Starting phenix.real_space_refine
on Fri Mar 14 01:34:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jl3_36387/03_2025/8jl3_36387.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jl3_36387/03_2025/8jl3_36387.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.59
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jl3_36387/03_2025/8jl3_36387.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jl3_36387/03_2025/8jl3_36387.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jl3_36387/03_2025/8jl3_36387.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jl3_36387/03_2025/8jl3_36387.cif"
  }
  resolution = 2.59
  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=   0.045
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: 5
    Type Number    sf(0)   Gaussians
     P       6      5.49       5
     S      40      5.16       5
     C    6470      2.51       5
     N    1366      2.21       5
     O    1526      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 9408
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 4189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4189
          Classifications: {'peptide': 527}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 501}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 4189
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 527, 4189
          Classifications: {'peptide': 527}
          Link IDs: {'PCIS': 2, 'PTRANS': 23, 'TRANS': 501}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 459
          Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 2, 'OCT': 16, 'R16': 1}
          Classifications: {'undetermined': 37}
          Link IDs: {None: 36}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ACO:plan-1': 1}
          Unresolved non-hydrogen planarities: 3
    Chain: "B"
      Number of atoms: 459
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 37, 459
          Unusual residues: {'ACO': 1, 'C14': 12, 'CLR': 1, 'D10': 1, 'D12': 3, 'NAG': 2, 'OCT': 16, 'R16': 1}
          Classifications: {'undetermined': 37}
          Link IDs: {None: 36}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ACO:plan-1': 1}
          Unresolved non-hydrogen planarities: 3
  Time building chain proxies: 7.56, per 1000 atoms: 0.80
  Number of scatterers: 9408
  At special positions: 0
  Unit cell: (108.73, 87.15, 105.41, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P       6     15.00
     O    1526      8.00
     N    1366      7.00
     C    6470      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 104 " - pdb=" SG  CYS A 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 151 " - pdb=" SG  CYS A 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 443 " - pdb=" SG  CYS A 462 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 104 " - pdb=" SG  CYS B 107 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 151 " - pdb=" SG  CYS B 179 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 443 " - pdb=" SG  CYS B 462 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG A 803 " - " ASN A  94 "
      " NAG B 804 " - " ASN B  94 "
      " NAG C   1 " - " ASN A 142 "
      " NAG D   1 " - " ASN A 162 "
      " NAG E   1 " - " ASN B 142 "
      " NAG F   1 " - " ASN B 162 "
  Time building additional restraints: 2.68
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1948

  Finding SS restraints...
    Secondary structure from input PDB file:
      40 helices and 4 sheets defined
      56.9% alpha, 9.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.94
  Creating SS restraints...
    Processing helix  chain 'A' and resid 191 through 215
    Processing helix  chain 'A' and resid 268 through 287
      removed outlier: 3.511A  pdb=" N   ASP A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 288 through 296
      removed outlier: 6.689A  pdb=" N   TRP A 293 " --> pdb=" O   GLY A 290 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   TYR A 294 " --> pdb=" O   LYS A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 307
    Processing helix  chain 'A' and resid 308 through 331
      removed outlier: 3.599A  pdb=" N   TRP A 312 " --> pdb=" O   LEU A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 334 through 356
    Processing helix  chain 'A' and resid 367 through 371
    Processing helix  chain 'A' and resid 375 through 394
    Processing helix  chain 'A' and resid 411 through 416
    Processing helix  chain 'A' and resid 417 through 438
      removed outlier: 3.564A  pdb=" N   LEU A 438 " --> pdb=" O   LEU A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 458
    Processing helix  chain 'A' and resid 465 through 475
    Processing helix  chain 'A' and resid 476 through 480
    Processing helix  chain 'A' and resid 486 through 491
    Processing helix  chain 'A' and resid 503 through 524
    Processing helix  chain 'A' and resid 527 through 551
    Processing helix  chain 'A' and resid 567 through 590
      Proline residue:  A 587  - end of helix
    Processing helix  chain 'A' and resid 600 through 605
    Processing helix  chain 'A' and resid 606 through 617
    Processing helix  chain 'A' and resid 632 through 657
    Processing helix  chain 'B' and resid 191 through 215
    Processing helix  chain 'B' and resid 268 through 287
      removed outlier: 3.510A  pdb=" N   ASP B 272 " --> pdb=" O   LEU B 268 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 288 through 296
      removed outlier: 6.689A  pdb=" N   TRP B 293 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   TYR B 294 " --> pdb=" O   LYS B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 307
    Processing helix  chain 'B' and resid 308 through 331
      removed outlier: 3.600A  pdb=" N   TRP B 312 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 334 through 356
    Processing helix  chain 'B' and resid 367 through 371
    Processing helix  chain 'B' and resid 375 through 394
    Processing helix  chain 'B' and resid 411 through 416
    Processing helix  chain 'B' and resid 417 through 438
      removed outlier: 3.564A  pdb=" N   LEU B 438 " --> pdb=" O   LEU B 434 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 454 through 458
    Processing helix  chain 'B' and resid 465 through 475
    Processing helix  chain 'B' and resid 476 through 480
    Processing helix  chain 'B' and resid 486 through 491
    Processing helix  chain 'B' and resid 503 through 524
    Processing helix  chain 'B' and resid 527 through 551
    Processing helix  chain 'B' and resid 567 through 590
      Proline residue:  B 587  - end of helix
    Processing helix  chain 'B' and resid 600 through 605
    Processing helix  chain 'B' and resid 606 through 617
    Processing helix  chain 'B' and resid 632 through 657
    Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 132
      removed outlier: 9.048A  pdb=" N   TYR A 163 " --> pdb=" O   GLN A  81 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   LEU A  83 " --> pdb=" O   TYR A 163 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   LEU A 165 " --> pdb=" O   LEU A  83 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   LEU A  85 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL A 167 " --> pdb=" O   LEU A  85 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   HIS A  87 " --> pdb=" O   VAL A 167 " (cutoff:3.500A)
      removed outlier: 6.579A  pdb=" N   ASN A 162 " --> pdb=" O   ASN A 184 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 115
      removed outlier: 6.890A  pdb=" N   VAL A  97 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ASN A 114 " --> pdb=" O   LEU A  95 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU A  95 " --> pdb=" O   ASN A 114 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS A 151 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ASP A 143 " --> pdb=" O   GLU A 149 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   GLU A 149 " --> pdb=" O   ASP A 143 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 125 through 132
      removed outlier: 9.047A  pdb=" N   TYR B 163 " --> pdb=" O   GLN B  81 " (cutoff:3.500A)
      removed outlier: 6.293A  pdb=" N   LEU B  83 " --> pdb=" O   TYR B 163 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   LEU B 165 " --> pdb=" O   LEU B  83 " (cutoff:3.500A)
      removed outlier: 6.433A  pdb=" N   LEU B  85 " --> pdb=" O   LEU B 165 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   VAL B 167 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 6.529A  pdb=" N   HIS B  87 " --> pdb=" O   VAL B 167 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   ASN B 162 " --> pdb=" O   ASN B 184 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 110 through 115
      removed outlier: 6.890A  pdb=" N   VAL B  97 " --> pdb=" O   LEU B 112 " (cutoff:3.500A)
      removed outlier: 4.873A  pdb=" N   ASN B 114 " --> pdb=" O   LEU B  95 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   LEU B  95 " --> pdb=" O   ASN B 114 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   CYS B 151 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 6.241A  pdb=" N   ASP B 143 " --> pdb=" O   GLU B 149 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   GLU B 149 " --> pdb=" O   ASP B 143 " (cutoff:3.500A)

