Starting phenix.real_space_refine
on Fri Aug 22 16:37:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8yhu_39301/08_2025/8yhu_39301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8yhu_39301/08_2025/8yhu_39301.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.88
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8yhu_39301/08_2025/8yhu_39301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8yhu_39301/08_2025/8yhu_39301.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8yhu_39301/08_2025/8yhu_39301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8yhu_39301/08_2025/8yhu_39301.map"
  }
  resolution = 2.88
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.022
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      19      5.16       5
     C    3805      2.51       5
     N     998      2.21       5
     O    1168      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model
  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5990
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 5323
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 663, 5323
          Classifications: {'peptide': 663}
          Link IDs: {'PTRANS': 26, 'TRANS': 636}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 457
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 457
          Classifications: {'peptide': 56}
          Link IDs: {'TRANS': 55}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "G"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.59, per 1000 atoms: 0.27
  Number of scatterers: 5990
  At special positions: 0
  Unit cell: (56.44, 103.584, 112.216, 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      19     16.00
     O    1168      8.00
     N     998      7.00
     C    3805      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  28 " - pdb=" SG  CYS A  37 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  95 " - pdb=" SG  CYS A 122 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 649 " - pdb=" SG  CYS A 677 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 651 " - pdb=" SG  CYS A 696 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
      " NAG G   1 " - " NAG G   2 "
    NAG-ASN
      " NAG A 801 " - " ASN A  57 "
      " NAG A 802 " - " ASN A 124 "
      " NAG A 803 " - " ASN A 252 "
      " NAG A 804 " - " ASN A 275 "
      " NAG A 805 " - " ASN A 291 "
      " NAG C   1 " - " ASN A  52 "
      " NAG D   1 " - " ASN A 247 "
      " NAG E   1 " - " ASN A 265 "
      " NAG F   1 " - " ASN A 398 "
      " NAG G   1 " - " ASN A 413 "
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 317.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1388

  Finding SS restraints...
    Secondary structure from input PDB file:
      14 helices and 8 sheets defined
      15.3% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 69 through 74
      removed outlier: 3.556A  pdb=" N   THR A  72 " --> pdb=" O   ALA A  69 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   ARG A  73 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 97
      removed outlier: 3.592A  pdb=" N   GLN A  96 " --> pdb=" O   PRO A  92 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   LYS A  97 " --> pdb=" O   GLU A  93 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 92 through 97'
    Processing helix  chain 'A' and resid 188 through 195
      removed outlier: 5.162A  pdb=" N   ILE A 193 " --> pdb=" O   GLU A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 237 through 245
      removed outlier: 3.796A  pdb=" N   LEU A 243 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 269 through 273
      removed outlier: 3.693A  pdb=" N   TRP A 273 " --> pdb=" O   GLY A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 401 through 405
    Processing helix  chain 'A' and resid 449 through 453
      removed outlier: 3.697A  pdb=" N   TRP A 452 " --> pdb=" O   GLY A 449 " (cutoff:3.500A)
      removed outlier: 3.931A  pdb=" N   ARG A 453 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 449 through 453'
    Processing helix  chain 'A' and resid 542 through 547
      removed outlier: 3.948A  pdb=" N   TRP A 546 " --> pdb=" O   ALA A 543 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LYS A 547 " --> pdb=" O   ARG A 544 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 655 through 661
    Processing helix  chain 'A' and resid 692 through 696
      removed outlier: 3.564A  pdb=" N   SER A 695 " --> pdb=" O   ASP A 692 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1 through 4
    Processing helix  chain 'B' and resid 5 through 17
      removed outlier: 3.892A  pdb=" N   VAL B   9 " --> pdb=" O   GLU B   5 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 38
    Processing helix  chain 'B' and resid 43 through 54
    Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30
      removed outlier: 4.367A  pdb=" N   THR A  29 " --> pdb=" O   ASP A  36 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A  56 " --> pdb=" O   SER A  79 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ASP A  81 " --> pdb=" O   LEU A  56 " (cutoff:3.500A)
      removed outlier: 7.933A  pdb=" N   LEU A  80 " --> pdb=" O   ASN A 105 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LEU A 104 " --> pdb=" O   GLU A 127 " (cutoff:3.500A)
      removed outlier: 6.806A  pdb=" N   LEU A 128 " --> pdb=" O   ASP A 153 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU A 152 " --> pdb=" O   GLU A 175 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 198 through 199
      removed outlier: 6.076A  pdb=" N   ARG A 222 " --> pdb=" O   LEU A 199 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 302 through 304
      removed outlier: 7.699A  pdb=" N   PHE A 303 " --> pdb=" O   ASN A 328 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 395 through 396
      removed outlier: 3.508A  pdb=" N   LEU A 396 " --> pdb=" O   LYS A 421 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'A' and resid 411 through 412
    Processing sheet with id=AA6, first strand: chain 'A' and resid 444 through 446
      removed outlier: 3.605A  pdb=" N   GLN A 470 " --> pdb=" O   GLN A 445 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 461 through 462
      removed outlier: 3.546A  pdb=" N   MET A 486 " --> pdb=" O   ILE A 461 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 615 through 616
      removed outlier: 7.880A  pdb=" N   LEU A 615 " --> pdb=" O   ASP A 641 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8

