Starting phenix.real_space_refine
on Thu Feb 13 21:11:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6qvc_4647/02_2025/6qvc_4647.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6qvc_4647/02_2025/6qvc_4647.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6qvc_4647/02_2025/6qvc_4647.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6qvc_4647/02_2025/6qvc_4647.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6qvc_4647/02_2025/6qvc_4647.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6qvc_4647/02_2025/6qvc_4647.cif"
  }
  resolution = 4.0
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
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      70      5.16       5
     C    6132      2.51       5
     N    1484      2.21       5
     O    1586      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib"
  Total number of atoms: 9272
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 4636
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 599, 4636
          Classifications: {'peptide': 599}
          Link IDs: {'CIS': 1, 'PTRANS': 28, 'TRANS': 569}
          Chain breaks: 3
  Restraints were copied for chains:
    B
  Time building chain proxies: 8.63, per 1000 atoms: 0.93
  Number of scatterers: 9272
  At special positions: 0
  Unit cell: (105.93, 103.79, 109.14, 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      70     16.00
     O    1586      8.00
     N    1484      7.00
     C    6132      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=0, symmetry=0
  Time building additional restraints: 2.22
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2216

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 6 sheets defined
      66.4% alpha, 4.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'B' and resid 116 through 153
    Processing helix  chain 'B' and resid 158 through 181
      Proline residue:  B 168  - end of helix
    Processing helix  chain 'B' and resid 190 through 199
      removed outlier: 4.413A  pdb=" N   MET B 194 " --> pdb=" O   GLY B 190 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 203 through 207
    Processing helix  chain 'B' and resid 208 through 225
      removed outlier: 3.627A  pdb=" N   PHE B 212 " --> pdb=" O   THR B 208 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL B 213 " --> pdb=" O   MET B 209 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   VAL B 217 " --> pdb=" O   VAL B 213 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ALA B 218 " --> pdb=" O   ALA B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 231 through 250
      removed outlier: 3.611A  pdb=" N   PHE B 235 " --> pdb=" O   LYS B 231 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 280
    Processing helix  chain 'B' and resid 281 through 291
    Processing helix  chain 'B' and resid 298 through 324
      removed outlier: 3.549A  pdb=" N   ARG B 317 " --> pdb=" O   ALA B 313 " (cutoff:3.500A)
      removed outlier: 3.871A  pdb=" N   ALA B 320 " --> pdb=" O   PHE B 316 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 347 through 377
      removed outlier: 4.151A  pdb=" N   CYS B 358 " --> pdb=" O   ILE B 354 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   GLY B 375 " --> pdb=" O   GLN B 371 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 379 through 389
    Processing helix  chain 'B' and resid 391 through 403
      removed outlier: 4.691A  pdb=" N   GLY B 395 " --> pdb=" O   LEU B 391 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE B 396 " --> pdb=" O   LEU B 392 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL B 397 " --> pdb=" O   TYR B 393 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 419 through 428
    Processing helix  chain 'B' and resid 444 through 450
      removed outlier: 3.516A  pdb=" N   ILE B 450 " --> pdb=" O   ALA B 447 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 455 through 477
      removed outlier: 3.530A  pdb=" N   ILE B 459 " --> pdb=" O   ASN B 455 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   ILE B 472 " --> pdb=" O   PHE B 468 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL B 473 " --> pdb=" O   TRP B 469 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   MET B 477 " --> pdb=" O   VAL B 473 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 484 through 506
    Processing helix  chain 'B' and resid 521 through 538
      removed outlier: 4.539A  pdb=" N   THR B 533 " --> pdb=" O   ALA B 529 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 540 through 551
      removed outlier: 3.948A  pdb=" N   VAL B 544 " --> pdb=" O   VAL B 540 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 574
    Processing helix  chain 'B' and resid 576 through 586
    Processing helix  chain 'B' and resid 621 through 632
    Processing helix  chain 'B' and resid 654 through 666
    Processing helix  chain 'B' and resid 833 through 845
    Processing helix  chain 'B' and resid 862 through 871
    Processing helix  chain 'A' and resid 116 through 153
    Processing helix  chain 'A' and resid 158 through 181
      Proline residue:  A 168  - end of helix
    Processing helix  chain 'A' and resid 190 through 199
      removed outlier: 4.413A  pdb=" N   MET A 194 " --> pdb=" O   GLY A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 203 through 207
    Processing helix  chain 'A' and resid 208 through 225
      removed outlier: 3.626A  pdb=" N   PHE A 212 " --> pdb=" O   THR A 208 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   VAL A 213 " --> pdb=" O   MET A 209 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   VAL A 217 " --> pdb=" O   VAL A 213 " (cutoff:3.500A)
      removed outlier: 4.636A  pdb=" N   ALA A 218 " --> pdb=" O   ALA A 214 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 250
      removed outlier: 3.610A  pdb=" N   PHE A 235 " --> pdb=" O   LYS A 231 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 263 through 280
    Processing helix  chain 'A' and resid 281 through 291
    Processing helix  chain 'A' and resid 298 through 324
      removed outlier: 3.550A  pdb=" N   ARG A 317 " --> pdb=" O   ALA A 313 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   ALA A 320 " --> pdb=" O   PHE A 316 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 347 through 377
      removed outlier: 4.151A  pdb=" N   CYS A 358 " --> pdb=" O   ILE A 354 " (cutoff:3.500A)
      removed outlier: 3.991A  pdb=" N   GLY A 375 " --> pdb=" O   GLN A 371 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 389
    Processing helix  chain 'A' and resid 391 through 403
      removed outlier: 4.691A  pdb=" N   GLY A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   ILE A 396 " --> pdb=" O   LEU A 392 " (cutoff:3.500A)
      removed outlier: 4.011A  pdb=" N   VAL A 397 " --> pdb=" O   TYR A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 428
    Processing helix  chain 'A' and resid 444 through 450
      removed outlier: 3.516A  pdb=" N   ILE A 450 " --> pdb=" O   ALA A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 477
      removed outlier: 3.530A  pdb=" N   ILE A 459 " --> pdb=" O   ASN A 455 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   ILE A 472 " --> pdb=" O   PHE A 468 " (cutoff:3.500A)
      removed outlier: 4.071A  pdb=" N   VAL A 473 " --> pdb=" O   TRP A 469 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   MET A 477 " --> pdb=" O   VAL A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 484 through 506
    Processing helix  chain 'A' and resid 521 through 538
      removed outlier: 4.538A  pdb=" N   THR A 533 " --> pdb=" O   ALA A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 540 through 551
      removed outlier: 3.949A  pdb=" N   VAL A 544 " --> pdb=" O   VAL A 540 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 574
    Processing helix  chain 'A' and resid 576 through 586
    Processing helix  chain 'A' and resid 621 through 632
    Processing helix  chain 'A' and resid 654 through 666
    Processing helix  chain 'A' and resid 833 through 845
    Processing helix  chain 'A' and resid 862 through 871
    Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 512
    Processing sheet with id=AA2, first strand: chain 'B' and resid 616 through 617
      removed outlier: 6.096A  pdb=" N   VAL B 616 " --> pdb=" O   VAL B 640 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP B 822 " --> pdb=" O   SER B 651 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 849 through 853
      removed outlier: 6.582A  pdb=" N   ALA B 849 " --> pdb=" O   VAL B 860 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL B 860 " --> pdb=" O   ALA B 849 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   VAL B 851 " --> pdb=" O   ARG B 858 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 510 through 512
    Processing sheet with id=AA5, first strand: chain 'A' and resid 616 through 617
      removed outlier: 6.096A  pdb=" N   VAL A 616 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ASP A 822 " --> pdb=" O   SER A 651 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 849 through 853
      removed outlier: 6.581A  pdb=" N   ALA A 849 " --> pdb=" O   VAL A 860 " (cutoff:3.500A)
      removed outlier: 4.419A  pdb=" N   VAL A 860 " --> pdb=" O   ALA A 849 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   VAL A 851 " --> pdb=" O   ARG A 858 " (cutoff:3.500A)

