Starting phenix.real_space_refine
on Tue Feb 11 21:13:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vke_43315/02_2025/8vke_43315.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vke_43315/02_2025/8vke_43315.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vke_43315/02_2025/8vke_43315.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vke_43315/02_2025/8vke_43315.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vke_43315/02_2025/8vke_43315.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vke_43315/02_2025/8vke_43315.cif"
  }
  resolution = 3.1
  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=  -0.000 sd=   0.022
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      30      5.16       5
     C    4218      2.51       5
     N    1114      2.21       5
     O    1290      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 6652
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "H"
      Number of atoms: 991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 991
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "L"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 825
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 7, 'TRANS': 105}
    Chain: "R"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1496
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 10, 'TRANS': 175}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 991
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 128, 991
          Classifications: {'peptide': 128}
          Link IDs: {'PTRANS': 5, 'TRANS': 122}
    Chain: "B"
      Number of atoms: 825
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 825
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 7, 'TRANS': 105}
    Chain: "C"
      Number of atoms: 1496
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 186, 1496
          Classifications: {'peptide': 186}
          Link IDs: {'PTRANS': 10, 'TRANS': 175}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 7.38, per 1000 atoms: 1.11
  Number of scatterers: 6652
  At special positions: 0
  Unit cell: (81.78, 88.36, 103.4, 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      30     16.00
     O    1290      8.00
     N    1114      7.00
     C    4218      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=12, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.02
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 336 " - pdb=" SG  CYS R 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 379 " - pdb=" SG  CYS R 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 391 " - pdb=" SG  CYS R 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 480 " - pdb=" SG  CYS R 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03

  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
  Links applied
    NAG-ASN
      " NAG C1301 " - " ASN C 343 "
      " NAG R1301 " - " ASN R 343 "
  Time building additional restraints: 1.66
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1572

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 20 sheets defined
      12.2% alpha, 35.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.91
  Creating SS restraints...
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'H' and resid 99 through 100A
      No H-bonds generated for 'chain 'H' and resid 99 through 100A'
    Processing helix  chain 'L' and resid 27A through 30
    Processing helix  chain 'R' and resid 338 through 343
    Processing helix  chain 'R' and resid 349 through 353
      removed outlier: 3.616A  pdb=" N   TRP R 353 " --> pdb=" O   VAL R 350 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 364 through 372
      removed outlier: 3.756A  pdb=" N   LEU R 368 " --> pdb=" O   ASP R 364 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 383 through 387
      removed outlier: 3.820A  pdb=" N   LEU R 387 " --> pdb=" O   PRO R 384 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 404 through 410
      removed outlier: 3.687A  pdb=" N   VAL R 407 " --> pdb=" O   GLY R 404 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   ARG R 408 " --> pdb=" O   ASP R 405 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   GLN R 409 " --> pdb=" O   GLU R 406 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 416 through 422
    Processing helix  chain 'A' and resid 83 through 87
    Processing helix  chain 'A' and resid 99 through 100A
      No H-bonds generated for 'chain 'A' and resid 99 through 100A'
    Processing helix  chain 'B' and resid 27A through 30
    Processing helix  chain 'C' and resid 338 through 343
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.575A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 364 through 372
      removed outlier: 3.566A  pdb=" N   LEU C 368 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 383 through 387
      removed outlier: 3.796A  pdb=" N   LEU C 387 " --> pdb=" O   PRO C 384 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 408
      removed outlier: 3.751A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6
    Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12
      removed outlier: 6.981A  pdb=" N   VAL H  35A" --> pdb=" O   ASP H  50 " (cutoff:3.500A)
      removed outlier: 4.585A  pdb=" N   ASP H  50 " --> pdb=" O   VAL H  35A" (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   TRP H  36 " --> pdb=" O   LEU H  48 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12
      removed outlier: 4.063A  pdb=" N   ASN H 102 " --> pdb=" O   ARG H  94 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   ALA H  96 " --> pdb=" O   PHE H 100K" (cutoff:3.500A)
      removed outlier: 4.967A  pdb=" N   PHE H 100K" --> pdb=" O   ALA H  96 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 100C through 100E
    Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 13
      removed outlier: 6.322A  pdb=" N   TRP L  35 " --> pdb=" O   LEU L  47 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 13
    Processing sheet with id=AA7, first strand: chain 'L' and resid 19 through 24
    Processing sheet with id=AA8, first strand: chain 'R' and resid 391 through 392
      removed outlier: 3.861A  pdb=" N   PHE R 392 " --> pdb=" O   VAL R 524 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   VAL R 524 " --> pdb=" O   PHE R 392 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'R' and resid 452 through 454
    Processing sheet with id=AB1, first strand: chain 'R' and resid 473 through 474
    Processing sheet with id=AB2, first strand: chain 'A' and resid 3 through 6
    Processing sheet with id=AB3, first strand: chain 'A' and resid 10 through 12
      removed outlier: 6.915A  pdb=" N   VAL A  35A" --> pdb=" O   ASP A  50 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   ASP A  50 " --> pdb=" O   VAL A  35A" (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   TRP A  36 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12
      removed outlier: 4.054A  pdb=" N   ASN A 102 " --> pdb=" O   ARG A  94 " (cutoff:3.500A)
      removed outlier: 6.953A  pdb=" N   ALA A  96 " --> pdb=" O   PHE A 100K" (cutoff:3.500A)
      removed outlier: 4.993A  pdb=" N   PHE A 100K" --> pdb=" O   ALA A  96 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 100C through 100E
    Processing sheet with id=AB6, first strand: chain 'B' and resid 9 through 13
      removed outlier: 6.330A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 9 through 13
    Processing sheet with id=AB8, first strand: chain 'B' and resid 19 through 24
    Processing sheet with id=AB9, first strand: chain 'C' and resid 361 through 362
      removed outlier: 6.766A  pdb=" N   CYS C 361 " --> pdb=" O   CYS C 525 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB9
    Processing sheet with id=AC1, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AC2, first strand: chain 'C' and resid 473 through 474