    59 hydrogen bonds defined for protein.
    141 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.71

  Time building geometry restraints manager: 0.68 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: 1934
        1.34 -     1.46: 1153
        1.46 -     1.58: 2990
        1.58 -     1.69: 0
        1.69 -     1.81: 27
  Bond restraints: 6104
  Sorted by residual:
  bond pdb=" N   GLY A 594 "
       pdb=" CA  GLY A 594 "
    ideal  model  delta    sigma   weight residual
    1.447  1.475 -0.028 9.30e-03 1.16e+04 9.12e+00
  bond pdb=" N   ILE A 622 "
       pdb=" CA  ILE A 622 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.035 1.24e-02 6.50e+03 8.07e+00
  bond pdb=" N   ASN A 596 "
       pdb=" CA  ASN A 596 "
    ideal  model  delta    sigma   weight residual
    1.457  1.487 -0.030 1.24e-02 6.50e+03 5.91e+00
  bond pdb=" N   LEU A 621 "
       pdb=" CA  LEU A 621 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.22e-02 6.72e+03 5.30e+00
  bond pdb=" N   ASN A 620 "
       pdb=" CA  ASN A 620 "
    ideal  model  delta    sigma   weight residual
    1.451  1.486 -0.034 1.62e-02 3.81e+03 4.48e+00
  ... (remaining 6099 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.32: 7724
        1.32 -     2.64: 437
        2.64 -     3.96: 88
        3.96 -     5.27: 25
        5.27 -     6.59: 4
  Bond angle restraints: 8278
  Sorted by residual:
  angle pdb=" N   ASN A 124 "
        pdb=" CA  ASN A 124 "
        pdb=" C   ASN A 124 "
      ideal   model   delta    sigma   weight residual
     111.71  107.09    4.62 1.34e+00 5.57e-01 1.19e+01
  angle pdb=" N   GLN A  62 "
        pdb=" CA  GLN A  62 "
        pdb=" C   GLN A  62 "
      ideal   model   delta    sigma   weight residual
     110.80  117.39   -6.59 2.13e+00 2.20e-01 9.58e+00
  angle pdb=" CA  GLY A 594 "
        pdb=" C   GLY A 594 "
        pdb=" O   GLY A 594 "
      ideal   model   delta    sigma   weight residual
     121.31  118.17    3.14 1.09e+00 8.42e-01 8.31e+00
  angle pdb=" C   VAL A 144 "
        pdb=" N   LYS A 145 "
        pdb=" CA  LYS A 145 "
      ideal   model   delta    sigma   weight residual
     121.71  117.82    3.89 1.39e+00 5.18e-01 7.85e+00
  angle pdb=" CA  LEU A 595 "
        pdb=" C   LEU A 595 "
        pdb=" O   LEU A 595 "
      ideal   model   delta    sigma   weight residual
     121.54  118.33    3.21 1.16e+00 7.43e-01 7.64e+00
  ... (remaining 8273 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.19: 3552
       21.19 -    42.38: 291
       42.38 -    63.57: 37
       63.57 -    84.76: 9
       84.76 -   105.96: 8
  Dihedral angle restraints: 3897
    sinusoidal: 1779
      harmonic: 2118
  Sorted by residual:
  dihedral pdb=" CB  CYS A 651 "
           pdb=" SG  CYS A 651 "
           pdb=" SG  CYS A 696 "
           pdb=" CB  CYS A 696 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   28.29   64.71     1      1.00e+01 1.00e-02 5.50e+01
  dihedral pdb=" CB  CYS A 649 "
           pdb=" SG  CYS A 649 "
           pdb=" SG  CYS A 677 "
           pdb=" CB  CYS A 677 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   50.31   42.69     1      1.00e+01 1.00e-02 2.54e+01
  dihedral pdb=" CA  HIS A  60 "
           pdb=" C   HIS A  60 "
           pdb=" N   ASN A  61 "
           pdb=" CA  ASN A  61 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -158.21  -21.79     0      5.00e+00 4.00e-02 1.90e+01
  ... (remaining 3894 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 912
       0.085 -    0.170: 84
       0.170 -    0.256: 6
       0.256 -    0.341: 1
       0.341 -    0.426: 1
  Chirality restraints: 1004
  Sorted by residual:
  chirality pdb=" C1  NAG A 804 "
            pdb=" ND2 ASN A 275 "
            pdb=" C2  NAG A 804 "
            pdb=" O5  NAG A 804 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.97   -0.43 2.00e-01 2.50e+01 4.54e+00
  chirality pdb=" CA  GLN A  62 "
            pdb=" N   GLN A  62 "
            pdb=" C   GLN A  62 "
            pdb=" CB  GLN A  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.23    0.28 2.00e-01 2.50e+01 1.92e+00
  chirality pdb=" C1  NAG A 805 "
            pdb=" ND2 ASN A 291 "
            pdb=" C2  NAG A 805 "
            pdb=" O5  NAG A 805 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.62e+00
  ... (remaining 1001 not shown)