    586 hydrogen bonds defined for protein.
    1710 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: 2.67

  Time building geometry restraints manager: 2.59 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2748
        1.34 -     1.46: 2200
        1.46 -     1.58: 4440
        1.58 -     1.70: 0
        1.70 -     1.82: 116
  Bond restraints: 9504
  Sorted by residual:
  bond pdb=" CG1 ILE B 527 "
       pdb=" CD1 ILE B 527 "
    ideal  model  delta    sigma   weight residual
    1.513  1.389  0.124 3.90e-02 6.57e+02 1.02e+01
  bond pdb=" CG1 ILE A 527 "
       pdb=" CD1 ILE A 527 "
    ideal  model  delta    sigma   weight residual
    1.513  1.389  0.124 3.90e-02 6.57e+02 1.01e+01
  bond pdb=" CB  ILE A 354 "
       pdb=" CG2 ILE A 354 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.68e+00
  bond pdb=" CB  ILE B 354 "
       pdb=" CG2 ILE B 354 "
    ideal  model  delta    sigma   weight residual
    1.521  1.436  0.085 3.30e-02 9.18e+02 6.63e+00
  bond pdb=" C   PHE A 343 "
       pdb=" N   ASP A 344 "
    ideal  model  delta    sigma   weight residual
    1.329  1.362 -0.033 1.40e-02 5.10e+03 5.68e+00
  ... (remaining 9499 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.15: 12606
        4.15 -     8.29: 262
        8.29 -    12.44: 36
       12.44 -    16.59: 8
       16.59 -    20.73: 2
  Bond angle restraints: 12914
  Sorted by residual:
  angle pdb=" C   PHE A 343 "
        pdb=" N   ASP A 344 "
        pdb=" CA  ASP A 344 "
      ideal   model   delta    sigma   weight residual
     121.70  132.56  -10.86 1.80e+00 3.09e-01 3.64e+01
  angle pdb=" C   PHE B 343 "
        pdb=" N   ASP B 344 "
        pdb=" CA  ASP B 344 "
      ideal   model   delta    sigma   weight residual
     121.70  132.48  -10.78 1.80e+00 3.09e-01 3.59e+01
  angle pdb=" CA  LEU A 171 "
        pdb=" CB  LEU A 171 "
        pdb=" CG  LEU A 171 "
      ideal   model   delta    sigma   weight residual
     116.30  137.03  -20.73 3.50e+00 8.16e-02 3.51e+01
  angle pdb=" CA  LEU B 171 "
        pdb=" CB  LEU B 171 "
        pdb=" CG  LEU B 171 "
      ideal   model   delta    sigma   weight residual
     116.30  136.99  -20.69 3.50e+00 8.16e-02 3.49e+01
  angle pdb=" C   THR B 621 "
        pdb=" N   TYR B 622 "
        pdb=" CA  TYR B 622 "
      ideal   model   delta    sigma   weight residual
     120.82  128.30   -7.48 1.50e+00 4.44e-01 2.49e+01
  ... (remaining 12909 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.08: 4989
       14.08 -    28.16: 433
       28.16 -    42.24: 108
       42.24 -    56.32: 20
       56.32 -    70.40: 6
  Dihedral angle restraints: 5556
    sinusoidal: 2114
      harmonic: 3442
  Sorted by residual:
  dihedral pdb=" CA  ALA A 326 "
           pdb=" C   ALA A 326 "
           pdb=" N   VAL A 327 "
           pdb=" CA  VAL A 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.06  -44.94     0      5.00e+00 4.00e-02 8.08e+01
  dihedral pdb=" CA  ALA B 326 "
           pdb=" C   ALA B 326 "
           pdb=" N   VAL B 327 "
           pdb=" CA  VAL B 327 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -135.14  -44.86     0      5.00e+00 4.00e-02 8.05e+01
  dihedral pdb=" CA  ILE B 290 "
           pdb=" C   ILE B 290 "
           pdb=" N   GLU B 291 "
           pdb=" CA  GLU B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.15  -34.85     0      5.00e+00 4.00e-02 4.86e+01
  ... (remaining 5553 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.112: 1322
       0.112 -    0.225: 171
       0.225 -    0.337: 31
       0.337 -    0.450: 0
       0.450 -    0.562: 2
  Chirality restraints: 1526
  Sorted by residual:
  chirality pdb=" CB  VAL B 321 "
            pdb=" CA  VAL B 321 "
            pdb=" CG1 VAL B 321 "
            pdb=" CG2 VAL B 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.90e+00
  chirality pdb=" CB  VAL A 321 "
            pdb=" CA  VAL A 321 "
            pdb=" CG1 VAL A 321 "
            pdb=" CG2 VAL A 321 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.07   -0.56 2.00e-01 2.50e+01 7.84e+00
  chirality pdb=" CB  ILE B 329 "
            pdb=" CA  ILE B 329 "
            pdb=" CG1 ILE B 329 "
            pdb=" CG2 ILE B 329 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.95   -0.31 2.00e-01 2.50e+01 2.36e+00
  ... (remaining 1523 not shown)

