Starting phenix.real_space_refine
on Fri Aug 22 21:32:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8irl_35678/08_2025/8irl_35678.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8irl_35678/08_2025/8irl_35678.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8irl_35678/08_2025/8irl_35678.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8irl_35678/08_2025/8irl_35678.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8irl_35678/08_2025/8irl_35678.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8irl_35678/08_2025/8irl_35678.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.004
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      52      5.16       5
     C    5280      2.51       5
     N    1306      2.21       5
     O    1470      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 8108
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 4026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4026
          Classifications: {'peptide': 540}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516}
    Chain: "B"
      Number of atoms: 4026
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 540, 4026
          Classifications: {'peptide': 540}
          Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 516}
    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
  Time building chain proxies: 2.07, per 1000 atoms: 0.26
  Number of scatterers: 8108
  At special positions: 0
  Unit cell: (97.865, 108.077, 102.12, 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      52     16.00
     O    1470      8.00
     N    1306      7.00
     C    5280      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  78 " - pdb=" SG  CYS A 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  83 " - pdb=" SG  CYS A 111 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A  87 " - pdb=" SG  CYS A  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 254 " - pdb=" SG  CYS A 287 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  78 " - pdb=" SG  CYS B 123 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  83 " - pdb=" SG  CYS B 111 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  87 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 254 " - pdb=" SG  CYS B 287 " 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-ASN
      " NAG C   1 " - " ASN A 270 "
      " NAG D   1 " - " ASN B 270 "
  Time building additional restraints: 0.49
  Conformation dependent library (CDL) restraints added in 377.3 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1940