  Planarity restraints: 1051
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 303 "   -0.021 2.00e-02 2.50e+03   1.70e-02 5.07e+00
        pdb=" CG  PHE A 303 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 303 "   -0.007 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 303 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 303 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 303 "   -0.003 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 303 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 297 "    0.033 5.00e-02 4.00e+02   5.08e-02 4.13e+00
        pdb=" N   PRO A 298 "   -0.088 5.00e-02 4.00e+02
        pdb=" CA  PRO A 298 "    0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO A 298 "    0.028 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 645 "   -0.029 5.00e-02 4.00e+02   4.36e-02 3.04e+00
        pdb=" N   PRO A 646 "    0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO A 646 "   -0.023 5.00e-02 4.00e+02
        pdb=" CD  PRO A 646 "   -0.024 5.00e-02 4.00e+02
  ... (remaining 1048 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 1242
        2.78 -     3.31: 5735
        3.31 -     3.84: 9412
        3.84 -     4.37: 11243
        4.37 -     4.90: 18707
  Nonbonded interactions: 46339
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 500 "
            pdb=" O   ASP A 524 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   ASP A 648 "
            pdb=" OG  SER A 653 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   THR A 248 "
            pdb=" OG1 THR A 274 "
     model   vdw
     2.275 3.040
  nonbonded pdb=" O   ASN A  85 "
            pdb=" ND2 ASN A 109 "
     model   vdw
     2.285 3.120
  nonbonded pdb=" OD1 ASP A 366 "
            pdb=" OG1 THR A 391 "
     model   vdw
     2.290 3.040
  ... (remaining 46334 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: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
  selection = chain 'G'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.990
  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:             0.000
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.710
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.380
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6271
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      :  0.004   0.035   6123  Z= 0.209
  Angle     :  0.744  11.119   8331  Z= 0.374
  Chirality :  0.052   0.426   1004
  Planarity :  0.004   0.051   1041
  Dihedral  : 15.503 105.956   2497
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 11.29
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  : 13.04 %
    Favored  : 86.82 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  0.30 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.42 (0.31), residues: 713
  helix: -0.83 (0.61), residues: 72
  sheet: -3.97 (0.53), residues: 75
  loop : -2.43 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 484 
 TYR   0.008   0.001   TYR A 283 
 PHE   0.038   0.002   PHE A 303 
 TRP   0.015   0.002   TRP A 546 
 HIS   0.003   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00419 ( 6104)
  covalent geometry    : angle       0.71835 ( 8278)
  SS BOND              : bond        0.00130 (    4)
  SS BOND              : angle       1.06445 (    8)
  hydrogen bonds       : bond        0.26987 (   59)
  hydrogen bonds       : angle       7.25241 (  141)
  link_BETA1-4         : bond        0.00302 (    5)
  link_BETA1-4         : angle       0.98513 (   15)
  link_NAG-ASN         : bond        0.00591 (   10)
  link_NAG-ASN         : angle       3.21791 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
REVERT: A  119 PHE cc_start: 0.6524 (p90) cc_final: 0.5817 (p90)
REVERT: A  621 LEU cc_start: 0.6014 (OUTLIER) cc_final: 0.5813 (mm)
  outliers start: 2
  outliers final: 1
  residues processed: 101
  average time/residue: 0.4061
  time to fit residues: 43.6059
Evaluate side-chains
  88 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 86
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  621 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    2.9990
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    0.9990
   chunk 51 optimal weight:    0.0000
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.3980
   overall best weight:    0.6186