    248 hydrogen bonds defined for protein.
    558 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.01

  Time building geometry restraints manager: 1.90 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 2123
        1.35 -     1.48: 1885
        1.48 -     1.60: 2772
        1.60 -     1.72: 0
        1.72 -     1.85: 36
  Bond restraints: 6816
  Sorted by residual:
  bond pdb=" N   VAL B  11 "
       pdb=" CA  VAL B  11 "
    ideal  model  delta    sigma   weight residual
    1.456  1.495 -0.040 1.11e-02 8.12e+03 1.28e+01
  bond pdb=" C   GLN B   6 "
       pdb=" N   PRO B   7 "
    ideal  model  delta    sigma   weight residual
    1.329  1.363 -0.034 1.18e-02 7.18e+03 8.35e+00
  bond pdb=" N   SER B   9 "
       pdb=" CA  SER B   9 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.030 1.23e-02 6.61e+03 5.97e+00
  bond pdb=" N   CYS R 480 "
       pdb=" CA  CYS R 480 "
    ideal  model  delta    sigma   weight residual
    1.456  1.486 -0.029 1.21e-02 6.83e+03 5.84e+00
  bond pdb=" N   LYS R 478 "
       pdb=" CA  LYS R 478 "
    ideal  model  delta    sigma   weight residual
    1.454  1.485 -0.030 1.45e-02 4.76e+03 4.34e+00
  ... (remaining 6811 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.49: 8977
        1.49 -     2.98: 260
        2.98 -     4.47: 31
        4.47 -     5.95: 1
        5.95 -     7.44: 1
  Bond angle restraints: 9270
  Sorted by residual:
  angle pdb=" CA  VAL B  11 "
        pdb=" C   VAL B  11 "
        pdb=" O   VAL B  11 "
      ideal   model   delta    sigma   weight residual
     121.67  118.17    3.50 1.05e+00 9.07e-01 1.11e+01
  angle pdb=" CA  CYS R 391 "
        pdb=" CB  CYS R 391 "
        pdb=" SG  CYS R 391 "
      ideal   model   delta    sigma   weight residual
     114.40  121.84   -7.44 2.30e+00 1.89e-01 1.05e+01
  angle pdb=" CA  SER B   9 "
        pdb=" C   SER B   9 "
        pdb=" O   SER B   9 "
      ideal   model   delta    sigma   weight residual
     121.23  118.05    3.18 1.07e+00 8.73e-01 8.85e+00
  angle pdb=" N   PRO B   7 "
        pdb=" CA  PRO B   7 "
        pdb=" C   PRO B   7 "
      ideal   model   delta    sigma   weight residual
     110.70  107.15    3.55 1.22e+00 6.72e-01 8.48e+00
  angle pdb=" O   GLN B   6 "
        pdb=" C   GLN B   6 "
        pdb=" N   PRO B   7 "
      ideal   model   delta    sigma   weight residual
     121.55  119.38    2.17 7.80e-01 1.64e+00 7.76e+00
  ... (remaining 9265 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.11: 3642
       17.11 -    34.22: 308
       34.22 -    51.33: 79
       51.33 -    68.45: 16
       68.45 -    85.56: 11
  Dihedral angle restraints: 4056
    sinusoidal: 1588
      harmonic: 2468
  Sorted by residual:
  dihedral pdb=" CB  CYS R 480 "
           pdb=" SG  CYS R 480 "
           pdb=" SG  CYS R 488 "
           pdb=" CB  CYS R 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.41  -75.41     1      1.00e+01 1.00e-02 7.18e+01
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  161.94  -68.94     1      1.00e+01 1.00e-02 6.15e+01
  dihedral pdb=" CB  CYS C 336 "
           pdb=" SG  CYS C 336 "
           pdb=" SG  CYS C 361 "
           pdb=" CB  CYS C 361 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -38.05  -47.95     1      1.00e+01 1.00e-02 3.17e+01
  ... (remaining 4053 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 693
       0.037 -    0.074: 217
       0.074 -    0.111: 78
       0.111 -    0.148: 31
       0.148 -    0.185: 3
  Chirality restraints: 1022
  Sorted by residual:
  chirality pdb=" CA  VAL B  11 "
            pdb=" N   VAL B  11 "
            pdb=" C   VAL B  11 "
            pdb=" CB  VAL B  11 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.18 2.00e-01 2.50e+01 8.52e-01
  chirality pdb=" CA  ILE B  48 "
            pdb=" N   ILE B  48 "
            pdb=" C   ILE B  48 "
            pdb=" CB  ILE B  48 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.59   -0.16 2.00e-01 2.50e+01 6.50e-01
  chirality pdb=" CA  ASN B  52 "
            pdb=" N   ASN B  52 "
            pdb=" C   ASN B  52 "
            pdb=" CB  ASN B  52 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.89e-01
  ... (remaining 1019 not shown)

