Starting phenix.real_space_refine
on Thu Mar  6 04:20:06 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ykj_33892/03_2025/7ykj_33892.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ykj_33892/03_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_33892/03_2025/7ykj_33892.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ykj_33892/03_2025/7ykj_33892.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ykj_33892/03_2025/7ykj_33892.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ykj_33892/03_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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/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: 3.76, per 1000 atoms: 0.78
  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: 1.15
  Conformation dependent library (CDL) restraints added in 592.9 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: 0.58
  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: 1.39 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:             2.700
  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:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.800
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.760
-------------------------------------------------------------------------------
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   4941  Z= 0.844
  Angle     :  1.781  13.371   6738  Z= 1.182
  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 

*********************** 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  : 0.553 
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: 0.2237
  time to fit residues: 34.7338
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  : 0.552 
-------------------------------------------------------------------------------
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:    0.9980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
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**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  90 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.175184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3736 r_free = 0.3736 target = 0.128521 restraints weight = 9639.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.131498 restraints weight = 5548.960|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3802 r_free = 0.3802 target = 0.133489 restraints weight = 3948.564|
|-----------------------------------------------------------------------------|
r_work (final): 0.3771
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7307
moved from start:          0.2229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4941  Z= 0.220
  Angle     :  0.675   6.743   6738  Z= 0.354
  Chirality :  0.047   0.200    728
  Planarity :  0.006   0.063    878
  Dihedral  :  6.107  43.639    702
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  5.02 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 18.29 %
    Favored  : 76.94 %
  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: -1.66 (0.34), residues: 618
  helix: -3.86 (0.49), residues: 43
  sheet: -1.15 (0.38), residues: 150
  loop : -0.76 (0.32), residues: 425

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 103 
 ARG   0.004   0.001   ARG C 408 

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

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

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

  1236 Ramachandran restraints generated.
    618 Oldfield, 0 Emsley, 618 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 110
  time to evaluate  : 0.511 
Fit side-chains
REVERT: B  400 PHE cc_start: 0.6167 (p90) cc_final: 0.5907 (p90)
REVERT: B  418 ILE cc_start: 0.7134 (OUTLIER) cc_final: 0.6867 (mm)
REVERT: B  457 ARG cc_start: 0.4909 (ttt-90) cc_final: 0.4657 (ttt180)
REVERT: A    3 GLN cc_start: 0.7067 (OUTLIER) cc_final: 0.6819 (pp30)
REVERT: A   28 THR cc_start: 0.9071 (m) cc_final: 0.8665 (p)
REVERT: A   57 ASP cc_start: 0.7958 (t70) cc_final: 0.7654 (t70)
REVERT: A   95 TYR cc_start: 0.8572 (m-80) cc_final: 0.8184 (m-80)
  outliers start: 24
  outliers final: 12
  residues processed: 125
  average time/residue: 0.1986
  time to fit residues: 30.4514
Evaluate side-chains
  101 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 87
  time to evaluate  : 0.551 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  331 ASN
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  383 SER
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   89 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:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 30 optimal weight:    2.9990
   chunk 2 optimal weight:    8.9990
   chunk 52 optimal weight:   20.0000
   chunk 23 optimal weight:    0.7980
   chunk 50 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 48 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    2.3186

-------------------------------------------------------------------------------
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 506 GLN
D  38 GLN
** D  91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.169399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 76)----------------|
| r_work = 0.3663 r_free = 0.3663 target = 0.124270 restraints weight = 9450.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.126665 restraints weight = 5991.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.128182 restraints weight = 4496.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7487
moved from start:          0.3197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.084   4941  Z= 0.357
  Angle     :  0.739   9.605   6738  Z= 0.385
  Chirality :  0.049   0.201    728
  Planarity :  0.006   0.066    878
  Dihedral  :  6.151  44.661    696
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 12.34
  Ramachandran Plot:
    Outliers :  0.81 %
    Allowed  :  6.63 %
    Favored  : 92.56 %
  Rotamer:
    Outliers :  7.36 %
    Allowed  : 18.69 %
    Favored  : 73.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 5.88 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.71 (0.33), residues: 618
  helix: -3.42 (0.57), residues: 43
  sheet: -0.72 (0.39), residues: 160
  loop : -1.06 (0.32), residues: 415

