Starting phenix.real_space_refine
on Wed Feb 12 08:54:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sgk_40458/02_2025/8sgk_40458.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sgk_40458/02_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_40458/02_2025/8sgk_40458.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sgk_40458/02_2025/8sgk_40458.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sgk_40458/02_2025/8sgk_40458.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sgk_40458/02_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-5592/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: 7.04, per 1000 atoms: 0.92
  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: 1.83
  Conformation dependent library (CDL) restraints added in 1.0 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: 0.93
  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: 2.57

  Time building geometry restraints manager: 2.08 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:             2.190
  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:          0.270
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     22.760
  Find NCS groups from input model:        0.120
  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:2.880
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.370
-------------------------------------------------------------------------------
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  : 0.918 
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: 0.2064
  time to fit residues: 22.5611
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  : 0.876 
-------------------------------------------------------------------------------
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 = 0.140952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.116099 restraints weight = 14794.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.119042 restraints weight = 11137.427|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.120950 restraints weight = 7877.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.3743
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7719
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  : 0.813 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   99 TYR cc_start: 0.8303 (t80) cc_final: 0.8062 (t80)
  outliers start: 13
  outliers final: 5
  residues processed: 94
  average time/residue: 0.1923
  time to fit residues: 25.1330
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  : 0.870 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 87 optimal weight:    0.1980
   chunk 97 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 43 optimal weight:   10.0000
   chunk 16 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 55 optimal weight:    3.9990
   chunk 18 optimal weight:    0.7980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.4026 r_free = 0.4026 target = 0.141916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.117972 restraints weight = 14997.456|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.120067 restraints weight = 10629.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3763 r_free = 0.3763 target = 0.122167 restraints weight = 8325.932|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7732
moved from start:          0.1353

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= 0.215
  Angle     :  0.553   6.888  10698  Z= 0.273
  Chirality :  0.040   0.132   1204
  Planarity :  0.004   0.031   1400
  Dihedral  :  5.624  52.425   1110
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 7.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.51 %
    Favored  : 99.49 %
  Rotamer:
    Outliers :  3.09 %
    Allowed  : 23.45 %
    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:  1.03 (0.41), residues: 170
  loop : -0.18 (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   0.013   0.002   TYR B 479 
 ARG   0.003   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
  106 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 82
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8555 (ttp) cc_final: 0.8339 (ttp)
REVERT: B  144 MET cc_start: 0.8522 (ttp) cc_final: 0.8292 (ttp)
  outliers start: 24
  outliers final: 10
  residues processed: 104
  average time/residue: 0.2308
  time to fit residues: 31.4834
Evaluate side-chains
  81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 71
  time to evaluate  : 0.863 
-------------------------------------------------------------------------------
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:    0.3980
   chunk 56 optimal weight:    0.6980
   chunk 22 optimal weight:    3.9990
   chunk 3 optimal weight:    4.9990
   chunk 10 optimal weight:    3.9990
   chunk 26 optimal weight:    0.6980
   chunk 91 optimal weight:    0.9990
   chunk 97 optimal weight:    0.9990
   chunk 96 optimal weight:    0.9980
   chunk 61 optimal weight:    4.9990
   overall best weight:    0.7582

-------------------------------------------------------------------------------
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 = 0.3951 r_free = 0.3951 target = 0.135689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108401 restraints weight = 14951.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.111531 restraints weight = 10382.561|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.113979 restraints weight = 8096.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.1778