    492 hydrogen bonds defined for protein.
    1386 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: 2.54

  Time building geometry restraints manager: 3.14 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2553
        1.34 -     1.46: 2203
        1.46 -     1.58: 4776
        1.58 -     1.70: 2
        1.70 -     1.82: 52
  Bond restraints: 9586
  Sorted by residual:
  bond pdb=" C1  NAG A 803 "
       pdb=" O5  NAG A 803 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.44e+00
  bond pdb=" C1  NAG B 804 "
       pdb=" O5  NAG B 804 "
    ideal  model  delta    sigma   weight residual
    1.406  1.437 -0.031 2.00e-02 2.50e+03 2.44e+00
  bond pdb=" C1  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.82e+00
  bond pdb=" C1  NAG F   2 "
       pdb=" O5  NAG F   2 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  bond pdb=" CB  PRO A 311 "
       pdb=" CG  PRO A 311 "
    ideal  model  delta    sigma   weight residual
    1.492  1.432  0.060 5.00e-02 4.00e+02 1.46e+00
  ... (remaining 9581 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 12557
        1.94 -     3.88: 199
        3.88 -     5.82: 30
        5.82 -     7.76: 2
        7.76 -     9.70: 2
  Bond angle restraints: 12790
  Sorted by residual:
  angle pdb=" CA  LEU A 348 "
        pdb=" CB  LEU A 348 "
        pdb=" CG  LEU A 348 "
      ideal   model   delta    sigma   weight residual
     116.30  126.00   -9.70 3.50e+00 8.16e-02 7.69e+00
  angle pdb=" CA  LEU B 348 "
        pdb=" CB  LEU B 348 "
        pdb=" CG  LEU B 348 "
      ideal   model   delta    sigma   weight residual
     116.30  126.00   -9.70 3.50e+00 8.16e-02 7.68e+00
  angle pdb=" CA  CYS B 104 "
        pdb=" CB  CYS B 104 "
        pdb=" SG  CYS B 104 "
      ideal   model   delta    sigma   weight residual
     114.40  119.06   -4.66 2.30e+00 1.89e-01 4.10e+00
  angle pdb=" CA  CYS A 104 "
        pdb=" CB  CYS A 104 "
        pdb=" SG  CYS A 104 "
      ideal   model   delta    sigma   weight residual
     114.40  119.04   -4.64 2.30e+00 1.89e-01 4.07e+00
  angle pdb=" N   SER A 607 "
        pdb=" CA  SER A 607 "
        pdb=" C   SER A 607 "
      ideal   model   delta    sigma   weight residual
     111.07  113.18   -2.11 1.07e+00 8.73e-01 3.91e+00
  ... (remaining 12785 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.80: 5129
       15.80 -    31.60: 593
       31.60 -    47.40: 182
       47.40 -    63.20: 70
       63.20 -    79.00: 8
  Dihedral angle restraints: 5982
    sinusoidal: 2940
      harmonic: 3042
  Sorted by residual:
  dihedral pdb=" CB  CYS A 443 "
           pdb=" SG  CYS A 443 "
           pdb=" SG  CYS A 462 "
           pdb=" CB  CYS A 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.74  -73.74     1      1.00e+01 1.00e-02 6.91e+01
  dihedral pdb=" CB  CYS B 443 "
           pdb=" SG  CYS B 443 "
           pdb=" SG  CYS B 462 "
           pdb=" CB  CYS B 462 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  166.72  -73.72     1      1.00e+01 1.00e-02 6.91e+01
  dihedral pdb=" CB  CYS B 151 "
           pdb=" SG  CYS B 151 "
           pdb=" SG  CYS B 179 "
           pdb=" CB  CYS B 179 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  141.67  -48.67     1      1.00e+01 1.00e-02 3.26e+01
  ... (remaining 5979 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 795
       0.034 -    0.067: 445
       0.067 -    0.101: 157
       0.101 -    0.135: 36
       0.135 -    0.168: 3
  Chirality restraints: 1436
  Sorted by residual:
  chirality pdb=" C1  NAG E   1 "
            pdb=" ND2 ASN B 142 "
            pdb=" C2  NAG E   1 "
            pdb=" O5  NAG E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.07e-01
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN A 142 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.24   -0.16 2.00e-01 2.50e+01 6.67e-01
  chirality pdb=" CA  PRO A 460 "
            pdb=" N   PRO A 460 "
            pdb=" C   PRO A 460 "
            pdb=" CB  PRO A 460 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.58    0.14 2.00e-01 2.50e+01 4.77e-01
  ... (remaining 1433 not shown)