  Planarity restraints: 1194
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS C 478 "   -0.052 5.00e-02 4.00e+02   7.77e-02 9.66e+00
        pdb=" N   PRO C 479 "    0.134 5.00e-02 4.00e+02
        pdb=" CA  PRO C 479 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO C 479 "   -0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 372 "    0.020 5.00e-02 4.00e+02   3.02e-02 1.46e+00
        pdb=" N   PRO C 373 "   -0.052 5.00e-02 4.00e+02
        pdb=" CA  PRO C 373 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 373 "    0.016 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL C 362 "    0.006 2.00e-02 2.50e+03   1.17e-02 1.37e+00
        pdb=" C   VAL C 362 "   -0.020 2.00e-02 2.50e+03
        pdb=" O   VAL C 362 "    0.008 2.00e-02 2.50e+03
        pdb=" N   ALA C 363 "    0.007 2.00e-02 2.50e+03
  ... (remaining 1191 not shown)

  Histogram of nonbonded interaction distances:
        2.10 -     2.66: 111
        2.66 -     3.22: 5977
        3.22 -     3.78: 10000
        3.78 -     4.34: 14631
        4.34 -     4.90: 24437
  Nonbonded interactions: 55156
  Sorted by model distance:
  nonbonded pdb=" O   SER C 366 "
            pdb=" ND2 ASN C 370 "
     model   vdw
     2.103 3.120
  nonbonded pdb=" O   PHE R 486 "
            pdb=" ND2 ASN C 450 "
     model   vdw
     2.240 3.120
  nonbonded pdb=" O   TRP R 353 "
            pdb=" NH1 ARG R 466 "
     model   vdw
     2.275 3.120
  nonbonded pdb=" NH1 ARG H  71 "
            pdb=" OG1 THR H  73 "
     model   vdw
     2.281 3.120
  nonbonded pdb=" N   GLN H 105 "
            pdb=" OE1 GLN H 105 "
     model   vdw
     2.294 3.120
  ... (remaining 55151 not shown)

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

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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             28.760
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.000
  Check model and map are aligned:         0.000
  Set scattering table:                    0.000
  Process input model:                     20.220
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  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:2.530
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   51.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8303
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      :  0.003   0.050   6816  Z= 0.224
  Angle     :  0.591   7.443   9270  Z= 0.349
  Chirality :  0.045   0.185   1022
  Planarity :  0.004   0.078   1192
  Dihedral  : 14.192  85.558   2448
  Min Nonbonded Distance : 2.103

