Starting phenix.real_space_refine
on Tue Mar  3 14:15:32 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ure_26710/03_2026/7ure_26710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ure_26710/03_2026/7ure_26710.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7ure_26710/03_2026/7ure_26710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ure_26710/03_2026/7ure_26710.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ure_26710/03_2026/7ure_26710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ure_26710/03_2026/7ure_26710.cif"
  }
  resolution = 3.19
  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=   0.005 sd=   0.092
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: 5
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     S      35      5.16       5
     C    3566      2.51       5
     N     895      2.21       5
     O     953      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5450
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3465
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3465
          Classifications: {'peptide': 432}
          Link IDs: {'PTRANS': 14, 'TRANS': 417}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 829
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 829
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
    Chain: "H"
      Number of atoms: 926
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 926
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
    Chain: "B"
      Number of atoms: 158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 158
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'DNP:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "A"
      Number of atoms: 55
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 55
          Unusual residues: {' ZN': 1, 'AJP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 34
          Unresolved non-hydrogen angles: 51
          Unresolved non-hydrogen dihedrals: 73
          Unresolved non-hydrogen chiralities: 14
    Chain: "B"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PAM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'PAM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2849  SG  CYS A 370      54.825  29.237  18.480  1.00101.61           S
  ATOM   2896  SG  CYS A 376      53.706  28.652  22.060  1.00110.68           S

  Time building chain proxies: 1.45, per 1000 atoms: 0.27
  Number of scatterers: 5450
  At special positions: 0
  Unit cell: (97.11, 70.55, 97.11, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      1     29.99
     S      35     16.00
     O     953      8.00
     N     895      7.00
     C    3566      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=5, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  17 " - pdb=" SG  CYS A 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  43 " - pdb=" SG  CYS L 108 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  41 " - pdb=" SG  CYS H 115 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 203 " - pdb=" SG  CYS B 217 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 205 " - pdb=" SG  CYS B 212 " 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.50
  Conformation dependent library (CDL) restraints added in 341.6 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 502 "
        pdb="ZN    ZN A 502 " - pdb=" ND1 HIS A 382 "
        pdb="ZN    ZN A 502 " - pdb=" SG  CYS A 370 "
        pdb="ZN    ZN A 502 " - pdb=" SG  CYS A 376 "


  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1254

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 7 sheets defined
      50.6% alpha, 16.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 43
      removed outlier: 4.015A  pdb=" N   GLN A  12 " --> pdb=" O   GLU A   8 " (cutoff:3.500A)
      removed outlier: 4.034A  pdb=" N   LEU A  14 " --> pdb=" O   PHE A  10 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   GLN A  15 " --> pdb=" O   GLN A  11 " (cutoff:3.500A)
      Proline residue:  A  20  - end of helix
      removed outlier: 5.369A  pdb=" N   LEU A  31 " --> pdb=" O   ASP A  27 " (cutoff:3.500A)
      removed outlier: 5.179A  pdb=" N   LEU A  32 " --> pdb=" O   GLN A  28 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 48 through 68
    Processing helix  chain 'A' and resid 72 through 89
    Processing helix  chain 'A' and resid 94 through 112
    Processing helix  chain 'A' and resid 116 through 144
      removed outlier: 5.316A  pdb=" N   GLY A 125 " --> pdb=" O   HIS A 121 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   ALA A 126 " --> pdb=" O   LYS A 122 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 160
    Processing helix  chain 'A' and resid 172 through 182
    Processing helix  chain 'A' and resid 186 through 210
      removed outlier: 3.719A  pdb=" N   LEU A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 265
      removed outlier: 3.616A  pdb=" N   GLY A 265 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 288
      removed outlier: 3.554A  pdb=" N   VAL A 287 " --> pdb=" O   LYS A 283 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 292 through 301
      removed outlier: 4.510A  pdb=" N   ASN A 301 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 317
    Processing helix  chain 'A' and resid 320 through 336
      removed outlier: 3.691A  pdb=" N   HIS A 336 " --> pdb=" O   SER A 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 343 through 367
    Processing helix  chain 'A' and resid 388 through 410
    Processing helix  chain 'A' and resid 411 through 413
      No H-bonds generated for 'chain 'A' and resid 411 through 413'
    Processing helix  chain 'A' and resid 426 through 437
    Processing helix  chain 'A' and resid 439 through 456
    Processing helix  chain 'L' and resid 99 through 103
      removed outlier: 4.091A  pdb=" N   PHE L 103 " --> pdb=" O   PRO L 100 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 47 through 51
      removed outlier: 4.185A  pdb=" N   TYR H  51 " --> pdb=" O   PHE H  48 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 271
      removed outlier: 3.679A  pdb=" N   GLU A 276 " --> pdb=" O   THR A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'L' and resid 24 through 27
      removed outlier: 4.126A  pdb=" N   GLN L  90 " --> pdb=" O   SER L  87 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   SER L  87 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   SER L  92 " --> pdb=" O   SER L  85 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'L' and resid 30 through 33
      removed outlier: 6.299A  pdb=" N   LEU L  31 " --> pdb=" O   GLU L 125 " (cutoff:3.500A)
      removed outlier: 6.468A  pdb=" N   LEU L  53 " --> pdb=" O   TYR L  69 " (cutoff:3.500A)
      removed outlier: 4.905A  pdb=" N   TYR L  69 " --> pdb=" O   LEU L  53 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   TRP L  55 " --> pdb=" O   LEU L  67 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 24 through 25
    Processing sheet with id=AA5, first strand: chain 'H' and resid 29 through 31
      removed outlier: 3.728A  pdb=" N   TYR H 113 " --> pdb=" O   THR H 132 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   MET H  53 " --> pdb=" O   ASN H  69 " (cutoff:3.500A)
      removed outlier: 4.542A  pdb=" N   ASN H  69 " --> pdb=" O   MET H  53 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   TRP H  55 " --> pdb=" O   ILE H  67 " (cutoff:3.500A)
      removed outlier: 3.859A  pdb=" N   SER H  76 " --> pdb=" O   ASN H  71 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31
      removed outlier: 3.728A  pdb=" N   TYR H 113 " --> pdb=" O   THR H 132 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   TYR H 127 " --> pdb=" O   ARG H 117 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 202 through 206
      removed outlier: 3.502A  pdb=" N   TRP B 218 " --> pdb=" O   LYS B 202 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LYS B 204 " --> pdb=" O   THR B 216 " (cutoff:3.500A)