  Planarity restraints: 1580
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 469 "    0.035 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRP B 469 "   -0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 469 "    0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 469 "   -0.005 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 469 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 469 "    0.006 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 469 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 469 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 469 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 469 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 469 "   -0.035 2.00e-02 2.50e+03   2.09e-02 1.09e+01
        pdb=" CG  TRP A 469 "    0.053 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 469 "   -0.011 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 469 "    0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 469 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 469 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 469 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 469 "   -0.013 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 469 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 469 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL A 327 "    0.016 2.00e-02 2.50e+03   3.21e-02 1.03e+01
        pdb=" C   VAL A 327 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   VAL A 327 "    0.021 2.00e-02 2.50e+03
        pdb=" N   THR A 328 "    0.019 2.00e-02 2.50e+03
  ... (remaining 1577 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.77: 1622
        2.77 -     3.30: 9375
        3.30 -     3.83: 15743
        3.83 -     4.37: 17403
        4.37 -     4.90: 28449
  Nonbonded interactions: 72592
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 472 "
            pdb=" OG1 THR A 476 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ILE B 472 "
            pdb=" OG1 THR B 476 "
     model   vdw
     2.232 3.040
  nonbonded pdb=" O   ILE B 401 "
            pdb=" OG1 THR B 405 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" O   ILE A 401 "
            pdb=" OG1 THR A 405 "
     model   vdw
     2.237 3.040
  nonbonded pdb=" OG1 THR B 632 "
            pdb=" NH1 ARG B 654 "
     model   vdw
     2.249 3.120
  ... (remaining 72587 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: 0.05
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:             1.100
  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:                    0.070
  Process input model:                     26.230
  Find NCS groups from input model:        0.170
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.590
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   30.580
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
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      :  0.008   0.124   9504  Z= 0.520
  Angle     :  1.474  20.735  12914  Z= 0.771
  Chirality :  0.080   0.562   1526
  Planarity :  0.010   0.059   1580
  Dihedral  : 11.978  70.398   3340
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.51 %
    Allowed  :  8.38 %
    Favored  : 91.12 %
  Rotamer:
    Outliers :  2.19 %
    Allowed  :  8.95 %
    Favored  : 88.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.71 %

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: -3.90 (0.20), residues: 1182
  helix: -2.23 (0.15), residues: 758
  sheet: -0.42 (0.90), residues: 20
  loop : -3.15 (0.28), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.005   TRP A 469 
 HIS   0.008   0.002   HIS A 835 
 PHE   0.037   0.004   PHE A 547 
 TYR   0.031   0.003   TYR B 589 
 ARG   0.008   0.001   ARG A 626 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 225
  time to evaluate  : 1.113 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  126 LEU cc_start: 0.9707 (tt) cc_final: 0.9435 (pp)
REVERT: B  128 MET cc_start: 0.9329 (tpp) cc_final: 0.8931 (tpp)
REVERT: B  194 MET cc_start: 0.8984 (ppp) cc_final: 0.8701 (ppp)
REVERT: B  277 CYS cc_start: 0.8164 (t) cc_final: 0.7599 (t)
REVERT: B  301 ASN cc_start: 0.8804 (m-40) cc_final: 0.8440 (m-40)
REVERT: B  302 TYR cc_start: 0.9326 (t80) cc_final: 0.9018 (t80)
REVERT: B  307 PHE cc_start: 0.8795 (t80) cc_final: 0.8593 (t80)
REVERT: B  323 ASN cc_start: 0.8838 (m-40) cc_final: 0.8169 (m-40)
REVERT: B  385 PHE cc_start: 0.8736 (t80) cc_final: 0.8525 (m-80)
REVERT: B  432 THR cc_start: 0.9306 (m) cc_final: 0.9076 (p)
REVERT: B  472 ILE cc_start: 0.9177 (OUTLIER) cc_final: 0.8956 (mt)
REVERT: B  609 MET cc_start: 0.7621 (ptp) cc_final: 0.7252 (pmm)
REVERT: B  614 LYS cc_start: 0.9531 (pmtt) cc_final: 0.9305 (tptp)
REVERT: B  865 GLU cc_start: 0.9364 (mp0) cc_final: 0.9076 (mp0)
REVERT: B  868 LYS cc_start: 0.9471 (mttt) cc_final: 0.9236 (mttt)
REVERT: A  126 LEU cc_start: 0.9734 (tt) cc_final: 0.9443 (pp)
REVERT: A  128 MET cc_start: 0.9410 (tpp) cc_final: 0.8982 (tpp)
REVERT: A  173 LEU cc_start: 0.8987 (pp) cc_final: 0.8774 (pp)
REVERT: A  194 MET cc_start: 0.8837 (ppp) cc_final: 0.8486 (ppp)
REVERT: A  250 MET cc_start: 0.9139 (tpt) cc_final: 0.8934 (tpp)
REVERT: A  277 CYS cc_start: 0.7868 (t) cc_final: 0.7333 (t)
REVERT: A  301 ASN cc_start: 0.8730 (m-40) cc_final: 0.8333 (m-40)
REVERT: A  302 TYR cc_start: 0.9336 (t80) cc_final: 0.9006 (t80)
REVERT: A  323 ASN cc_start: 0.8910 (m-40) cc_final: 0.8260 (m-40)
REVERT: A  432 THR cc_start: 0.9388 (m) cc_final: 0.9105 (p)
REVERT: A  466 MET cc_start: 0.8711 (tpt) cc_final: 0.8471 (tpt)
REVERT: A  472 ILE cc_start: 0.9306 (OUTLIER) cc_final: 0.8952 (tt)
REVERT: A  865 GLU cc_start: 0.9546 (mp0) cc_final: 0.9319 (mp0)
REVERT: A  868 LYS cc_start: 0.9536 (mttt) cc_final: 0.9322 (mttt)
  outliers start: 22
  outliers final: 1
  residues processed: 234
  average time/residue: 0.2205
  time to fit residues: 70.9500
Evaluate side-chains
  135 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 132
  time to evaluate  : 1.052 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  472 ILE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  472 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 99 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 49 optimal weight:    9.9990
   chunk 30 optimal weight:    8.9990
   chunk 60 optimal weight:    0.9990
   chunk 47 optimal weight:    3.9990
   chunk 92 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 56 optimal weight:    8.9990
   chunk 68 optimal weight:    0.0570
   chunk 107 optimal weight:   30.0000
   overall best weight:    0.7100