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  : 13.86 %
    Favored  : 86.01 %
  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: -0.05 (0.28), residues: 838
  helix: -3.52 (0.46), residues: 64
  sheet:  1.18 (0.33), residues: 276
  loop : -0.22 (0.25), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  47 
 HIS   0.001   0.000   HIS C 505 
 PHE   0.013   0.001   PHE R 392 
 TYR   0.018   0.001   TYR L  49 
 ARG   0.004   0.000   ARG C 346 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 0.740 
Fit side-chains
REVERT: L   17 GLN cc_start: 0.7476 (mm-40) cc_final: 0.7062 (tt0)
REVERT: L   78 LEU cc_start: 0.7864 (tp) cc_final: 0.7593 (mt)
REVERT: R  466 ARG cc_start: 0.8088 (ptm160) cc_final: 0.7887 (ptt180)
  outliers start: 1
  outliers final: 1
  residues processed: 109
  average time/residue: 0.1935
  time to fit residues: 28.0552
Evaluate side-chains
  105 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 104
  time to evaluate  : 0.704 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  427 ASP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 69 optimal weight:    1.9990
   chunk 62 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 21 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 33 optimal weight:    0.6980
   chunk 64 optimal weight:    0.6980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
R 487 ASN
C 448 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.133950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.107965 restraints weight = 8282.215|
|-----------------------------------------------------------------------------|
r_work (start): 0.3202 rms_B_bonded: 1.93
r_work: 0.3069 rms_B_bonded: 2.29 restraints_weight: 0.5000
r_work: 0.2930 rms_B_bonded: 3.80 restraints_weight: 0.2500
r_work (final): 0.2930
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8389
moved from start:          0.1002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.037   6816  Z= 0.352
  Angle     :  0.608   7.729   9270  Z= 0.330
  Chirality :  0.048   0.172   1022
  Planarity :  0.005   0.052   1192
  Dihedral  :  5.979  53.158    980
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 3.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 12.91 %
    Favored  : 84.65 %
  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: -0.40 (0.27), residues: 838
  helix: -3.90 (0.44), residues: 54
  sheet:  0.81 (0.32), residues: 278
  loop : -0.44 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.002   0.001   HIS B  34 
 PHE   0.012   0.002   PHE R 392 
 TYR   0.027   0.002   TYR L  49 
 ARG   0.003   0.000   ARG C 403 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.747 
Fit side-chains
REVERT: L   17 GLN cc_start: 0.7320 (mm-40) cc_final: 0.7084 (tt0)
REVERT: L   69 THR cc_start: 0.9082 (t) cc_final: 0.8542 (m)
REVERT: L   78 LEU cc_start: 0.7986 (tp) cc_final: 0.7621 (mt)
REVERT: A   56 GLU cc_start: 0.8639 (mp0) cc_final: 0.8419 (mt-10)
  outliers start: 18
  outliers final: 11
  residues processed: 112
  average time/residue: 0.2042
  time to fit residues: 30.1623
Evaluate side-chains
  111 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.700 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  415 THR
Chi-restraints excluded: chain C residue  470 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 39 optimal weight:    0.9980
   chunk 78 optimal weight:    3.9990
   chunk 22 optimal weight:    0.6980
   chunk 3 optimal weight:    1.9990
   chunk 79 optimal weight:    0.0870
   chunk 7 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 68 optimal weight:    0.3980
   chunk 25 optimal weight:    0.0870
   chunk 53 optimal weight:    0.2980
   chunk 69 optimal weight:    0.7980
   overall best weight:    0.3136

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

Flipped N/Q/H residues before XYZ refinement:
C 370 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.139641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.110953 restraints weight = 8230.787|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 1.93
r_work: 0.3079 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8263
moved from start:          0.1185

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6816  Z= 0.173
  Angle     :  0.510   7.645   9270  Z= 0.276
  Chirality :  0.044   0.170   1022
  Planarity :  0.004   0.046   1192
  Dihedral  :  5.572  53.146    978
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.86 %
    Favored  : 97.14 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.81 %
    Favored  : 83.02 %
  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: -0.41 (0.27), residues: 838
  helix: -3.83 (0.44), residues: 54
  sheet:  0.81 (0.32), residues: 278
  loop : -0.46 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.002   0.000   HIS B  34 
 PHE   0.007   0.001   PHE L  91 
 TYR   0.014   0.001   TYR B  49 
 ARG   0.004   0.000   ARG R 466 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 105
  time to evaluate  : 1.290 
Fit side-chains
REVERT: H   76 SER cc_start: 0.8405 (m) cc_final: 0.8043 (p)
REVERT: L   17 GLN cc_start: 0.7249 (mm-40) cc_final: 0.6959 (tt0)
REVERT: L   69 THR cc_start: 0.9064 (t) cc_final: 0.8549 (m)
REVERT: L   78 LEU cc_start: 0.7895 (tp) cc_final: 0.7543 (mt)
REVERT: R  466 ARG cc_start: 0.8305 (ptm-80) cc_final: 0.7982 (ptt180)
REVERT: A   56 GLU cc_start: 0.8538 (OUTLIER) cc_final: 0.8243 (mt-10)
  outliers start: 16
  outliers final: 12
  residues processed: 114
  average time/residue: 0.2100
  time to fit residues: 31.7859
Evaluate side-chains
  116 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 103
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   97 ASN
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  470 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 71 optimal weight:    0.5980
   chunk 1 optimal weight:    0.4980
   chunk 18 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 5 optimal weight:    1.9990
   chunk 8 optimal weight:    0.2980
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0980
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.4580