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 111 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.016   0.002   PHE B 338 
 TYR   0.023   0.002   TYR A  60 
 ARG   0.004   0.001   ARG D  78 

*********************** 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
  131 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 94
  time to evaluate  : 0.564 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5686 (OUTLIER) cc_final: 0.4950 (p90)
REVERT: B  418 ILE cc_start: 0.7115 (OUTLIER) cc_final: 0.6856 (mm)
REVERT: A   32 TYR cc_start: 0.7862 (m-80) cc_final: 0.7350 (m-10)
REVERT: A   57 ASP cc_start: 0.8023 (t70) cc_final: 0.7767 (t70)
REVERT: A   84 ASN cc_start: 0.7985 (p0) cc_final: 0.7640 (m-40)
REVERT: A   95 TYR cc_start: 0.8550 (m-80) cc_final: 0.8336 (m-80)
  outliers start: 37
  outliers final: 24
  residues processed: 116
  average time/residue: 0.1773
  time to fit residues: 26.1376
Evaluate side-chains
  110 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 84
  time to evaluate  : 0.504 
-------------------------------------------------------------------------------
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  368 LEU
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  398 ASP
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue  333 THR
Chi-restraints excluded: chain C residue  383 SER
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  389 ASP
Chi-restraints excluded: chain C residue  401 VAL
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  515 PHE
Chi-restraints excluded: chain A residue   12 VAL
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Chi-restraints excluded: chain D residue   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:    9.9990
   chunk 52 optimal weight:    6.9990
   chunk 43 optimal weight:    0.0370
   chunk 56 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9990
   chunk 20 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 4 optimal weight:    9.9990
   chunk 47 optimal weight:    3.9990
   chunk 58 optimal weight:    6.9990
   overall best weight:    1.3864

-------------------------------------------------------------------------------
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 = 0.4252 r_free = 0.4252 target = 0.171500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 84)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.126750 restraints weight = 9662.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.129254 restraints weight = 5987.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.130976 restraints weight = 4455.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.3725
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7437
moved from start:          0.3578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   4941  Z= 0.242
  Angle     :  0.650   8.497   6738  Z= 0.336
  Chirality :  0.047   0.213    728
  Planarity :  0.005   0.066    878
  Dihedral  :  5.732  43.174    696
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.51
  Ramachandran Plot:
    Outliers :  0.65 %
    Allowed  :  5.18 %
    Favored  : 94.17 %
  Rotamer:
    Outliers :  6.76 %
    Allowed  : 20.28 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.34), residues: 618
  helix: -2.85 (0.69), residues: 43
  sheet: -0.54 (0.41), residues: 156
  loop : -1.06 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.002   TRP A 111 
 HIS   0.002   0.001   HIS B 519 
 PHE   0.010   0.001   PHE D 100 
 TYR   0.016   0.002   TYR D  37 
 ARG   0.003   0.000   ARG A  19 

*********************** 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
  131 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 0.508 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5927 (OUTLIER) cc_final: 0.5001 (p90)
REVERT: B  403 ARG cc_start: 0.4944 (OUTLIER) cc_final: 0.4646 (ptm-80)
REVERT: B  418 ILE cc_start: 0.7170 (OUTLIER) cc_final: 0.6968 (mm)
REVERT: B  457 ARG cc_start: 0.5116 (ttt-90) cc_final: 0.4846 (ttt180)
REVERT: A   18 LEU cc_start: 0.7942 (tp) cc_final: 0.7739 (mt)
REVERT: A   32 TYR cc_start: 0.7777 (m-80) cc_final: 0.7356 (m-10)
REVERT: A   57 ASP cc_start: 0.8003 (OUTLIER) cc_final: 0.7653 (t70)
REVERT: D   55 ARG cc_start: 0.8244 (ttm110) cc_final: 0.8038 (ttm110)
  outliers start: 34
  outliers final: 24
  residues processed: 117
  average time/residue: 0.2019
  time to fit residues: 29.0555
Evaluate side-chains
  116 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 88
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
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  368 LEU
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  403 ARG
Chi-restraints excluded: chain B residue  418 ILE
Chi-restraints excluded: chain B residue  434 ILE
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  415 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   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   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
Chi-restraints excluded: chain D residue   89 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 49 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   chunk 54 optimal weight:    0.4980
   chunk 9 optimal weight:    7.9990
   chunk 56 optimal weight:   10.0000
   chunk 22 optimal weight:    0.8980
   chunk 44 optimal weight:    1.9990
   chunk 27 optimal weight:    0.8980
   chunk 2 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.4265 r_free = 0.4265 target = 0.172623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.128571 restraints weight = 9661.213|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3759 r_free = 0.3759 target = 0.131148 restraints weight = 5942.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.132876 restraints weight = 4319.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7374
moved from start:          0.3864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4941  Z= 0.179
  Angle     :  0.618   7.321   6738  Z= 0.319
  Chirality :  0.046   0.277    728
  Planarity :  0.005   0.060    878
  Dihedral  :  5.443  38.790    696
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.66 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.37 %
    Allowed  : 22.07 %
    Favored  : 72.56 %
  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: -1.37 (0.34), residues: 618
  helix: -2.96 (0.74), residues: 37
  sheet: -0.42 (0.41), residues: 158
  loop : -0.92 (0.32), residues: 423