    319 hydrogen bonds defined for protein.
    900 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: 0.81

  Time building geometry restraints manager: 0.65 seconds

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

  Histogram of bond lengths:
        1.00 -     1.20: 5
        1.20 -     1.40: 2365
        1.40 -     1.60: 3182
        1.60 -     1.79: 21
        1.79 -     1.99: 39
  Bond restraints: 5612
  Sorted by residual:
  bond pdb=" C07 AJP A 501 "
       pdb=" C08 AJP A 501 "
    ideal  model  delta    sigma   weight residual
    1.550  1.991 -0.441 2.00e-02 2.50e+03 4.86e+02
  bond pdb=" C01 AJP A 501 "
       pdb=" C02 AJP A 501 "
    ideal  model  delta    sigma   weight residual
    1.521  1.950 -0.429 2.00e-02 2.50e+03 4.59e+02
  bond pdb=" C08 AJP A 501 "
       pdb=" O09 AJP A 501 "
    ideal  model  delta    sigma   weight residual
    1.410  1.002  0.408 2.00e-02 2.50e+03 4.16e+02
  bond pdb=" C05 AJP A 501 "
       pdb=" O09 AJP A 501 "
    ideal  model  delta    sigma   weight residual
    1.407  1.803 -0.396 2.00e-02 2.50e+03 3.92e+02
  bond pdb=" C02 AJP A 501 "
       pdb=" C03 AJP A 501 "
    ideal  model  delta    sigma   weight residual
    1.525  1.130  0.395 2.00e-02 2.50e+03 3.91e+02
  ... (remaining 5607 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.41: 7561
        3.41 -     6.82: 55
        6.82 -    10.22: 9
       10.22 -    13.63: 3
       13.63 -    17.04: 2
  Bond angle restraints: 7630
  Sorted by residual:
  angle pdb=" C2  PAM B 601 "
        pdb=" C1  PAM B 601 "
        pdb=" O1  PAM B 601 "
      ideal   model   delta    sigma   weight residual
     115.96   98.92   17.04 3.00e+00 1.11e-01 3.23e+01
  angle pdb=" C11 AJP A 501 "
        pdb=" C12 AJP A 501 "
        pdb=" C81 AJP A 501 "
      ideal   model   delta    sigma   weight residual
     114.35  100.70   13.65 3.00e+00 1.11e-01 2.07e+01
  angle pdb=" C03 AJP A 501 "
        pdb=" C02 AJP A 501 "
        pdb=" C85 AJP A 501 "
      ideal   model   delta    sigma   weight residual
     109.14  122.46  -13.32 3.00e+00 1.11e-01 1.97e+01
  angle pdb=" C04 AJP A 501 "
        pdb=" C05 AJP A 501 "
        pdb=" O84 AJP A 501 "
      ideal   model   delta    sigma   weight residual
     111.01  122.20  -11.19 3.00e+00 1.11e-01 1.39e+01
  angle pdb=" C06 AJP A 501 "
        pdb=" C07 AJP A 501 "
        pdb=" C12 AJP A 501 "
      ideal   model   delta    sigma   weight residual
     120.30  130.92  -10.62 3.00e+00 1.11e-01 1.25e+01
  ... (remaining 7625 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.23: 3179
       35.23 -    70.45: 83
       70.45 -   105.68: 24
      105.68 -   140.90: 35
      140.90 -   176.13: 9
  Dihedral angle restraints: 3330
    sinusoidal: 1368
      harmonic: 1962
  Sorted by residual:
  dihedral pdb=" C06 AJP A 501 "
           pdb=" C07 AJP A 501 "
           pdb=" C12 AJP A 501 "
           pdb=" C13 AJP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     109.15  -74.72 -176.13     1      3.00e+01 1.11e-03 2.13e+01
  dihedral pdb=" C29 AJP A 501 "
           pdb=" C30 AJP A 501 "
           pdb=" C32 AJP A 501 "
           pdb=" O33 AJP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.96  108.71 -169.67     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C08 AJP A 501 "
           pdb=" C07 AJP A 501 "
           pdb=" C12 AJP A 501 "
           pdb=" C81 AJP A 501 "
      ideal   model   delta sinusoidal    sigma   weight residual
     101.32  -65.22  166.54     1      3.00e+01 1.11e-03 2.10e+01
  ... (remaining 3327 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.102: 832
       1.102 -    2.205: 0
       2.205 -    3.307: 0
       3.307 -    4.409: 2
       4.409 -    5.512: 19
  Chirality restraints: 853
  Sorted by residual:
  chirality pdb=" C15 AJP A 501 "
            pdb=" C14 AJP A 501 "
            pdb=" C16 AJP A 501 "
            pdb=" C20 AJP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42    3.09   -5.51 2.00e-01 2.50e+01 7.59e+02
  chirality pdb=" C20 AJP A 501 "
            pdb=" C15 AJP A 501 "
            pdb=" C19 AJP A 501 "
            pdb=" C21 AJP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.96   -2.52    5.48 2.00e-01 2.50e+01 7.51e+02
  chirality pdb=" C16 AJP A 501 "
            pdb=" C11 AJP A 501 "
            pdb=" C15 AJP A 501 "
            pdb=" C17 AJP A 501 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.70    2.76   -5.47 2.00e-01 2.50e+01 7.47e+02
  ... (remaining 850 not shown)