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

Flipped N/Q/H residues before XYZ refinement:
R 448 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.138682 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.109667 restraints weight = 8234.985|
|-----------------------------------------------------------------------------|
r_work (start): 0.3199 rms_B_bonded: 1.95
r_work: 0.3075 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2933 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2933
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8290
moved from start:          0.1393

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6816  Z= 0.221
  Angle     :  0.516   6.139   9270  Z= 0.279
  Chirality :  0.045   0.167   1022
  Planarity :  0.004   0.033   1192
  Dihedral  :  5.539  52.759    978
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 3.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.10 %
    Favored  : 96.90 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.40 %
    Favored  : 82.61 %
  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: -0.47 (0.27), residues: 838
  helix: -3.75 (0.47), residues: 54
  sheet:  0.76 (0.31), residues: 278
  loop : -0.51 (0.25), residues: 506

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  47 
 HIS   0.001   0.001   HIS B  34 
 PHE   0.008   0.001   PHE B  91 
 TYR   0.020   0.001   TYR L  49 
 ARG   0.003   0.000   ARG C 346 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 108
  time to evaluate  : 0.870 
Fit side-chains
REVERT: H   76 SER cc_start: 0.8377 (m) cc_final: 0.8051 (p)
REVERT: L   17 GLN cc_start: 0.7303 (mm-40) cc_final: 0.6948 (tt0)
REVERT: L   69 THR cc_start: 0.9152 (t) cc_final: 0.8668 (m)
REVERT: L   78 LEU cc_start: 0.7914 (tp) cc_final: 0.7605 (mt)
REVERT: A   56 GLU cc_start: 0.8591 (OUTLIER) cc_final: 0.8223 (mt-10)
REVERT: C  501 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.8039 (m-10)
  outliers start: 22
  outliers final: 16
  residues processed: 122
  average time/residue: 0.2010
  time to fit residues: 32.4247
Evaluate side-chains
  119 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 6 optimal weight:    2.9990
   chunk 72 optimal weight:    0.6980
   chunk 67 optimal weight:    0.9980
   chunk 34 optimal weight:    1.9990
   chunk 8 optimal weight:    6.9990
   chunk 32 optimal weight:    0.5980
   chunk 25 optimal weight:    0.2980
   chunk 61 optimal weight:    0.9980
   chunk 24 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
C 370 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.134846 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.105832 restraints weight = 8151.896|
|-----------------------------------------------------------------------------|
r_work (start): 0.3163 rms_B_bonded: 1.96
r_work: 0.3039 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2897 rms_B_bonded: 3.95 restraints_weight: 0.2500
r_work (final): 0.2897
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8323
moved from start:          0.1637

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   6816  Z= 0.293
  Angle     :  0.553   5.495   9270  Z= 0.299
  Chirality :  0.046   0.171   1022
  Planarity :  0.004   0.037   1192
  Dihedral  :  5.682  52.704    978
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 14.54 %
    Favored  : 82.07 %
  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: -0.63 (0.27), residues: 838
  helix: -3.76 (0.48), residues: 50
  sheet:  0.64 (0.32), residues: 278
  loop : -0.67 (0.24), residues: 510