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

Flipped N/Q/H residues before XYZ refinement:
B 451 HIS
B 658 GLN
A 451 HIS
A 658 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.077355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.057638 restraints weight = 40211.310|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.059335 restraints weight = 23011.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.060626 restraints weight = 15484.326|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.2865

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   9504  Z= 0.219
  Angle     :  0.907  12.802  12914  Z= 0.440
  Chirality :  0.046   0.181   1526
  Planarity :  0.006   0.050   1580
  Dihedral  :  7.051  51.009   1268
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.02 %
    Favored  : 92.98 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 16.30 %
    Favored  : 80.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.18 %

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: -1.69 (0.24), residues: 1182
  helix: -0.27 (0.17), residues: 776
  sheet: -0.20 (0.97), residues: 20
  loop : -2.90 (0.32), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 469 
 HIS   0.009   0.001   HIS B 838 
 PHE   0.040   0.002   PHE A 547 
 TYR   0.010   0.001   TYR B 137 
 ARG   0.005   0.001   ARG A 199 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 172
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9142 (tpp) cc_final: 0.8869 (tpp)
REVERT: B  194 MET cc_start: 0.8794 (ppp) cc_final: 0.8518 (ppp)
REVERT: B  302 TYR cc_start: 0.9440 (t80) cc_final: 0.9085 (t80)
REVERT: B  397 VAL cc_start: 0.9286 (m) cc_final: 0.9084 (p)
REVERT: B  504 MET cc_start: 0.9062 (tmm) cc_final: 0.8783 (tmm)
REVERT: B  609 MET cc_start: 0.7730 (ptp) cc_final: 0.7396 (pmm)
REVERT: B  826 PHE cc_start: 0.6780 (p90) cc_final: 0.6418 (p90)
REVERT: B  868 LYS cc_start: 0.9534 (mttt) cc_final: 0.9333 (mttm)
REVERT: A  128 MET cc_start: 0.9223 (tpp) cc_final: 0.8863 (tpp)
REVERT: A  194 MET cc_start: 0.8611 (ppp) cc_final: 0.8286 (ppp)
REVERT: A  302 TYR cc_start: 0.9414 (t80) cc_final: 0.9104 (t80)
REVERT: A  466 MET cc_start: 0.8699 (tpt) cc_final: 0.8218 (tpp)
REVERT: A  470 MET cc_start: 0.8450 (mmm) cc_final: 0.7559 (mmm)
REVERT: A  472 ILE cc_start: 0.9343 (OUTLIER) cc_final: 0.9028 (tt)
REVERT: A  504 MET cc_start: 0.9012 (tmm) cc_final: 0.8649 (ppp)
  outliers start: 34
  outliers final: 10
  residues processed: 192
  average time/residue: 0.1780
  time to fit residues: 50.8331
Evaluate side-chains
  145 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 134
  time to evaluate  : 0.963 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  397 VAL
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  614 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 61 optimal weight:    0.9990
   chunk 103 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 96 optimal weight:    5.9990
   chunk 21 optimal weight:    0.3980
   chunk 93 optimal weight:    0.1980
   chunk 81 optimal weight:    3.9990
   chunk 37 optimal weight:    0.4980
   chunk 58 optimal weight:   10.0000
   chunk 64 optimal weight:    0.7980
   chunk 111 optimal weight:    8.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.077678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.057750 restraints weight = 40271.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.059566 restraints weight = 22983.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.060908 restraints weight = 15348.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8198
moved from start:          0.3719