  Planarity restraints: 921
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 310 "   -0.011 2.00e-02 2.50e+03   2.24e-02 5.00e+00
        pdb=" C   ASN A 310 "    0.039 2.00e-02 2.50e+03
        pdb=" O   ASN A 310 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   TYR A 311 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 309 "   -0.011 2.00e-02 2.50e+03   2.11e-02 4.44e+00
        pdb=" C   ASN A 309 "    0.036 2.00e-02 2.50e+03
        pdb=" O   ASN A 309 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ASN A 310 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 215 "   -0.033 5.00e-02 4.00e+02   4.92e-02 3.87e+00
        pdb=" N   PRO A 216 "    0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO A 216 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO A 216 "   -0.028 5.00e-02 4.00e+02
  ... (remaining 918 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 84
        2.67 -     3.23: 5166
        3.23 -     3.79: 8435
        3.79 -     4.34: 11495
        4.34 -     4.90: 19542
  Nonbonded interactions: 44722
  Sorted by model distance:
  nonbonded pdb=" O   LEU A 319 "
            pdb=" OG  SER A 323 "
     model   vdw
     2.118 3.040
  nonbonded pdb=" O33 AJP A 501 "
            pdb=" O40 AJP A 501 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   ARG A  90 "
            pdb=" NH1 ARG A  95 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" O   PHE A 340 "
            pdb=" ND1 HIS A 341 "
     model   vdw
     2.276 3.120
  nonbonded pdb=" ND1 HIS A  53 "
            pdb=" OH  TYR A 176 "
     model   vdw
     2.315 3.120
  ... (remaining 44717 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
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:             1.420
  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:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.710
  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:1.230
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.560
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8139
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      :  0.018   0.441   5621  Z= 0.882
  Angle     :  0.781  17.041   7640  Z= 0.350
  Chirality :  0.778   5.512    853
  Planarity :  0.005   0.049    921
  Dihedral  : 25.750 176.131   2061
  Min Nonbonded Distance : 2.118