  Finding SS restraints...
    Secondary structure from input PDB file:
      54 helices and 6 sheets defined
      67.0% alpha, 5.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.18
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 30
    Processing helix  chain 'A' and resid 31 through 37
    Processing helix  chain 'A' and resid 46 through 61
    Processing helix  chain 'A' and resid 62 through 73
      removed outlier: 4.284A  pdb=" N   ALA A  68 " --> pdb=" O   LEU A  64 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 93 through 97
    Processing helix  chain 'A' and resid 108 through 113
    Processing helix  chain 'A' and resid 117 through 150
    Processing helix  chain 'A' and resid 159 through 169
    Processing helix  chain 'A' and resid 172 through 176
    Processing helix  chain 'A' and resid 180 through 201
      removed outlier: 3.508A  pdb=" N   ILE A 201 " --> pdb=" O   PHE A 197 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 208
    Processing helix  chain 'A' and resid 212 through 232
      removed outlier: 4.913A  pdb=" N   SER A 220 " --> pdb=" O   ARG A 216 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ALA A 221 " --> pdb=" O   ILE A 217 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 257
      No H-bonds generated for 'chain 'A' and resid 255 through 257'
    Processing helix  chain 'A' and resid 294 through 313
    Processing helix  chain 'A' and resid 317 through 330
    Processing helix  chain 'A' and resid 343 through 355
      removed outlier: 3.883A  pdb=" N   LYS A 355 " --> pdb=" O   ASP A 351 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 371 through 375
      removed outlier: 3.960A  pdb=" N   ILE A 374 " --> pdb=" O   PHE A 371 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ASN A 375 " --> pdb=" O   SER A 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 371 through 375'
    Processing helix  chain 'A' and resid 376 through 405
      removed outlier: 3.942A  pdb=" N   TRP A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   TYR A 399 " --> pdb=" O   THR A 395 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER A 400 " --> pdb=" O   GLY A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 435
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 4.013A  pdb=" N   GLY A 448 " --> pdb=" O   GLU A 444 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 456 through 470
    Processing helix  chain 'A' and resid 472 through 477
    Processing helix  chain 'A' and resid 484 through 496
      removed outlier: 4.083A  pdb=" N   LEU A 488 " --> pdb=" O   VAL A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 497 through 502
      removed outlier: 3.714A  pdb=" N   THR A 500 " --> pdb=" O   LYS A 497 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   GLU A 501 " --> pdb=" O   SER A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 523
      Proline residue:  A 512  - end of helix
      Proline residue:  A 521  - end of helix
    Processing helix  chain 'A' and resid 525 through 554
      removed outlier: 3.918A  pdb=" N   GLY A 529 " --> pdb=" O   SER A 525 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   TRP A 543 " --> pdb=" O   VAL A 539 " (cutoff:3.500A)
      removed outlier: 5.300A  pdb=" N   ASP A 544 " --> pdb=" O   LEU A 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 19 through 30
    Processing helix  chain 'B' and resid 31 through 37
    Processing helix  chain 'B' and resid 46 through 61
    Processing helix  chain 'B' and resid 62 through 73
      removed outlier: 4.289A  pdb=" N   ALA B  68 " --> pdb=" O   LEU B  64 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 79 through 83
    Processing helix  chain 'B' and resid 93 through 97
    Processing helix  chain 'B' and resid 108 through 113
    Processing helix  chain 'B' and resid 117 through 150
    Processing helix  chain 'B' and resid 159 through 169
    Processing helix  chain 'B' and resid 172 through 176
    Processing helix  chain 'B' and resid 180 through 201
      removed outlier: 3.503A  pdb=" N   ILE B 201 " --> pdb=" O   PHE B 197 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 208
    Processing helix  chain 'B' and resid 212 through 232
      removed outlier: 4.902A  pdb=" N   SER B 220 " --> pdb=" O   ARG B 216 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ALA B 221 " --> pdb=" O   ILE B 217 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 255 through 257
      No H-bonds generated for 'chain 'B' and resid 255 through 257'
    Processing helix  chain 'B' and resid 294 through 313
    Processing helix  chain 'B' and resid 317 through 330
    Processing helix  chain 'B' and resid 343 through 355
      removed outlier: 3.869A  pdb=" N   LYS B 355 " --> pdb=" O   ASP B 351 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 371 through 375
      removed outlier: 3.954A  pdb=" N   ILE B 374 " --> pdb=" O   PHE B 371 " (cutoff:3.500A)
      removed outlier: 4.553A  pdb=" N   ASN B 375 " --> pdb=" O   SER B 372 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 371 through 375'
    Processing helix  chain 'B' and resid 376 through 405
      removed outlier: 3.988A  pdb=" N   TRP B 380 " --> pdb=" O   LYS B 376 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   TYR B 399 " --> pdb=" O   THR B 395 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   SER B 400 " --> pdb=" O   GLY B 396 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 416 through 435
    Processing helix  chain 'B' and resid 444 through 450
      removed outlier: 4.007A  pdb=" N   GLY B 448 " --> pdb=" O   GLU B 444 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 456 through 470
    Processing helix  chain 'B' and resid 472 through 477
    Processing helix  chain 'B' and resid 484 through 496
      removed outlier: 4.088A  pdb=" N   LEU B 488 " --> pdb=" O   VAL B 484 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 497 through 502
      removed outlier: 3.680A  pdb=" N   THR B 500 " --> pdb=" O   LYS B 497 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLU B 501 " --> pdb=" O   SER B 498 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 523
      Proline residue:  B 512  - end of helix
      Proline residue:  B 521  - end of helix
    Processing helix  chain 'B' and resid 525 through 554
      removed outlier: 3.926A  pdb=" N   GLY B 529 " --> pdb=" O   SER B 525 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   TRP B 543 " --> pdb=" O   VAL B 539 " (cutoff:3.500A)
      removed outlier: 5.286A  pdb=" N   ASP B 544 " --> pdb=" O   LEU B 540 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 156 through 158
    Processing sheet with id=AA2, first strand: chain 'A' and resid 241 through 244
    Processing sheet with id=AA3, first strand: chain 'A' and resid 273 through 275
      removed outlier: 11.871A  pdb=" N   ARG A 259 " --> pdb=" O   THR B 267 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   THR B 267 " --> pdb=" O   ARG A 259 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER A 261 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   SER B 261 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   THR A 267 " --> pdb=" O   ARG B 259 " (cutoff:3.500A)
      removed outlier: 11.838A  pdb=" N   ARG B 259 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 286 through 287
      removed outlier: 11.871A  pdb=" N   ARG A 259 " --> pdb=" O   THR B 267 " (cutoff:3.500A)
      removed outlier: 8.376A  pdb=" N   THR B 267 " --> pdb=" O   ARG A 259 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   SER A 261 " --> pdb=" O   VAL B 265 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   SER B 261 " --> pdb=" O   VAL A 265 " (cutoff:3.500A)
      removed outlier: 8.391A  pdb=" N   THR A 267 " --> pdb=" O   ARG B 259 " (cutoff:3.500A)
      removed outlier: 11.838A  pdb=" N   ARG B 259 " --> pdb=" O   THR A 267 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 156 through 158
    Processing sheet with id=AA6, first strand: chain 'B' and resid 241 through 244

    504 hydrogen bonds defined for protein.
    1440 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.83

