Starting phenix.real_space_refine
on Wed Mar 12 09:00:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sgk_40458/03_2025/8sgk_40458.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sgk_40458/03_2025/8sgk_40458.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sgk_40458/03_2025/8sgk_40458.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sgk_40458/03_2025/8sgk_40458.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sgk_40458/03_2025/8sgk_40458.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sgk_40458/03_2025/8sgk_40458.cif"
  }
  resolution = 3.7
  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=  -0.001 sd=   0.038
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      22      5.16       5
     C    4856      2.51       5
     N    1350      2.21       5
     O    1394      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7622
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3768
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3768
          Classifications: {'peptide': 493}
          Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 453}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 43
          Unusual residues: {'LBV': 1}
          Classifications: {'undetermined': 1}
  Restraints were copied for chains:
    B
  Time building chain proxies: 7.49, per 1000 atoms: 0.98
  Number of scatterers: 7622
  At special positions: 0
  Unit cell: (88.596, 93.564, 110.124, 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      22     16.00
     O    1394      8.00
     N    1350      7.00
     C    4856      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.98
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1812

  Finding SS restraints...
    Secondary structure from input PDB file:
      36 helices and 8 sheets defined
      42.8% alpha, 18.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 15
      removed outlier: 3.917A  pdb=" N   GLY A  15 " --> pdb=" O   LEU A  12 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 27
      removed outlier: 3.684A  pdb=" N   CYS A  24 " --> pdb=" O   THR A  21 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU A  25 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU A  27 " --> pdb=" O   CYS A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 57 through 63
    Processing helix  chain 'A' and resid 65 through 70
    Processing helix  chain 'A' and resid 73 through 78
    Processing helix  chain 'A' and resid 80 through 89
      removed outlier: 4.261A  pdb=" N   ALA A  84 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 149
      removed outlier: 3.576A  pdb=" N   GLU A 148 " --> pdb=" O   MET A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 152 through 169
      removed outlier: 3.869A  pdb=" N   GLU A 158 " --> pdb=" O   ARG A 154 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL A 159 " --> pdb=" O   ALA A 155 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 209 through 217
    Processing helix  chain 'A' and resid 257 through 267
      removed outlier: 3.833A  pdb=" N   MET A 267 " --> pdb=" O   TYR A 263 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 298 through 330
      removed outlier: 3.953A  pdb=" N   THR A 304 " --> pdb=" O   ASP A 300 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   GLN A 317 " --> pdb=" O   SER A 313 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 344
      removed outlier: 4.111A  pdb=" N   HIS A 344 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 353
    Processing helix  chain 'A' and resid 358 through 363
      removed outlier: 3.788A  pdb=" N   MET A 363 " --> pdb=" O   LEU A 359 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 398
    Processing helix  chain 'A' and resid 407 through 412
      removed outlier: 3.935A  pdb=" N   LEU A 411 " --> pdb=" O   ALA A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 414 through 418
    Processing helix  chain 'A' and resid 484 through 518
      removed outlier: 3.835A  pdb=" N   GLY A 503 " --> pdb=" O   THR A 499 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLU A 504 " --> pdb=" O   GLY A 500 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 11 through 15
      removed outlier: 3.915A  pdb=" N   GLY B  15 " --> pdb=" O   LEU B  12 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 21 through 27
      removed outlier: 3.684A  pdb=" N   CYS B  24 " --> pdb=" O   THR B  21 " (cutoff:3.500A)
      removed outlier: 4.359A  pdb=" N   GLU B  25 " --> pdb=" O   GLU B  22 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   GLU B  27 " --> pdb=" O   CYS B  24 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 63
    Processing helix  chain 'B' and resid 65 through 70