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.73 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.14 %
    Favored  : 95.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole: -2.27 (0.30), residues: 663
  helix: -0.41 (0.25), residues: 331
  sheet: -2.23 (0.46), residues: 125
  loop : -2.62 (0.40), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG H 117 
 TYR   0.016   0.002   TYR A  83 
 PHE   0.010   0.001   PHE A 268 
 TRP   0.007   0.001   TRP H  66 
 HIS   0.005   0.001   HIS L 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.01736 ( 5612)
  covalent geometry    : angle       0.78063 ( 7630)
  SS BOND              : bond        0.00159 (    5)
  SS BOND              : angle       0.71560 (   10)
  hydrogen bonds       : bond        0.13546 (  313)
  hydrogen bonds       : angle       6.66551 (  900)
  metal coordination   : bond        0.14268 (    3)
  Misc. bond           : bond        0.10044 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 83
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.8161 (t80) cc_final: 0.7925 (t80)
REVERT: A  201 LEU cc_start: 0.7964 (mt) cc_final: 0.7760 (mm)
REVERT: A  407 TYR cc_start: 0.8170 (t80) cc_final: 0.7482 (t80)
REVERT: A  434 TRP cc_start: 0.8299 (m-10) cc_final: 0.8018 (m-10)
REVERT: A  452 TYR cc_start: 0.6613 (t80) cc_final: 0.6403 (t80)
REVERT: L  116 TYR cc_start: 0.9007 (m-80) cc_final: 0.8725 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 83
  average time/residue: 0.1015
  time to fit residues: 10.5379
Evaluate side-chains
  73 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.157 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    2.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   chunk 27 optimal weight:    3.9990
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A  71 HIS
A  91 HIS
A 121 HIS
A 127 GLN
A 181 GLN
A 315 ASN
A 394 ASN
L  96 ASN
L 111 HIS
H  22 GLN
H  78 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.151107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.114775 restraints weight = 6011.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3226 rms_B_bonded: 2.33
r_work: 0.3089 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2938 rms_B_bonded: 4.63 restraints_weight: 0.2500
r_work (final): 0.2938
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.1135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   5621  Z= 0.135
  Angle     :  1.118  34.391   7640  Z= 0.427
  Chirality :  0.121   2.260    853
  Planarity :  0.005   0.044    921
  Dihedral  : 21.344 172.924    893
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 6.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  9.48 %
    Favored  : 89.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole: -0.78 (0.32), residues: 663
  helix:  0.95 (0.27), residues: 328
  sheet: -1.62 (0.45), residues: 134
  loop : -2.10 (0.42), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 318 
 TYR   0.017   0.002   TYR A  83 
 PHE   0.008   0.001   PHE A 268 
 TRP   0.007   0.001   TRP H  66 
 HIS   0.007   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5612)
  covalent geometry    : angle       1.11870 ( 7630)
  SS BOND              : bond        0.00276 (    5)
  SS BOND              : angle       0.54874 (   10)
  hydrogen bonds       : bond        0.03455 (  313)
  hydrogen bonds       : angle       4.98498 (  900)
  metal coordination   : bond        0.00106 (    3)
  Misc. bond           : bond        0.00015 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 67
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.7846 (t80) cc_final: 0.7623 (t80)
REVERT: A  112 MET cc_start: 0.5795 (tmm) cc_final: 0.5232 (ttm)
REVERT: A  341 HIS cc_start: 0.7624 (OUTLIER) cc_final: 0.7089 (p-80)
REVERT: A  342 LEU cc_start: 0.7526 (tp) cc_final: 0.7182 (tp)
REVERT: A  434 TRP cc_start: 0.7701 (m-10) cc_final: 0.7305 (m-10)
REVERT: L  116 TYR cc_start: 0.9196 (m-80) cc_final: 0.8896 (m-80)
REVERT: B  217 CYS cc_start: 0.7443 (m) cc_final: 0.7179 (m)
  outliers start: 4
  outliers final: 2
  residues processed: 71
  average time/residue: 0.0877
  time to fit residues: 7.9341
Evaluate side-chains
  65 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 62
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  371 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 8 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 12 optimal weight:    1.9990
   chunk 56 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 127 GLN
** H 123 HIS ** 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 = 0.3679 r_free = 0.3679 target = 0.151240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.115119 restraints weight = 5914.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3205 rms_B_bonded: 2.32
r_work: 0.3067 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2916 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7762
moved from start:          0.1425

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5621  Z= 0.132
  Angle     :  1.096  34.733   7640  Z= 0.416
  Chirality :  0.120   2.221    853
  Planarity :  0.004   0.044    921
  Dihedral  : 21.101 174.284    893
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 11.03 %
    Favored  : 87.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole: -0.11 (0.33), residues: 663
  helix:  1.57 (0.28), residues: 327
  sheet: -1.38 (0.44), residues: 135
  loop : -1.83 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 365 
 TYR   0.021   0.002   TYR L  52 
 PHE   0.009   0.001   PHE A 248 
 TRP   0.006   0.001   TRP A  74 
 HIS   0.005   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00301 ( 5612)
  covalent geometry    : angle       1.09678 ( 7630)
  SS BOND              : bond        0.00236 (    5)
  SS BOND              : angle       0.51392 (   10)
  hydrogen bonds       : bond        0.03136 (  313)
  hydrogen bonds       : angle       4.62187 (  900)
  metal coordination   : bond        0.00124 (    3)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.7859 (t80) cc_final: 0.7612 (t80)
REVERT: A  341 HIS cc_start: 0.7615 (OUTLIER) cc_final: 0.7231 (p-80)
REVERT: A  342 LEU cc_start: 0.7567 (tp) cc_final: 0.7259 (tp)
REVERT: A  388 LEU cc_start: 0.7754 (tt) cc_final: 0.7126 (pp)
REVERT: A  434 TRP cc_start: 0.7690 (m-10) cc_final: 0.7300 (m-10)
REVERT: L  116 TYR cc_start: 0.9205 (m-80) cc_final: 0.8926 (m-80)
REVERT: B  217 CYS cc_start: 0.7315 (m) cc_final: 0.7075 (m)
  outliers start: 8
  outliers final: 4
  residues processed: 68
  average time/residue: 0.0840
  time to fit residues: 7.3939
Evaluate side-chains
  67 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 62
  time to evaluate  : 0.183 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain B residue  214 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 60 optimal weight:    4.9990
   chunk 62 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9980
   chunk 47 optimal weight:    0.1980
   chunk 61 optimal weight:    3.9990
   chunk 46 optimal weight:    0.9980
   chunk 55 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 32 optimal weight:    7.9990
   chunk 36 optimal weight:    3.9990
   overall best weight:    1.6384

