Starting phenix.real_space_refine
on Tue Mar 11 15:03:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7urd_26709/03_2025/7urd_26709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7urd_26709/03_2025/7urd_26709.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7urd_26709/03_2025/7urd_26709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7urd_26709/03_2025/7urd_26709.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7urd_26709/03_2025/7urd_26709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7urd_26709/03_2025/7urd_26709.cif"
  }
  resolution = 2.92
  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=   0.007 sd=   0.087
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    3642      2.51       5
     N     897      2.21       5
     O     959      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 5534
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 3449
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 432, 3449
          Classifications: {'peptide': 432}
          Incomplete info: {'truncation_to_alanine': 4}
          Link IDs: {'PTRANS': 14, 'TRANS': 417}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 17
          Unresolved non-hydrogen angles: 21
          Unresolved non-hydrogen dihedrals: 15
          Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 12
    Chain: "B"
      Number of atoms: 158
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 20, 158
          Classifications: {'peptide': 20}
          Link IDs: {'TRANS': 19}
    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: "A"
      Number of atoms: 172
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 172
          Unusual residues: {' ZN': 1, 'AJP': 1, 'CLR': 2, 'O50': 1, 'OLA': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 22
          Unresolved non-hydrogen angles: 33
          Unresolved non-hydrogen dihedrals: 47
          Unresolved non-hydrogen chiralities: 9

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2833  SG  CYS A 370      56.521  29.274  19.732  1.00108.35           S
  ATOM   2880  SG  CYS A 376      55.636  28.723  23.034  1.00118.02           S
  ATOM   2908  SG  CYS A 380      59.361  29.098  21.112  1.00127.74           S

  Time building chain proxies: 4.07, per 1000 atoms: 0.74
  Number of scatterers: 5534
  At special positions: 0
  Unit cell: (98.77, 69.72, 93.79, 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     959      8.00
     N     897      7.00
     C    3642      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 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
    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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.78
  Conformation dependent library (CDL) restraints added in 790.1 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 506 "
        pdb="ZN    ZN A 506 " - pdb=" SG  CYS A 370 "
        pdb="ZN    ZN A 506 " - pdb=" ND1 HIS A 382 "
        pdb="ZN    ZN A 506 " - pdb=" SG  CYS A 376 "
        pdb="ZN    ZN A 506 " - pdb=" SG  CYS A 380 "
      Number of angles added : 3