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= 0.215
  Angle     :  0.551   7.263  10698  Z= 0.276
  Chirality :  0.040   0.133   1204
  Planarity :  0.004   0.031   1400
  Dihedral  :  5.702  52.331   1110
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.29 %
    Favored  : 74.36 %
  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:  0.98 (0.27), residues: 974
  helix:  1.53 (0.27), residues: 354
  sheet:  0.99 (0.40), residues: 170
  loop : -0.13 (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   0.007   0.001   PHE B 145 
 TYR   0.013   0.002   TYR B 479 
 ARG   0.007   0.000   ARG B 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
  99 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 73
  time to evaluate  : 0.866 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  144 MET cc_start: 0.8653 (ttp) cc_final: 0.8415 (ttp)
REVERT: B  279 VAL cc_start: 0.7856 (t) cc_final: 0.7560 (t)
  outliers start: 26
  outliers final: 15
  residues processed: 95
  average time/residue: 0.1931
  time to fit residues: 25.4631
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  : 0.781 
-------------------------------------------------------------------------------
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  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   57 ASN
Chi-restraints excluded: chain B residue  122 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 73 optimal weight:    0.5980
   chunk 67 optimal weight:    0.6980
   chunk 81 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 72 optimal weight:    0.9990
   chunk 78 optimal weight:    1.9990
   chunk 43 optimal weight:    9.9990
   chunk 30 optimal weight:    0.9990
   chunk 14 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3949 r_free = 0.3949 target = 0.135538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.107906 restraints weight = 15003.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.111204 restraints weight = 10315.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.113632 restraints weight = 8003.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7818  Z= 0.222
  Angle     :  0.562   7.710  10698  Z= 0.277
  Chirality :  0.040   0.143   1204
  Planarity :  0.004   0.031   1400
  Dihedral  :  5.709  52.057   1110
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  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:  1.01 (0.27), residues: 974
  helix:  1.56 (0.27), residues: 354
  sheet:  0.93 (0.41), residues: 170
  loop : -0.08 (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   0.007   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
  91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 70
  time to evaluate  : 0.846 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 21
  outliers final: 14
  residues processed: 88
  average time/residue: 0.1986
  time to fit residues: 24.2547
Evaluate side-chains
  81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.768 
-------------------------------------------------------------------------------
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  296 VAL
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain B residue    8 PHE
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:    0.0980
   chunk 39 optimal weight:    2.9990
   chunk 81 optimal weight:    6.9990
   chunk 15 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 96 optimal weight:    0.9980
   chunk 77 optimal weight:    0.6980
   chunk 7 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 97 optimal weight:    0.8980
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.135527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.108022 restraints weight = 14930.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.111257 restraints weight = 10340.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.113636 restraints weight = 8063.492|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7789
moved from start:          0.2098

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= 0.214
  Angle     :  0.550   7.115  10698  Z= 0.273
  Chirality :  0.040   0.135   1204
  Planarity :  0.004   0.031   1400
  Dihedral  :  5.729  51.412   1110
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  3.35 %
    Allowed  : 22.68 %
    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:  1.00 (0.27), residues: 974
  helix:  1.64 (0.27), residues: 350
  sheet:  0.90 (0.41), residues: 170
  loop : -0.15 (0.29), residues: 454

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 412 
 HIS   0.004   0.001   HIS B 116 
 PHE   0.013   0.001   PHE A   9 
 TYR   0.012   0.002   TYR B 479 
 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
  96 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 70
  time to evaluate  : 0.823 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 TYR cc_start: 0.8464 (m-80) cc_final: 0.8215 (m-80)
  outliers start: 26
  outliers final: 24
  residues processed: 91
  average time/residue: 0.1782
  time to fit residues: 23.2544
Evaluate side-chains
  94 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 70
  time to evaluate  : 0.817 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 HIS
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  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 A residue  506 LEU
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   57 ASN
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
Chi-restraints excluded: chain B residue  506 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 59 optimal weight:    0.0170
   chunk 22 optimal weight:    0.8980
   chunk 66 optimal weight:    0.7980
   chunk 9 optimal weight:    0.3980
   chunk 89 optimal weight:    1.9990
   chunk 34 optimal weight:    0.7980
   chunk 46 optimal weight:    0.7980
   chunk 76 optimal weight:    0.6980
   chunk 38 optimal weight:    0.0470
   chunk 80 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9980
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
A  36 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.136878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.109608 restraints weight = 14938.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.113030 restraints weight = 10197.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.115468 restraints weight = 7862.089|
|-----------------------------------------------------------------------------|
r_work (final): 0.3671
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.2189