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

Flipped N/Q/H residues before XYZ refinement:
A  62 GLN
A 328 ASN
A 361 ASN
A 540 ASN
A 609 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4451 r_free = 0.4451 target = 0.177237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.155686 restraints weight = 8075.446|
|-----------------------------------------------------------------------------|
r_work (start): 0.4214 rms_B_bonded: 2.76
r_work: 0.4064 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4064
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6629
moved from start:          0.0974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6123  Z= 0.152
  Angle     :  0.719  10.563   8331  Z= 0.345
  Chirality :  0.050   0.395   1004
  Planarity :  0.004   0.041   1041
  Dihedral  : 10.689  80.150   1074
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.64 %
    Favored  : 88.36 %
  Rotamer:
    Outliers :  1.20 %
    Allowed  : 10.34 %
    Favored  : 88.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.36 (0.31), residues: 713
  helix: -0.77 (0.59), residues: 74
  sheet: -4.14 (0.51), residues: 80
  loop : -2.33 (0.26), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B  29 
 TYR   0.010   0.001   TYR A 307 
 PHE   0.025   0.002   PHE A 303 
 TRP   0.009   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A  60 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 ( 6104)
  covalent geometry    : angle       0.69574 ( 8278)
  SS BOND              : bond        0.00117 (    4)
  SS BOND              : angle       0.76988 (    8)
  hydrogen bonds       : bond        0.05083 (   59)
  hydrogen bonds       : angle       5.53320 (  141)
  link_BETA1-4         : bond        0.00477 (    5)
  link_BETA1-4         : angle       1.24810 (   15)
  link_NAG-ASN         : bond        0.00564 (   10)
  link_NAG-ASN         : angle       3.03164 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8078 (p) cc_final: 0.7828 (t)
REVERT: A  119 PHE cc_start: 0.6666 (p90) cc_final: 0.5903 (p90)
REVERT: A  363 GLU cc_start: 0.6318 (tp30) cc_final: 0.6087 (tp30)
REVERT: A  418 LYS cc_start: 0.7978 (mppt) cc_final: 0.7771 (mppt)
REVERT: A  531 LYS cc_start: 0.7083 (pttp) cc_final: 0.6758 (pttp)
  outliers start: 8
  outliers final: 3
  residues processed: 97
  average time/residue: 0.3822
  time to fit residues: 39.5142
Evaluate side-chains
  92 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   61 ASN
Chi-restraints excluded: chain A residue   90 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 61 optimal weight:    0.0980
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   overall best weight:    0.7384

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 207 ASN
A 328 ASN
A 361 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4441 r_free = 0.4441 target = 0.176478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.155098 restraints weight = 8063.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.4202 rms_B_bonded: 2.73
r_work: 0.4051 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4051
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6644
moved from start:          0.1233

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   6123  Z= 0.170
  Angle     :  0.696  10.502   8331  Z= 0.336
  Chirality :  0.049   0.381   1004
  Planarity :  0.004   0.041   1041
  Dihedral  :  9.039  57.571   1070
  Min Nonbonded Distance : 2.466

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.34 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.04 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.33 (0.31), residues: 713
  helix: -0.60 (0.59), residues: 74
  sheet: -4.37 (0.51), residues: 73
  loop : -2.33 (0.26), residues: 566

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.009   0.001   TYR A 675 
 PHE   0.026   0.002   PHE A 647 
 TRP   0.008   0.002   TRP A 546 
 HIS   0.004   0.001   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00392 ( 6104)
  covalent geometry    : angle       0.67029 ( 8278)
  SS BOND              : bond        0.00118 (    4)
  SS BOND              : angle       0.65738 (    8)
  hydrogen bonds       : bond        0.04852 (   59)
  hydrogen bonds       : angle       5.20680 (  141)
  link_BETA1-4         : bond        0.00479 (    5)
  link_BETA1-4         : angle       1.37462 (   15)
  link_NAG-ASN         : bond        0.00594 (   10)
  link_NAG-ASN         : angle       3.06691 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.245 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8062 (OUTLIER) cc_final: 0.7824 (t)
REVERT: A  119 PHE cc_start: 0.6731 (p90) cc_final: 0.5956 (p90)
REVERT: A  363 GLU cc_start: 0.6294 (tp30) cc_final: 0.6030 (tp30)
REVERT: A  381 LEU cc_start: 0.7349 (tp) cc_final: 0.7043 (tt)
REVERT: A  418 LYS cc_start: 0.8008 (mppt) cc_final: 0.7803 (mppt)
REVERT: A  531 LYS cc_start: 0.7147 (pttp) cc_final: 0.6784 (pttp)
  outliers start: 14
  outliers final: 5
  residues processed: 99
  average time/residue: 0.4215
  time to fit residues: 44.5188
Evaluate side-chains
  94 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 88
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  593 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 46 optimal weight:    0.9990
   chunk 45 optimal weight:    0.4980
   chunk 54 optimal weight:    0.0010
   chunk 3 optimal weight:    0.8980
   chunk 8 optimal weight:    2.9990
   chunk 44 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 18 optimal weight:    0.8980
   chunk 58 optimal weight:    0.8980
   chunk 13 optimal weight:    4.9990
   chunk 70 optimal weight:    0.1980
   overall best weight:    0.4386