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

Flipped N/Q/H residues before XYZ refinement:
A 127 GLN
** H  52 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 = 0.3835 r_free = 0.3835 target = 0.157208 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.124720 restraints weight = 6148.703|
|-----------------------------------------------------------------------------|
r_work (start): 0.3466 rms_B_bonded: 1.98
r_work: 0.3293 rms_B_bonded: 2.82 restraints_weight: 0.5000
r_work: 0.3150 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3150
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8448
moved from start:          0.1497

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   5621  Z= 0.203
  Angle     :  1.132  35.173   7640  Z= 0.440
  Chirality :  0.120   2.208    853
  Planarity :  0.004   0.043    921
  Dihedral  : 21.322 176.165    893
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.49 %
    Favored  : 93.51 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 11.72 %
    Favored  : 86.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole:  0.00 (0.33), residues: 663
  helix:  1.53 (0.28), residues: 329
  sheet: -1.20 (0.45), residues: 135
  loop : -1.67 (0.44), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 238 
 TYR   0.020   0.002   TYR A 311 
 PHE   0.013   0.001   PHE A 215 
 TRP   0.010   0.001   TRP A  74 
 HIS   0.005   0.001   HIS A  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00482 ( 5612)
  covalent geometry    : angle       1.13283 ( 7630)
  SS BOND              : bond        0.00241 (    5)
  SS BOND              : angle       0.61046 (   10)
  hydrogen bonds       : bond        0.03675 (  313)
  hydrogen bonds       : angle       4.74099 (  900)
  metal coordination   : bond        0.00196 (    3)
  Misc. bond           : bond        0.00010 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A  112 MET cc_start: 0.6291 (tmm) cc_final: 0.5905 (ttm)
REVERT: A  318 ARG cc_start: 0.6602 (mtp85) cc_final: 0.6333 (mtm-85)
REVERT: A  341 HIS cc_start: 0.7981 (OUTLIER) cc_final: 0.7406 (p-80)
REVERT: A  407 TYR cc_start: 0.8557 (t80) cc_final: 0.7988 (t80)
REVERT: A  434 TRP cc_start: 0.8412 (m-10) cc_final: 0.7938 (m-10)
REVERT: L   90 GLN cc_start: 0.8071 (OUTLIER) cc_final: 0.7632 (tm-30)
REVERT: B  217 CYS cc_start: 0.7666 (m) cc_final: 0.7428 (m)
  outliers start: 13
  outliers final: 8
  residues processed: 74
  average time/residue: 0.0887
  time to fit residues: 8.3270
Evaluate side-chains
  72 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 62
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain L residue   78 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue   97 THR
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain B residue  214 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 14 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 53 optimal weight:    0.0370
   chunk 33 optimal weight:    0.9980
   chunk 18 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0970
   chunk 22 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.6256

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

Flipped N/Q/H residues before XYZ refinement:
A 127 GLN
A 336 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3878 r_free = 0.3878 target = 0.160194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3498 r_free = 0.3498 target = 0.127503 restraints weight = 6169.942|
|-----------------------------------------------------------------------------|
r_work (start): 0.3495 rms_B_bonded: 2.01
r_work: 0.3353 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3213 rms_B_bonded: 4.41 restraints_weight: 0.2500
r_work (final): 0.3213
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1712

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   5621  Z= 0.112
  Angle     :  1.089  34.763   7640  Z= 0.409
  Chirality :  0.119   2.211    853
  Planarity :  0.004   0.042    921
  Dihedral  : 21.038 176.599    893
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.10 %
    Favored  : 85.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole:  0.43 (0.34), residues: 663
  helix:  1.98 (0.28), residues: 327
  sheet: -1.08 (0.44), residues: 135
  loop : -1.57 (0.44), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 385 
 TYR   0.018   0.001   TYR A  83 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.005   0.001   TRP H 128 
 HIS   0.004   0.001   HIS L 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00248 ( 5612)
  covalent geometry    : angle       1.08946 ( 7630)
  SS BOND              : bond        0.00195 (    5)
  SS BOND              : angle       0.38381 (   10)
  hydrogen bonds       : bond        0.02875 (  313)
  hydrogen bonds       : angle       4.38835 (  900)
  metal coordination   : bond        0.00064 (    3)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.6281 (tmm) cc_final: 0.5921 (ttm)
REVERT: A  186 SER cc_start: 0.8623 (t) cc_final: 0.8073 (p)
REVERT: A  341 HIS cc_start: 0.7749 (OUTLIER) cc_final: 0.7547 (p-80)
REVERT: A  388 LEU cc_start: 0.7752 (tt) cc_final: 0.7031 (pp)
REVERT: A  434 TRP cc_start: 0.8214 (m-10) cc_final: 0.7870 (m-10)
REVERT: L   90 GLN cc_start: 0.8012 (OUTLIER) cc_final: 0.7596 (tm-30)
REVERT: L  116 TYR cc_start: 0.9154 (m-80) cc_final: 0.8892 (m-80)
REVERT: B  217 CYS cc_start: 0.7616 (m) cc_final: 0.7411 (m)
  outliers start: 11
  outliers final: 5
  residues processed: 75
  average time/residue: 0.0803
  time to fit residues: 7.8578
Evaluate side-chains
  70 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 63
  time to evaluate  : 0.146 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain L residue   78 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain B residue  206 HIS
Chi-restraints excluded: chain B residue  214 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 21 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 39 optimal weight:    4.9990
   chunk 17 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 53 optimal weight:    0.8980
   chunk 54 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   chunk 20 optimal weight:    0.6980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
H  25 GLN
** H  52 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 = 0.3842 r_free = 0.3842 target = 0.156944 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.125260 restraints weight = 6100.443|
|-----------------------------------------------------------------------------|
r_work (start): 0.3503 rms_B_bonded: 1.94
r_work: 0.3355 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8377
moved from start:          0.1763