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 111 
 HIS   0.002   0.001   HIS B 505 
 PHE   0.009   0.001   PHE D 100 
 TYR   0.015   0.001   TYR D  37 
 ARG   0.005   0.001   ARG B 357 

*********************** 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
  128 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 101
  time to evaluate  : 0.511 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5745 (OUTLIER) cc_final: 0.4881 (p90)
REVERT: B  403 ARG cc_start: 0.4874 (ptm-80) cc_final: 0.4639 (ptm-80)
REVERT: A   32 TYR cc_start: 0.7716 (m-80) cc_final: 0.7232 (m-10)
REVERT: A   57 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7644 (t70)
REVERT: D   87 TYR cc_start: 0.8473 (m-10) cc_final: 0.8239 (m-10)
  outliers start: 27
  outliers final: 17
  residues processed: 115
  average time/residue: 0.1829
  time to fit residues: 26.1817
Evaluate side-chains
  109 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 90
  time to evaluate  : 0.519 
-------------------------------------------------------------------------------
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  503 VAL
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  415 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain C residue  441 LEU
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   64 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 14 optimal weight:    5.9990
   chunk 22 optimal weight:    2.9990
   chunk 48 optimal weight:    3.9990
   chunk 23 optimal weight:    0.5980
   chunk 1 optimal weight:    1.9990
   chunk 40 optimal weight:    0.3980
   chunk 8 optimal weight:    9.9990
   chunk 3 optimal weight:    0.7980
   chunk 46 optimal weight:   10.0000
   chunk 0 optimal weight:    0.6980
   chunk 47 optimal weight:    0.2980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.4284 r_free = 0.4284 target = 0.174156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 77)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.130557 restraints weight = 9641.341|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.132986 restraints weight = 5972.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.134697 restraints weight = 4347.437|
|-----------------------------------------------------------------------------|
r_work (final): 0.3782
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7354
moved from start:          0.4182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4941  Z= 0.164
  Angle     :  0.597   8.126   6738  Z= 0.308
  Chirality :  0.046   0.258    728
  Planarity :  0.005   0.054    878
  Dihedral  :  5.203  36.575    696
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.18 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 21.47 %
    Favored  : 73.36 %
  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: -1.21 (0.35), residues: 618
  helix: -2.75 (0.78), residues: 37
  sheet: -0.26 (0.41), residues: 156
  loop : -0.84 (0.32), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 105 
 HIS   0.001   0.000   HIS B 519 
 PHE   0.008   0.001   PHE D 100 
 TYR   0.014   0.001   TYR D  37 
 ARG   0.004   0.001   ARG B 357 