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 328 ASN
A 361 ASN
A 609 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4455 r_free = 0.4455 target = 0.177754 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.156329 restraints weight = 8109.015|
|-----------------------------------------------------------------------------|
r_work (start): 0.4219 rms_B_bonded: 2.74
r_work: 0.4069 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4069
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6616
moved from start:          0.1382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6123  Z= 0.122
  Angle     :  0.656  10.105   8331  Z= 0.314
  Chirality :  0.047   0.370   1004
  Planarity :  0.004   0.037   1041
  Dihedral  :  7.823  55.897   1070
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 14.54 %
    Favored  : 83.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.31), residues: 713
  helix: -0.34 (0.61), residues: 74
  sheet: -3.92 (0.59), residues: 65
  loop : -2.33 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.007   0.001   TYR A 383 
 PHE   0.018   0.001   PHE A 647 
 TRP   0.007   0.001   TRP A 546 
 HIS   0.003   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00279 ( 6104)
  covalent geometry    : angle       0.63085 ( 8278)
  SS BOND              : bond        0.00090 (    4)
  SS BOND              : angle       0.66376 (    8)
  hydrogen bonds       : bond        0.03811 (   59)
  hydrogen bonds       : angle       4.89170 (  141)
  link_BETA1-4         : bond        0.00482 (    5)
  link_BETA1-4         : angle       1.55065 (   15)
  link_NAG-ASN         : bond        0.00559 (   10)
  link_NAG-ASN         : angle       2.92124 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8055 (OUTLIER) cc_final: 0.7815 (t)
REVERT: A  119 PHE cc_start: 0.6716 (p90) cc_final: 0.5919 (p90)
REVERT: A  150 ILE cc_start: 0.5887 (OUTLIER) cc_final: 0.5649 (mp)
REVERT: A  418 LYS cc_start: 0.8009 (mppt) cc_final: 0.7805 (mppt)
REVERT: A  507 ASN cc_start: 0.7375 (m-40) cc_final: 0.7130 (m-40)
REVERT: A  531 LYS cc_start: 0.7131 (pttp) cc_final: 0.6659 (pttp)
REVERT: A  642 MET cc_start: 0.7668 (mmm) cc_final: 0.7145 (tmm)
  outliers start: 16
  outliers final: 8
  residues processed: 102
  average time/residue: 0.3966
  time to fit residues: 43.4274
Evaluate side-chains
  95 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 85
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  605 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 15 optimal weight:    3.9990
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.0030
   chunk 65 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 19 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 4 optimal weight:    0.5980
   chunk 30 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6994

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 361 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4445 r_free = 0.4445 target = 0.176652 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.155086 restraints weight = 8237.550|
|-----------------------------------------------------------------------------|
r_work (start): 0.4206 rms_B_bonded: 2.77
r_work: 0.4056 rms_B_bonded: 3.44 restraints_weight: 0.5000
r_work (final): 0.4056
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6642
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   6123  Z= 0.156
  Angle     :  0.673  10.229   8331  Z= 0.323
  Chirality :  0.048   0.374   1004
  Planarity :  0.004   0.042   1041
  Dihedral  :  7.407  55.705   1070
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.78 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 15.29 %
    Favored  : 81.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.20 (0.31), residues: 713
  helix: -0.38 (0.61), residues: 74
  sheet: -4.15 (0.58), residues: 63
  loop : -2.34 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 484 
 TYR   0.007   0.001   TYR A 383 
 PHE   0.024   0.002   PHE A 557 
 TRP   0.007   0.001   TRP A 296 
 HIS   0.004   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6104)
  covalent geometry    : angle       0.64681 ( 8278)
  SS BOND              : bond        0.00139 (    4)
  SS BOND              : angle       0.62827 (    8)
  hydrogen bonds       : bond        0.04214 (   59)
  hydrogen bonds       : angle       4.85413 (  141)
  link_BETA1-4         : bond        0.00485 (    5)
  link_BETA1-4         : angle       1.64907 (   15)
  link_NAG-ASN         : bond        0.00574 (   10)
  link_NAG-ASN         : angle       2.97952 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.241 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8039 (OUTLIER) cc_final: 0.7801 (t)
REVERT: A  119 PHE cc_start: 0.6737 (p90) cc_final: 0.5929 (p90)
REVERT: A  150 ILE cc_start: 0.5876 (OUTLIER) cc_final: 0.5641 (mp)
REVERT: A  363 GLU cc_start: 0.6312 (tp30) cc_final: 0.6024 (tp30)
REVERT: A  642 MET cc_start: 0.7616 (mmm) cc_final: 0.6944 (tmm)
  outliers start: 19
  outliers final: 11
  residues processed: 104
  average time/residue: 0.3895
  time to fit residues: 43.2199
Evaluate side-chains
  100 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.228 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 SER
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  621 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 65 optimal weight:    0.0170
   chunk 30 optimal weight:    1.9990
   chunk 56 optimal weight:    0.7980
   chunk 36 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   chunk 1 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0670
   chunk 46 optimal weight:    0.9990
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    0.0570
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.3674

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 299 GLN
A 361 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.178178 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.156775 restraints weight = 8043.438|
|-----------------------------------------------------------------------------|
r_work (start): 0.4224 rms_B_bonded: 2.75
r_work: 0.4075 rms_B_bonded: 3.43 restraints_weight: 0.5000
r_work (final): 0.4075
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6609
moved from start:          0.1611