  Planarity restraints: 1452
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL B 115 "    0.051 5.00e-02 4.00e+02   7.79e-02 9.72e+00
        pdb=" N   PRO B 116 "   -0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO B 116 "    0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO B 116 "    0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 115 "   -0.051 5.00e-02 4.00e+02   7.79e-02 9.71e+00
        pdb=" N   PRO A 116 "    0.135 5.00e-02 4.00e+02
        pdb=" CA  PRO A 116 "   -0.041 5.00e-02 4.00e+02
        pdb=" CD  PRO A 116 "   -0.042 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 566 "   -0.002 2.00e-02 2.50e+03   1.07e-02 2.87e+00
        pdb=" CG  TRP A 566 "    0.025 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 566 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 566 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 566 "    0.006 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 566 "    0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 566 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 566 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 566 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 566 "    0.000 2.00e-02 2.50e+03
  ... (remaining 1449 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1440
        2.76 -     3.30: 8015
        3.30 -     3.83: 15144
        3.83 -     4.37: 19548
        4.37 -     4.90: 32576
  Nonbonded interactions: 76723
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 447 "
            pdb=" OD2 ASP A 455 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OH  TYR B 447 "
            pdb=" OD2 ASP B 455 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   LYS A 296 "
            pdb=" OG1 THR A 304 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" O   LYS B 296 "
            pdb=" OG1 THR B 304 "
     model   vdw
     2.302 3.040
  nonbonded pdb=" ND2 ASN B 506 "
            pdb=" O   TRP B 566 "
     model   vdw
     2.355 3.120
  ... (remaining 76718 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: 0.04
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 75 through 663 or resid 806 through 807 or (resid 809 and  \ 
(name C03 or name C04 or name C05 or name C06 or name C07 or name C08 or name C0 \ 
9 or name C10 or name C11 or name C12 or name C13 or name C14)) or resid 810 thr \ 
ough 812 or resid 819 or resid 824 through 826 or (resid 828 and (name C03 or na \ 
me C04 or name C05 or name C06 or name C07 or name C08 or name C09 or name C10 o \ 
r name C11 or name C12 or name C13 or name C14)) or resid 829 through 830 or res \ 
id 832 or resid 835 through 836))
  selection = (chain 'B' and (resid 75 through 663 or resid 806 through 807 or resid 809 throu \ 
gh 812 or resid 819 or resid 824 through 826 or resid 828 through 830 or resid 8 \ 
32 or resid 835 through 836))
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