    Processing helix  chain 'B' and resid 73 through 78
    Processing helix  chain 'B' and resid 80 through 89
      removed outlier: 4.261A  pdb=" N   ALA B  84 " --> pdb=" O   GLU B  80 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 149
      removed outlier: 3.575A  pdb=" N   GLU B 148 " --> pdb=" O   MET B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 152 through 169
      removed outlier: 3.868A  pdb=" N   GLU B 158 " --> pdb=" O   ARG B 154 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL B 159 " --> pdb=" O   ALA B 155 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 209 through 217
    Processing helix  chain 'B' and resid 257 through 267
      removed outlier: 3.833A  pdb=" N   MET B 267 " --> pdb=" O   TYR B 263 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 298 through 330
      removed outlier: 3.953A  pdb=" N   THR B 304 " --> pdb=" O   ASP B 300 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   GLN B 317 " --> pdb=" O   SER B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 344
      removed outlier: 4.111A  pdb=" N   HIS B 344 " --> pdb=" O   LEU B 340 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 353
    Processing helix  chain 'B' and resid 358 through 363
      removed outlier: 3.788A  pdb=" N   MET B 363 " --> pdb=" O   LEU B 359 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 384 through 398
    Processing helix  chain 'B' and resid 407 through 412
      removed outlier: 3.935A  pdb=" N   LEU B 411 " --> pdb=" O   ALA B 407 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 414 through 418
    Processing helix  chain 'B' and resid 484 through 518
      removed outlier: 3.835A  pdb=" N   GLY B 503 " --> pdb=" O   THR B 499 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLU B 504 " --> pdb=" O   GLY B 500 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 3.633A  pdb=" N   MET A  54 " --> pdb=" O   ASP A 235 " (cutoff:3.500A)
      removed outlier: 6.636A  pdb=" N   THR A  43 " --> pdb=" O   LEU A  52 " (cutoff:3.500A)
      removed outlier: 4.716A  pdb=" N   MET A  54 " --> pdb=" O   LEU A  41 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   LEU A  41 " --> pdb=" O   MET A  54 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 202 through 203
      removed outlier: 5.084A  pdb=" N   VAL A 186 " --> pdb=" O   LYS A 177 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LYS A 177 " --> pdb=" O   VAL A 186 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   ALA A 188 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   TRP A 284 " --> pdb=" O   PHE A 178 " (cutoff:3.500A)
      removed outlier: 5.251A  pdb=" N   LEU A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
      removed outlier: 5.964A  pdb=" N   VAL A 279 " --> pdb=" O   LEU A 283 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 376 through 380
      removed outlier: 4.340A  pdb=" N   GLU A 436 " --> pdb=" O   VAL A 430 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 450
      removed outlier: 4.452A  pdb=" N   VAL A 449 " --> pdb=" O   GLU A 474 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLU A 474 " --> pdb=" O   VAL A 449 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 34 through 35
      removed outlier: 3.634A  pdb=" N   MET B  54 " --> pdb=" O   ASP B 235 " (cutoff:3.500A)
      removed outlier: 6.635A  pdb=" N   THR B  43 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 4.717A  pdb=" N   MET B  54 " --> pdb=" O   LEU B  41 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   LEU B  41 " --> pdb=" O   MET B  54 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 202 through 203
      removed outlier: 5.083A  pdb=" N   VAL B 186 " --> pdb=" O   LYS B 177 " (cutoff:3.500A)
      removed outlier: 6.622A  pdb=" N   LYS B 177 " --> pdb=" O   VAL B 186 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   ALA B 188 " --> pdb=" O   LEU B 175 " (cutoff:3.500A)
      removed outlier: 6.555A  pdb=" N   TRP B 284 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 5.252A  pdb=" N   LEU B 283 " --> pdb=" O   VAL B 279 " (cutoff:3.500A)
      removed outlier: 5.965A  pdb=" N   VAL B 279 " --> pdb=" O   LEU B 283 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 376 through 380
      removed outlier: 4.341A  pdb=" N   GLU B 436 " --> pdb=" O   VAL B 430 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 448 through 450
      removed outlier: 4.451A  pdb=" N   VAL B 449 " --> pdb=" O   GLU B 474 " (cutoff:3.500A)
      removed outlier: 4.085A  pdb=" N   GLU B 474 " --> pdb=" O   VAL B 449 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    382 hydrogen bonds defined for protein.
    1068 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: 2.34

