Starting phenix.real_space_refine
on Thu Jul 24 10:05:32 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7ure_26710/07_2025/7ure_26710.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7ure_26710/07_2025/7ure_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_26710/07_2025/7ure_26710.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2025/7ure_26710.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2025/7ure_26710.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7ure_26710/07_2025/7ure_26710.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.005 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 4.22, per 1000 atoms: 0.77
  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: 1.57
  Conformation dependent library (CDL) restraints added in 828.4 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: 0.60
  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: 1.50

  Time building geometry restraints manager: 1.78 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:             1.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     18.840
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.750
-------------------------------------------------------------------------------
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 : 9.65
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.007   0.001   TRP H  66 
 HIS   0.005   0.001   HIS L 111 
 PHE   0.010   0.001   PHE A 268 
 TYR   0.016   0.002   TYR A  83 
 ARG   0.002   0.000   ARG H 117 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.13546 (  313)
  hydrogen bonds       : angle       6.66551 (  900)
  metal coordination   : bond        0.14268 (    3)
  SS BOND              : bond        0.00159 (    5)
  SS BOND              : angle       0.71560 (   10)
  covalent geometry    : bond        0.01736 ( 5612)
  covalent geometry    : angle       0.78063 ( 7630)
  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  : 0.600 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.8162 (t80) cc_final: 0.7925 (t80)
REVERT: A  201 LEU cc_start: 0.7965 (mt) cc_final: 0.7760 (mm)
REVERT: A  407 TYR cc_start: 0.8170 (t80) cc_final: 0.7481 (t80)
REVERT: A  434 TRP cc_start: 0.8298 (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: 0.2292
  time to fit residues: 23.8778
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  : 0.616 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 55 optimal weight:    2.9990
   chunk 50 optimal weight:    6.9990
   chunk 27 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 33 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    3.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A  24 GLN
A  91 HIS
A 121 HIS
A 127 GLN
A 181 GLN
A 315 ASN
** A 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L  96 ASN
L 111 HIS
H  22 GLN
** H  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  78 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.147913 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3240 r_free = 0.3240 target = 0.112091 restraints weight = 5942.995|
|-----------------------------------------------------------------------------|
r_work (start): 0.3125 rms_B_bonded: 2.24
r_work: 0.2986 rms_B_bonded: 2.77 restraints_weight: 0.5000
r_work: 0.2837 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7647
moved from start:          0.1110

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.031   5621  Z= 0.197
  Angle     :  1.139  34.430   7640  Z= 0.443
  Chirality :  0.122   2.301    853
  Planarity :  0.005   0.045    921
  Dihedral  : 21.340 171.726    893
  Min Nonbonded Distance : 2.542