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= 0.173
  Angle     :  0.543   7.406  10698  Z= 0.271
  Chirality :  0.039   0.137   1204
  Planarity :  0.004   0.032   1400
  Dihedral  :  5.699  51.697   1110
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.82 %
    Favored  : 99.18 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 23.84 %
    Favored  : 73.58 %
  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:  1.05 (0.27), residues: 974
  helix:  1.66 (0.27), residues: 354
  sheet:  0.87 (0.41), residues: 170
  loop : -0.09 (0.29), residues: 450

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 412 
 HIS   0.003   0.001   HIS B  38 
 PHE   0.009   0.001   PHE A  61 
 TYR   0.012   0.002   TYR B 216 
 ARG   0.006   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
  94 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 TYR cc_start: 0.8453 (m-80) cc_final: 0.8221 (m-80)
  outliers start: 20
  outliers final: 13
  residues processed: 91
  average time/residue: 0.1828
  time to fit residues: 23.5172
Evaluate side-chains
  81 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.852 
-------------------------------------------------------------------------------
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  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   30 HIS
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:    0.9990
   chunk 58 optimal weight:    0.7980
   chunk 22 optimal weight:    0.7980
   chunk 71 optimal weight:    0.9980
   chunk 9 optimal weight:    0.0670
   chunk 69 optimal weight:    0.9990
   chunk 93 optimal weight:    3.9990
   chunk 88 optimal weight:    3.9990
   chunk 85 optimal weight:    2.9990
   chunk 7 optimal weight:    0.4980
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.6318

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3959 r_free = 0.3959 target = 0.136308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.108797 restraints weight = 15162.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.112134 restraints weight = 10444.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3660 r_free = 0.3660 target = 0.114536 restraints weight = 8129.622|
|-----------------------------------------------------------------------------|
r_work (final): 0.3655
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7770
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   7818  Z= 0.200
  Angle     :  0.559   8.354  10698  Z= 0.277
  Chirality :  0.040   0.137   1204
  Planarity :  0.004   0.033   1400
  Dihedral  :  5.671  52.143   1110
  Min Nonbonded Distance : 2.603

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.23 %
    Favored  : 98.77 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 23.84 %
    Favored  : 73.20 %
  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: 350
  sheet:  0.96 (0.42), residues: 170
  loop : -0.08 (0.29), 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  38 
 PHE   0.007   0.001   PHE A   9 
 TYR   0.014   0.002   TYR B 479 
 ARG   0.011   0.000   ARG B 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
  91 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 68
  time to evaluate  : 1.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  216 TYR cc_start: 0.8481 (m-80) cc_final: 0.8244 (m-80)
  outliers start: 23
  outliers final: 19
  residues processed: 86
  average time/residue: 0.1789
  time to fit residues: 22.0421
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  : 0.783 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 HIS
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  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   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  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
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:    0.5980
   chunk 30 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 57 optimal weight:    0.0370
   chunk 22 optimal weight:    0.9980
   chunk 88 optimal weight:    2.9990
   overall best weight:    0.7058

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

Flipped N/Q/H residues before XYZ refinement:
A  57 ASN
B  57 ASN
B 329 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.135814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.108195 restraints weight = 15278.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.111677 restraints weight = 11732.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.114602 restraints weight = 8246.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7785
moved from start:          0.2410

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   7818  Z= 0.209
  Angle     :  0.570  10.633  10698  Z= 0.286
  Chirality :  0.040   0.135   1204
  Planarity :  0.004   0.034   1400
  Dihedral  :  5.737  52.092   1110
  Min Nonbonded Distance : 2.602