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP H  47 
 HIS   0.002   0.001   HIS R 505 
 PHE   0.009   0.001   PHE A  52 
 TYR   0.022   0.002   TYR L  49 
 ARG   0.004   0.000   ARG H  71 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 105
  time to evaluate  : 0.708 
Fit side-chains
REVERT: H   76 SER cc_start: 0.8419 (m) cc_final: 0.8099 (p)
REVERT: L   17 GLN cc_start: 0.7355 (mm-40) cc_final: 0.6978 (tt0)
REVERT: L   69 THR cc_start: 0.9163 (t) cc_final: 0.8692 (m)
REVERT: L   78 LEU cc_start: 0.7854 (tp) cc_final: 0.7516 (mt)
REVERT: A   56 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8139 (mt-10)
REVERT: C  501 TYR cc_start: 0.8666 (OUTLIER) cc_final: 0.8148 (m-10)
  outliers start: 25
  outliers final: 18
  residues processed: 121
  average time/residue: 0.2052
  time to fit residues: 32.3219
Evaluate side-chains
  123 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  415 THR
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 63 optimal weight:    0.1980
   chunk 71 optimal weight:    0.5980
   chunk 2 optimal weight:    0.4980
   chunk 70 optimal weight:    0.4980
   chunk 41 optimal weight:    2.9990
   chunk 31 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0770
   chunk 79 optimal weight:    0.5980
   chunk 58 optimal weight:    0.7980
   chunk 26 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0980
   overall best weight:    0.2738

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.139400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.111756 restraints weight = 8103.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3279 rms_B_bonded: 1.95
r_work: 0.3152 rms_B_bonded: 2.32 restraints_weight: 0.5000
r_work: 0.3009 rms_B_bonded: 3.86 restraints_weight: 0.2500
r_work (final): 0.3009
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8324
moved from start:          0.1720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   6816  Z= 0.159
  Angle     :  0.490   5.649   9270  Z= 0.265
  Chirality :  0.043   0.166   1022
  Planarity :  0.004   0.032   1192
  Dihedral  :  5.482  52.979    978
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 4.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.34 %
    Favored  : 96.66 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.08 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.61 (0.27), residues: 838
  helix: -3.82 (0.46), residues: 54
  sheet:  0.90 (0.33), residues: 248
  loop : -0.67 (0.24), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.007   0.001   PHE L  91 
 TYR   0.013   0.001   TYR L  49 
 ARG   0.002   0.000   ARG H  71 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 108
  time to evaluate  : 0.806 
Fit side-chains
REVERT: L   17 GLN cc_start: 0.7372 (mm-40) cc_final: 0.7105 (tt0)
REVERT: L   69 THR cc_start: 0.9091 (t) cc_final: 0.8604 (m)
REVERT: L   78 LEU cc_start: 0.7924 (tp) cc_final: 0.7707 (mt)
REVERT: R  409 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8868 (pt0)
REVERT: A   56 GLU cc_start: 0.8635 (OUTLIER) cc_final: 0.8238 (mt-10)
REVERT: C  501 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7976 (m-10)
  outliers start: 26
  outliers final: 19
  residues processed: 125
  average time/residue: 0.2237
  time to fit residues: 36.1115
Evaluate side-chains
  122 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 0.787 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  389 ASP
Chi-restraints excluded: chain R residue  409 GLN
Chi-restraints excluded: chain R residue  415 THR
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 77 optimal weight:    0.9980
   chunk 42 optimal weight:    2.9990
   chunk 56 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0070
   chunk 69 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 1 optimal weight:    0.8980
   overall best weight:    0.5798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.135863 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.105344 restraints weight = 8098.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3141 rms_B_bonded: 2.18
r_work: 0.3015 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8021
moved from start:          0.1839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6816  Z= 0.261
  Angle     :  0.537   5.107   9270  Z= 0.290
  Chirality :  0.045   0.169   1022
  Planarity :  0.004   0.038   1192
  Dihedral  :  5.557  52.670    978
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 4.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 15.35 %
    Favored  : 81.25 %
  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: -0.67 (0.27), residues: 838
  helix: -3.79 (0.46), residues: 54
  sheet:  0.85 (0.33), residues: 248
  loop : -0.72 (0.24), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS B  34 
 PHE   0.009   0.001   PHE A  52 
 TYR   0.021   0.002   TYR L  49 
 ARG   0.004   0.000   ARG H  71 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 104
  time to evaluate  : 0.732 
Fit side-chains
REVERT: H   64 LYS cc_start: 0.7509 (OUTLIER) cc_final: 0.7122 (tptm)
REVERT: L   17 GLN cc_start: 0.7194 (mm-40) cc_final: 0.6638 (tt0)
REVERT: L   69 THR cc_start: 0.8936 (t) cc_final: 0.8457 (m)
REVERT: L   78 LEU cc_start: 0.7644 (tp) cc_final: 0.7378 (mt)
REVERT: A   56 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7982 (mt-10)
REVERT: C  501 TYR cc_start: 0.8511 (OUTLIER) cc_final: 0.7844 (m-10)
  outliers start: 25
  outliers final: 19
  residues processed: 120
  average time/residue: 0.2208
  time to fit residues: 34.5509
Evaluate side-chains
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.727 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  389 ASP
Chi-restraints excluded: chain R residue  415 THR
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 70 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 69 optimal weight:    0.5980
   chunk 71 optimal weight:    0.5980
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0470
   chunk 19 optimal weight:    0.6980
   chunk 39 optimal weight:    0.0970
   overall best weight:    0.3876