  Time building geometry restraints manager: 2.31 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 1412
        1.32 -     1.45: 1902
        1.45 -     1.57: 4468
        1.57 -     1.69: 0
        1.69 -     1.81: 36
  Bond restraints: 7818
  Sorted by residual:
  bond pdb=" CA  TRP A 412 "
       pdb=" CB  TRP A 412 "
    ideal  model  delta    sigma   weight residual
    1.522  1.535 -0.012 1.75e-02 3.27e+03 5.06e-01
  bond pdb=" CA  TRP B 412 "
       pdb=" CB  TRP B 412 "
    ideal  model  delta    sigma   weight residual
    1.522  1.534 -0.012 1.75e-02 3.27e+03 4.60e-01
  bond pdb=" CG  PRO A 236 "
       pdb=" CD  PRO A 236 "
    ideal  model  delta    sigma   weight residual
    1.512  1.494  0.018 2.70e-02 1.37e+03 4.36e-01
  bond pdb=" CG  PRO B 236 "
       pdb=" CD  PRO B 236 "
    ideal  model  delta    sigma   weight residual
    1.512  1.496  0.016 2.70e-02 1.37e+03 3.73e-01
  bond pdb=" CB  LYS B 476 "
       pdb=" CG  LYS B 476 "
    ideal  model  delta    sigma   weight residual
    1.520  1.503  0.017 3.00e-02 1.11e+03 3.28e-01
  ... (remaining 7813 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.42: 10436
        1.42 -     2.83: 199
        2.83 -     4.25: 47
        4.25 -     5.67: 6
        5.67 -     7.09: 10
  Bond angle restraints: 10698
  Sorted by residual:
  angle pdb=" CA  ARG A 332 "
        pdb=" CB  ARG A 332 "
        pdb=" CG  ARG A 332 "
      ideal   model   delta    sigma   weight residual
     114.10  120.50   -6.40 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" CA  ARG B 332 "
        pdb=" CB  ARG B 332 "
        pdb=" CG  ARG B 332 "
      ideal   model   delta    sigma   weight residual
     114.10  120.49   -6.39 2.00e+00 2.50e-01 1.02e+01
  angle pdb=" C   VAL A 296 "
        pdb=" N   LEU A 297 "
        pdb=" CA  LEU A 297 "
      ideal   model   delta    sigma   weight residual
     122.65  118.83    3.82 1.66e+00 3.63e-01 5.29e+00
  angle pdb=" C   VAL B 296 "
        pdb=" N   LEU B 297 "
        pdb=" CA  LEU B 297 "
      ideal   model   delta    sigma   weight residual
     122.65  118.84    3.81 1.66e+00 3.63e-01 5.25e+00
  angle pdb=" N   GLY A 478 "
        pdb=" CA  GLY A 478 "
        pdb=" C   GLY A 478 "
      ideal   model   delta    sigma   weight residual
     113.76  117.67   -3.91 1.80e+00 3.09e-01 4.71e+00
  ... (remaining 10693 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 4029
       17.85 -    35.69: 429
       35.69 -    53.54: 152
       53.54 -    71.39: 40
       71.39 -    89.23: 6
  Dihedral angle restraints: 4656
    sinusoidal: 1846
      harmonic: 2810
  Sorted by residual:
  dihedral pdb=" CA  ARG B 477 "
           pdb=" C   ARG B 477 "
           pdb=" N   GLY B 478 "
           pdb=" CA  GLY B 478 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.85   19.15     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  ARG A 477 "
           pdb=" C   ARG A 477 "
           pdb=" N   GLY A 478 "
           pdb=" CA  GLY A 478 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.90   19.10     0      5.00e+00 4.00e-02 1.46e+01
  dihedral pdb=" CA  TRP A 412 "
           pdb=" C   TRP A 412 "
           pdb=" N   PRO A 413 "
           pdb=" CA  PRO A 413 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.29  -17.71     0      5.00e+00 4.00e-02 1.26e+01
  ... (remaining 4653 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.024: 696
       0.024 -    0.048: 310
       0.048 -    0.072: 99
       0.072 -    0.095: 53
       0.095 -    0.119: 46
  Chirality restraints: 1204
  Sorted by residual:
  chirality pdb=" CA  ILE A 287 "
            pdb=" N   ILE A 287 "
            pdb=" C   ILE A 287 "
            pdb=" CB  ILE A 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.56e-01
  chirality pdb=" CA  ILE B 287 "
            pdb=" N   ILE B 287 "
            pdb=" C   ILE B 287 "
            pdb=" CB  ILE B 287 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.52e-01
  chirality pdb=" CA  VAL B 449 "
            pdb=" N   VAL B 449 "
            pdb=" C   VAL B 449 "
            pdb=" CB  VAL B 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.56   -0.12 2.00e-01 2.50e+01 3.32e-01
  ... (remaining 1201 not shown)