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9504  Z= 0.200
  Angle     :  0.882  13.656  12914  Z= 0.413
  Chirality :  0.046   0.205   1526
  Planarity :  0.005   0.049   1580
  Dihedral  :  5.994  43.656   1264
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 16.90 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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: -0.66 (0.25), residues: 1182
  helix:  0.68 (0.19), residues: 756
  sheet: -0.04 (0.99), residues: 20
  loop : -2.66 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP B 469 
 HIS   0.007   0.001   HIS B 838 
 PHE   0.038   0.002   PHE A 547 
 TYR   0.011   0.001   TYR A 620 
 ARG   0.003   0.000   ARG B 669 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  201 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 160
  time to evaluate  : 1.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.9074 (tpp) cc_final: 0.8793 (tpp)
REVERT: B  194 MET cc_start: 0.8869 (ppp) cc_final: 0.8550 (ppp)
REVERT: B  246 LEU cc_start: 0.9738 (tp) cc_final: 0.9533 (tp)
REVERT: B  302 TYR cc_start: 0.9483 (t80) cc_final: 0.9014 (t80)
REVERT: B  504 MET cc_start: 0.8870 (tmm) cc_final: 0.8648 (ppp)
REVERT: B  548 GLU cc_start: 0.8664 (tt0) cc_final: 0.8463 (tt0)
REVERT: B  609 MET cc_start: 0.7924 (ptp) cc_final: 0.7428 (pmm)
REVERT: B  826 PHE cc_start: 0.6680 (p90) cc_final: 0.6435 (p90)
REVERT: A  128 MET cc_start: 0.9167 (tpp) cc_final: 0.8881 (tpp)
REVERT: A  194 MET cc_start: 0.8656 (ppp) cc_final: 0.8319 (ppp)
REVERT: A  302 TYR cc_start: 0.9506 (t80) cc_final: 0.9053 (t80)
REVERT: A  466 MET cc_start: 0.8643 (tpt) cc_final: 0.8339 (tpp)
REVERT: A  470 MET cc_start: 0.8395 (mmm) cc_final: 0.7540 (mmm)
REVERT: A  548 GLU cc_start: 0.8784 (tt0) cc_final: 0.8473 (tt0)
REVERT: A  826 PHE cc_start: 0.6703 (p90) cc_final: 0.6209 (p90)
  outliers start: 41
  outliers final: 17
  residues processed: 185
  average time/residue: 0.1671
  time to fit residues: 46.4091
Evaluate side-chains
  154 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 137
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  568 MET
Chi-restraints excluded: chain B residue  615 PHE
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  567 ASN
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  614 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 86 optimal weight:    0.9990
   chunk 6 optimal weight:    0.3980
   chunk 78 optimal weight:    2.9990
   chunk 110 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 12 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9990
   chunk 101 optimal weight:    0.6980
   chunk 95 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 49 optimal weight:   20.0000
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** B 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 323 ASN
B 567 ASN
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.077498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.057757 restraints weight = 39834.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.059442 restraints weight = 23280.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.060729 restraints weight = 15903.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3115
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.4178

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   9504  Z= 0.199
  Angle     :  0.865  14.585  12914  Z= 0.403
  Chirality :  0.046   0.217   1526
  Planarity :  0.005   0.046   1580
  Dihedral  :  5.631  44.333   1264
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 14.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.45 %
    Favored  : 92.55 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 19.58 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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: -0.31 (0.25), residues: 1182
  helix:  0.94 (0.19), residues: 758
  sheet:  0.06 (0.99), residues: 20
  loop : -2.52 (0.31), residues: 404

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP B 469 
 HIS   0.004   0.001   HIS B 838 
 PHE   0.033   0.002   PHE A 547 
 TYR   0.010   0.001   TYR A 137 
 ARG   0.002   0.000   ARG A 199 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 153
  time to evaluate  : 1.051 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  153 MET cc_start: 0.8552 (ppp) cc_final: 0.8077 (ppp)
REVERT: B  194 MET cc_start: 0.8737 (ppp) cc_final: 0.8470 (ppp)
REVERT: B  302 TYR cc_start: 0.9388 (t80) cc_final: 0.8936 (t80)
REVERT: B  609 MET cc_start: 0.7970 (ptp) cc_final: 0.7298 (pmm)
REVERT: B  826 PHE cc_start: 0.6645 (p90) cc_final: 0.6365 (p90)
REVERT: A  153 MET cc_start: 0.8541 (ppp) cc_final: 0.8193 (ppp)
REVERT: A  194 MET cc_start: 0.8598 (ppp) cc_final: 0.8295 (ppp)
REVERT: A  302 TYR cc_start: 0.9403 (t80) cc_final: 0.9013 (t80)
REVERT: A  470 MET cc_start: 0.8414 (mmm) cc_final: 0.7683 (mmm)
  outliers start: 37
  outliers final: 19
  residues processed: 177
  average time/residue: 0.1683
  time to fit residues: 44.9060
Evaluate side-chains
  158 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 139
  time to evaluate  : 0.973 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  614 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 110 optimal weight:    8.9990
   chunk 61 optimal weight:    0.9980
   chunk 47 optimal weight:    0.4980
   chunk 112 optimal weight:    2.9990
   chunk 78 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 103 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 3 optimal weight:    0.5980
   chunk 83 optimal weight:    0.6980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.077037 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3040 r_free = 0.3040 target = 0.057319 restraints weight = 40128.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.059028 restraints weight = 23517.752|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.060265 restraints weight = 16046.751|
|-----------------------------------------------------------------------------|
r_work (final): 0.3102
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.4529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9504  Z= 0.204
  Angle     :  0.867  13.544  12914  Z= 0.402
  Chirality :  0.046   0.217   1526
  Planarity :  0.005   0.055   1580
  Dihedral  :  5.436  38.985   1264
  Min Nonbonded Distance : 2.543