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.137063 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.106562 restraints weight = 8095.641|
|-----------------------------------------------------------------------------|
r_work (start): 0.3157 rms_B_bonded: 2.18
r_work: 0.3032 rms_B_bonded: 2.59 restraints_weight: 0.5000
r_work: 0.2886 rms_B_bonded: 4.17 restraints_weight: 0.2500
r_work (final): 0.2886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6816  Z= 0.193
  Angle     :  0.505   4.429   9270  Z= 0.273
  Chirality :  0.044   0.168   1022
  Planarity :  0.004   0.032   1192
  Dihedral  :  5.493  52.810    978
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 4.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.35 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.64 (0.27), residues: 838
  helix: -3.73 (0.48), residues: 54
  sheet:  0.83 (0.33), residues: 248
  loop : -0.68 (0.24), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 HIS   0.001   0.000   HIS B  34 
 PHE   0.007   0.001   PHE L  91 
 TYR   0.017   0.001   TYR L  49 
 ARG   0.004   0.000   ARG C 346 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 103
  time to evaluate  : 0.715 
Fit side-chains
REVERT: H   64 LYS cc_start: 0.7503 (OUTLIER) cc_final: 0.7124 (tptm)
REVERT: L   17 GLN cc_start: 0.7168 (mm-40) cc_final: 0.6626 (tt0)
REVERT: L   69 THR cc_start: 0.8919 (t) cc_final: 0.8439 (m)
REVERT: L   78 LEU cc_start: 0.7602 (tp) cc_final: 0.7384 (mt)
REVERT: A   56 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7990 (mt-10)
REVERT: C  501 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.7740 (m-10)
  outliers start: 24
  outliers final: 19
  residues processed: 118
  average time/residue: 0.2183
  time to fit residues: 33.3983
Evaluate side-chains
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 102
  time to evaluate  : 0.728 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain H residue  108 LEU
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  389 ASP
Chi-restraints excluded: chain R residue  415 THR
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9980
   chunk 49 optimal weight:    0.3980
   chunk 29 optimal weight:    0.6980
   chunk 30 optimal weight:    0.6980
   chunk 9 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 45 optimal weight:    0.5980
   overall best weight:    0.6180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.135387 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.104317 restraints weight = 8190.712|
|-----------------------------------------------------------------------------|
r_work (start): 0.3142 rms_B_bonded: 2.26
r_work: 0.3013 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.2864 rms_B_bonded: 4.32 restraints_weight: 0.2500
r_work (final): 0.2864
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8023
moved from start:          0.1942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6816  Z= 0.271
  Angle     :  0.539   5.512   9270  Z= 0.291
  Chirality :  0.045   0.169   1022
  Planarity :  0.004   0.033   1192
  Dihedral  :  5.590  52.715    978
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.70 %
    Favored  : 96.30 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 15.35 %
    Favored  : 81.11 %
  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: -0.68 (0.27), residues: 838
  helix: -3.37 (0.49), residues: 66
  sheet:  0.81 (0.34), residues: 248
  loop : -0.68 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  47 
 HIS   0.001   0.001   HIS B  34 
 PHE   0.009   0.001   PHE A  52 
 TYR   0.021   0.002   TYR L  49 
 ARG   0.004   0.000   ARG C 346 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 104
  time to evaluate  : 0.677 
Fit side-chains
REVERT: H   64 LYS cc_start: 0.7617 (OUTLIER) cc_final: 0.7224 (tptm)
REVERT: L   17 GLN cc_start: 0.7172 (mm-40) cc_final: 0.6606 (tt0)
REVERT: L   69 THR cc_start: 0.8934 (t) cc_final: 0.8467 (m)
REVERT: L   78 LEU cc_start: 0.7639 (tp) cc_final: 0.7386 (mt)
REVERT: A   56 GLU cc_start: 0.8575 (OUTLIER) cc_final: 0.7959 (mt-10)
REVERT: C  501 TYR cc_start: 0.8525 (OUTLIER) cc_final: 0.7754 (m-10)
  outliers start: 26
  outliers final: 17
  residues processed: 121
  average time/residue: 0.2140
  time to fit residues: 33.5362
Evaluate side-chains
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.679 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  389 ASP
Chi-restraints excluded: chain R residue  415 THR
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 79 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 80 optimal weight:    0.9980
   chunk 52 optimal weight:    0.0870
   chunk 5 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 3 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   overall best weight:    0.6960