  Planarity restraints: 1400
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 479 "   -0.008 2.00e-02 2.50e+03   1.18e-02 2.79e+00
        pdb=" CG  TYR A 479 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 479 "   -0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 479 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 479 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 479 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 479 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR A 479 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 479 "    0.008 2.00e-02 2.50e+03   1.17e-02 2.75e+00
        pdb=" CG  TYR B 479 "   -0.028 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 479 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 479 "    0.009 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 479 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 479 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 479 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 479 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 484 "    0.022 5.00e-02 4.00e+02   3.28e-02 1.73e+00
        pdb=" N   PRO A 485 "   -0.057 5.00e-02 4.00e+02
        pdb=" CA  PRO A 485 "    0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 485 "    0.018 5.00e-02 4.00e+02
  ... (remaining 1397 not shown)

  Histogram of nonbonded interaction distances:
        2.27 -     2.80: 1799
        2.80 -     3.32: 7185
        3.32 -     3.85: 13029
        3.85 -     4.37: 14203
        4.37 -     4.90: 25152
  Nonbonded interactions: 61368
  Sorted by model distance:
  nonbonded pdb=" O   ARG A 328 "
            pdb=" NH1 ARG A 332 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   ARG B 328 "
            pdb=" NH1 ARG B 332 "
     model   vdw
     2.269 3.120
  nonbonded pdb=" O   TRP B 394 "
            pdb=" OG1 THR B 397 "
     model   vdw
     2.287 3.040
  nonbonded pdb=" O   TRP A 394 "
            pdb=" OG1 THR A 397 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" O   GLN B 329 "
            pdb=" NE2 GLN B 329 "
     model   vdw
     2.295 3.120
  ... (remaining 61363 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'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.860
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.090
  Process input model:                     24.070
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   31.550
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7642
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      :  0.002   0.024   7818  Z= 0.149
  Angle     :  0.556   7.087  10698  Z= 0.287
  Chirality :  0.037   0.119   1204
  Planarity :  0.004   0.033   1400
  Dihedral  : 17.409  89.232   2844
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  : 26.80 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.76 (0.26), residues: 974
  helix:  1.38 (0.27), residues: 336
  sheet:  1.02 (0.42), residues: 150
  loop : -0.23 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 412 
 HIS   0.004   0.001   HIS A 335 
 PHE   0.003   0.000   PHE B 469 
 TYR   0.028   0.002   TYR A 479 
 ARG   0.011   0.000   ARG A 332 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8524 (tmm) cc_final: 0.8197 (ttp)
REVERT: A  332 ARG cc_start: 0.6996 (mmm160) cc_final: 0.6791 (ptp-110)
REVERT: B   99 TYR cc_start: 0.8256 (t80) cc_final: 0.8016 (t80)
REVERT: B  144 MET cc_start: 0.8513 (tmm) cc_final: 0.8118 (ttp)
  outliers start: 2
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1930
  time to fit residues: 21.0652
Evaluate side-chains
  71 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 71
  time to evaluate  : 0.778 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 50 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9980
   chunk 76 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    0.9990
   chunk 57 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A 410 GLN
B  57 ASN
B 410 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.140951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.116081 restraints weight = 14794.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.119051 restraints weight = 11141.886|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.120932 restraints weight = 7877.794|
|-----------------------------------------------------------------------------|
r_work (final): 0.3742
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7720
moved from start:          0.1013