*********************** 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
  121 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 95
  time to evaluate  : 0.642 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5630 (OUTLIER) cc_final: 0.4780 (p90)
REVERT: B  403 ARG cc_start: 0.4873 (OUTLIER) cc_final: 0.4504 (ptm-80)
REVERT: C  467 ASP cc_start: 0.6834 (t0) cc_final: 0.6604 (t0)
REVERT: A   18 LEU cc_start: 0.8085 (tp) cc_final: 0.7832 (tp)
REVERT: A   32 TYR cc_start: 0.7632 (m-80) cc_final: 0.7160 (m-10)
REVERT: A   57 ASP cc_start: 0.7866 (OUTLIER) cc_final: 0.7561 (t70)
REVERT: D  108 ILE cc_start: 0.4662 (OUTLIER) cc_final: 0.4048 (tp)
  outliers start: 26
  outliers final: 19
  residues processed: 109
  average time/residue: 0.2430
  time to fit residues: 33.8492
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  : 1.242 
-------------------------------------------------------------------------------
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  403 ARG
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain C residue  335 LEU
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   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   64 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 1 optimal weight:    0.0670
   chunk 52 optimal weight:    9.9990
   chunk 2 optimal weight:    5.9990
   chunk 26 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 43 optimal weight:    4.9990
   chunk 8 optimal weight:   10.0000
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   overall best weight:    1.1722

-------------------------------------------------------------------------------
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 = 0.4251 r_free = 0.4251 target = 0.171668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.127792 restraints weight = 9456.293|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.130263 restraints weight = 5833.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.131745 restraints weight = 4329.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.4390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058   4941  Z= 0.220
  Angle     :  0.627   7.864   6738  Z= 0.320
  Chirality :  0.046   0.263    728
  Planarity :  0.005   0.054    878
  Dihedral  :  5.290  36.513    696
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.83 %
    Favored  : 93.85 %
  Rotamer:
    Outliers :  5.96 %
    Allowed  : 20.68 %
    Favored  : 73.36 %
  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 (0.35), residues: 618
  helix: -2.39 (0.88), residues: 31
  sheet: -0.12 (0.42), residues: 156
  loop : -0.87 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 111 
 HIS   0.001   0.001   HIS B 505 
 PHE   0.010   0.001   PHE C 377 
 TYR   0.013   0.001   TYR C 473 
 ARG   0.005   0.001   ARG A  19 

*********************** 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
  126 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 96
  time to evaluate  : 1.033 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5848 (OUTLIER) cc_final: 0.4949 (p90)
REVERT: B  403 ARG cc_start: 0.4904 (OUTLIER) cc_final: 0.4573 (ptm-80)
REVERT: C  467 ASP cc_start: 0.6919 (t0) cc_final: 0.6603 (t0)
REVERT: A   18 LEU cc_start: 0.8113 (tp) cc_final: 0.7869 (tp)
REVERT: A   32 TYR cc_start: 0.7862 (m-80) cc_final: 0.7343 (m-10)
REVERT: A   57 ASP cc_start: 0.7952 (OUTLIER) cc_final: 0.7671 (t70)
REVERT: D  108 ILE cc_start: 0.4347 (OUTLIER) cc_final: 0.3730 (tp)
  outliers start: 30
  outliers final: 20
  residues processed: 113
  average time/residue: 0.2475
  time to fit residues: 35.0043
Evaluate side-chains
  113 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 89
  time to evaluate  : 0.693 
-------------------------------------------------------------------------------
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  403 ARG
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain B residue  519 HIS
Chi-restraints excluded: chain C residue  332 ILE
Chi-restraints excluded: chain C residue  385 THR
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    3 GLN
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   64 SER
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 ILE
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:    0.8980
   chunk 17 optimal weight:   20.0000
   chunk 8 optimal weight:    0.0030
   chunk 14 optimal weight:    0.6980
   chunk 46 optimal weight:   10.0000
   chunk 59 optimal weight:    0.3980
   chunk 45 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 6 optimal weight:    9.9990
   chunk 40 optimal weight:    0.5980
   overall best weight:    0.5190

-------------------------------------------------------------------------------
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 = 0.4292 r_free = 0.4292 target = 0.174950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.132769 restraints weight = 9542.804|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.135324 restraints weight = 5722.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.135512 restraints weight = 3712.427|
|-----------------------------------------------------------------------------|
r_work (final): 0.3781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.4606

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   4941  Z= 0.160
  Angle     :  0.599   6.371   6738  Z= 0.310
  Chirality :  0.046   0.241    728
  Planarity :  0.005   0.054    878
  Dihedral  :  5.046  33.286    696
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  4.85 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  4.37 %
    Allowed  : 21.87 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (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: -1.04 (0.35), residues: 618
  helix: -2.36 (0.87), residues: 31
  sheet: -0.01 (0.43), residues: 154
  loop : -0.83 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 105 
 HIS   0.001   0.000   HIS A  59 
 PHE   0.009   0.001   PHE D 100 
 TYR   0.014   0.001   TYR D  37 
 ARG   0.010   0.001   ARG A  19 