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.36 %
    Favored  : 92.64 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 20.78 %
    Favored  : 75.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.01 (0.25), residues: 1182
  helix:  1.23 (0.19), residues: 760
  sheet:  0.02 (0.99), residues: 20
  loop : -2.48 (0.30), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 469 
 HIS   0.006   0.001   HIS B 838 
 PHE   0.031   0.001   PHE A 547 
 TYR   0.009   0.001   TYR A 137 
 ARG   0.002   0.000   ARG B 199 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  195 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 157
  time to evaluate  : 0.970 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  194 MET cc_start: 0.8737 (ppp) cc_final: 0.8513 (ppp)
REVERT: B  302 TYR cc_start: 0.9373 (t80) cc_final: 0.8920 (t80)
REVERT: B  609 MET cc_start: 0.7962 (ptp) cc_final: 0.7354 (pmm)
REVERT: A  128 MET cc_start: 0.8920 (tpp) cc_final: 0.8622 (tpp)
REVERT: A  153 MET cc_start: 0.8564 (ppp) cc_final: 0.8311 (ppp)
REVERT: A  194 MET cc_start: 0.8572 (ppp) cc_final: 0.8326 (ppp)
REVERT: A  302 TYR cc_start: 0.9373 (t80) cc_final: 0.8972 (t80)
REVERT: A  303 TRP cc_start: 0.8881 (m-10) cc_final: 0.8634 (m-10)
REVERT: A  854 MET cc_start: 0.8528 (tmm) cc_final: 0.8234 (tmm)
  outliers start: 38
  outliers final: 24
  residues processed: 180
  average time/residue: 0.1625
  time to fit residues: 44.4371
Evaluate side-chains
  165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 141
  time to evaluate  : 1.112 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  330 THR
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain B residue  568 MET
Chi-restraints excluded: chain B residue  581 ILE
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  354 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  614 LYS
Chi-restraints excluded: chain A residue  861 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 96 optimal weight:    0.5980
   chunk 16 optimal weight:    0.5980
   chunk 115 optimal weight:    8.9990
   chunk 107 optimal weight:    0.0070
   chunk 51 optimal weight:   10.0000
   chunk 52 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 69 optimal weight:    0.4980
   chunk 102 optimal weight:    0.8980
   chunk 113 optimal weight:    3.9990
   overall best weight:    0.5198

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3508 r_free = 0.3508 target = 0.077949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.058225 restraints weight = 39587.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3113 r_free = 0.3113 target = 0.059965 restraints weight = 23233.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.061188 restraints weight = 15864.891|
|-----------------------------------------------------------------------------|
r_work (final): 0.3125
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8218
moved from start:          0.4838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   9504  Z= 0.200
  Angle     :  0.924  14.544  12914  Z= 0.419
  Chirality :  0.047   0.225   1526
  Planarity :  0.005   0.049   1580
  Dihedral  :  5.305  40.284   1264
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 15.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 23.56 %
    Favored  : 73.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.16 (0.25), residues: 1182
  helix:  1.35 (0.19), residues: 752
  sheet:  0.08 (1.01), residues: 20
  loop : -2.36 (0.30), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 469 
 HIS   0.013   0.001   HIS B 369 
 PHE   0.032   0.001   PHE A 547 
 TYR   0.009   0.001   TYR B 137 
 ARG   0.002   0.000   ARG A 334 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 1.047 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  302 TYR cc_start: 0.9386 (t80) cc_final: 0.8899 (t80)
REVERT: B  609 MET cc_start: 0.7949 (ptp) cc_final: 0.7225 (pmm)
REVERT: B  826 PHE cc_start: 0.6511 (p90) cc_final: 0.6247 (p90)
REVERT: A  194 MET cc_start: 0.8569 (ppp) cc_final: 0.8275 (ppp)
REVERT: A  302 TYR cc_start: 0.9372 (t80) cc_final: 0.8950 (t80)
REVERT: A  303 TRP cc_start: 0.8928 (m-10) cc_final: 0.8688 (m-10)
REVERT: A  826 PHE cc_start: 0.6525 (p90) cc_final: 0.6204 (p90)
  outliers start: 30
  outliers final: 20
  residues processed: 176
  average time/residue: 0.1589
  time to fit residues: 42.6791
Evaluate side-chains
  162 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 142
  time to evaluate  : 1.026 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  392 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  861 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 77 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9990
   chunk 101 optimal weight:    0.8980
   chunk 54 optimal weight:    1.9990
   chunk 90 optimal weight:    0.1980
   chunk 60 optimal weight:    0.8980
   chunk 88 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   chunk 95 optimal weight:    0.6980
   chunk 107 optimal weight:    8.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.077860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.058185 restraints weight = 39967.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.059992 restraints weight = 23318.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.061260 restraints weight = 15858.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.5077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   9504  Z= 0.213
  Angle     :  0.961  15.717  12914  Z= 0.435
  Chirality :  0.048   0.227   1526
  Planarity :  0.005   0.047   1580
  Dihedral  :  5.252  43.518   1264
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 15.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.11 %
    Favored  : 92.89 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 23.96 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.24 (0.25), residues: 1182
  helix:  1.40 (0.19), residues: 754
  sheet:  0.11 (1.02), residues: 20
  loop : -2.33 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP B 469 
 HIS   0.015   0.001   HIS B 369 
 PHE   0.033   0.001   PHE B 547 
 TYR   0.009   0.001   TYR B 524 
 ARG   0.002   0.000   ARG B 370 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 150
  time to evaluate  : 0.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8832 (tpp) cc_final: 0.8476 (tpp)
REVERT: B  153 MET cc_start: 0.8532 (ppp) cc_final: 0.8118 (ppp)
REVERT: B  250 MET cc_start: 0.8594 (tpp) cc_final: 0.8306 (tpt)
REVERT: B  302 TYR cc_start: 0.9346 (t80) cc_final: 0.8894 (t80)
REVERT: B  325 ASP cc_start: 0.7906 (OUTLIER) cc_final: 0.7690 (p0)
REVERT: B  609 MET cc_start: 0.7867 (ptp) cc_final: 0.7097 (pmm)
REVERT: B  826 PHE cc_start: 0.6502 (p90) cc_final: 0.6219 (p90)
REVERT: A  178 PHE cc_start: 0.8858 (OUTLIER) cc_final: 0.8553 (m-80)
REVERT: A  194 MET cc_start: 0.8558 (ppp) cc_final: 0.8278 (ppp)
REVERT: A  302 TYR cc_start: 0.9367 (t80) cc_final: 0.8962 (t80)
REVERT: A  303 TRP cc_start: 0.8920 (m-10) cc_final: 0.8718 (m-10)
REVERT: A  487 VAL cc_start: 0.9600 (OUTLIER) cc_final: 0.9335 (p)
REVERT: A  826 PHE cc_start: 0.6445 (p90) cc_final: 0.6068 (p90)
  outliers start: 33
  outliers final: 24
  residues processed: 172
  average time/residue: 0.1525
  time to fit residues: 40.6378
Evaluate side-chains
  163 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 136
  time to evaluate  : 1.093 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  169 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  517 TYR
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  861 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 73 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 86 optimal weight:    0.9980
   chunk 66 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 36 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 39 optimal weight:    6.9990
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
B 567 ASN
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.077012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.057284 restraints weight = 40809.074|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.059046 restraints weight = 24037.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.060251 restraints weight = 16432.295|
|-----------------------------------------------------------------------------|
r_work (final): 0.3100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.5233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9504  Z= 0.220
  Angle     :  0.957  14.248  12914  Z= 0.434
  Chirality :  0.047   0.227   1526
  Planarity :  0.005   0.046   1580
  Dihedral  :  5.222  43.848   1264
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.58 %
    Allowed  : 23.66 %
    Favored  : 72.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.33 (0.25), residues: 1182
  helix:  1.45 (0.19), residues: 754
  sheet:  0.02 (1.01), residues: 20
  loop : -2.24 (0.31), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP B 469 
 HIS   0.010   0.001   HIS B 369 
 PHE   0.033   0.001   PHE B 547 
 TYR   0.008   0.001   TYR A 137 
 ARG   0.002   0.000   ARG B 334 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 147
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8896 (tpp) cc_final: 0.8545 (tpp)
REVERT: B  250 MET cc_start: 0.8626 (tpp) cc_final: 0.8367 (tpt)
REVERT: B  302 TYR cc_start: 0.9360 (t80) cc_final: 0.8948 (t80)
REVERT: B  325 ASP cc_start: 0.7867 (OUTLIER) cc_final: 0.7641 (p0)
REVERT: B  609 MET cc_start: 0.7868 (ptp) cc_final: 0.7122 (pmm)
REVERT: B  826 PHE cc_start: 0.6543 (p90) cc_final: 0.6259 (p90)
REVERT: B  868 LYS cc_start: 0.9555 (mttt) cc_final: 0.9328 (mttm)
REVERT: A  178 PHE cc_start: 0.8979 (OUTLIER) cc_final: 0.8583 (m-80)
REVERT: A  194 MET cc_start: 0.8570 (ppp) cc_final: 0.8277 (ppp)
REVERT: A  302 TYR cc_start: 0.9376 (t80) cc_final: 0.8947 (t80)
REVERT: A  303 TRP cc_start: 0.8945 (m-10) cc_final: 0.8711 (m-10)
REVERT: A  487 VAL cc_start: 0.9616 (OUTLIER) cc_final: 0.9390 (p)
  outliers start: 36
  outliers final: 23
  residues processed: 172
  average time/residue: 0.1571
  time to fit residues: 41.6405
Evaluate side-chains
  165 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 139
  time to evaluate  : 0.981 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  539 THR
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  581 ILE
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  861 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 36 optimal weight:    0.8980
   chunk 107 optimal weight:    0.7980
   chunk 81 optimal weight:    0.9980
   chunk 94 optimal weight:    0.0170
   chunk 17 optimal weight:    0.5980
   chunk 91 optimal weight:    0.9980
   chunk 68 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 64 optimal weight:    0.0270
   chunk 23 optimal weight:    0.9990
   chunk 60 optimal weight:    0.8980
   overall best weight:    0.4676