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   7818  Z= 0.218
  Angle     :  0.567   6.832  10698  Z= 0.286
  Chirality :  0.040   0.134   1204
  Planarity :  0.005   0.031   1400
  Dihedral  :  5.611  53.182   1110
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.03 %
    Favored  : 98.97 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 26.03 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.90 (0.26), residues: 974
  helix:  1.29 (0.27), residues: 350
  sheet:  1.55 (0.42), residues: 162
  loop : -0.24 (0.28), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 412 
 HIS   0.006   0.001   HIS A 335 
 PHE   0.005   0.001   PHE B 469 
 TYR   0.015   0.002   TYR B 216 
 ARG   0.003   0.000   ARG B 371 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 TYR cc_start: 0.8304 (t80) cc_final: 0.8063 (t80)
  outliers start: 13
  outliers final: 5
  residues processed: 94
  average time/residue: 0.2065
  time to fit residues: 26.7700
Evaluate side-chains
  80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 75
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   51 VAL
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   57 ASN
Chi-restraints excluded: chain B residue  122 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 67 optimal weight:    6.9990
   chunk 83 optimal weight:    0.0970
   chunk 87 optimal weight:    0.8980
   chunk 97 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 16 optimal weight:    0.7980
   chunk 59 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
B  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.141999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.118074 restraints weight = 14994.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.120249 restraints weight = 10566.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.122347 restraints weight = 8276.881|
|-----------------------------------------------------------------------------|
r_work (final): 0.3769
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7728
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7818  Z= 0.212
  Angle     :  0.552   6.922  10698  Z= 0.273
  Chirality :  0.040   0.132   1204
  Planarity :  0.004   0.031   1400
  Dihedral  :  5.620  52.408   1110
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.58 %
    Favored  : 73.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.27), residues: 974
  helix:  1.49 (0.27), residues: 354
  sheet:  1.04 (0.41), residues: 170
  loop : -0.17 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 412 
 HIS   0.006   0.001   HIS A 335 
 PHE   0.007   0.001   PHE B 145 
 TYR   0.014   0.002   TYR B 479 
 ARG   0.002   0.000   ARG A 332 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 82
  time to evaluate  : 0.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8547 (ttp) cc_final: 0.8318 (ttp)
REVERT: B   99 TYR cc_start: 0.8298 (t80) cc_final: 0.8032 (t80)
REVERT: B  144 MET cc_start: 0.8522 (ttp) cc_final: 0.8290 (ttp)
  outliers start: 23
  outliers final: 10
  residues processed: 104
  average time/residue: 0.2208
  time to fit residues: 30.4725
Evaluate side-chains
  82 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.777 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 HIS
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  349 HIS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0060
   chunk 22 optimal weight:    0.3980
   chunk 3 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.7980
   chunk 91 optimal weight:    0.9980
   chunk 97 optimal weight:    0.7980
   chunk 96 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
A  72 GLN
B  57 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.136904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.109211 restraints weight = 15048.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.112603 restraints weight = 10320.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.115113 restraints weight = 7989.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7758
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7818  Z= 0.192
  Angle     :  0.543   7.049  10698  Z= 0.271
  Chirality :  0.039   0.132   1204
  Planarity :  0.004   0.032   1400
  Dihedral  :  5.661  51.836   1110
  Min Nonbonded Distance : 2.531

