47 optimal weight:    0.9990
   chunk 2 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 7 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    7.9990
   chunk 10 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 35 optimal weight:    0.2980
   overall best weight:    1.4386

-------------------------------------------------------------------------------
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**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.171815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.128040 restraints weight = 9498.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.130591 restraints weight = 5863.663|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.132272 restraints weight = 4296.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7391
moved from start:          0.4943

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.072   4950  Z= 0.167
  Angle     :  0.672   9.760   6756  Z= 0.340
  Chirality :  0.046   0.160    728
  Planarity :  0.005   0.060    878
  Dihedral  :  5.079  33.293    696
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.66 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 22.07 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.00 (0.34), residues: 618
  helix: -2.42 (0.86), residues: 31
  sheet:  0.19 (0.43), residues: 155
  loop : -0.89 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.002   TRP A 111 
 HIS   0.005   0.001   HIS B 505 
 PHE   0.014   0.001   PHE C 377 
 TYR   0.020   0.002   TYR D  50 
 ARG   0.007   0.001   ARG B 403 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03171 (  140)
  hydrogen bonds       : angle       5.82440 (  333)
  SS BOND              : bond        0.00536 (    9)
  SS BOND              : angle       1.62947 (   18)
  covalent geometry    : bond        0.00401 ( 4941)
  covalent geometry    : angle       0.66799 ( 6738)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2301.94 seconds
wall clock time: 40 minutes 47.88 seconds (2447.88 seconds total)