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6123  Z= 0.112
  Angle     :  0.659   9.926   8331  Z= 0.314
  Chirality :  0.046   0.380   1004
  Planarity :  0.004   0.040   1041
  Dihedral  :  7.065  55.863   1070
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.66 %
    Favored  : 89.34 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.39 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.08 (0.31), residues: 713
  helix: -0.22 (0.61), residues: 74
  sheet: -3.89 (0.59), residues: 65
  loop : -2.27 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 484 
 TYR   0.007   0.001   TYR A 383 
 PHE   0.014   0.001   PHE A 119 
 TRP   0.007   0.001   TRP A 452 
 HIS   0.003   0.000   HIS A 539 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 6104)
  covalent geometry    : angle       0.63249 ( 8278)
  SS BOND              : bond        0.00091 (    4)
  SS BOND              : angle       0.67991 (    8)
  hydrogen bonds       : bond        0.03557 (   59)
  hydrogen bonds       : angle       4.68833 (  141)
  link_BETA1-4         : bond        0.00454 (    5)
  link_BETA1-4         : angle       1.64439 (   15)
  link_NAG-ASN         : bond        0.00557 (   10)
  link_NAG-ASN         : angle       2.94901 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8031 (OUTLIER) cc_final: 0.7790 (t)
REVERT: A  119 PHE cc_start: 0.6720 (p90) cc_final: 0.5882 (p90)
REVERT: A  150 ILE cc_start: 0.5880 (OUTLIER) cc_final: 0.5641 (mp)
REVERT: A  363 GLU cc_start: 0.6332 (tp30) cc_final: 0.6029 (tp30)
REVERT: A  418 LYS cc_start: 0.8038 (mppt) cc_final: 0.7833 (mppt)
REVERT: A  642 MET cc_start: 0.7537 (mmm) cc_final: 0.6875 (tmm)
  outliers start: 17
  outliers final: 9
  residues processed: 103
  average time/residue: 0.4359
  time to fit residues: 47.8627
Evaluate side-chains
  99 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.221 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  621 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 25 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 34 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 48 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 361 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4444 r_free = 0.4444 target = 0.176912 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.155669 restraints weight = 8065.110|
|-----------------------------------------------------------------------------|
r_work (start): 0.4210 rms_B_bonded: 2.72
r_work: 0.4060 rms_B_bonded: 3.39 restraints_weight: 0.5000
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6642
moved from start:          0.1666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   6123  Z= 0.164
  Angle     :  0.682  10.324   8331  Z= 0.325
  Chirality :  0.049   0.380   1004
  Planarity :  0.004   0.039   1041
  Dihedral  :  6.993  55.790   1070
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.34 %
    Favored  : 87.66 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 15.89 %
    Favored  : 80.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.18 (0.31), residues: 713
  helix: -0.33 (0.60), residues: 74
  sheet: -4.09 (0.59), residues: 63
  loop : -2.33 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 484 
 TYR   0.008   0.001   TYR A 383 
 PHE   0.026   0.002   PHE A 557 
 TRP   0.008   0.001   TRP A 296 
 HIS   0.004   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6104)
  covalent geometry    : angle       0.65495 ( 8278)
  SS BOND              : bond        0.00130 (    4)
  SS BOND              : angle       0.64558 (    8)
  hydrogen bonds       : bond        0.04245 (   59)
  hydrogen bonds       : angle       4.87498 (  141)
  link_BETA1-4         : bond        0.00454 (    5)
  link_BETA1-4         : angle       1.62402 (   15)
  link_NAG-ASN         : bond        0.00579 (   10)
  link_NAG-ASN         : angle       3.03472 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 90
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8029 (OUTLIER) cc_final: 0.7796 (t)
REVERT: A  119 PHE cc_start: 0.6744 (p90) cc_final: 0.5909 (p90)
REVERT: A  150 ILE cc_start: 0.5871 (OUTLIER) cc_final: 0.5620 (mp)
REVERT: A  363 GLU cc_start: 0.6324 (tp30) cc_final: 0.6023 (tp30)
REVERT: A  617 LEU cc_start: 0.7961 (OUTLIER) cc_final: 0.7705 (mt)
REVERT: A  642 MET cc_start: 0.7504 (mmm) cc_final: 0.6864 (tmm)
  outliers start: 22
  outliers final: 11
  residues processed: 107
  average time/residue: 0.4225
  time to fit residues: 48.0615
Evaluate side-chains
  99 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.256 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  621 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 60 optimal weight:    0.8980
   chunk 59 optimal weight:    0.7980
   chunk 30 optimal weight:    1.9990
   chunk 0 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 46 optimal weight:    0.5980
   chunk 61 optimal weight:    0.7980
   chunk 54 optimal weight:    0.1980
   chunk 41 optimal weight:    0.5980
   chunk 50 optimal weight:    0.4980
   chunk 43 optimal weight:    0.9980
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN
A 361 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4452 r_free = 0.4452 target = 0.177522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4221 r_free = 0.4221 target = 0.156256 restraints weight = 8051.363|
|-----------------------------------------------------------------------------|
r_work (start): 0.4218 rms_B_bonded: 2.72
r_work: 0.4071 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6623
moved from start:          0.1734