  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 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:
      24 helices and 7 sheets defined
      51.5% alpha, 17.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.56
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 28
      removed outlier: 4.921A  pdb=" N   LEU A  14 " --> pdb=" O   PHE A  10 " (cutoff:3.500A)
      removed outlier: 5.901A  pdb=" N   GLN A  15 " --> pdb=" O   GLN A  11 " (cutoff:3.500A)
      removed outlier: 5.323A  pdb=" N   LEU A  19 " --> pdb=" O   GLN A  15 " (cutoff:3.500A)
      Proline residue:  A  20  - end of helix
    Processing helix  chain 'A' and resid 29 through 43
    Processing helix  chain 'A' and resid 48 through 68
    Processing helix  chain 'A' and resid 72 through 89
      removed outlier: 3.952A  pdb=" N   LEU A  78 " --> pdb=" O   TRP A  74 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   CYS A  89 " --> pdb=" O   VAL A  85 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 94 through 111
    Processing helix  chain 'A' and resid 116 through 123
      removed outlier: 3.686A  pdb=" N   HIS A 121 " --> pdb=" O   THR A 117 " (cutoff:3.500A)
      removed outlier: 3.818A  pdb=" N   MET A 123 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 123 through 143
      removed outlier: 3.570A  pdb=" N   ILE A 129 " --> pdb=" O   GLY A 125 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ASP A 142 " --> pdb=" O   GLY A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 160
    Processing helix  chain 'A' and resid 172 through 181
      removed outlier: 3.842A  pdb=" N   ALA A 179 " --> pdb=" O   SER A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 186 through 209
      removed outlier: 3.870A  pdb=" N   LEU A 190 " --> pdb=" O   SER A 186 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 235 through 264
      removed outlier: 3.654A  pdb=" N   VAL A 253 " --> pdb=" O   SER A 249 " (cutoff:3.500A)
      removed outlier: 3.742A  pdb=" N   ALA A 264 " --> pdb=" O   THR A 260 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 289
    Processing helix  chain 'A' and resid 292 through 301
      removed outlier: 4.359A  pdb=" N   ASN A 301 " --> pdb=" O   VAL A 297 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 312
    Processing helix  chain 'A' and resid 312 through 317
    Processing helix  chain 'A' and resid 320 through 336
    Processing helix  chain 'A' and resid 339 through 367
      removed outlier: 3.610A  pdb=" N   ALA A 350 " --> pdb=" O   LEU A 346 " (cutoff:3.500A)
      removed outlier: 3.694A  pdb=" N   PHE A 351 " --> pdb=" O   LEU A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 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 436
    Processing helix  chain 'A' and resid 439 through 455
      removed outlier: 3.713A  pdb=" N   PHE A 446 " --> pdb=" O   HIS A 442 " (cutoff:3.500A)
    Processing helix  chain 'L' and resid 99 through 103
      removed outlier: 3.891A  pdb=" N   PHE L 103 " --> pdb=" O   PRO L 100 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 47 through 51
      removed outlier: 4.201A  pdb=" N   TYR H  51 " --> pdb=" O   PHE H  48 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 106 through 110
      removed outlier: 3.740A  pdb=" N   SER H 110 " --> pdb=" O   SER H 107 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 269 through 270
    Processing sheet with id=AA2, first strand: chain 'B' and resid 202 through 206
    Processing sheet with id=AA3, first strand: chain 'L' and resid 24 through 27
      removed outlier: 5.677A  pdb=" N   THR L  89 " --> pdb=" O   THR L  45 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 30 through 33
      removed outlier: 6.863A  pdb=" N   LEU L  31 " --> pdb=" O   GLU L 125 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   TRP L  55 " --> pdb=" O   LEU L  67 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25
    Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 31
      removed outlier: 6.573A  pdb=" N   GLU H  29 " --> pdb=" O   THR H 135 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   GLY H  68 " --> pdb=" O   TRP H  55 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   LYS H  57 " --> pdb=" O   TRP H  66 " (cutoff:3.500A)
      removed outlier: 5.496A  pdb=" N   TRP H  66 " --> pdb=" O   LYS H  57 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 31
      removed outlier: 6.573A  pdb=" N   GLU H  29 " --> pdb=" O   THR H 135 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   TYR H 127 " --> pdb=" O   ARG H 117 " (cutoff:3.500A)

    300 hydrogen bonds defined for protein.
    849 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: 1.61