  Time building geometry restraints manager: 0.71 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1258
        1.31 -     1.44: 2228
        1.44 -     1.57: 4722
        1.57 -     1.69: 2
        1.69 -     1.82: 84
  Bond restraints: 8294
  Sorted by residual:
  bond pdb=" C5  NAG D   2 "
       pdb=" O5  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.537 -0.124 2.00e-02 2.50e+03 3.87e+01
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.532 -0.119 2.00e-02 2.50e+03 3.55e+01
  bond pdb=" C5  NAG D   1 "
       pdb=" O5  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.529 -0.116 2.00e-02 2.50e+03 3.38e+01
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.529 -0.116 2.00e-02 2.50e+03 3.36e+01
  bond pdb=" C7  NAG D   1 "
       pdb=" N2  NAG D   1 "
    ideal  model  delta    sigma   weight residual
    1.346  1.453 -0.107 2.00e-02 2.50e+03 2.85e+01
  ... (remaining 8289 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.58: 10890
        1.58 -     3.17: 319
        3.17 -     4.75: 53
        4.75 -     6.33: 24
        6.33 -     7.91: 4
  Bond angle restraints: 11290
  Sorted by residual:
  angle pdb=" C   GLY A 485 "
        pdb=" N   PRO A 486 "
        pdb=" CA  PRO A 486 "
      ideal   model   delta    sigma   weight residual
     120.38  114.94    5.44 1.03e+00 9.43e-01 2.79e+01
  angle pdb=" C   GLY B 485 "
        pdb=" N   PRO B 486 "
        pdb=" CA  PRO B 486 "
      ideal   model   delta    sigma   weight residual
     120.38  114.96    5.42 1.03e+00 9.43e-01 2.77e+01
  angle pdb=" N   GLY B 485 "
        pdb=" CA  GLY B 485 "
        pdb=" C   GLY B 485 "
      ideal   model   delta    sigma   weight residual
     112.34  120.25   -7.91 2.04e+00 2.40e-01 1.50e+01
  angle pdb=" N   GLY A 485 "
        pdb=" CA  GLY A 485 "
        pdb=" C   GLY A 485 "
      ideal   model   delta    sigma   weight residual
     112.34  120.12   -7.78 2.04e+00 2.40e-01 1.46e+01
  angle pdb=" C   THR B 247 "
        pdb=" N   LEU B 248 "
        pdb=" CA  LEU B 248 "
      ideal   model   delta    sigma   weight residual
     121.54  128.61   -7.07 1.91e+00 2.74e-01 1.37e+01
  ... (remaining 11285 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    23.67: 4680
       23.67 -    47.34: 192
       47.34 -    71.01: 16
       71.01 -    94.68: 5
       94.68 -   118.35: 3
  Dihedral angle restraints: 4896
    sinusoidal: 1844
      harmonic: 3052
  Sorted by residual:
  dihedral pdb=" CB  CYS B 254 "
           pdb=" SG  CYS B 254 "
           pdb=" SG  CYS B 287 "
           pdb=" CB  CYS B 287 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.44  -69.44     1      1.00e+01 1.00e-02 6.23e+01
  dihedral pdb=" CB  CYS A 254 "
           pdb=" SG  CYS A 254 "
           pdb=" SG  CYS A 287 "
           pdb=" CB  CYS A 287 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  162.41  -69.41     1      1.00e+01 1.00e-02 6.22e+01
  dihedral pdb=" CA  ASN A 235 "
           pdb=" C   ASN A 235 "
           pdb=" N   GLN A 236 "
           pdb=" CA  GLN A 236 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.12  -21.88     0      5.00e+00 4.00e-02 1.91e+01
  ... (remaining 4893 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 1051
       0.050 -    0.101: 254
       0.101 -    0.151: 46
       0.151 -    0.201: 1
       0.201 -    0.252: 4
  Chirality restraints: 1356
  Sorted by residual:
  chirality pdb=" C5  NAG C   1 "
            pdb=" C4  NAG C   1 "
            pdb=" C6  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.66    0.25 2.00e-01 2.50e+01 1.58e+00
  chirality pdb=" CB  THR B 250 "
            pdb=" CA  THR B 250 "
            pdb=" OG1 THR B 250 "
            pdb=" CG2 THR B 250 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.34    0.22 2.00e-01 2.50e+01 1.16e+00
  chirality pdb=" C5  NAG C   2 "
            pdb=" C4  NAG C   2 "
            pdb=" C6  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.41   -2.62    0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1353 not shown)

  Planarity restraints: 1398
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 248 "    0.017 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   LEU A 248 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   LEU A 248 "    0.021 2.00e-02 2.50e+03
        pdb=" N   VAL A 249 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 248 "    0.017 2.00e-02 2.50e+03   3.32e-02 1.10e+01
        pdb=" C   LEU B 248 "   -0.057 2.00e-02 2.50e+03
        pdb=" O   LEU B 248 "    0.021 2.00e-02 2.50e+03
        pdb=" N   VAL B 249 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO A 486 "   -0.044 5.00e-02 4.00e+02   6.63e-02 7.03e+00
        pdb=" N   PRO A 487 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO A 487 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO A 487 "   -0.037 5.00e-02 4.00e+02
  ... (remaining 1395 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 31
        2.59 -     3.17: 7024
        3.17 -     3.75: 12140
        3.75 -     4.32: 16886
        4.32 -     4.90: 28488
  Nonbonded interactions: 64569
  Sorted by model distance:
  nonbonded pdb=" O   VAL A 539 "
            pdb=" OH  TYR B 309 "
     model   vdw
     2.014 3.040
  nonbonded pdb=" OG  SER A 268 "
            pdb=" OD1 ASN A 270 "
     model   vdw
     2.094 3.040
  nonbonded pdb=" OG  SER B 268 "
            pdb=" OD1 ASN B 270 "
     model   vdw
     2.131 3.040
  nonbonded pdb=" OD1 ASN A 163 "
            pdb=" OG  SER A 437 "
     model   vdw
     2.142 3.040
  nonbonded pdb=" OD1 ASN B 163 "
            pdb=" OG  SER B 437 "
     model   vdw
     2.142 3.040
  ... (remaining 64564 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 'B'
}
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
}

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:                  0.010
  Normalize map: mean=0, sd=1:             0.860
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     7.230
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.020
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8475
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      :  0.007   0.124   8306  Z= 0.338
  Angle     :  0.683   7.914  11318  Z= 0.372
  Chirality :  0.045   0.252   1356
  Planarity :  0.006   0.066   1396
  Dihedral  : 12.790 118.352   2932
  Min Nonbonded Distance : 2.014