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   6123  Z= 0.133
  Angle     :  0.684  11.963   8331  Z= 0.324
  Chirality :  0.047   0.385   1004
  Planarity :  0.004   0.042   1041
  Dihedral  :  6.806  55.974   1070
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.92 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  2.85 %
    Allowed  : 17.09 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.12 (0.31), residues: 713
  helix: -0.37 (0.59), residues: 74
  sheet: -4.08 (0.59), residues: 63
  loop : -2.27 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 484 
 TYR   0.008   0.001   TYR A 383 
 PHE   0.018   0.001   PHE A 557 
 TRP   0.007   0.001   TRP A 452 
 HIS   0.003   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6104)
  covalent geometry    : angle       0.65914 ( 8278)
  SS BOND              : bond        0.00088 (    4)
  SS BOND              : angle       0.61024 (    8)
  hydrogen bonds       : bond        0.03947 (   59)
  hydrogen bonds       : angle       4.94265 (  141)
  link_BETA1-4         : bond        0.00440 (    5)
  link_BETA1-4         : angle       1.55484 (   15)
  link_NAG-ASN         : bond        0.00554 (   10)
  link_NAG-ASN         : angle       2.94007 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 86
  time to evaluate  : 0.269 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8003 (OUTLIER) cc_final: 0.7769 (t)
REVERT: A  119 PHE cc_start: 0.6746 (p90) cc_final: 0.5897 (p90)
REVERT: A  150 ILE cc_start: 0.5866 (OUTLIER) cc_final: 0.5616 (mp)
REVERT: A  363 GLU cc_start: 0.6304 (tp30) cc_final: 0.6007 (tp30)
REVERT: A  642 MET cc_start: 0.7438 (mmm) cc_final: 0.6869 (tmm)
  outliers start: 19
  outliers final: 12
  residues processed: 101
  average time/residue: 0.4431
  time to fit residues: 47.7783
Evaluate side-chains
  99 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.226 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  617 LEU
Chi-restraints excluded: chain A residue  621 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 63 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 37 optimal weight:    0.7980
   chunk 24 optimal weight:    0.1980
   chunk 66 optimal weight:    0.1980
   chunk 28 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8182

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4424 r_free = 0.4424 target = 0.175701 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.154600 restraints weight = 8130.923|
|-----------------------------------------------------------------------------|
r_work (start): 0.4193 rms_B_bonded: 2.73
r_work: 0.4041 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6655
moved from start:          0.1770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046   6123  Z= 0.176
  Angle     :  0.698  10.767   8331  Z= 0.334
  Chirality :  0.049   0.389   1004
  Planarity :  0.004   0.041   1041
  Dihedral  :  6.845  55.853   1070
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.90 %
    Favored  : 87.10 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 17.39 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.20 (0.31), residues: 713
  helix: -0.48 (0.59), residues: 74
  sheet: -4.23 (0.57), residues: 63
  loop : -2.31 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 544 
 TYR   0.008   0.001   TYR A 675 
 PHE   0.027   0.002   PHE A 557 
 TRP   0.007   0.002   TRP A 546 
 HIS   0.006   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00406 ( 6104)
  covalent geometry    : angle       0.67203 ( 8278)
  SS BOND              : bond        0.00153 (    4)
  SS BOND              : angle       0.67388 (    8)
  hydrogen bonds       : bond        0.04498 (   59)
  hydrogen bonds       : angle       4.99659 (  141)
  link_BETA1-4         : bond        0.00446 (    5)
  link_BETA1-4         : angle       1.50110 (   15)
  link_NAG-ASN         : bond        0.00590 (   10)
  link_NAG-ASN         : angle       3.05504 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8037 (OUTLIER) cc_final: 0.7803 (t)
REVERT: A  119 PHE cc_start: 0.6788 (p90) cc_final: 0.5957 (p90)
REVERT: A  150 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5578 (mp)
REVERT: A  363 GLU cc_start: 0.6349 (tp30) cc_final: 0.6016 (tp30)
REVERT: A  642 MET cc_start: 0.7413 (mmm) cc_final: 0.6823 (tmm)
  outliers start: 17
  outliers final: 11
  residues processed: 104
  average time/residue: 0.4434
  time to fit residues: 49.2658
Evaluate side-chains
  101 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 88
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  675 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 30 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 66 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9980
   chunk 15 optimal weight:    0.4980
   chunk 56 optimal weight:    0.7980
   chunk 63 optimal weight:    0.9980
   chunk 68 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    1.9990
   chunk 38 optimal weight:    0.4980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4433 r_free = 0.4433 target = 0.176347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4206 r_free = 0.4206 target = 0.155308 restraints weight = 8062.280|
|-----------------------------------------------------------------------------|
r_work (start): 0.4203 rms_B_bonded: 2.71
r_work: 0.4052 rms_B_bonded: 3.41 restraints_weight: 0.5000
r_work (final): 0.4052
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6640
moved from start:          0.1803