*********************** 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
  115 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.669 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5656 (OUTLIER) cc_final: 0.4820 (p90)
REVERT: B  403 ARG cc_start: 0.4868 (OUTLIER) cc_final: 0.4567 (ptm-80)
REVERT: C  467 ASP cc_start: 0.6845 (t0) cc_final: 0.6530 (t0)
REVERT: A   32 TYR cc_start: 0.7672 (m-80) cc_final: 0.7257 (m-10)
REVERT: A   57 ASP cc_start: 0.7888 (t70) cc_final: 0.7620 (t70)
REVERT: D   43 GLN cc_start: 0.8363 (mt0) cc_final: 0.7998 (mt0)
REVERT: D  108 ILE cc_start: 0.3696 (OUTLIER) cc_final: 0.3100 (tp)
  outliers start: 22
  outliers final: 16
  residues processed: 104
  average time/residue: 0.2184
  time to fit residues: 28.9677
Evaluate side-chains
  105 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.682 
-------------------------------------------------------------------------------
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  403 ARG
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue    3 GLN
Chi-restraints excluded: chain A residue   40 THR
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   48 LEU
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 4 optimal weight:    3.9990
   chunk 12 optimal weight:    6.9990
   chunk 8 optimal weight:    8.9990
   chunk 16 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 9 optimal weight:    7.9990
   chunk 43 optimal weight:    0.0470
   chunk 10 optimal weight:    8.9990
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.9682

-------------------------------------------------------------------------------
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 = 0.4271 r_free = 0.4271 target = 0.173072 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.129347 restraints weight = 9538.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.131813 restraints weight = 5836.650|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.133571 restraints weight = 4265.801|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7370
moved from start:          0.4700

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   4941  Z= 0.201
  Angle     :  0.631   8.105   6738  Z= 0.322
  Chirality :  0.046   0.249    728
  Planarity :  0.005   0.054    878
  Dihedral  :  5.073  33.230    696
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 9.98
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.34 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.47 %
    Favored  : 73.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (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: -1.15 (0.34), residues: 618
  helix: -2.42 (0.80), residues: 37
  sheet:  0.01 (0.42), residues: 155
  loop : -0.93 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 111 
 HIS   0.001   0.000   HIS B 505 
 PHE   0.011   0.001   PHE C 377 
 TYR   0.017   0.001   TYR A  95 
 ARG   0.005   0.001   ARG C 346 

*********************** 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
  115 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.605 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5715 (OUTLIER) cc_final: 0.4952 (p90)
REVERT: C  467 ASP cc_start: 0.6924 (t0) cc_final: 0.6579 (t0)
REVERT: A   32 TYR cc_start: 0.7818 (m-80) cc_final: 0.7285 (m-10)
REVERT: A   57 ASP cc_start: 0.7967 (OUTLIER) cc_final: 0.7651 (t70)
REVERT: D  108 ILE cc_start: 0.3755 (OUTLIER) cc_final: 0.3131 (tp)
  outliers start: 24
  outliers final: 18
  residues processed: 101
  average time/residue: 0.2089
  time to fit residues: 26.4471
Evaluate side-chains
  108 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 87
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain B residue  503 VAL
Chi-restraints excluded: chain C residue  385 THR
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   40 THR
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue    3 VAL
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 22 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 36 optimal weight:    2.9990
   chunk 29 optimal weight:    0.6980
   chunk 19 optimal weight:    0.5980
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:   10.0000
   chunk 56 optimal weight:    0.1980
   chunk 58 optimal weight:    6.9990
   chunk 47 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
B 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 = 0.4284 r_free = 0.4284 target = 0.174014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.130944 restraints weight = 9526.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.133457 restraints weight = 5808.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.135157 restraints weight = 4247.945|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7344
moved from start:          0.4841