Molprobity Statistics.
  All-atom Clashscore : 3.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.23 %
    Favored  : 99.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.48 (0.25), residues: 1076
  helix:  1.07 (0.21), residues: 640
  sheet: -4.16 (0.76), residues: 20
  loop : -0.55 (0.29), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A 216 
 TYR   0.021   0.002   TYR B 309 
 PHE   0.021   0.002   PHE B 229 
 TRP   0.013   0.001   TRP B 380 
 HIS   0.004   0.001   HIS B 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00708 ( 8294)
  covalent geometry    : angle       0.67572 (11290)
  SS BOND              : bond        0.00375 (    8)
  SS BOND              : angle       2.33507 (   16)
  hydrogen bonds       : bond        0.16563 (  500)
  hydrogen bonds       : angle       6.59204 ( 1440)
  link_BETA1-4         : bond        0.00663 (    2)
  link_BETA1-4         : angle       2.13132 (    6)
  link_NAG-ASN         : bond        0.00327 (    2)
  link_NAG-ASN         : angle       1.66492 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.269 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.5079
  time to fit residues: 45.3159
Evaluate side-chains
  73 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.298 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    0.0980
   chunk 53 optimal weight:   10.0000
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.0020
   chunk 51 optimal weight:    2.9990
   chunk 100 optimal weight:    4.9990
   chunk 106 optimal weight:    0.9980
   chunk 38 optimal weight:    5.9990
   overall best weight:    0.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 541 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.122279 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.089291 restraints weight = 10129.449|
|-----------------------------------------------------------------------------|
r_work (start): 0.2998 rms_B_bonded: 2.07
r_work: 0.2891 rms_B_bonded: 2.43 restraints_weight: 0.5000
r_work: 0.2777 rms_B_bonded: 3.94 restraints_weight: 0.2500
r_work (final): 0.2777
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8578
moved from start:          0.0988

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   8306  Z= 0.128
  Angle     :  0.554   7.363  11318  Z= 0.294
  Chirality :  0.041   0.171   1356
  Planarity :  0.005   0.059   1396
  Dihedral  :  7.026 107.520   1230
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 2.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  6.64 %
    Favored  : 92.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.54 (0.26), residues: 1076
  helix:  2.12 (0.21), residues: 632
  sheet: -4.11 (0.78), residues: 20
  loop : -0.39 (0.30), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B 204 
 TYR   0.011   0.001   TYR A 388 
 PHE   0.012   0.001   PHE A 166 
 TRP   0.014   0.001   TRP A 380 
 HIS   0.002   0.001   HIS B 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 ( 8294)
  covalent geometry    : angle       0.54575 (11290)
  SS BOND              : bond        0.00159 (    8)
  SS BOND              : angle       1.57986 (   16)
  hydrogen bonds       : bond        0.05670 (  500)
  hydrogen bonds       : angle       4.47346 ( 1440)
  link_BETA1-4         : bond        0.00672 (    2)
  link_BETA1-4         : angle       3.14775 (    6)
  link_NAG-ASN         : bond        0.00390 (    2)
  link_NAG-ASN         : angle       1.68401 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.195 
Fit side-chains
REVERT: A  207 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.7993 (tt)
  outliers start: 6
  outliers final: 2
  residues processed: 75
  average time/residue: 0.4921
  time to fit residues: 39.2775
Evaluate side-chains
  73 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 70
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  374 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 28 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 6 optimal weight:    8.9990
   chunk 57 optimal weight:    6.9990
   chunk 72 optimal weight:    5.9990
   chunk 30 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 75 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9990
   chunk 86 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   overall best weight:    1.3786

-------------------------------------------------------------------------------
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 = 0.3437 r_free = 0.3437 target = 0.121137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.087988 restraints weight = 9954.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.05
r_work: 0.2875 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8600
moved from start:          0.1093

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   8306  Z= 0.137
  Angle     :  0.545   7.873  11318  Z= 0.290
  Chirality :  0.041   0.161   1356
  Planarity :  0.005   0.052   1396
  Dihedral  :  6.885 107.080   1230
  Min Nonbonded Distance : 2.591