  Time building geometry restraints manager: 1.75 seconds

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

  Histogram of bond lengths:
        1.00 -     1.19: 4
        1.19 -     1.39: 2353
        1.39 -     1.59: 3288
        1.59 -     1.78: 10
        1.78 -     1.98: 50
  Bond restraints: 5705
  Sorted by residual:
  bond pdb=" C07 AJP A 504 "
       pdb=" C08 AJP A 504 "
    ideal  model  delta    sigma   weight residual
    1.550  1.980 -0.430 2.00e-02 2.50e+03 4.62e+02
  bond pdb=" C01 AJP A 504 "
       pdb=" C02 AJP A 504 "
    ideal  model  delta    sigma   weight residual
    1.521  1.947 -0.426 2.00e-02 2.50e+03 4.55e+02
  bond pdb=" C08 AJP A 504 "
       pdb=" O09 AJP A 504 "
    ideal  model  delta    sigma   weight residual
    1.410  0.998  0.412 2.00e-02 2.50e+03 4.24e+02
  bond pdb=" C02 AJP A 504 "
       pdb=" C03 AJP A 504 "
    ideal  model  delta    sigma   weight residual
    1.525  1.133  0.392 2.00e-02 2.50e+03 3.85e+02
  bond pdb=" C05 AJP A 504 "
       pdb=" O09 AJP A 504 "
    ideal  model  delta    sigma   weight residual
    1.407  1.784 -0.377 2.00e-02 2.50e+03 3.55e+02
  ... (remaining 5700 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.20: 7706
        4.20 -     8.40: 54
        8.40 -    12.60: 7
       12.60 -    16.80: 4
       16.80 -    20.99: 1
  Bond angle restraints: 7772
  Sorted by residual:
  angle pdb=" C06 AJP A 504 "
        pdb=" C07 AJP A 504 "
        pdb=" C12 AJP A 504 "
      ideal   model   delta    sigma   weight residual
     120.30  141.29  -20.99 3.00e+00 1.11e-01 4.90e+01
  angle pdb=" C11 AJP A 504 "
        pdb=" C12 AJP A 504 "
        pdb=" C81 AJP A 504 "
      ideal   model   delta    sigma   weight residual
     114.35   98.09   16.26 3.00e+00 1.11e-01 2.94e+01
  angle pdb=" C07 AJP A 504 "
        pdb=" C12 AJP A 504 "
        pdb=" C13 AJP A 504 "
      ideal   model   delta    sigma   weight residual
     114.18  129.16  -14.98 3.00e+00 1.11e-01 2.49e+01
  angle pdb=" C07 AJP A 504 "
        pdb=" C08 AJP A 504 "
        pdb=" C10 AJP A 504 "
      ideal   model   delta    sigma   weight residual
     107.39   93.44   13.95 3.00e+00 1.11e-01 2.16e+01
  angle pdb=" C   PRO A 377 "
        pdb=" N   PRO A 378 "
        pdb=" CA  PRO A 378 "
      ideal   model   delta    sigma   weight residual
     119.47  124.77   -5.30 1.16e+00 7.43e-01 2.09e+01
  ... (remaining 7767 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.55: 3322
       34.55 -    69.10: 79
       69.10 -   103.65: 34
      103.65 -   138.20: 37
      138.20 -   172.75: 14
  Dihedral angle restraints: 3486
    sinusoidal: 1524
      harmonic: 1962
  Sorted by residual:
  dihedral pdb=" CA  TYR H  74 "
           pdb=" C   TYR H  74 "
           pdb=" N   VAL H  75 "
           pdb=" CA  VAL H  75 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.22  -27.78     0      5.00e+00 4.00e-02 3.09e+01
  dihedral pdb=" C06 AJP A 504 "
           pdb=" C07 AJP A 504 "
           pdb=" C12 AJP A 504 "
           pdb=" C13 AJP A 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     109.15  -63.60  172.75     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C12 AJP A 504 "
           pdb=" C10 AJP A 504 "
           pdb=" C11 AJP A 504 "
           pdb=" O82 AJP A 504 "
      ideal   model   delta sinusoidal    sigma   weight residual
     287.38  117.68  169.70     1      3.00e+01 1.11e-03 2.12e+01
  ... (remaining 3483 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.107: 849
       1.107 -    2.213: 0
       2.213 -    3.320: 0
       3.320 -    4.426: 1
       4.426 -    5.533: 24
  Chirality restraints: 874
  Sorted by residual:
  chirality pdb=" C15 AJP A 504 "
            pdb=" C14 AJP A 504 "
            pdb=" C16 AJP A 504 "
            pdb=" C20 AJP A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.42    3.11   -5.53 2.00e-01 2.50e+01 7.65e+02
  chirality pdb=" C16 AJP A 504 "
            pdb=" C11 AJP A 504 "
            pdb=" C15 AJP A 504 "
            pdb=" C17 AJP A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.70    2.76   -5.46 2.00e-01 2.50e+01 7.45e+02
  chirality pdb=" C20 AJP A 504 "
            pdb=" C15 AJP A 504 "
            pdb=" C19 AJP A 504 "
            pdb=" C21 AJP A 504 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.96   -2.42    5.38 2.00e-01 2.50e+01 7.23e+02
  ... (remaining 871 not shown)