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

Flipped N/Q/H residues before XYZ refinement:
** A 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 301 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 = 0.3527 r_free = 0.3527 target = 0.078646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.058491 restraints weight = 39517.070|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.060309 restraints weight = 22840.237|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3148 r_free = 0.3148 target = 0.061527 restraints weight = 15499.086|
|-----------------------------------------------------------------------------|
r_work (final): 0.3133
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.5455

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9504  Z= 0.209
  Angle     :  0.990  15.739  12914  Z= 0.441
  Chirality :  0.048   0.244   1526
  Planarity :  0.005   0.045   1580
  Dihedral  :  5.162  42.363   1264
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 15.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.51 %
    Favored  : 93.49 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.06 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.35 (0.25), residues: 1182
  helix:  1.45 (0.19), residues: 756
  sheet: -0.02 (1.03), residues: 20
  loop : -2.21 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP B 469 
 HIS   0.011   0.001   HIS B 369 
 PHE   0.035   0.001   PHE B 547 
 TYR   0.008   0.001   TYR A 137 
 ARG   0.002   0.000   ARG B 199 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 156
  time to evaluate  : 1.109 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  128 MET cc_start: 0.8939 (tpp) cc_final: 0.8501 (tpp)
REVERT: B  225 SER cc_start: 0.8601 (OUTLIER) cc_final: 0.8252 (p)
REVERT: B  250 MET cc_start: 0.8836 (tpp) cc_final: 0.8608 (tpt)
REVERT: B  302 TYR cc_start: 0.9464 (t80) cc_final: 0.8958 (t80)
REVERT: B  325 ASP cc_start: 0.7963 (OUTLIER) cc_final: 0.7746 (p0)
REVERT: B  609 MET cc_start: 0.7737 (ptp) cc_final: 0.6834 (pmm)
REVERT: B  826 PHE cc_start: 0.6425 (p90) cc_final: 0.6125 (p90)
REVERT: A  178 PHE cc_start: 0.9084 (OUTLIER) cc_final: 0.8726 (m-80)
REVERT: A  194 MET cc_start: 0.8623 (ppp) cc_final: 0.8345 (ppp)
REVERT: A  302 TYR cc_start: 0.9469 (t80) cc_final: 0.8970 (t80)
REVERT: A  303 TRP cc_start: 0.9061 (m-10) cc_final: 0.8804 (m-10)
REVERT: A  487 VAL cc_start: 0.9598 (OUTLIER) cc_final: 0.9374 (p)
REVERT: A  826 PHE cc_start: 0.6613 (p90) cc_final: 0.6261 (p90)
  outliers start: 30
  outliers final: 20
  residues processed: 172
  average time/residue: 0.1564
  time to fit residues: 41.6963
Evaluate side-chains
  173 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 149
  time to evaluate  : 1.001 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  487 VAL
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  861 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 56 optimal weight:   10.0000
   chunk 70 optimal weight:    0.9980
   chunk 15 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9990
   chunk 109 optimal weight:    6.9990
   chunk 17 optimal weight:    5.9990
   chunk 84 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 101 optimal weight:    0.5980
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** A 160 GLN ** 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 = 0.3505 r_free = 0.3505 target = 0.077620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.057395 restraints weight = 40423.577|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.059248 restraints weight = 23276.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.060439 restraints weight = 15687.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.5546