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.40 %
    Allowed  :  8.16 %
    Favored  : 90.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.60 (0.26), residues: 1076
  helix:  2.21 (0.21), residues: 644
  sheet: -4.02 (0.79), residues: 20
  loop : -0.54 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 216 
 TYR   0.014   0.001   TYR B 388 
 PHE   0.014   0.001   PHE A 166 
 TRP   0.011   0.001   TRP A 380 
 HIS   0.002   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 8294)
  covalent geometry    : angle       0.53698 (11290)
  SS BOND              : bond        0.00225 (    8)
  SS BOND              : angle       1.60915 (   16)
  hydrogen bonds       : bond        0.05932 (  500)
  hydrogen bonds       : angle       4.35146 ( 1440)
  link_BETA1-4         : bond        0.00677 (    2)
  link_BETA1-4         : angle       2.99627 (    6)
  link_NAG-ASN         : bond        0.00311 (    2)
  link_NAG-ASN         : angle       1.65291 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 72
  time to evaluate  : 0.317 
Fit side-chains
REVERT: A  505 GLU cc_start: 0.8578 (mp0) cc_final: 0.8303 (mp0)
  outliers start: 12
  outliers final: 5
  residues processed: 76
  average time/residue: 0.5888
  time to fit residues: 47.5759
Evaluate side-chains
  75 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 70
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 35 optimal weight:    0.1980
   chunk 10 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 41 optimal weight:    0.6980
   chunk 11 optimal weight:    0.9990
   chunk 101 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 5 optimal weight:    2.9990
   chunk 1 optimal weight:   10.0000
   chunk 59 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3460 r_free = 0.3460 target = 0.123015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3016 r_free = 0.3016 target = 0.089755 restraints weight = 10201.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3005 rms_B_bonded: 2.09
r_work: 0.2898 rms_B_bonded: 2.44 restraints_weight: 0.5000
r_work: 0.2783 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2783
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8565
moved from start:          0.1303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   8306  Z= 0.117
  Angle     :  0.515   8.091  11318  Z= 0.272
  Chirality :  0.040   0.161   1356
  Planarity :  0.004   0.048   1396
  Dihedral  :  6.693 105.527   1230
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.70 %
    Favored  : 97.30 %
  Rotamer:
    Outliers :  0.70 %
    Allowed  :  9.91 %
    Favored  : 89.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.80 (0.26), residues: 1076
  helix:  2.38 (0.21), residues: 644
  sheet: -4.02 (0.79), residues: 20
  loop : -0.46 (0.30), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 216 
 TYR   0.010   0.001   TYR B 418 
 PHE   0.014   0.001   PHE B 166 
 TRP   0.010   0.001   TRP A 380 
 HIS   0.002   0.001   HIS B 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 8294)
  covalent geometry    : angle       0.50744 (11290)
  SS BOND              : bond        0.00173 (    8)
  SS BOND              : angle       1.31362 (   16)
  hydrogen bonds       : bond        0.05145 (  500)
  hydrogen bonds       : angle       4.27037 ( 1440)
  link_BETA1-4         : bond        0.00673 (    2)
  link_BETA1-4         : angle       2.95405 (    6)
  link_NAG-ASN         : bond        0.00270 (    2)
  link_NAG-ASN         : angle       1.58853 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 71
  time to evaluate  : 0.200 
Fit side-chains
REVERT: A  207 LEU cc_start: 0.8328 (OUTLIER) cc_final: 0.7992 (tt)
REVERT: A  505 GLU cc_start: 0.8582 (mp0) cc_final: 0.8325 (mp0)
  outliers start: 6
  outliers final: 4
  residues processed: 73
  average time/residue: 0.5445
  time to fit residues: 42.2640
Evaluate side-chains
  74 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.243 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  494 MET
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  494 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 64 optimal weight:    2.9990
   chunk 85 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 24 optimal weight:    2.9990
   chunk 74 optimal weight:    6.9990
   chunk 68 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 79 optimal weight:    4.9990
   chunk 28 optimal weight:    2.9990
   chunk 37 optimal weight:    3.9990
   overall best weight:    2.5988

-------------------------------------------------------------------------------
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 = 0.3392 r_free = 0.3392 target = 0.117619 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2931 r_free = 0.2931 target = 0.084273 restraints weight = 10152.404|
|-----------------------------------------------------------------------------|
r_work (start): 0.2932 rms_B_bonded: 2.06
r_work: 0.2824 rms_B_bonded: 2.38 restraints_weight: 0.5000
r_work: 0.2711 rms_B_bonded: 3.82 restraints_weight: 0.2500
r_work (final): 0.2711
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8651
moved from start:          0.1157

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048   8306  Z= 0.200
  Angle     :  0.610   8.507  11318  Z= 0.326
  Chirality :  0.044   0.169   1356
  Planarity :  0.005   0.046   1396
  Dihedral  :  6.768 103.832   1230
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 2.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.66 %
    Favored  : 87.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.58 (0.26), residues: 1076
  helix:  2.24 (0.21), residues: 642
  sheet:  None (None), residues: 0
  loop : -0.84 (0.28), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 216 
 TYR   0.018   0.002   TYR A 388 
 PHE   0.016   0.002   PHE A 166 
 TRP   0.011   0.002   TRP A 380 
 HIS   0.003   0.001   HIS A 174 

Details of bonding type rmsd
  covalent geometry    : bond        0.00492 ( 8294)
  covalent geometry    : angle       0.59962 (11290)
  SS BOND              : bond        0.00345 (    8)
  SS BOND              : angle       2.17636 (   16)
  hydrogen bonds       : bond        0.07278 (  500)
  hydrogen bonds       : angle       4.36194 ( 1440)
  link_BETA1-4         : bond        0.00780 (    2)
  link_BETA1-4         : angle       2.94796 (    6)
  link_NAG-ASN         : bond        0.00394 (    2)
  link_NAG-ASN         : angle       1.81161 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 79
  time to evaluate  : 0.330 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.6454 (OUTLIER) cc_final: 0.6236 (tt)
REVERT: A  207 LEU cc_start: 0.8389 (OUTLIER) cc_final: 0.8048 (tt)
REVERT: B  207 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7979 (tp)
  outliers start: 11
  outliers final: 4
  residues processed: 83
  average time/residue: 0.5122
  time to fit residues: 45.4549
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  551 VAL
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  551 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 101 optimal weight:    0.6980
   chunk 6 optimal weight:    0.7980
   chunk 70 optimal weight:    5.9990
   chunk 14 optimal weight:    0.9980
   chunk 68 optimal weight:    0.8980
   chunk 63 optimal weight:    0.9990
   chunk 45 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 39 optimal weight:    0.5980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
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 = 0.3466 r_free = 0.3466 target = 0.123776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3029 r_free = 0.3029 target = 0.090821 restraints weight = 10051.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.06
r_work: 0.2913 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2799 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2799
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8554
moved from start:          0.1475