  Planarity restraints: 924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 215 "   -0.029 5.00e-02 4.00e+02   4.31e-02 2.97e+00
        pdb=" N   PRO A 216 "    0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A 216 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 216 "   -0.025 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE A 219 "    0.026 5.00e-02 4.00e+02   3.92e-02 2.46e+00
        pdb=" N   PRO A 220 "   -0.068 5.00e-02 4.00e+02
        pdb=" CA  PRO A 220 "    0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO A 220 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  14 "   -0.007 2.00e-02 2.50e+03   1.48e-02 2.20e+00
        pdb=" C   LEU A  14 "    0.026 2.00e-02 2.50e+03
        pdb=" O   LEU A  14 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   GLN A  15 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 921 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 267
        2.72 -     3.27: 5456
        3.27 -     3.81: 9026
        3.81 -     4.36: 11401
        4.36 -     4.90: 19866
  Nonbonded interactions: 46016
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 242 "
            pdb=" OD1 ASP A 413 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" NH1 ARG A 360 "
            pdb=" O   VAL A 371 "
     model   vdw
     2.196 3.120
  nonbonded pdb=" OG  SER H  26 "
            pdb=" OG  SER H  40 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG  SER L  27 "
            pdb=" OG1 THR L  42 "
     model   vdw
     2.266 3.040
  nonbonded pdb=" OG  SER A  79 "
            pdb=" OH  TYR A 160 "
     model   vdw
     2.280 3.040
  ... (remaining 46011 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:             0.930
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.630
  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:13.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8184
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      :  0.017   0.430   5705  Z= 1.120
  Angle     :  0.954  20.994   7772  Z= 0.412
  Chirality :  0.833   5.533    874
  Planarity :  0.004   0.043    924
  Dihedral  : 26.242 172.752   2217
  Min Nonbonded Distance : 2.177

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  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: -2.44 (0.28), residues: 666
  helix: -0.91 (0.25), residues: 324
  sheet: -1.58 (0.42), residues: 129
  loop : -2.50 (0.37), residues: 213

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP H  66 
 HIS   0.006   0.001   HIS A  94 
 PHE   0.018   0.001   PHE A 403 
 TYR   0.013   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  235 ARG cc_start: 0.7350 (mmt180) cc_final: 0.6938 (mtm180)
REVERT: A  361 LYS cc_start: 0.7957 (tttt) cc_final: 0.7605 (ttpt)
REVERT: A  432 HIS cc_start: 0.8143 (t-90) cc_final: 0.7735 (t70)
REVERT: L   23 HIS cc_start: 0.8141 (m-70) cc_final: 0.7933 (m-70)
REVERT: H  101 GLN cc_start: 0.8481 (tt0) cc_final: 0.8253 (tt0)
REVERT: H  119 TYR cc_start: 0.6625 (t80) cc_final: 0.6393 (t80)
  outliers start: 0
  outliers final: 0
  residues processed: 101
  average time/residue: 1.1695
  time to fit residues: 123.5445
Evaluate side-chains
  73 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.548 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 17 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 26 optimal weight:    0.6980
   chunk 51 optimal weight:    3.9990
   chunk 20 optimal weight:    0.4980
   chunk 31 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
A  12 GLN
A  24 GLN
A  66 HIS
A  91 HIS
A  94 HIS
A 174 HIS
A 247 HIS
L 111 HIS
H  52 ASN
H  78 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.128218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.092067 restraints weight = 6250.320|
|-----------------------------------------------------------------------------|
r_work (start): 0.2975 rms_B_bonded: 2.27
r_work: 0.2839 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2699 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2699
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8154
moved from start:          0.1255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5705  Z= 0.181
  Angle     :  1.095  32.247   7772  Z= 0.414
  Chirality :  0.118   2.107    874
  Planarity :  0.004   0.040    924
  Dihedral  : 20.285 179.650   1059
  Min Nonbonded Distance : 2.592