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:             79.400
  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:          0.390
  Check model and map are aligned:         0.070
  Set scattering table:                    0.100
  Process input model:                     26.250
  Find NCS groups from input model:        0.470
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:13.480
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  120.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8666
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      :  0.006   0.060   9586  Z= 0.364
  Angle     :  0.630   9.704  12790  Z= 0.307
  Chirality :  0.045   0.168   1436
  Planarity :  0.005   0.078   1446
  Dihedral  : 15.268  78.999   4016
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.33 %
    Favored  : 99.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.25), residues: 1038
  helix:  1.62 (0.22), residues: 508
  sheet:  1.00 (0.40), residues: 114
  loop : -0.31 (0.30), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 566 
 HIS   0.010   0.001   HIS A 614 
 PHE   0.016   0.002   PHE B 322 
 TYR   0.013   0.002   TYR B 496 
 ARG   0.003   0.001   ARG A 275 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 1.031 
Fit side-chains
REVERT: A  461 ASN cc_start: 0.8740 (m110) cc_final: 0.8438 (m-40)
REVERT: B  461 ASN cc_start: 0.8709 (m110) cc_final: 0.8440 (m-40)
  outliers start: 0
  outliers final: 0
  residues processed: 97
  average time/residue: 1.1678
  time to fit residues: 122.6815
Evaluate side-chains
  71 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 1.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 87 optimal weight:    1.9990
   chunk 78 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 53 optimal weight:    5.9990
   chunk 42 optimal weight:    0.6980
   chunk 81 optimal weight:    0.9980
   chunk 31 optimal weight:    0.0670
   chunk 49 optimal weight:    0.9980
   chunk 60 optimal weight:    0.8980
   chunk 94 optimal weight:    0.5980
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
A 114 ASN
A 286 ASN
A 461 ASN
A 491 HIS
B 114 ASN
B 286 ASN
B 461 ASN
B 491 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3480 r_free = 0.3480 target = 0.134275 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.102272 restraints weight = 8710.188|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 1.19
r_work: 0.2950 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2830 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.2830
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.0912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   9586  Z= 0.166
  Angle     :  0.512   6.589  12790  Z= 0.263
  Chirality :  0.040   0.136   1436
  Planarity :  0.004   0.057   1446
  Dihedral  : 12.937  59.821   2124
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 4.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  :  6.56 %
    Favored  : 92.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.91 (0.25), residues: 1038
  helix:  2.61 (0.22), residues: 500
  sheet:  1.38 (0.39), residues: 112
  loop : -0.42 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 647 
 HIS   0.003   0.001   HIS A 491 
 PHE   0.017   0.001   PHE B 322 
 TYR   0.010   0.001   TYR B 155 
 ARG   0.002   0.000   ARG B 275 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  88 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 75
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  153 LEU cc_start: 0.8303 (OUTLIER) cc_final: 0.7934 (mp)
REVERT: A  461 ASN cc_start: 0.8690 (m-40) cc_final: 0.8403 (m-40)
REVERT: A  478 ASP cc_start: 0.8050 (OUTLIER) cc_final: 0.7466 (m-30)
REVERT: A  630 ASN cc_start: 0.8463 (m-40) cc_final: 0.8215 (t0)
REVERT: B  153 LEU cc_start: 0.8324 (OUTLIER) cc_final: 0.7952 (mp)
REVERT: B  461 ASN cc_start: 0.8671 (m-40) cc_final: 0.8432 (m-40)
REVERT: B  478 ASP cc_start: 0.8027 (OUTLIER) cc_final: 0.7447 (m-30)
REVERT: B  630 ASN cc_start: 0.8464 (m-40) cc_final: 0.8202 (t0)
  outliers start: 13
  outliers final: 4
  residues processed: 84
  average time/residue: 1.0772
  time to fit residues: 99.0242
Evaluate side-chains
  79 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  478 ASP
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  478 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 68 optimal weight:    3.9990
   chunk 46 optimal weight:    0.4980
   chunk 41 optimal weight:    3.9990
   chunk 31 optimal weight:    1.9990
   chunk 91 optimal weight:    0.5980
   chunk 2 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 18 optimal weight:    1.9990
   chunk 34 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9990
   overall best weight:    1.2186

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

Flipped N/Q/H residues before XYZ refinement:
B 358 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.132936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.099629 restraints weight = 8710.627|
|-----------------------------------------------------------------------------|
r_work (start): 0.3023 rms_B_bonded: 1.25
r_work: 0.2921 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8529
moved from start:          0.0967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   9586  Z= 0.271
  Angle     :  0.560   6.571  12790  Z= 0.284
  Chirality :  0.043   0.144   1436
  Planarity :  0.004   0.051   1446
  Dihedral  : 13.238  64.615   2124
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 3.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  :  8.64 %
    Favored  : 90.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.04 (0.25), residues: 1038
  helix:  2.61 (0.21), residues: 500
  sheet:  1.32 (0.40), residues: 126
  loop : -0.23 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP B 647 
 HIS   0.003   0.001   HIS A 614 
 PHE   0.019   0.002   PHE B 322 
 TYR   0.013   0.002   TYR A 496 
 ARG   0.003   0.000   ARG B 275 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.927 
Fit side-chains
REVERT: A  153 LEU cc_start: 0.8340 (OUTLIER) cc_final: 0.7944 (mp)
REVERT: A  369 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.8008 (p0)
REVERT: A  461 ASN cc_start: 0.8749 (m-40) cc_final: 0.8395 (m-40)
REVERT: A  630 ASN cc_start: 0.8489 (m-40) cc_final: 0.8223 (t0)
REVERT: B  153 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7948 (mp)
REVERT: B  369 ASP cc_start: 0.8375 (OUTLIER) cc_final: 0.8013 (p0)
REVERT: B  461 ASN cc_start: 0.8721 (m-40) cc_final: 0.8394 (m-40)
REVERT: B  630 ASN cc_start: 0.8494 (m-40) cc_final: 0.8227 (t0)
  outliers start: 11
  outliers final: 5
  residues processed: 84
  average time/residue: 1.1310
  time to fit residues: 102.6904
Evaluate side-chains
  83 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 74
  time to evaluate  : 0.903 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  369 ASP
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 16 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 59 optimal weight:    3.9990
   chunk 84 optimal weight:    2.9990
   chunk 54 optimal weight:    0.5980
   chunk 18 optimal weight:    0.8980
   chunk 82 optimal weight:    0.0770
   chunk 38 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 33 optimal weight:    1.9990
   overall best weight:    0.8740