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036   8306  Z= 0.110
  Angle     :  0.502   8.296  11318  Z= 0.265
  Chirality :  0.039   0.160   1356
  Planarity :  0.004   0.044   1396
  Dihedral  :  6.567 104.123   1230
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 12.47 %
    Favored  : 86.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.84 (0.26), residues: 1076
  helix:  2.42 (0.21), residues: 646
  sheet: -4.04 (0.78), residues: 20
  loop : -0.48 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 216 
 TYR   0.010   0.001   TYR B 418 
 PHE   0.014   0.001   PHE B 166 
 TRP   0.010   0.001   TRP A 380 
 HIS   0.002   0.000   HIS B 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00228 ( 8294)
  covalent geometry    : angle       0.49437 (11290)
  SS BOND              : bond        0.00164 (    8)
  SS BOND              : angle       1.19368 (   16)
  hydrogen bonds       : bond        0.04782 (  500)
  hydrogen bonds       : angle       4.26027 ( 1440)
  link_BETA1-4         : bond        0.00724 (    2)
  link_BETA1-4         : angle       2.93582 (    6)
  link_NAG-ASN         : bond        0.00238 (    2)
  link_NAG-ASN         : angle       1.53923 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.307 
Fit side-chains
REVERT: A  207 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8007 (tt)
  outliers start: 11
  outliers final: 5
  residues processed: 78
  average time/residue: 0.5815
  time to fit residues: 48.1454
Evaluate side-chains
  78 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 72
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  451 GLU
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  250 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 38 optimal weight:   10.0000
   chunk 9 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 78 optimal weight:    1.9990
   chunk 26 optimal weight:    4.9990
   chunk 97 optimal weight:    5.9990
   chunk 60 optimal weight:    4.9990
   chunk 90 optimal weight:    4.9990
   chunk 24 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   overall best weight:    2.3388

-------------------------------------------------------------------------------
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 = 0.3397 r_free = 0.3397 target = 0.118132 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2943 r_free = 0.2943 target = 0.085022 restraints weight = 10152.291|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 2.04
r_work: 0.2819 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2703 rms_B_bonded: 3.84 restraints_weight: 0.2500
r_work (final): 0.2703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8653
moved from start:          0.1274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   8306  Z= 0.186
  Angle     :  0.593   8.611  11318  Z= 0.316
  Chirality :  0.043   0.166   1356
  Planarity :  0.005   0.046   1396
  Dihedral  :  6.655 103.013   1230
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.04 %
    Favored  : 97.96 %
  Rotamer:
    Outliers :  1.63 %
    Allowed  : 12.35 %
    Favored  : 86.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.26), residues: 1076
  helix:  2.33 (0.21), residues: 644
  sheet:  None (None), residues: 0
  loop : -0.83 (0.28), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 216 
 TYR   0.019   0.002   TYR B 388 
 PHE   0.015   0.002   PHE A 166 
 TRP   0.011   0.001   TRP A 380 
 HIS   0.002   0.001   HIS B 364 

Details of bonding type rmsd
  covalent geometry    : bond        0.00454 ( 8294)
  covalent geometry    : angle       0.58394 (11290)
  SS BOND              : bond        0.00311 (    8)
  SS BOND              : angle       2.04838 (   16)
  hydrogen bonds       : bond        0.06946 (  500)
  hydrogen bonds       : angle       4.32453 ( 1440)
  link_BETA1-4         : bond        0.00749 (    2)
  link_BETA1-4         : angle       2.90620 (    6)
  link_NAG-ASN         : bond        0.00373 (    2)
  link_NAG-ASN         : angle       1.78042 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.264 
Fit side-chains
REVERT: A   20 LEU cc_start: 0.6401 (OUTLIER) cc_final: 0.6175 (tt)
REVERT: A  207 LEU cc_start: 0.8359 (OUTLIER) cc_final: 0.8030 (tt)
REVERT: A  524 TYR cc_start: 0.9295 (OUTLIER) cc_final: 0.8930 (t80)
REVERT: B  207 LEU cc_start: 0.8393 (OUTLIER) cc_final: 0.7967 (tp)
REVERT: B  524 TYR cc_start: 0.9300 (OUTLIER) cc_final: 0.8921 (t80)
  outliers start: 14
  outliers final: 6
  residues processed: 82
  average time/residue: 0.4747
  time to fit residues: 41.6763
Evaluate side-chains
  79 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.246 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  524 TYR
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  207 LEU
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  320 ILE
Chi-restraints excluded: chain B residue  524 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 72 optimal weight:    5.9990
   chunk 63 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 76 optimal weight:    0.0470
   chunk 102 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9980
   chunk 59 optimal weight:    0.5980
   chunk 85 optimal weight:    0.0370
   chunk 105 optimal weight:    3.9990
   overall best weight:    0.4756