Molprobity Statistics.
  All-atom Clashscore : 4.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.58 %
    Favored  : 94.42 %
  Rotamer:
    Outliers :  1.03 %
    Allowed  :  9.66 %
    Favored  : 89.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.32), residues: 663
  helix:  0.79 (0.27), residues: 328
  sheet: -1.65 (0.45), residues: 135
  loop : -2.10 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP H  66 
 HIS   0.006   0.001   HIS L 111 
 PHE   0.012   0.001   PHE A 268 
 TYR   0.018   0.002   TYR A 311 
 ARG   0.002   0.000   ARG A 318 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03852 (  313)
  hydrogen bonds       : angle       5.08922 (  900)
  metal coordination   : bond        0.00224 (    3)
  SS BOND              : bond        0.00305 (    5)
  SS BOND              : angle       0.64232 (   10)
  covalent geometry    : bond        0.00463 ( 5612)
  covalent geometry    : angle       1.14001 ( 7630)
  Misc. bond           : bond        0.00009 (    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
  76 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 70
  time to evaluate  : 0.568 
Fit side-chains
   revert: symmetry clash
REVERT: A    5 SER cc_start: 0.8372 (t) cc_final: 0.8162 (p)
REVERT: A  112 MET cc_start: 0.5732 (tmm) cc_final: 0.5114 (ttm)
REVERT: A  341 HIS cc_start: 0.7604 (OUTLIER) cc_final: 0.7031 (p-80)
REVERT: A  407 TYR cc_start: 0.7939 (t80) cc_final: 0.7315 (t80)
REVERT: A  434 TRP cc_start: 0.7701 (m-10) cc_final: 0.7240 (m-10)
REVERT: A  452 TYR cc_start: 0.5876 (t80) cc_final: 0.5629 (t80)
  outliers start: 6
  outliers final: 3
  residues processed: 75
  average time/residue: 0.2195
  time to fit residues: 21.0275
Evaluate side-chains
  70 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 66
  time to evaluate  : 0.874 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain H residue   97 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 30 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 32 optimal weight:    8.9990
   chunk 21 optimal weight:    0.2980
   chunk 11 optimal weight:    6.9990
   chunk 33 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9990
   chunk 35 optimal weight:    0.0980
   chunk 57 optimal weight:    0.7980
   chunk 24 optimal weight:    0.6980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 127 GLN
A 394 ASN
** H 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.152725 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.116656 restraints weight = 5937.686|
|-----------------------------------------------------------------------------|
r_work (start): 0.3224 rms_B_bonded: 2.34
r_work: 0.3087 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2935 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2935
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7740
moved from start:          0.1478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020   5621  Z= 0.109
  Angle     :  1.088  34.531   7640  Z= 0.410
  Chirality :  0.120   2.218    853
  Planarity :  0.004   0.044    921
  Dihedral  : 21.114 174.338    893
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 11.90 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.08 (0.33), residues: 663
  helix:  1.61 (0.28), residues: 327
  sheet: -1.41 (0.44), residues: 135
  loop : -1.83 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP H 128 
 HIS   0.006   0.001   HIS A  53 
 PHE   0.009   0.001   PHE A  67 
 TYR   0.020   0.001   TYR L  52 
 ARG   0.002   0.000   ARG A 365 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02985 (  313)
  hydrogen bonds       : angle       4.59358 (  900)
  metal coordination   : bond        0.00088 (    3)
  SS BOND              : bond        0.00234 (    5)
  SS BOND              : angle       0.46469 (   10)
  covalent geometry    : bond        0.00238 ( 5612)
  covalent geometry    : angle       1.08836 ( 7630)
  Misc. bond           : bond        0.00013 (    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
  78 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 69
  time to evaluate  : 0.573 
Fit side-chains
   revert: symmetry clash
REVERT: A  186 SER cc_start: 0.8238 (t) cc_final: 0.7696 (p)
REVERT: A  341 HIS cc_start: 0.7571 (OUTLIER) cc_final: 0.7218 (p-80)
REVERT: A  388 LEU cc_start: 0.7760 (tt) cc_final: 0.7105 (pp)
REVERT: B  217 CYS cc_start: 0.7315 (m) cc_final: 0.7088 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 76
  average time/residue: 0.1928
  time to fit residues: 18.9516
Evaluate side-chains
  72 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 66
  time to evaluate  : 0.518 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   97 VAL
Chi-restraints excluded: chain A residue  341 HIS
Chi-restraints excluded: chain L residue   78 VAL
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 19 optimal weight:    3.9990
   chunk 58 optimal weight:    0.8980
   chunk 51 optimal weight:    2.9990
   chunk 65 optimal weight:    5.9990
   chunk 1 optimal weight:    6.9990
   chunk 4 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 55 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.0984