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.92 %
    Favored  : 99.08 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 22.81 %
    Favored  : 74.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.99 (0.27), residues: 974
  helix:  1.54 (0.27), residues: 354
  sheet:  1.01 (0.40), residues: 170
  loop : -0.14 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 412 
 HIS   0.007   0.001   HIS A 335 
 PHE   0.006   0.001   PHE B 145 
 TYR   0.011   0.002   TYR A 216 
 ARG   0.005   0.000   ARG A 442 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 76
  time to evaluate  : 0.840 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  279 VAL cc_start: 0.7769 (t) cc_final: 0.7462 (t)
  outliers start: 24
  outliers final: 13
  residues processed: 96
  average time/residue: 0.2057
  time to fit residues: 27.0346
Evaluate side-chains
  84 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.848 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 HIS
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue   30 HIS
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue   57 ASN
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  349 HIS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    0.8980
   chunk 67 optimal weight:    0.6980
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 29 optimal weight:    0.9990
   chunk 72 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 30 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
B  57 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.135473 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3564 r_free = 0.3564 target = 0.108178 restraints weight = 15011.556|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111316 restraints weight = 10401.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.113647 restraints weight = 8080.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7818  Z= 0.231
  Angle     :  0.561   7.483  10698  Z= 0.277
  Chirality :  0.040   0.139   1204
  Planarity :  0.004   0.031   1400
  Dihedral  :  5.687  51.626   1110
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 22.81 %
    Favored  : 74.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.02 (0.27), residues: 974
  helix:  1.58 (0.27), residues: 354
  sheet:  0.96 (0.41), residues: 170
  loop : -0.10 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 412 
 HIS   0.004   0.001   HIS A 335 
 PHE   0.006   0.001   PHE A 372 
 TYR   0.012   0.001   TYR B 216 
 ARG   0.006   0.000   ARG B 442 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 69
  time to evaluate  : 0.898 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 16
  residues processed: 85
  average time/residue: 0.1808
  time to fit residues: 21.8214
Evaluate side-chains
  82 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 66
  time to evaluate  : 0.853 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 HIS
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue    8 PHE
Chi-restraints excluded: chain B residue   30 HIS
Chi-restraints excluded: chain B residue   51 VAL
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  349 HIS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 20 optimal weight:    0.0870
   chunk 39 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    0.2980
   chunk 96 optimal weight:    0.7980
   chunk 77 optimal weight:    0.3980
   chunk 7 optimal weight:    0.9980
   chunk 13 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 97 optimal weight:    0.6980
   overall best weight:    0.4558

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN
A  57 ASN
B  57 ASN
B 513 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.137262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.109794 restraints weight = 14977.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.113168 restraints weight = 10235.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.115702 restraints weight = 7901.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7747
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   7818  Z= 0.172
  Angle     :  0.536   7.315  10698  Z= 0.266
  Chirality :  0.039   0.136   1204
  Planarity :  0.004   0.032   1400
  Dihedral  :  5.642  50.784   1110
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 6.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 23.58 %
    Favored  : 74.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.10 (0.27), residues: 974
  helix:  1.72 (0.28), residues: 354
  sheet:  0.91 (0.41), residues: 170
  loop : -0.07 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 412 
 HIS   0.003   0.001   HIS A 335 
 PHE   0.005   0.001   PHE A 372 
 TYR   0.013   0.001   TYR A 216 
 ARG   0.006   0.000   ARG B 442 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.792 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 17
  outliers final: 14
  residues processed: 88
  average time/residue: 0.1794
  time to fit residues: 22.5092
Evaluate side-chains
  84 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.860 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   57 ASN
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  235 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain B residue   57 ASN
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  412 TRP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 59 optimal weight:    0.0370
   chunk 22 optimal weight:    0.2980
   chunk 66 optimal weight:    0.3980
   chunk 9 optimal weight:    0.0980
   chunk 89 optimal weight:    9.9990
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    0.6980
   chunk 76 optimal weight:    1.9990
   chunk 38 optimal weight:    0.8980
   chunk 80 optimal weight:    0.8980
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.3058