-------------------------------------------------------------------------------
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 = 0.3469 r_free = 0.3469 target = 0.124085 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.091152 restraints weight = 10011.162|
|-----------------------------------------------------------------------------|
r_work (start): 0.3011 rms_B_bonded: 2.05
r_work: 0.2906 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2792 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8549
moved from start:          0.1546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8306  Z= 0.105
  Angle     :  0.502   8.330  11318  Z= 0.263
  Chirality :  0.039   0.159   1356
  Planarity :  0.004   0.044   1396
  Dihedral  :  6.492 103.535   1230
  Min Nonbonded Distance : 2.623

Molprobity Statistics.
  All-atom Clashscore : 2.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.42 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 13.17 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.93 (0.26), residues: 1076
  helix:  2.51 (0.21), residues: 646
  sheet: -4.07 (0.78), residues: 20
  loop : -0.47 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 508 
 TYR   0.010   0.001   TYR A 418 
 PHE   0.013   0.001   PHE A 166 
 TRP   0.011   0.001   TRP B 380 
 HIS   0.002   0.000   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00201 ( 8294)
  covalent geometry    : angle       0.49544 (11290)
  SS BOND              : bond        0.00150 (    8)
  SS BOND              : angle       1.13019 (   16)
  hydrogen bonds       : bond        0.04649 (  500)
  hydrogen bonds       : angle       4.22421 ( 1440)
  link_BETA1-4         : bond        0.00738 (    2)
  link_BETA1-4         : angle       2.89370 (    6)
  link_NAG-ASN         : bond        0.00219 (    2)
  link_NAG-ASN         : angle       1.51473 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 72
  time to evaluate  : 0.231 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.6373 (OUTLIER) cc_final: 0.6162 (tt)
REVERT: A  207 LEU cc_start: 0.8318 (OUTLIER) cc_final: 0.7998 (tt)
REVERT: A  524 TYR cc_start: 0.9222 (OUTLIER) cc_final: 0.8822 (t80)
REVERT: B  524 TYR cc_start: 0.9213 (OUTLIER) cc_final: 0.8797 (t80)
  outliers start: 11
  outliers final: 4
  residues processed: 79
  average time/residue: 0.5039
  time to fit residues: 42.4273
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 74
  time to evaluate  : 0.312 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  524 TYR
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  524 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 65 optimal weight:    1.9990
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0980
   chunk 59 optimal weight:    0.7980
   chunk 70 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:    2.9990
   overall best weight:    1.1786

-------------------------------------------------------------------------------
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 = 0.3446 r_free = 0.3446 target = 0.122125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3005 r_free = 0.3005 target = 0.089171 restraints weight = 10027.784|
|-----------------------------------------------------------------------------|
r_work (start): 0.2981 rms_B_bonded: 2.04
r_work: 0.2875 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2760 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8580
moved from start:          0.1502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   8306  Z= 0.123
  Angle     :  0.523   8.488  11318  Z= 0.275
  Chirality :  0.040   0.161   1356
  Planarity :  0.004   0.044   1396
  Dihedral  :  6.455 102.865   1230
  Min Nonbonded Distance : 2.621

Molprobity Statistics.
  All-atom Clashscore : 2.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.52 %
    Allowed  : 13.29 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.95 (0.26), residues: 1076
  helix:  2.53 (0.21), residues: 646
  sheet: -3.94 (0.80), residues: 20
  loop : -0.49 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 216 
 TYR   0.023   0.001   TYR B 388 
 PHE   0.015   0.001   PHE B 166 
 TRP   0.010   0.001   TRP A 380 
 HIS   0.002   0.001   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00270 ( 8294)
  covalent geometry    : angle       0.51549 (11290)
  SS BOND              : bond        0.00214 (    8)
  SS BOND              : angle       1.45289 (   16)
  hydrogen bonds       : bond        0.05326 (  500)
  hydrogen bonds       : angle       4.19413 ( 1440)
  link_BETA1-4         : bond        0.00731 (    2)
  link_BETA1-4         : angle       2.84676 (    6)
  link_NAG-ASN         : bond        0.00286 (    2)
  link_NAG-ASN         : angle       1.52523 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.6357 (OUTLIER) cc_final: 0.6144 (tt)
REVERT: A  207 LEU cc_start: 0.8338 (OUTLIER) cc_final: 0.8015 (tt)
REVERT: A  524 TYR cc_start: 0.9250 (OUTLIER) cc_final: 0.8849 (t80)
REVERT: B  524 TYR cc_start: 0.9247 (OUTLIER) cc_final: 0.8851 (t80)
  outliers start: 13
  outliers final: 5
  residues processed: 81
  average time/residue: 0.4956
  time to fit residues: 42.7836
Evaluate side-chains
  81 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 72
  time to evaluate  : 0.317 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   20 LEU
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  320 ILE
Chi-restraints excluded: chain A residue  524 TYR
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  524 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 103 optimal weight:    1.9990
   chunk 25 optimal weight:    0.0010
   chunk 7 optimal weight:    2.9990
   chunk 88 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0670
   chunk 60 optimal weight:    0.0060
   chunk 82 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9980
   chunk 87 optimal weight:    0.7980
   chunk 101 optimal weight:    0.9990
   overall best weight:    0.3740