-------------------------------------------------------------------------------
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 = 0.3722 r_free = 0.3722 target = 0.151560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.116409 restraints weight = 6014.247|
|-----------------------------------------------------------------------------|
r_work (start): 0.3297 rms_B_bonded: 2.16
r_work: 0.3168 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3025 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3025
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8062
moved from start:          0.1549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   5621  Z= 0.153
  Angle     :  1.110  34.856   7640  Z= 0.424
  Chirality :  0.119   2.189    853
  Planarity :  0.004   0.043    921
  Dihedral  : 21.227 175.875    893
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.03 %
    Favored  : 93.97 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.10 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.20 (0.34), residues: 663
  helix:  1.77 (0.28), residues: 327
  sheet: -1.15 (0.45), residues: 134
  loop : -1.65 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A  74 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.010   0.001   PHE A 248 
 TYR   0.019   0.002   TYR A  83 
 ARG   0.001   0.000   ARG A 238 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03249 (  313)
  hydrogen bonds       : angle       4.57634 (  900)
  metal coordination   : bond        0.00122 (    3)
  SS BOND              : bond        0.00219 (    5)
  SS BOND              : angle       0.49475 (   10)
  covalent geometry    : bond        0.00356 ( 5612)
  covalent geometry    : angle       1.11080 ( 7630)
  Misc. bond           : bond        0.00011 (    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: 12
    poor density    : 65
  time to evaluate  : 1.097 
Fit side-chains
REVERT: A  112 MET cc_start: 0.5866 (tmm) cc_final: 0.5415 (ttm)
REVERT: A  318 ARG cc_start: 0.6501 (mtp85) cc_final: 0.6061 (mtt-85)
REVERT: A  341 HIS cc_start: 0.7773 (OUTLIER) cc_final: 0.7271 (p-80)
REVERT: A  388 LEU cc_start: 0.7811 (tt) cc_final: 0.7082 (pp)
REVERT: A  407 TYR cc_start: 0.8224 (t80) cc_final: 0.7626 (t80)
REVERT: A  434 TRP cc_start: 0.7984 (m-10) cc_final: 0.7586 (m-10)
REVERT: B  217 CYS cc_start: 0.7443 (m) cc_final: 0.7201 (m)
  outliers start: 12
  outliers final: 7
  residues processed: 74
  average time/residue: 0.2104
  time to fit residues: 19.9737
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  : 0.596 
-------------------------------------------------------------------------------
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 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 61 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 47 optimal weight:    0.5980
   chunk 26 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.153318 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.118508 restraints weight = 5976.633|
|-----------------------------------------------------------------------------|
r_work (start): 0.3326 rms_B_bonded: 2.14
r_work: 0.3199 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3054 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3054
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.1711

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5621  Z= 0.120
  Angle     :  1.088  34.715   7640  Z= 0.410
  Chirality :  0.119   2.237    853
  Planarity :  0.004   0.036    921
  Dihedral  : 21.027 176.556    893
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 13.45 %
    Favored  : 84.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.34), residues: 663
  helix:  2.00 (0.28), residues: 327
  sheet: -0.99 (0.45), residues: 134
  loop : -1.57 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  74 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.008   0.001   PHE A 248 
 TYR   0.018   0.002   TYR A  83 
 ARG   0.002   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02937 (  313)
  hydrogen bonds       : angle       4.38442 (  900)
  metal coordination   : bond        0.00089 (    3)
  SS BOND              : bond        0.00197 (    5)
  SS BOND              : angle       0.40250 (   10)
  covalent geometry    : bond        0.00269 ( 5612)
  covalent geometry    : angle       1.08858 ( 7630)
  Misc. bond           : bond        0.00008 (    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
  77 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 67
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
REVERT: A  112 MET cc_start: 0.6080 (tmm) cc_final: 0.5537 (ttm)
REVERT: A  186 SER cc_start: 0.8395 (t) cc_final: 0.7821 (p)
REVERT: A  341 HIS cc_start: 0.7774 (OUTLIER) cc_final: 0.7246 (p-80)
REVERT: A  388 LEU cc_start: 0.7768 (tt) cc_final: 0.7038 (pp)
REVERT: A  434 TRP cc_start: 0.7918 (m-10) cc_final: 0.7531 (m-10)
REVERT: B  217 CYS cc_start: 0.7469 (m) cc_final: 0.7256 (m)
  outliers start: 10
  outliers final: 7
  residues processed: 75
  average time/residue: 0.1906
  time to fit residues: 18.6630
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  : 0.591 
-------------------------------------------------------------------------------
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 L residue   78 VAL
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 27 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9990
   chunk 49 optimal weight:    7.9990
   chunk 40 optimal weight:    7.9990
   chunk 18 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    0.6980
   chunk 57 optimal weight:    5.9990
   chunk 28 optimal weight:    0.0470
   chunk 30 optimal weight:    6.9990
   overall best weight:    0.9282

-------------------------------------------------------------------------------
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 = 0.3862 r_free = 0.3862 target = 0.158626 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.126388 restraints weight = 6024.066|
|-----------------------------------------------------------------------------|
r_work (start): 0.3506 rms_B_bonded: 1.96
r_work: 0.3358 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.1742