-------------------------------------------------------------------------------
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 = 0.3470 r_free = 0.3470 target = 0.133519 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.101150 restraints weight = 8735.766|
|-----------------------------------------------------------------------------|
r_work (start): 0.3040 rms_B_bonded: 1.20
r_work: 0.2935 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8530
moved from start:          0.1150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9586  Z= 0.210
  Angle     :  0.512   6.606  12790  Z= 0.262
  Chirality :  0.041   0.138   1436
  Planarity :  0.004   0.046   1446
  Dihedral  : 12.815  68.184   2124
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  :  9.63 %
    Favored  : 88.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.24 (0.25), residues: 1038
  helix:  2.81 (0.21), residues: 500
  sheet:  1.51 (0.40), residues: 126
  loop : -0.22 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.002   0.001   HIS B 636 
 PHE   0.017   0.001   PHE A 322 
 TYR   0.010   0.001   TYR B 294 
 ARG   0.002   0.000   ARG A 275 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 1.022 
Fit side-chains
REVERT: A  153 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.7953 (mp)
REVERT: A  369 ASP cc_start: 0.8323 (OUTLIER) cc_final: 0.8027 (p0)
REVERT: A  461 ASN cc_start: 0.8748 (m-40) cc_final: 0.8547 (m-40)
REVERT: A  630 ASN cc_start: 0.8519 (m-40) cc_final: 0.8250 (t0)
REVERT: B  153 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.7972 (mp)
REVERT: B  369 ASP cc_start: 0.8374 (OUTLIER) cc_final: 0.8053 (p0)
REVERT: B  630 ASN cc_start: 0.8505 (m-40) cc_final: 0.8219 (t0)
  outliers start: 18
  outliers final: 10
  residues processed: 90
  average time/residue: 1.0623
  time to fit residues: 103.9692
Evaluate side-chains
  89 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 1.005 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  369 ASP
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 79 optimal weight:    1.9990
   chunk 68 optimal weight:    2.9990
   chunk 98 optimal weight:    0.6980
   chunk 52 optimal weight:    3.9990
   chunk 72 optimal weight:    3.9990
   chunk 99 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 28 optimal weight:    0.9980
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
A 358 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.133317 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.100844 restraints weight = 8747.944|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 1.20
r_work: 0.2929 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2808 rms_B_bonded: 3.05 restraints_weight: 0.2500
r_work (final): 0.2808
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8601
moved from start:          0.1219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9586  Z= 0.211
  Angle     :  0.515   6.631  12790  Z= 0.262
  Chirality :  0.041   0.137   1436
  Planarity :  0.004   0.044   1446
  Dihedral  : 12.709  68.415   2124
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 3.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.30 %
    Favored  : 88.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.29 (0.25), residues: 1038
  helix:  2.84 (0.21), residues: 500
  sheet:  1.64 (0.40), residues: 126
  loop : -0.23 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 647 
 HIS   0.003   0.001   HIS B 614 
 PHE   0.017   0.001   PHE A 322 
 TYR   0.011   0.001   TYR A 294 
 ARG   0.002   0.000   ARG B 156 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 73
  time to evaluate  : 1.000 
Fit side-chains
REVERT: A  153 LEU cc_start: 0.8405 (OUTLIER) cc_final: 0.7992 (mp)
REVERT: A  170 ILE cc_start: 0.6677 (OUTLIER) cc_final: 0.6132 (mt)
REVERT: A  369 ASP cc_start: 0.8386 (OUTLIER) cc_final: 0.8094 (p0)
REVERT: A  630 ASN cc_start: 0.8556 (m-40) cc_final: 0.8305 (t0)
REVERT: B  110 GLN cc_start: 0.7904 (OUTLIER) cc_final: 0.7556 (mt0)
REVERT: B  153 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.8018 (mp)
REVERT: B  170 ILE cc_start: 0.6706 (OUTLIER) cc_final: 0.6153 (mt)
REVERT: B  630 ASN cc_start: 0.8545 (m-40) cc_final: 0.8276 (t0)
  outliers start: 23
  outliers final: 12
  residues processed: 91
  average time/residue: 1.2878
  time to fit residues: 128.3444
Evaluate side-chains
  90 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  416 SER
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 80 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 55 optimal weight:    0.9990
   chunk 0 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 5 optimal weight:    1.9990
   chunk 38 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.3450 r_free = 0.3450 target = 0.131897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3018 r_free = 0.3018 target = 0.098461 restraints weight = 8608.814|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 1.24
r_work: 0.2912 rms_B_bonded: 1.77 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 2.89 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8557
moved from start:          0.1194