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.44 %
    Favored  : 98.56 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 25.13 %
    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:  1.02 (0.27), residues: 974
  helix:  1.53 (0.27), residues: 350
  sheet:  0.96 (0.43), residues: 170
  loop : -0.02 (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 A 116 
 PHE   0.007   0.001   PHE A   9 
 TYR   0.017   0.002   TYR B 479 
 ARG   0.008   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
  87 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 67
  time to evaluate  : 0.860 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 20
  outliers final: 19
  residues processed: 82
  average time/residue: 0.1776
  time to fit residues: 20.8701
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  : 0.893 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   30 HIS
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  273 LEU
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   30 HIS
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  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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 34 optimal weight:    0.3980
   chunk 57 optimal weight:    0.0030
   chunk 78 optimal weight:    0.6980
   chunk 43 optimal weight:   10.0000
   chunk 84 optimal weight:    1.9990
   chunk 90 optimal weight:    0.8980
   chunk 55 optimal weight:    4.9990
   chunk 18 optimal weight:    0.0970
   chunk 88 optimal weight:    0.5980
   overall best weight:    0.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 329 GLN
A 335 HIS
B 335 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3954 r_free = 0.3954 target = 0.135841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.108384 restraints weight = 15224.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.111656 restraints weight = 10560.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.113976 restraints weight = 8221.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3648
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7778
moved from start:          0.2466

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.154   7818  Z= 0.315
  Angle     :  1.061  59.200  10698  Z= 0.649
  Chirality :  0.045   0.549   1204
  Planarity :  0.006   0.136   1400
  Dihedral  :  5.790  52.080   1110
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 25.13 %
    Favored  : 72.55 %
  Cbeta Deviations :  0.11 %
  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:  1.00 (0.27), residues: 974
  helix:  1.54 (0.28), residues: 350
  sheet:  0.95 (0.43), residues: 170
  loop : -0.07 (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 A  38 
 PHE   0.006   0.001   PHE A   9 
 TYR   0.029   0.002   TYR A 216 
 ARG   0.014   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
  86 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 68
  time to evaluate  : 0.820 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 17
  residues processed: 81
  average time/residue: 0.1825
  time to fit residues: 21.2026
Evaluate side-chains
  83 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 66
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
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  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    8 PHE
Chi-restraints excluded: chain B residue   30 HIS
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
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 4 optimal weight:    0.9980
   chunk 33 optimal weight:    0.5980
   chunk 49 optimal weight:    6.9990
   chunk 89 optimal weight:    7.9990
   chunk 88 optimal weight:    0.8980
   chunk 80 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 90 optimal weight:    2.9990
   chunk 9 optimal weight:    0.0020
   chunk 23 optimal weight:    0.0770
   chunk 63 optimal weight:    0.8980
   overall best weight:    0.4946

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

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.135723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.108451 restraints weight = 15144.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.111691 restraints weight = 10504.823|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.114037 restraints weight = 8153.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3653
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7773
moved from start:          0.2473

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.154   7818  Z= 0.315
  Angle     :  1.061  59.200  10698  Z= 0.649
  Chirality :  0.045   0.549   1204
  Planarity :  0.006   0.136   1400
  Dihedral  :  5.790  52.080   1110
  Min Nonbonded Distance : 0.815

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.54 %
    Favored  : 98.46 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  : 25.52 %
    Favored  : 72.29 %
  Cbeta Deviations :  0.11 %
  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:  1.00 (0.27), residues: 974
  helix:  1.54 (0.28), residues: 350
  sheet:  0.95 (0.43), residues: 170
  loop : -0.07 (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 A  38 
 PHE   0.006   0.001   PHE A   9 
 TYR   0.029   0.002   TYR A 216 
 ARG   0.014   0.000   ARG A 222 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2338.08 seconds
wall clock time: 42 minutes 32.82 seconds (2552.82 seconds total)