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

Flipped N/Q/H residues before XYZ refinement:
B  36 GLN
B  57 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.137920 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.110582 restraints weight = 15002.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.114101 restraints weight = 10096.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.116662 restraints weight = 7732.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3684
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7722
moved from start:          0.2149

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   7818  Z= 0.158
  Angle     :  0.532   7.346  10698  Z= 0.265
  Chirality :  0.039   0.135   1204
  Planarity :  0.004   0.045   1400
  Dihedral  :  5.571  51.219   1110
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 6.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.84 %
    Allowed  : 23.20 %
    Favored  : 73.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.17 (0.27), residues: 974
  helix:  1.71 (0.28), residues: 354
  sheet:  1.01 (0.42), residues: 170
  loop :  0.00 (0.30), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 412 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.009   0.001   PHE A   9 
 TYR   0.012   0.001   TYR B 216 
 ARG   0.005   0.000   ARG B 222 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.881 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 TYR cc_start: 0.8094 (t80) cc_final: 0.7779 (t80)
  outliers start: 22
  outliers final: 13
  residues processed: 90
  average time/residue: 0.1877
  time to fit residues: 23.6526
Evaluate side-chains
  80 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.871 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  235 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  412 TRP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 96 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 22 optimal weight:    2.9990
   chunk 71 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 69 optimal weight:    0.8980
   chunk 93 optimal weight:    0.8980
   chunk 88 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 7 optimal weight:    0.0470
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.6878

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
** B  57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 329 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3960 r_free = 0.3960 target = 0.136437 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.108705 restraints weight = 15092.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.112065 restraints weight = 10360.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.114537 restraints weight = 8030.224|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7766
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   7818  Z= 0.205
  Angle     :  0.560   6.720  10698  Z= 0.280
  Chirality :  0.040   0.134   1204
  Planarity :  0.004   0.032   1400
  Dihedral  :  5.600  51.021   1110
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.13 %
    Favored  : 98.87 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 24.61 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.12 (0.27), residues: 974
  helix:  1.70 (0.28), residues: 350
  sheet:  1.01 (0.42), residues: 170
  loop : -0.05 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 412 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.007   0.001   PHE A   9 
 TYR   0.012   0.001   TYR A 216 
 ARG   0.008   0.000   ARG A 222 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 66
  time to evaluate  : 0.894 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 17
  residues processed: 79
  average time/residue: 0.1887
  time to fit residues: 21.2751
Evaluate side-chains
  81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  235 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain A residue  479 TYR
Chi-restraints excluded: chain B residue    8 PHE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  412 TRP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 62 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 83 optimal weight:    2.9990
   chunk 50 optimal weight:    5.9990
   chunk 30 optimal weight:    0.6980
   chunk 80 optimal weight:    3.9990
   chunk 40 optimal weight:    0.6980
   chunk 57 optimal weight:    0.8980
   chunk 22 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.8180

-------------------------------------------------------------------------------
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 = 0.3945 r_free = 0.3945 target = 0.135183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.107420 restraints weight = 15234.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.110746 restraints weight = 10410.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.113174 restraints weight = 8066.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   7818  Z= 0.224
  Angle     :  0.573  10.749  10698  Z= 0.285
  Chirality :  0.040   0.137   1204
  Planarity :  0.004   0.031   1400
  Dihedral  :  5.702  50.364   1110
  Min Nonbonded Distance : 2.624

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 24.87 %
    Favored  : 72.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.11 (0.27), residues: 974
  helix:  1.67 (0.28), residues: 350
  sheet:  0.98 (0.43), residues: 170
  loop : -0.04 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 412 
 HIS   0.004   0.001   HIS A 116 
 PHE   0.009   0.001   PHE A   9 
 TYR   0.016   0.002   TYR B 479 
 ARG   0.009   0.000   ARG B 222 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.929 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 19
  outliers final: 17
  residues processed: 78
  average time/residue: 0.1739
  time to fit residues: 19.6937
Evaluate side-chains
  81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.846 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  235 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  296 VAL
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain B residue    8 PHE
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  296 VAL
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  412 TRP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 5 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 57 optimal weight:    0.9990
   chunk 78 optimal weight:    0.6980
   chunk 43 optimal weight:    0.0570
   chunk 84 optimal weight:    1.9990
   chunk 90 optimal weight:    1.9990
   chunk 55 optimal weight:    0.6980
   chunk 18 optimal weight:    0.0000
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.3702