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5621  Z= 0.132
  Angle     :  1.092  34.869   7640  Z= 0.412
  Chirality :  0.119   2.214    853
  Planarity :  0.004   0.041    921
  Dihedral  : 21.032 176.940    893
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.62 %
    Favored  : 84.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole:  0.59 (0.34), residues: 663
  helix:  2.07 (0.28), residues: 327
  sheet: -0.88 (0.44), residues: 134
  loop : -1.51 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.018   0.002   TYR A  83 
 PHE   0.008   0.001   PHE A 248 
 TRP   0.007   0.001   TRP A  74 
 HIS   0.004   0.001   HIS A  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 5612)
  covalent geometry    : angle       1.09265 ( 7630)
  SS BOND              : bond        0.00200 (    5)
  SS BOND              : angle       0.43724 (   10)
  hydrogen bonds       : bond        0.03005 (  313)
  hydrogen bonds       : angle       4.38036 (  900)
  metal coordination   : bond        0.00105 (    3)
  Misc. bond           : bond        0.00008 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  388 LEU cc_start: 0.7748 (tt) cc_final: 0.7046 (pp)
REVERT: A  407 TYR cc_start: 0.8464 (t80) cc_final: 0.7947 (t80)
REVERT: A  434 TRP cc_start: 0.8236 (m-10) cc_final: 0.7914 (m-10)
REVERT: L   90 GLN cc_start: 0.7979 (OUTLIER) cc_final: 0.7568 (tm-30)
REVERT: L  116 TYR cc_start: 0.9158 (m-80) cc_final: 0.8906 (m-80)
REVERT: B  217 CYS cc_start: 0.7591 (m) cc_final: 0.7374 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 73
  average time/residue: 0.0823
  time to fit residues: 7.8158
Evaluate side-chains
  71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.272 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain L residue   78 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain B residue  206 HIS
Chi-restraints excluded: chain B residue  214 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 57 optimal weight:    0.4980
   chunk 18 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 32 optimal weight:    4.9990
   chunk 60 optimal weight:    0.5980
   chunk 54 optimal weight:    0.9990
   chunk 34 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 10 optimal weight:    0.0870
   chunk 7 optimal weight:    0.9980
   overall best weight:    0.6360