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= 0.133
  Angle     :  1.090  34.841   7640  Z= 0.411
  Chirality :  0.119   2.207    853
  Planarity :  0.004   0.040    921
  Dihedral  : 21.054 177.034    893
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.98 %
    Favored  : 95.02 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 13.79 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.33), residues: 663
  helix:  2.05 (0.28), residues: 327
  sheet: -0.84 (0.45), residues: 134
  loop : -1.51 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  74 
 HIS   0.004   0.001   HIS A  94 
 PHE   0.009   0.001   PHE A 248 
 TYR   0.018   0.002   TYR A  83 
 ARG   0.002   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03034 (  313)
  hydrogen bonds       : angle       4.37336 (  900)
  metal coordination   : bond        0.00100 (    3)
  SS BOND              : bond        0.00187 (    5)
  SS BOND              : angle       0.40510 (   10)
  covalent geometry    : bond        0.00306 ( 5612)
  covalent geometry    : angle       1.09053 ( 7630)
  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
  70 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 59
  time to evaluate  : 0.889 
Fit side-chains
REVERT: A  341 HIS cc_start: 0.7935 (OUTLIER) cc_final: 0.7258 (p-80)
REVERT: A  434 TRP cc_start: 0.8250 (m-10) cc_final: 0.7917 (m-10)
REVERT: B  217 CYS cc_start: 0.7560 (m) cc_final: 0.7333 (m)
  outliers start: 11
  outliers final: 8
  residues processed: 67
  average time/residue: 0.3642
  time to fit residues: 34.7009
Evaluate side-chains
  68 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 59
  time to evaluate  : 0.536 
-------------------------------------------------------------------------------
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 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 51 optimal weight:    2.9990
   chunk 44 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   chunk 63 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 15 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 21 optimal weight:    0.7980
   chunk 22 optimal weight:    3.9990
   chunk 57 optimal weight:    0.8980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3870 r_free = 0.3870 target = 0.159505 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.127250 restraints weight = 6055.495|
|-----------------------------------------------------------------------------|
r_work (start): 0.3511 rms_B_bonded: 1.97
r_work: 0.3363 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3225 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.1821

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= 0.122
  Angle     :  1.101  34.667   7640  Z= 0.415
  Chirality :  0.118   2.190    853
  Planarity :  0.004   0.039    921
  Dihedral  : 21.026 177.145    893
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.14 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.33), residues: 663
  helix:  2.17 (0.28), residues: 327
  sheet: -0.68 (0.44), residues: 134
  loop : -1.46 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  74 
 HIS   0.004   0.001   HIS L 111 
 PHE   0.008   0.001   PHE A 248 
 TYR   0.018   0.001   TYR A  83 
 ARG   0.003   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02898 (  313)
  hydrogen bonds       : angle       4.28952 (  900)
  metal coordination   : bond        0.00087 (    3)
  SS BOND              : bond        0.00169 (    5)
  SS BOND              : angle       0.36422 (   10)
  covalent geometry    : bond        0.00275 ( 5612)
  covalent geometry    : angle       1.10138 ( 7630)
  Misc. bond           : bond        0.00007 (    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
  74 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 63
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.7867 (t80) cc_final: 0.7553 (t80)
REVERT: A  112 MET cc_start: 0.6256 (tmm) cc_final: 0.5914 (ttm)
REVERT: A  186 SER cc_start: 0.8634 (t) cc_final: 0.8069 (p)
REVERT: A  341 HIS cc_start: 0.7934 (OUTLIER) cc_final: 0.7293 (p-80)
REVERT: A  388 LEU cc_start: 0.7735 (tt) cc_final: 0.7018 (pp)
REVERT: B  217 CYS cc_start: 0.7508 (m) cc_final: 0.7275 (m)
  outliers start: 11
  outliers final: 8
  residues processed: 70
  average time/residue: 0.2038
  time to fit residues: 18.5685
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  : 0.618 
-------------------------------------------------------------------------------
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 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 16 optimal weight:    0.7980
   chunk 48 optimal weight:    0.0570
   chunk 23 optimal weight:    0.5980
   chunk 64 optimal weight:    0.9980
   chunk 22 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 40 optimal weight:    3.9990
   chunk 7 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 = 0.3883 r_free = 0.3883 target = 0.160634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.128232 restraints weight = 6098.027|
|-----------------------------------------------------------------------------|
r_work (start): 0.3524 rms_B_bonded: 1.99
r_work: 0.3375 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3235 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8354
moved from start:          0.1931