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053   9586  Z= 0.329
  Angle     :  0.606   6.686  12790  Z= 0.303
  Chirality :  0.044   0.144   1436
  Planarity :  0.005   0.043   1446
  Dihedral  : 13.323  68.674   2124
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 3.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.52 %
    Favored  : 87.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.08 (0.25), residues: 1038
  helix:  2.56 (0.21), residues: 504
  sheet:  1.68 (0.41), residues: 126
  loop : -0.25 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B 647 
 HIS   0.004   0.001   HIS A 614 
 PHE   0.021   0.002   PHE B 322 
 TYR   0.014   0.002   TYR A 496 
 ARG   0.004   0.001   ARG A 275 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 1.074 
Fit side-chains
REVERT: A  153 LEU cc_start: 0.8376 (OUTLIER) cc_final: 0.8136 (mp)
REVERT: A  170 ILE cc_start: 0.6568 (OUTLIER) cc_final: 0.6038 (mt)
REVERT: A  369 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8079 (p0)
REVERT: A  630 ASN cc_start: 0.8589 (m-40) cc_final: 0.8284 (t0)
REVERT: B  153 LEU cc_start: 0.8351 (OUTLIER) cc_final: 0.8112 (mp)
REVERT: B  170 ILE cc_start: 0.6601 (OUTLIER) cc_final: 0.6067 (mt)
REVERT: B  369 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8083 (p0)
REVERT: B  630 ASN cc_start: 0.8590 (m-40) cc_final: 0.8291 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 93
  average time/residue: 1.3698
  time to fit residues: 141.2687
Evaluate side-chains
  94 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 1.073 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  369 ASP
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  416 SER
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 47 optimal weight:    2.9990
   chunk 65 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 90 optimal weight:    2.9990
   chunk 30 optimal weight:    0.0670
   chunk 103 optimal weight:    2.9990
   chunk 10 optimal weight:    0.3980
   overall best weight:    1.2522

-------------------------------------------------------------------------------
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 = 0.3463 r_free = 0.3463 target = 0.132882 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3034 r_free = 0.3034 target = 0.099490 restraints weight = 8708.079|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.24
r_work: 0.2905 rms_B_bonded: 1.79 restraints_weight: 0.5000
r_work: 0.2781 rms_B_bonded: 2.92 restraints_weight: 0.2500
r_work (final): 0.2781
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8556
moved from start:          0.1238

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   9586  Z= 0.278
  Angle     :  0.564   6.644  12790  Z= 0.285
  Chirality :  0.043   0.139   1436
  Planarity :  0.004   0.041   1446
  Dihedral  : 13.145  67.898   2124
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  :  9.41 %
    Favored  : 88.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.14 (0.25), residues: 1038
  helix:  2.62 (0.21), residues: 504
  sheet:  1.78 (0.41), residues: 126
  loop : -0.27 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B 647 
 HIS   0.003   0.001   HIS B 614 
 PHE   0.019   0.002   PHE B 322 
 TYR   0.013   0.002   TYR B 496 
 ARG   0.003   0.000   ARG B 275 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 1.037 
Fit side-chains
REVERT: A  153 LEU cc_start: 0.8346 (OUTLIER) cc_final: 0.8125 (mp)
REVERT: A  170 ILE cc_start: 0.6578 (OUTLIER) cc_final: 0.6056 (mt)
REVERT: A  369 ASP cc_start: 0.8394 (OUTLIER) cc_final: 0.8073 (p0)
REVERT: A  630 ASN cc_start: 0.8584 (m-40) cc_final: 0.8287 (t0)
REVERT: B  153 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8116 (mp)
REVERT: B  170 ILE cc_start: 0.6616 (OUTLIER) cc_final: 0.6087 (mt)
REVERT: B  630 ASN cc_start: 0.8573 (m-40) cc_final: 0.8281 (t0)
  outliers start: 23
  outliers final: 16
  residues processed: 94
  average time/residue: 1.1481
  time to fit residues: 117.7095
Evaluate side-chains
  95 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 74
  time to evaluate  : 0.962 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  369 ASP
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  416 SER
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  416 SER
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 55 optimal weight:    0.9990
   chunk 4 optimal weight:    0.0040
   chunk 103 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 57 optimal weight:    4.9990
   chunk 6 optimal weight:    4.9990
   chunk 76 optimal weight:    1.9990
   chunk 101 optimal weight:    0.0070
   chunk 84 optimal weight:    0.0020
   chunk 48 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   overall best weight:    0.3820