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6123  Z= 0.149
  Angle     :  0.694  10.926   8331  Z= 0.332
  Chirality :  0.048   0.394   1004
  Planarity :  0.004   0.041   1041
  Dihedral  :  6.781  55.963   1070
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 8.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.92 %
    Favored  : 88.08 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 17.69 %
    Favored  : 80.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.16 (0.31), residues: 713
  helix: -0.42 (0.59), residues: 74
  sheet: -4.02 (0.58), residues: 65
  loop : -2.30 (0.26), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 484 
 TYR   0.007   0.001   TYR A 383 
 PHE   0.022   0.001   PHE A 557 
 TRP   0.008   0.001   TRP A 546 
 HIS   0.004   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00347 ( 6104)
  covalent geometry    : angle       0.67013 ( 8278)
  SS BOND              : bond        0.00112 (    4)
  SS BOND              : angle       0.63283 (    8)
  hydrogen bonds       : bond        0.04150 (   59)
  hydrogen bonds       : angle       4.94127 (  141)
  link_BETA1-4         : bond        0.00409 (    5)
  link_BETA1-4         : angle       1.43571 (   15)
  link_NAG-ASN         : bond        0.00575 (   10)
  link_NAG-ASN         : angle       2.97682 (   30)

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

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

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1426 Ramachandran restraints generated.
    713 Oldfield, 0 Emsley, 713 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  103 VAL cc_start: 0.8032 (OUTLIER) cc_final: 0.7798 (t)
REVERT: A  119 PHE cc_start: 0.6788 (p90) cc_final: 0.5962 (p90)
REVERT: A  150 ILE cc_start: 0.5828 (OUTLIER) cc_final: 0.5577 (mp)
REVERT: A  363 GLU cc_start: 0.6317 (tp30) cc_final: 0.5985 (tp30)
REVERT: A  437 ASP cc_start: 0.5658 (OUTLIER) cc_final: 0.5430 (t70)
  outliers start: 15
  outliers final: 11
  residues processed: 98
  average time/residue: 0.4408
  time to fit residues: 45.9713
Evaluate side-chains
  100 residues out of total 667 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 86
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 LEU
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  150 ILE
Chi-restraints excluded: chain A residue  169 GLN
Chi-restraints excluded: chain A residue  297 LEU
Chi-restraints excluded: chain A residue  367 ILE
Chi-restraints excluded: chain A residue  402 VAL
Chi-restraints excluded: chain A residue  437 ASP
Chi-restraints excluded: chain A residue  445 GLN
Chi-restraints excluded: chain A residue  495 VAL
Chi-restraints excluded: chain A residue  593 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  610 VAL
Chi-restraints excluded: chain A residue  621 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 71
   random chunks:
   chunk 55 optimal weight:    0.0980
   chunk 33 optimal weight:    0.5980
   chunk 10 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 5 optimal weight:    0.8980
   chunk 7 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0970
   chunk 31 optimal weight:    1.9990
   chunk 61 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 107 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4427 r_free = 0.4427 target = 0.175746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4200 r_free = 0.4200 target = 0.154715 restraints weight = 8067.029|
|-----------------------------------------------------------------------------|
r_work (start): 0.4196 rms_B_bonded: 2.70
r_work: 0.4044 rms_B_bonded: 3.40 restraints_weight: 0.5000
r_work (final): 0.4044
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6654
moved from start:          0.1880

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6123  Z= 0.165
  Angle     :  0.694  10.692   8331  Z= 0.335
  Chirality :  0.048   0.395   1004
  Planarity :  0.004   0.041   1041
  Dihedral  :  6.776  55.864   1070
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.62 %
    Favored  : 87.38 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.39 %
    Favored  : 79.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -3.22 (0.31), residues: 713
  helix: -0.49 (0.59), residues: 74
  sheet: -4.23 (0.57), residues: 63
  loop : -2.33 (0.26), residues: 576

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 643 
 TYR   0.007   0.001   TYR A 383 
 PHE   0.025   0.002   PHE A 557 
 TRP   0.008   0.002   TRP A 546 
 HIS   0.004   0.001   HIS A 359 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6104)
  covalent geometry    : angle       0.66917 ( 8278)
  SS BOND              : bond        0.00144 (    4)
  SS BOND              : angle       0.65749 (    8)
  hydrogen bonds       : bond        0.04354 (   59)
  hydrogen bonds       : angle       4.94376 (  141)
  link_BETA1-4         : bond        0.00400 (    5)
  link_BETA1-4         : angle       1.36745 (   15)
  link_NAG-ASN         : bond        0.00583 (   10)
  link_NAG-ASN         : angle       3.01325 (   30)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2399.99 seconds
wall clock time: 41 minutes 45.63 seconds (2505.63 seconds total)