-------------------------------------------------------------------------------
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 = 0.3502 r_free = 0.3502 target = 0.126666 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.094313 restraints weight = 9963.846|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.03
r_work: 0.2956 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2842 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work (final): 0.2842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8504
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8306  Z= 0.098
  Angle     :  0.485   8.475  11318  Z= 0.252
  Chirality :  0.039   0.155   1356
  Planarity :  0.004   0.044   1396
  Dihedral  :  6.320 102.402   1230
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 2.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.60 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 13.75 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.26), residues: 1076
  helix:  2.64 (0.21), residues: 646
  sheet: -3.87 (0.81), residues: 20
  loop : -0.33 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 204 
 TYR   0.009   0.001   TYR B 418 
 PHE   0.012   0.001   PHE A 166 
 TRP   0.010   0.001   TRP A 482 
 HIS   0.001   0.000   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00189 ( 8294)
  covalent geometry    : angle       0.47925 (11290)
  SS BOND              : bond        0.00112 (    8)
  SS BOND              : angle       0.95004 (   16)
  hydrogen bonds       : bond        0.04009 (  500)
  hydrogen bonds       : angle       4.14253 ( 1440)
  link_BETA1-4         : bond        0.00813 (    2)
  link_BETA1-4         : angle       2.83272 (    6)
  link_NAG-ASN         : bond        0.00206 (    2)
  link_NAG-ASN         : angle       1.38263 (    6)

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

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

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2152 Ramachandran restraints generated.
    1076 Oldfield, 0 Emsley, 1076 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  207 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8002 (tt)
REVERT: A  468 LEU cc_start: 0.7485 (mm) cc_final: 0.7185 (mp)
REVERT: A  524 TYR cc_start: 0.9194 (OUTLIER) cc_final: 0.8838 (t80)
REVERT: B  524 TYR cc_start: 0.9188 (OUTLIER) cc_final: 0.8824 (t80)
  outliers start: 9
  outliers final: 4
  residues processed: 81
  average time/residue: 0.5431
  time to fit residues: 46.8794
Evaluate side-chains
  82 residues out of total 858 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 75
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 ILE
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  250 THR
Chi-restraints excluded: chain A residue  524 TYR
Chi-restraints excluded: chain B residue  198 ILE
Chi-restraints excluded: chain B residue  250 THR
Chi-restraints excluded: chain B residue  524 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 108
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 80 optimal weight:    8.9990
   chunk 103 optimal weight:    0.9990
   chunk 14 optimal weight:    0.5980
   chunk 91 optimal weight:    5.9990
   chunk 20 optimal weight:    0.8980
   chunk 27 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 106 optimal weight:    4.9990
   chunk 54 optimal weight:   10.0000
   overall best weight:    0.8780

-------------------------------------------------------------------------------
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 = 0.124414 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.091553 restraints weight = 10053.092|
|-----------------------------------------------------------------------------|
r_work (start): 0.3030 rms_B_bonded: 2.05
r_work: 0.2927 rms_B_bonded: 2.42 restraints_weight: 0.5000
r_work: 0.2813 rms_B_bonded: 3.93 restraints_weight: 0.2500
r_work (final): 0.2813
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8545
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8306  Z= 0.110
  Angle     :  0.509   8.597  11318  Z= 0.264
  Chirality :  0.039   0.155   1356
  Planarity :  0.004   0.044   1396
  Dihedral  :  6.266 101.508   1230
  Min Nonbonded Distance : 2.622

Molprobity Statistics.
  All-atom Clashscore : 1.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.93 %
    Allowed  : 13.87 %
    Favored  : 85.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.14 (0.26), residues: 1076
  helix:  2.65 (0.21), residues: 646
  sheet: -3.79 (0.83), residues: 20
  loop : -0.34 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 216 
 TYR   0.026   0.001   TYR B 388 
 PHE   0.013   0.001   PHE A 166 
 TRP   0.009   0.001   TRP B 380 
 HIS   0.002   0.000   HIS A 541 

Details of bonding type rmsd
  covalent geometry    : bond        0.00233 ( 8294)
  covalent geometry    : angle       0.50232 (11290)
  SS BOND              : bond        0.00189 (    8)
  SS BOND              : angle       1.25501 (   16)
  hydrogen bonds       : bond        0.04696 (  500)
  hydrogen bonds       : angle       4.12331 ( 1440)
  link_BETA1-4         : bond        0.00711 (    2)
  link_BETA1-4         : angle       2.80621 (    6)
  link_NAG-ASN         : bond        0.00263 (    2)
  link_NAG-ASN         : angle       1.38907 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2549.83 seconds
wall clock time: 44 minutes 7.80 seconds (2647.80 seconds total)