-------------------------------------------------------------------------------
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 = 0.3501 r_free = 0.3501 target = 0.136091 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.102966 restraints weight = 8703.381|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 1.24
r_work: 0.2957 rms_B_bonded: 1.81 restraints_weight: 0.5000
r_work: 0.2836 rms_B_bonded: 2.94 restraints_weight: 0.2500
r_work (final): 0.2836
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8501
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   9586  Z= 0.139
  Angle     :  0.462   6.658  12790  Z= 0.239
  Chirality :  0.039   0.135   1436
  Planarity :  0.004   0.038   1446
  Dihedral  : 12.069  67.677   2124
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 4.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Rotamer:
    Outliers :  1.42 %
    Allowed  : 10.94 %
    Favored  : 87.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.41 (0.25), residues: 1038
  helix:  2.93 (0.22), residues: 512
  sheet:  1.90 (0.41), residues: 126
  loop : -0.32 (0.29), residues: 400

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.002   0.001   HIS B 633 
 PHE   0.013   0.001   PHE A 315 
 TYR   0.012   0.001   TYR A 570 
 ARG   0.002   0.000   ARG B 156 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 79
  time to evaluate  : 0.998 
Fit side-chains
REVERT: A  110 GLN cc_start: 0.7773 (OUTLIER) cc_final: 0.7566 (mp10)
REVERT: A  153 LEU cc_start: 0.8366 (OUTLIER) cc_final: 0.7990 (mp)
REVERT: A  170 ILE cc_start: 0.6590 (OUTLIER) cc_final: 0.6077 (mt)
REVERT: A  630 ASN cc_start: 0.8491 (m-40) cc_final: 0.8240 (t0)
REVERT: B  110 GLN cc_start: 0.7770 (OUTLIER) cc_final: 0.7564 (mp10)
REVERT: B  153 LEU cc_start: 0.8384 (OUTLIER) cc_final: 0.7956 (mp)
REVERT: B  170 ILE cc_start: 0.6638 (OUTLIER) cc_final: 0.6108 (mt)
REVERT: B  630 ASN cc_start: 0.8478 (m-40) cc_final: 0.8230 (t0)
  outliers start: 13
  outliers final: 7
  residues processed: 88
  average time/residue: 1.0229
  time to fit residues: 98.3382
Evaluate side-chains
  91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.992 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 77 optimal weight:    2.9990
   chunk 1 optimal weight:    5.9990
   chunk 98 optimal weight:    0.0870
   chunk 58 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 76 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 29 optimal weight:    1.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.6166

-------------------------------------------------------------------------------
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 = 0.3455 r_free = 0.3455 target = 0.132198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3024 r_free = 0.3024 target = 0.098863 restraints weight = 8586.240|
|-----------------------------------------------------------------------------|
r_work (start): 0.3003 rms_B_bonded: 1.24
r_work: 0.2899 rms_B_bonded: 1.76 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 2.85 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8542
moved from start:          0.1291

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055   9586  Z= 0.338
  Angle     :  0.608   6.707  12790  Z= 0.305
  Chirality :  0.044   0.141   1436
  Planarity :  0.005   0.041   1446
  Dihedral  : 13.066  67.616   2124
  Min Nonbonded Distance : 2.565

Molprobity Statistics.
  All-atom Clashscore : 3.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 10.39 %
    Favored  : 87.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.25), residues: 1038
  helix:  2.50 (0.21), residues: 516
  sheet:  1.89 (0.41), residues: 126
  loop : -0.28 (0.29), residues: 396

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 647 
 HIS   0.004   0.001   HIS A 614 
 PHE   0.021   0.002   PHE A 322 
 TYR   0.015   0.002   TYR B 496 
 ARG   0.004   0.001   ARG B 275 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 71
  time to evaluate  : 0.965 
Fit side-chains
REVERT: A  110 GLN cc_start: 0.7830 (OUTLIER) cc_final: 0.7452 (mt0)
REVERT: A  153 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.7975 (mp)
REVERT: A  170 ILE cc_start: 0.6632 (OUTLIER) cc_final: 0.6147 (mt)
REVERT: A  630 ASN cc_start: 0.8577 (OUTLIER) cc_final: 0.8270 (t0)
REVERT: B  110 GLN cc_start: 0.7833 (OUTLIER) cc_final: 0.7456 (mt0)
REVERT: B  153 LEU cc_start: 0.8343 (OUTLIER) cc_final: 0.8116 (mp)
REVERT: B  170 ILE cc_start: 0.6656 (OUTLIER) cc_final: 0.6171 (mt)
REVERT: B  369 ASP cc_start: 0.8407 (OUTLIER) cc_final: 0.8085 (p0)
REVERT: B  630 ASN cc_start: 0.8579 (m-40) cc_final: 0.8280 (t0)
  outliers start: 23
  outliers final: 14
  residues processed: 89
  average time/residue: 0.9712
  time to fit residues: 94.8686
Evaluate side-chains
  91 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 1.201 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  369 ASP
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 71 optimal weight:    3.9990
   chunk 96 optimal weight:    2.9990
   chunk 99 optimal weight:    1.9990
   chunk 13 optimal weight:    4.9990
   chunk 62 optimal weight:    0.1980
   chunk 48 optimal weight:    2.9990
   chunk 69 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.6388