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

Flipped N/Q/H residues before XYZ refinement:
** H  52 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 = 0.3884 r_free = 0.3884 target = 0.160736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.128145 restraints weight = 6145.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3535 rms_B_bonded: 2.01
r_work: 0.3361 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.1907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   5621  Z= 0.113
  Angle     :  1.100  34.641   7640  Z= 0.414
  Chirality :  0.118   2.185    853
  Planarity :  0.004   0.041    921
  Dihedral  : 21.003 177.097    893
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.31 %
    Favored  : 83.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole:  0.77 (0.34), residues: 663
  helix:  2.11 (0.28), residues: 333
  sheet: -0.73 (0.44), residues: 134
  loop : -1.38 (0.45), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.017   0.001   TYR A  83 
 PHE   0.008   0.001   PHE A  67 
 TRP   0.006   0.001   TRP A  74 
 HIS   0.004   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 5612)
  covalent geometry    : angle       1.10011 ( 7630)
  SS BOND              : bond        0.00199 (    5)
  SS BOND              : angle       0.51141 (   10)
  hydrogen bonds       : bond        0.02819 (  313)
  hydrogen bonds       : angle       4.31161 (  900)
  metal coordination   : bond        0.00071 (    3)
  Misc. bond           : bond        0.00008 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 68
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.6217 (tmm) cc_final: 0.5850 (ttm)
REVERT: A  186 SER cc_start: 0.8608 (t) cc_final: 0.8061 (p)
REVERT: A  276 GLU cc_start: 0.7651 (mm-30) cc_final: 0.7361 (mm-30)
REVERT: A  388 LEU cc_start: 0.7755 (tt) cc_final: 0.7060 (pp)
REVERT: L   90 GLN cc_start: 0.7981 (OUTLIER) cc_final: 0.7573 (tm-30)
REVERT: B  217 CYS cc_start: 0.7617 (m) cc_final: 0.7397 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 75
  average time/residue: 0.0803
  time to fit residues: 7.7950
Evaluate side-chains
  71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain L residue   78 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue   39 MET
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain B residue  206 HIS
Chi-restraints excluded: chain B residue  214 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 61 optimal weight:    7.9990
   chunk 65 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 24 optimal weight:    0.5980
   chunk 49 optimal weight:    7.9990
   chunk 19 optimal weight:    0.5980
   chunk 59 optimal weight:    0.3980
   chunk 6 optimal weight:    3.9990
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** H  52 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 = 0.3882 r_free = 0.3882 target = 0.160571 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.128160 restraints weight = 6042.764|
|-----------------------------------------------------------------------------|
r_work (start): 0.3526 rms_B_bonded: 1.98
r_work: 0.3377 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8364
moved from start:          0.1982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   5621  Z= 0.116
  Angle     :  1.097  34.595   7640  Z= 0.414
  Chirality :  0.118   2.177    853
  Planarity :  0.004   0.040    921
  Dihedral  : 20.982 177.155    893
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 5.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.48 %
    Favored  : 83.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole:  0.82 (0.34), residues: 663
  helix:  2.03 (0.28), residues: 339
  sheet: -0.59 (0.44), residues: 134
  loop : -1.32 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.017   0.001   TYR A  83 
 PHE   0.007   0.001   PHE A  67 
 TRP   0.006   0.001   TRP A  74 
 HIS   0.003   0.001   HIS L 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 5612)
  covalent geometry    : angle       1.09776 ( 7630)
  SS BOND              : bond        0.00173 (    5)
  SS BOND              : angle       0.46030 (   10)
  hydrogen bonds       : bond        0.02867 (  313)
  hydrogen bonds       : angle       4.35147 (  900)
  metal coordination   : bond        0.00089 (    3)
  Misc. bond           : bond        0.00007 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.225 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.6298 (tmm) cc_final: 0.5917 (ttm)
REVERT: A  186 SER cc_start: 0.8625 (t) cc_final: 0.8084 (p)
REVERT: A  341 HIS cc_start: 0.7942 (OUTLIER) cc_final: 0.7709 (p-80)
REVERT: A  388 LEU cc_start: 0.7733 (tt) cc_final: 0.7044 (pp)
REVERT: L   90 GLN cc_start: 0.7947 (OUTLIER) cc_final: 0.7567 (tm-30)
REVERT: B  217 CYS cc_start: 0.7436 (m) cc_final: 0.7230 (m)
  outliers start: 12
  outliers final: 9
  residues processed: 70
  average time/residue: 0.0849
  time to fit residues: 7.7187
Evaluate side-chains
  73 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain L residue   78 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue   39 MET
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain B residue  206 HIS
Chi-restraints excluded: chain B residue  214 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 53 optimal weight:    3.9990
   chunk 35 optimal weight:    3.9990
   chunk 21 optimal weight:    0.2980
   chunk 46 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 59 optimal weight:    0.0270
   chunk 50 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 47 optimal weight:    0.8980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** H  52 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 = 0.3868 r_free = 0.3868 target = 0.159417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.127827 restraints weight = 6058.546|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.95
r_work: 0.3386 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3249 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3249
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8348
moved from start:          0.2054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   5621  Z= 0.113
  Angle     :  1.093  34.493   7640  Z= 0.411
  Chirality :  0.118   2.167    853
  Planarity :  0.004   0.040    921
  Dihedral  : 20.931 177.196    893
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 14.83 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole:  0.93 (0.34), residues: 663
  helix:  2.09 (0.28), residues: 339
  sheet: -0.45 (0.44), residues: 134
  loop : -1.29 (0.45), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 453 
 TYR   0.017   0.001   TYR A  83 
 PHE   0.007   0.001   PHE A 248 
 TRP   0.005   0.001   TRP A  74 
 HIS   0.003   0.001   HIS A  53 