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   5621  Z= 0.112
  Angle     :  1.094  34.523   7640  Z= 0.411
  Chirality :  0.118   2.171    853
  Planarity :  0.004   0.041    921
  Dihedral  : 20.999 177.220    893
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  1.72 %
    Allowed  : 14.83 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.88 (0.33), residues: 663
  helix:  2.25 (0.28), residues: 327
  sheet: -0.56 (0.44), residues: 134
  loop : -1.42 (0.43), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  74 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.007   0.001   PHE A 248 
 TYR   0.018   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02823 (  313)
  hydrogen bonds       : angle       4.29460 (  900)
  metal coordination   : bond        0.00083 (    3)
  SS BOND              : bond        0.00168 (    5)
  SS BOND              : angle       0.33173 (   10)
  covalent geometry    : bond        0.00251 ( 5612)
  covalent geometry    : angle       1.09508 ( 7630)
  Misc. bond           : bond        0.00005 (    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
  75 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 65
  time to evaluate  : 0.604 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.7808 (t80) cc_final: 0.7479 (t80)
REVERT: A  112 MET cc_start: 0.6400 (tmm) cc_final: 0.5914 (ttm)
REVERT: A  186 SER cc_start: 0.8613 (t) cc_final: 0.8071 (p)
REVERT: A  341 HIS cc_start: 0.7901 (OUTLIER) cc_final: 0.7226 (p-80)
REVERT: A  388 LEU cc_start: 0.7687 (tt) cc_final: 0.6999 (pp)
REVERT: B  217 CYS cc_start: 0.7501 (m) cc_final: 0.7283 (m)
  outliers start: 10
  outliers final: 8
  residues processed: 72
  average time/residue: 0.1987
  time to fit residues: 18.5097
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  : 0.553 
-------------------------------------------------------------------------------
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 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 13 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9990
   chunk 0 optimal weight:    6.9990
   chunk 61 optimal weight:    7.9990
   chunk 10 optimal weight:    0.0040
   chunk 32 optimal weight:    1.9990
   chunk 6 optimal weight:    0.5980
   chunk 11 optimal weight:    2.9990
   chunk 37 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.6596

-------------------------------------------------------------------------------
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 = 0.3863 r_free = 0.3863 target = 0.159011 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3500 r_free = 0.3500 target = 0.127405 restraints weight = 6069.134|
|-----------------------------------------------------------------------------|
r_work (start): 0.3534 rms_B_bonded: 1.95
r_work: 0.3364 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.3218 rms_B_bonded: 4.62 restraints_weight: 0.2500
r_work (final): 0.3218
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1989

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   5621  Z= 0.114
  Angle     :  1.095  34.493   7640  Z= 0.411
  Chirality :  0.118   2.166    853
  Planarity :  0.004   0.039    921
  Dihedral  : 20.972 177.237    893
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 4.92
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.98 (0.33), residues: 663
  helix:  2.29 (0.28), residues: 327
  sheet: -0.47 (0.44), residues: 135
  loop : -1.32 (0.43), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  74 
 HIS   0.003   0.001   HIS L 111 
 PHE   0.008   0.001   PHE A 248 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02809 (  313)
  hydrogen bonds       : angle       4.29890 (  900)
  metal coordination   : bond        0.00082 (    3)
  SS BOND              : bond        0.00172 (    5)
  SS BOND              : angle       0.48572 (   10)
  covalent geometry    : bond        0.00255 ( 5612)
  covalent geometry    : angle       1.09544 ( 7630)
  Misc. bond           : bond        0.00005 (    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
  71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.538 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.7827 (t80) cc_final: 0.7492 (t80)
REVERT: A  112 MET cc_start: 0.6529 (tmm) cc_final: 0.5856 (ttp)
REVERT: A  186 SER cc_start: 0.8654 (t) cc_final: 0.8113 (p)
REVERT: A  341 HIS cc_start: 0.7873 (OUTLIER) cc_final: 0.7203 (p-80)
REVERT: A  388 LEU cc_start: 0.7733 (tt) cc_final: 0.7021 (pp)
REVERT: B  217 CYS cc_start: 0.7460 (m) cc_final: 0.7233 (m)
  outliers start: 9
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1899
  time to fit residues: 16.8847
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  : 0.577 
-------------------------------------------------------------------------------
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 H residue   39 MET
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 49 optimal weight:    0.9980
   chunk 19 optimal weight:    0.2980
   chunk 57 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 18 optimal weight:    2.9990
   chunk 42 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 13 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 48 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3731 r_free = 0.3731 target = 0.152411 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.117549 restraints weight = 6100.658|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 2.24
r_work: 0.3198 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3055 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3055
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.2012