-------------------------------------------------------------------------------
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 = 0.3971 r_free = 0.3971 target = 0.137302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.109852 restraints weight = 15182.296|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.113323 restraints weight = 10258.175|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.115849 restraints weight = 7893.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7737
moved from start:          0.2474

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   7818  Z= 0.168
  Angle     :  0.567   8.094  10698  Z= 0.279
  Chirality :  0.040   0.134   1204
  Planarity :  0.004   0.033   1400
  Dihedral  :  5.635  50.295   1110
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.72 %
    Favored  : 99.28 %
  Rotamer:
    Outliers :  2.06 %
    Allowed  : 25.39 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.23 (0.28), residues: 974
  helix:  1.73 (0.28), residues: 350
  sheet:  1.55 (0.44), residues: 158
  loop : -0.11 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 412 
 HIS   0.003   0.001   HIS A  38 
 PHE   0.009   0.001   PHE A   9 
 TYR   0.009   0.001   TYR A 176 
 ARG   0.006   0.000   ARG A 222 

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

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

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1948 Ramachandran restraints generated.
    974 Oldfield, 0 Emsley, 974 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 68
  time to evaluate  : 0.826 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 TYR cc_start: 0.8071 (t80) cc_final: 0.7758 (t80)
REVERT: A  141 ARG cc_start: 0.8202 (ttt90) cc_final: 0.7886 (ttp80)
REVERT: B   99 TYR cc_start: 0.8053 (t80) cc_final: 0.7749 (t80)
REVERT: B  141 ARG cc_start: 0.8245 (ttt90) cc_final: 0.7913 (ttp80)
  outliers start: 16
  outliers final: 15
  residues processed: 79
  average time/residue: 0.2032
  time to fit residues: 22.1359
Evaluate side-chains
  84 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.795 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  122 LEU
Chi-restraints excluded: chain A residue  174 MET
Chi-restraints excluded: chain A residue  235 ASP
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  412 TRP
Chi-restraints excluded: chain B residue  122 LEU
Chi-restraints excluded: chain B residue  174 MET
Chi-restraints excluded: chain B residue  235 ASP
Chi-restraints excluded: chain B residue  253 LEU
Chi-restraints excluded: chain B residue  273 LEU
Chi-restraints excluded: chain B residue  349 HIS
Chi-restraints excluded: chain B residue  412 TRP
Chi-restraints excluded: chain B residue  479 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 49 optimal weight:    9.9990
   chunk 89 optimal weight:    0.1980
   chunk 88 optimal weight:    0.9990
   chunk 80 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 90 optimal weight:    2.9990
   chunk 9 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   overall best weight:    0.6782

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.136099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108501 restraints weight = 15103.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.111841 restraints weight = 10326.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.114333 restraints weight = 8003.422|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.2535

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   7818  Z= 0.203
  Angle     :  0.567   7.135  10698  Z= 0.280
  Chirality :  0.040   0.133   1204
  Planarity :  0.004   0.034   1400
  Dihedral  :  5.661  50.632   1110
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 8.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 25.77 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.14 (0.27), residues: 974
  helix:  1.65 (0.27), residues: 350
  sheet:  0.95 (0.43), residues: 170
  loop :  0.06 (0.30), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 412 
 HIS   0.003   0.001   HIS B 116 
 PHE   0.009   0.001   PHE A   9 
 TYR   0.013   0.002   TYR B 479 
 ARG   0.006   0.000   ARG A 222 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2472.79 seconds
wall clock time: 43 minutes 42.82 seconds (2622.82 seconds total)