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

Flipped N/Q/H residues before XYZ refinement:
A  97 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.135024 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.104166 restraints weight = 8248.615|
|-----------------------------------------------------------------------------|
r_work (start): 0.3150 rms_B_bonded: 2.21
r_work: 0.3026 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.2879 rms_B_bonded: 4.16 restraints_weight: 0.2500
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8040
moved from start:          0.2021

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6816  Z= 0.300
  Angle     :  0.557   5.393   9270  Z= 0.301
  Chirality :  0.046   0.169   1022
  Planarity :  0.004   0.042   1192
  Dihedral  :  5.672  52.675    978
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 16.03 %
    Favored  : 81.11 %
  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: -0.77 (0.27), residues: 838
  helix: -3.50 (0.46), residues: 66
  sheet:  0.75 (0.34), residues: 248
  loop : -0.74 (0.24), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP H  47 
 HIS   0.001   0.001   HIS B  34 
 PHE   0.009   0.001   PHE A  52 
 TYR   0.023   0.002   TYR L  49 
 ARG   0.004   0.000   ARG H  71 

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

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

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1676 Ramachandran restraints generated.
    838 Oldfield, 0 Emsley, 838 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 105
  time to evaluate  : 0.752 
Fit side-chains
REVERT: H   64 LYS cc_start: 0.7655 (OUTLIER) cc_final: 0.7267 (tptm)
REVERT: L   17 GLN cc_start: 0.7197 (mm-40) cc_final: 0.6654 (tt0)
REVERT: L   69 THR cc_start: 0.8977 (t) cc_final: 0.8521 (m)
REVERT: L   78 LEU cc_start: 0.7664 (tp) cc_final: 0.7413 (mt)
REVERT: A   56 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.7935 (mt-10)
REVERT: C  501 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.7732 (m-10)
  outliers start: 21
  outliers final: 18
  residues processed: 117
  average time/residue: 0.2141
  time to fit residues: 32.3373
Evaluate side-chains
  124 residues out of total 736 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 103
  time to evaluate  : 0.811 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   64 LYS
Chi-restraints excluded: chain H residue   97 ASN
Chi-restraints excluded: chain L residue    5 THR
Chi-restraints excluded: chain L residue   56 SER
Chi-restraints excluded: chain L residue   63 SER
Chi-restraints excluded: chain L residue   95 LEU
Chi-restraints excluded: chain R residue  362 VAL
Chi-restraints excluded: chain R residue  389 ASP
Chi-restraints excluded: chain R residue  415 THR
Chi-restraints excluded: chain R residue  468 ILE
Chi-restraints excluded: chain R residue  470 THR
Chi-restraints excluded: chain A residue    3 THR
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   75 LYS
Chi-restraints excluded: chain A residue  108 LEU
Chi-restraints excluded: chain B residue    5 THR
Chi-restraints excluded: chain B residue   42 THR
Chi-restraints excluded: chain B residue   63 SER
Chi-restraints excluded: chain C residue  345 THR
Chi-restraints excluded: chain C residue  390 LEU
Chi-restraints excluded: chain C residue  501 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 82
   random chunks:
   chunk 68 optimal weight:    0.9980
   chunk 23 optimal weight:    0.7980
   chunk 20 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9980
   chunk 28 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9990
   chunk 80 optimal weight:    0.2980
   chunk 54 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.7380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.133883 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.103246 restraints weight = 8158.652|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.21
r_work: 0.3030 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2882 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2882
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8048
moved from start:          0.2081

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   6816  Z= 0.315
  Angle     :  0.564   5.612   9270  Z= 0.305
  Chirality :  0.046   0.170   1022
  Planarity :  0.004   0.037   1192
  Dihedral  :  5.733  52.687    978
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 4.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 15.62 %
    Favored  : 81.11 %
  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: -0.85 (0.27), residues: 838
  helix: -3.52 (0.46), residues: 66
  sheet:  0.70 (0.34), residues: 248
  loop : -0.81 (0.23), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP H  47 
 HIS   0.002   0.001   HIS R 505 
 PHE   0.009   0.001   PHE B  91 
 TYR   0.023   0.002   TYR L  49 
 ARG   0.004   0.000   ARG C 346 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4223.96 seconds
wall clock time: 76 minutes 58.74 seconds (4618.74 seconds total)