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= 0.115
  Angle     :  1.093  34.473   7640  Z= 0.410
  Chirality :  0.118   2.164    853
  Planarity :  0.004   0.040    921
  Dihedral  : 20.909 177.227    893
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 4.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.68 %
    Favored  : 95.32 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.33), residues: 663
  helix:  2.31 (0.28), residues: 327
  sheet: -0.36 (0.44), residues: 134
  loop : -1.30 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A  74 
 HIS   0.003   0.001   HIS L 111 
 PHE   0.008   0.001   PHE A 248 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02828 (  313)
  hydrogen bonds       : angle       4.30198 (  900)
  metal coordination   : bond        0.00095 (    3)
  SS BOND              : bond        0.00169 (    5)
  SS BOND              : angle       0.46648 (   10)
  covalent geometry    : bond        0.00260 ( 5612)
  covalent geometry    : angle       1.09342 ( 7630)
  Misc. bond           : bond        0.00007 (    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
  71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 62
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
REVERT: A   62 PHE cc_start: 0.7782 (t80) cc_final: 0.7446 (t80)
REVERT: A  112 MET cc_start: 0.6453 (tmm) cc_final: 0.5700 (ttp)
REVERT: A  186 SER cc_start: 0.8539 (t) cc_final: 0.7979 (p)
REVERT: A  341 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7180 (p-80)
REVERT: A  388 LEU cc_start: 0.7742 (tt) cc_final: 0.7068 (pp)
REVERT: L  125 GLU cc_start: 0.7109 (tt0) cc_final: 0.6594 (tm-30)
REVERT: B  217 CYS cc_start: 0.7399 (m) cc_final: 0.7180 (m)
  outliers start: 9
  outliers final: 7
  residues processed: 68
  average time/residue: 0.1900
  time to fit residues: 16.9592
Evaluate side-chains
  70 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 62
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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 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 54 optimal weight:    0.0980
   chunk 2 optimal weight:    0.9990
   chunk 31 optimal weight:    6.9990
   chunk 42 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 64 optimal weight:    6.9990
   chunk 16 optimal weight:    0.3980
   chunk 24 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.5980

-------------------------------------------------------------------------------
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 = 0.3741 r_free = 0.3741 target = 0.153375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.118527 restraints weight = 6150.781|
|-----------------------------------------------------------------------------|
r_work (start): 0.3347 rms_B_bonded: 2.25
r_work: 0.3212 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.3068 rms_B_bonded: 4.68 restraints_weight: 0.2500
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   5621  Z= 0.109
  Angle     :  1.091  34.391   7640  Z= 0.409
  Chirality :  0.118   2.155    853
  Planarity :  0.004   0.038    921
  Dihedral  : 20.832 177.181    893
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 4.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.37 %
    Favored  : 95.63 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.86 %
    Favored  : 82.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.34), residues: 663
  helix:  2.40 (0.28), residues: 327
  sheet: -0.23 (0.45), residues: 134
  loop : -1.25 (0.44), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A  74 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.007   0.001   PHE A  67 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 385 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02762 (  313)
  hydrogen bonds       : angle       4.28743 (  900)
  metal coordination   : bond        0.00072 (    3)
  SS BOND              : bond        0.00151 (    5)
  SS BOND              : angle       0.44677 (   10)
  covalent geometry    : bond        0.00240 ( 5612)
  covalent geometry    : angle       1.09197 ( 7630)
  Misc. bond           : bond        0.00006 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3202.30 seconds
wall clock time: 56 minutes 52.31 seconds (3412.31 seconds total)