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044   9504  Z= 0.225
  Angle     :  1.010  15.028  12914  Z= 0.453
  Chirality :  0.048   0.266   1526
  Planarity :  0.005   0.048   1580
  Dihedral  :  5.212  43.517   1264
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 16.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.26 %
    Favored  : 93.74 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 24.16 %
    Favored  : 72.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    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:  0.37 (0.25), residues: 1182
  helix:  1.44 (0.19), residues: 756
  sheet:  0.04 (1.02), residues: 20
  loop : -2.14 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 469 
 HIS   0.011   0.001   HIS B 369 
 PHE   0.032   0.001   PHE B 547 
 TYR   0.008   0.001   TYR B 524 
 ARG   0.002   0.000   ARG B 334 

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

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

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2364 Ramachandran restraints generated.
    1182 Oldfield, 0 Emsley, 1182 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  171 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 142
  time to evaluate  : 1.089 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  302 TYR cc_start: 0.9477 (t80) cc_final: 0.9058 (t80)
REVERT: B  325 ASP cc_start: 0.7983 (OUTLIER) cc_final: 0.7770 (p0)
REVERT: B  609 MET cc_start: 0.7857 (ptp) cc_final: 0.6916 (pmm)
REVERT: A  178 PHE cc_start: 0.9110 (OUTLIER) cc_final: 0.8721 (m-80)
REVERT: A  194 MET cc_start: 0.8652 (ppp) cc_final: 0.8360 (ppp)
REVERT: A  302 TYR cc_start: 0.9487 (t80) cc_final: 0.8980 (t80)
REVERT: A  303 TRP cc_start: 0.9060 (m-10) cc_final: 0.8797 (m-10)
REVERT: A  826 PHE cc_start: 0.6625 (p90) cc_final: 0.6257 (p90)
  outliers start: 29
  outliers final: 24
  residues processed: 159
  average time/residue: 0.1540
  time to fit residues: 37.8443
Evaluate side-chains
  164 residues out of total 1006 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 138
  time to evaluate  : 1.054 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  225 SER
Chi-restraints excluded: chain B residue  246 LEU
Chi-restraints excluded: chain B residue  301 ASN
Chi-restraints excluded: chain B residue  325 ASP
Chi-restraints excluded: chain B residue  391 LEU
Chi-restraints excluded: chain B residue  459 ILE
Chi-restraints excluded: chain B residue  515 ILE
Chi-restraints excluded: chain B residue  536 VAL
Chi-restraints excluded: chain B residue  539 THR
Chi-restraints excluded: chain B residue  559 MET
Chi-restraints excluded: chain A residue  123 LEU
Chi-restraints excluded: chain A residue  178 PHE
Chi-restraints excluded: chain A residue  225 SER
Chi-restraints excluded: chain A residue  290 ILE
Chi-restraints excluded: chain A residue  330 THR
Chi-restraints excluded: chain A residue  360 LEU
Chi-restraints excluded: chain A residue  391 LEU
Chi-restraints excluded: chain A residue  459 ILE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  510 ILE
Chi-restraints excluded: chain A residue  515 ILE
Chi-restraints excluded: chain A residue  519 ILE
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  590 LEU
Chi-restraints excluded: chain A residue  861 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 76 optimal weight:    3.9990
   chunk 39 optimal weight:    7.9990
   chunk 21 optimal weight:    0.5980
   chunk 13 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 73 optimal weight:    1.9990
   chunk 34 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 88 optimal weight:    2.9990
   chunk 114 optimal weight:    6.9990
   overall best weight:    0.8784

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

Flipped N/Q/H residues before XYZ refinement:
** A 160 GLN ** 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 = 0.3497 r_free = 0.3497 target = 0.077110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.057078 restraints weight = 39985.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.058832 restraints weight = 23316.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.060004 restraints weight = 15881.660|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.5671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9504  Z= 0.228
  Angle     :  1.016  14.917  12914  Z= 0.456
  Chirality :  0.048   0.279   1526
  Planarity :  0.005   0.049   1580
  Dihedral  :  5.193  43.444   1264
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 16.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.09 %
    Favored  : 93.91 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 24.55 %
    Favored  : 72.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.18 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.40 (0.25), residues: 1182
  helix:  1.45 (0.19), residues: 756
  sheet: -0.01 (1.03), residues: 20
  loop : -2.09 (0.31), residues: 406

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP B 469 
 HIS   0.008   0.001   HIS B 369 
 PHE   0.032   0.001   PHE B 547 
 TYR   0.007   0.001   TYR B 146 
 ARG   0.002   0.000   ARG B 199 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2555.06 seconds
wall clock time: 46 minutes 53.85 seconds (2813.85 seconds total)