-------------------------------------------------------------------------------
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 = 0.3612 r_free = 0.3612 target = 0.142623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3227 r_free = 0.3227 target = 0.111728 restraints weight = 9580.574|
|-----------------------------------------------------------------------------|
r_work (start): 0.3188 rms_B_bonded: 1.34
r_work: 0.3111 rms_B_bonded: 1.82 restraints_weight: 0.5000
r_work: 0.3012 rms_B_bonded: 2.99 restraints_weight: 0.2500
r_work (final): 0.3012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8636
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057   9586  Z= 0.344
  Angle     :  0.614   6.674  12790  Z= 0.308
  Chirality :  0.045   0.143   1436
  Planarity :  0.005   0.042   1446
  Dihedral  : 13.353  67.697   2124
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 3.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.35 %
    Favored  : 98.65 %
  Rotamer:
    Outliers :  2.74 %
    Allowed  :  9.96 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.24), residues: 1038
  helix:  2.51 (0.21), residues: 504
  sheet:  1.84 (0.41), residues: 126
  loop : -0.26 (0.29), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B 647 
 HIS   0.004   0.001   HIS B 614 
 PHE   0.021   0.002   PHE B 322 
 TYR   0.015   0.002   TYR A 496 
 ARG   0.004   0.001   ARG B 275 

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

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

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2076 Ramachandran restraints generated.
    1038 Oldfield, 0 Emsley, 1038 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 71
  time to evaluate  : 0.989 
Fit side-chains
REVERT: A  110 GLN cc_start: 0.7963 (OUTLIER) cc_final: 0.7571 (mt0)
REVERT: A  170 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6237 (mt)
REVERT: A  630 ASN cc_start: 0.8636 (OUTLIER) cc_final: 0.8367 (t0)
REVERT: B  110 GLN cc_start: 0.7950 (OUTLIER) cc_final: 0.7554 (mt0)
REVERT: B  153 LEU cc_start: 0.8388 (OUTLIER) cc_final: 0.8155 (mp)
REVERT: B  170 ILE cc_start: 0.6708 (OUTLIER) cc_final: 0.6244 (mt)
REVERT: B  369 ASP cc_start: 0.8382 (OUTLIER) cc_final: 0.8065 (p0)
REVERT: B  630 ASN cc_start: 0.8610 (m-40) cc_final: 0.8338 (t0)
  outliers start: 25
  outliers final: 17
  residues processed: 89
  average time/residue: 0.9587
  time to fit residues: 93.8416
Evaluate side-chains
  93 residues out of total 914 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 69
  time to evaluate  : 0.970 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  110 GLN
Chi-restraints excluded: chain A residue  131 VAL
Chi-restraints excluded: chain A residue  144 THR
Chi-restraints excluded: chain A residue  167 VAL
Chi-restraints excluded: chain A residue  170 ILE
Chi-restraints excluded: chain A residue  285 VAL
Chi-restraints excluded: chain A residue  327 SER
Chi-restraints excluded: chain A residue  393 LEU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  614 HIS
Chi-restraints excluded: chain A residue  630 ASN
Chi-restraints excluded: chain B residue  110 GLN
Chi-restraints excluded: chain B residue  131 VAL
Chi-restraints excluded: chain B residue  144 THR
Chi-restraints excluded: chain B residue  153 LEU
Chi-restraints excluded: chain B residue  167 VAL
Chi-restraints excluded: chain B residue  170 ILE
Chi-restraints excluded: chain B residue  285 VAL
Chi-restraints excluded: chain B residue  327 SER
Chi-restraints excluded: chain B residue  369 ASP
Chi-restraints excluded: chain B residue  393 LEU
Chi-restraints excluded: chain B residue  416 SER
Chi-restraints excluded: chain B residue  422 LEU
Chi-restraints excluded: chain B residue  614 HIS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 104
   random chunks:
   chunk 40 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 32 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   chunk 96 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 58 optimal weight:    0.9990
   chunk 102 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.3474 r_free = 0.3474 target = 0.134506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.101995 restraints weight = 8760.121|
|-----------------------------------------------------------------------------|
r_work (start): 0.3010 rms_B_bonded: 1.24
r_work: 0.2899 rms_B_bonded: 1.87 restraints_weight: 0.5000
r_work: 0.2778 rms_B_bonded: 3.02 restraints_weight: 0.2500
r_work (final): 0.2778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8593
moved from start:          0.1379

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   9586  Z= 0.204
  Angle     :  0.518   6.617  12790  Z= 0.265
  Chirality :  0.041   0.136   1436
  Planarity :  0.004   0.040   1446
  Dihedral  : 12.645  67.564   2124
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 3.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.16 %
    Favored  : 98.84 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 10.61 %
    Favored  : 87.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 8.33 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.25), residues: 1038
  helix:  2.80 (0.21), residues: 502
  sheet:  1.92 (0.42), residues: 126
  loop : -0.20 (0.28), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 647 
 HIS   0.002   0.001   HIS A 614 
 PHE   0.016   0.001   PHE A 322 
 TYR   0.011   0.001   TYR B 570 
 ARG   0.002   0.000   ARG A 156 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 7214.37 seconds
wall clock time: 127 minutes 6.26 seconds (7626.26 seconds total)