Details of bonding type rmsd
  covalent geometry    : bond        0.00253 ( 5612)
  covalent geometry    : angle       1.09317 ( 7630)
  SS BOND              : bond        0.00177 (    5)
  SS BOND              : angle       0.45334 (   10)
  hydrogen bonds       : bond        0.02805 (  313)
  hydrogen bonds       : angle       4.30875 (  900)
  metal coordination   : bond        0.00088 (    3)
  Misc. bond           : bond        0.00009 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 65
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.7576 (mmt) cc_final: 0.7345 (mmp)
REVERT: A  112 MET cc_start: 0.6482 (tmm) cc_final: 0.5745 (ttm)
REVERT: A  186 SER cc_start: 0.8604 (t) cc_final: 0.8069 (p)
REVERT: A  388 LEU cc_start: 0.7692 (tt) cc_final: 0.7056 (pp)
REVERT: L   90 GLN cc_start: 0.7911 (OUTLIER) cc_final: 0.7524 (tm-30)
REVERT: L  125 GLU cc_start: 0.7445 (tt0) cc_final: 0.7201 (tt0)
REVERT: H   38 LYS cc_start: 0.8198 (tttp) cc_final: 0.7982 (tptm)
REVERT: B  217 CYS cc_start: 0.7409 (m) cc_final: 0.7193 (m)
  outliers start: 12
  outliers final: 8
  residues processed: 73
  average time/residue: 0.0904
  time to fit residues: 8.5332
Evaluate side-chains
  72 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain L residue   78 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain B residue  206 HIS
Chi-restraints excluded: chain B residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 61 optimal weight:    5.9990
   chunk 34 optimal weight:    5.9990
   chunk 4 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 43 optimal weight:    0.7980
   chunk 29 optimal weight:    0.5980
   chunk 33 optimal weight:    0.6980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** H  52 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 = 0.3859 r_free = 0.3859 target = 0.158483 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.126912 restraints weight = 6140.566|
|-----------------------------------------------------------------------------|
r_work (start): 0.3525 rms_B_bonded: 1.95
r_work: 0.3377 rms_B_bonded: 2.66 restraints_weight: 0.5000
r_work: 0.3239 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8360
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5621  Z= 0.125
  Angle     :  1.099  34.572   7640  Z= 0.415
  Chirality :  0.118   2.173    853
  Planarity :  0.004   0.039    921
  Dihedral  : 20.883 177.175    893
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 5.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.34 %
    Favored  : 83.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole:  0.92 (0.33), residues: 663
  helix:  2.04 (0.28), residues: 339
  sheet: -0.39 (0.45), residues: 134
  loop : -1.26 (0.45), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 238 
 TYR   0.018   0.001   TYR A  83 
 PHE   0.008   0.001   PHE A 248 
 TRP   0.006   0.001   TRP A  74 
 HIS   0.004   0.001   HIS A  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 ( 5612)
  covalent geometry    : angle       1.09926 ( 7630)
  SS BOND              : bond        0.00163 (    5)
  SS BOND              : angle       0.43714 (   10)
  hydrogen bonds       : bond        0.02908 (  313)
  hydrogen bonds       : angle       4.34144 (  900)
  metal coordination   : bond        0.00101 (    3)
  Misc. bond           : bond        0.00009 (    1)

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

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

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1326 Ramachandran restraints generated.
    663 Oldfield, 0 Emsley, 663 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 64
  time to evaluate  : 0.189 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.7925 (t80) cc_final: 0.7617 (t80)
REVERT: A  112 MET cc_start: 0.6564 (tmm) cc_final: 0.5903 (ttp)
REVERT: A  186 SER cc_start: 0.8680 (t) cc_final: 0.8129 (p)
REVERT: A  388 LEU cc_start: 0.7703 (tt) cc_final: 0.7068 (pp)
REVERT: L   90 GLN cc_start: 0.7908 (OUTLIER) cc_final: 0.7529 (tm-30)
REVERT: H   38 LYS cc_start: 0.8214 (tttp) cc_final: 0.8009 (tptm)
REVERT: B  217 CYS cc_start: 0.7411 (m) cc_final: 0.7199 (m)
  outliers start: 9
  outliers final: 8
  residues processed: 70
  average time/residue: 0.0830
  time to fit residues: 7.5152
Evaluate side-chains
  72 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 63
  time to evaluate  : 0.165 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  148 THR
Chi-restraints excluded: chain A residue  347 LEU
Chi-restraints excluded: chain L residue   78 VAL
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain H residue  103 ASP
Chi-restraints excluded: chain H residue  135 THR
Chi-restraints excluded: chain B residue  206 HIS
Chi-restraints excluded: chain B residue  214 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 40 optimal weight:    5.9990
   chunk 29 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    4.9990
   chunk 63 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 37 optimal weight:    4.9990
   chunk 36 optimal weight:    0.3980
   overall best weight:    1.0582

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

Flipped N/Q/H residues before XYZ refinement:
** H  52 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 = 0.3843 r_free = 0.3843 target = 0.156878 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.125053 restraints weight = 6167.055|
|-----------------------------------------------------------------------------|
r_work (start): 0.3475 rms_B_bonded: 1.96
r_work: 0.3332 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3195 rms_B_bonded: 4.35 restraints_weight: 0.2500
r_work (final): 0.3195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8380
moved from start:          0.1952

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5621  Z= 0.148
  Angle     :  1.108  34.740   7640  Z= 0.422
  Chirality :  0.118   2.188    853
  Planarity :  0.004   0.040    921
  Dihedral  : 20.784 177.069    893
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.52 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    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 are not related in a simple way.
  whole:  0.87 (0.33), residues: 663
  helix:  1.94 (0.28), residues: 339
  sheet: -0.32 (0.45), residues: 134
  loop : -1.22 (0.46), residues: 190

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 238 
 TYR   0.018   0.002   TYR L  52 
 PHE   0.010   0.001   PHE A 248 
 TRP   0.008   0.001   TRP A  74 
 HIS   0.005   0.001   HIS A  94 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 5612)
  covalent geometry    : angle       1.10845 ( 7630)
  SS BOND              : bond        0.00174 (    5)
  SS BOND              : angle       0.48798 (   10)
  hydrogen bonds       : bond        0.03128 (  313)
  hydrogen bonds       : angle       4.43082 (  900)
  metal coordination   : bond        0.00139 (    3)
  Misc. bond           : bond        0.00012 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1473.51 seconds
wall clock time: 25 minutes 56.79 seconds (1556.79 seconds total)