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4941  Z= 0.180
  Angle     :  0.623   7.124   6738  Z= 0.320
  Chirality :  0.046   0.239    728
  Planarity :  0.005   0.053    878
  Dihedral  :  5.038  31.983    696
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 10.08
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  5.18 %
    Favored  : 94.50 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 22.66 %
    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: -1.04 (0.35), residues: 618
  helix: -2.64 (0.75), residues: 37
  sheet:  0.07 (0.42), residues: 155
  loop : -0.82 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 436 
 HIS   0.003   0.001   HIS B 505 
 PHE   0.009   0.001   PHE C 377 
 TYR   0.018   0.001   TYR A  60 
 ARG   0.008   0.001   ARG C 346 

********************** 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
  112 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 93
  time to evaluate  : 0.737 
Fit side-chains
REVERT: B  369 TYR cc_start: 0.5785 (OUTLIER) cc_final: 0.5046 (p90)
REVERT: C  467 ASP cc_start: 0.6860 (t0) cc_final: 0.6534 (t0)
REVERT: A   32 TYR cc_start: 0.7683 (m-80) cc_final: 0.7272 (m-10)
REVERT: A   57 ASP cc_start: 0.7856 (OUTLIER) cc_final: 0.7533 (t70)
REVERT: A   69 THR cc_start: 0.7888 (p) cc_final: 0.7586 (m)
REVERT: D   43 GLN cc_start: 0.8096 (mt0) cc_final: 0.7782 (pm20)
REVERT: D  108 ILE cc_start: 0.3594 (OUTLIER) cc_final: 0.2958 (tp)
  outliers start: 19
  outliers final: 16
  residues processed: 101
  average time/residue: 0.1837
  time to fit residues: 23.8080
Evaluate side-chains
  105 residues out of total 537 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.588 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  362 VAL
Chi-restraints excluded: chain B residue  364 ASP
Chi-restraints excluded: chain B residue  369 TYR
Chi-restraints excluded: chain B residue  399 SER
Chi-restraints excluded: chain B residue  434 ILE
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  385 THR
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  430 THR
Chi-restraints excluded: chain A residue   40 THR
Chi-restraints excluded: chain A residue   57 ASP
Chi-restraints excluded: chain A residue   79 VAL
Chi-restraints excluded: chain A residue  116 LEU
Chi-restraints excluded: chain A residue  117 VAL
Chi-restraints excluded: chain A residue  118 THR
Chi-restraints excluded: chain D residue   23 CYS
Chi-restraints excluded: chain D residue   94 THR
Chi-restraints excluded: chain D residue   98 LEU
Chi-restraints excluded: chain D residue  108 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 60
   random chunks:
   chunk 17 optimal weight:    6.9990
   chunk 47 optimal weight:    2.9990
   chunk 2 optimal weight:    0.9990
   chunk 11 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:   10.0000
   chunk 10 optimal weight:    8.9990
   chunk 22 optimal weight:    0.0170
   chunk 35 optimal weight:    0.5980
   overall best weight:    1.3224

-------------------------------------------------------------------------------
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 = 0.4261 r_free = 0.4261 target = 0.174268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.131161 restraints weight = 9618.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.133719 restraints weight = 5859.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.135430 restraints weight = 4254.653|
|-----------------------------------------------------------------------------|
r_work (final): 0.3751
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.5008

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   4941  Z= 0.240
  Angle     :  0.650   9.464   6738  Z= 0.332
  Chirality :  0.046   0.251    728
  Planarity :  0.005   0.055    878
  Dihedral  :  5.209  35.360    696
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 12.12
  Ramachandran Plot:
    Outliers :  0.49 %
    Allowed  :  5.50 %
    Favored  : 94.01 %
  Rotamer:
    Outliers :  4.97 %
    Allowed  : 22.07 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.94 %
    Twisted General : 0.00 %

Rama-Z (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 (0.35), residues: 618
  helix: -2.45 (0.85), residues: 31
  sheet:  0.14 (0.42), residues: 154
  loop : -0.85 (0.32), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.002   TRP A 111 
 HIS   0.002   0.001   HIS A  59 
 PHE   0.013   0.001   PHE C 377 
 TYR   0.013   0.001   TYR A  95 
 ARG   0.008   0.001   ARG C 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2522.27 seconds
wall clock time: 45 minutes 35.61 seconds (2735.61 seconds total)