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  :  9.71 %
    Favored  : 88.56 %
  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: -0.65 (0.32), residues: 666
  helix:  0.62 (0.27), residues: 329
  sheet: -1.03 (0.43), residues: 129
  loop : -1.58 (0.43), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H  66 
 HIS   0.005   0.001   HIS A  53 
 PHE   0.015   0.001   PHE A 403 
 TYR   0.018   0.001   TYR A  83 
 ARG   0.005   0.000   ARG A 362 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 89
  time to evaluate  : 0.533 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.7100 (mmt) cc_final: 0.6385 (mtm)
REVERT: A  124 ARG cc_start: 0.7514 (OUTLIER) cc_final: 0.7168 (mtm-85)
REVERT: A  142 ASP cc_start: 0.8504 (m-30) cc_final: 0.8192 (m-30)
REVERT: A  154 GLU cc_start: 0.8008 (OUTLIER) cc_final: 0.7671 (mt-10)
REVERT: A  235 ARG cc_start: 0.7453 (mmt180) cc_final: 0.6646 (mtm180)
REVERT: A  270 GLU cc_start: 0.8300 (pt0) cc_final: 0.8009 (pt0)
REVERT: A  361 LYS cc_start: 0.7651 (tttt) cc_final: 0.7370 (ttpt)
REVERT: A  375 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7802 (mtt-85)
REVERT: A  432 HIS cc_start: 0.7886 (t-90) cc_final: 0.7437 (t70)
REVERT: L   23 HIS cc_start: 0.8295 (m-70) cc_final: 0.7998 (m-70)
REVERT: H  101 GLN cc_start: 0.8228 (tt0) cc_final: 0.7963 (tt0)
REVERT: H  119 TYR cc_start: 0.6781 (t80) cc_final: 0.6422 (t80)
  outliers start: 10
  outliers final: 2
  residues processed: 94
  average time/residue: 1.1745
  time to fit residues: 115.4166
Evaluate side-chains
  88 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  285 LEU
Chi-restraints excluded: chain A residue  375 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 51 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 54 optimal weight:    0.9980
   chunk 25 optimal weight:    2.9990
   chunk 35 optimal weight:    0.0970
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.3418 r_free = 0.3418 target = 0.127539 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.091478 restraints weight = 6269.608|
|-----------------------------------------------------------------------------|
r_work (start): 0.2965 rms_B_bonded: 2.26
r_work: 0.2827 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2688 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2688
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5705  Z= 0.192
  Angle     :  1.076  31.573   7772  Z= 0.405
  Chirality :  0.118   2.112    874
  Planarity :  0.004   0.040    924
  Dihedral  : 20.153 179.594   1059
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 13.69 %
    Favored  : 84.40 %
  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:  0.17 (0.33), residues: 666
  helix:  1.32 (0.28), residues: 329
  sheet: -0.76 (0.43), residues: 129
  loop : -1.17 (0.45), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  66 
 HIS   0.004   0.001   HIS A  53 
 PHE   0.014   0.001   PHE A 403 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7747 (ptt)
REVERT: A  109 MET cc_start: 0.7028 (mmt) cc_final: 0.6266 (mtm)
REVERT: A  112 MET cc_start: 0.7893 (mtp) cc_final: 0.7681 (mtp)
REVERT: A  124 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.7227 (mtm-85)
REVERT: A  142 ASP cc_start: 0.8493 (m-30) cc_final: 0.8285 (m-30)
REVERT: A  154 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7686 (mt-10)
REVERT: A  235 ARG cc_start: 0.7438 (mmt180) cc_final: 0.6662 (mtm180)
REVERT: A  270 GLU cc_start: 0.8172 (pt0) cc_final: 0.7963 (pt0)
REVERT: A  375 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7805 (mtt-85)
REVERT: A  432 HIS cc_start: 0.7841 (t-90) cc_final: 0.7501 (t-170)
REVERT: L   81 ARG cc_start: 0.7872 (ptp90) cc_final: 0.7645 (ptp-170)
REVERT: H  101 GLN cc_start: 0.8217 (tt0) cc_final: 0.7961 (tt0)
REVERT: H  119 TYR cc_start: 0.6759 (t80) cc_final: 0.6402 (t80)
  outliers start: 11
  outliers final: 1
  residues processed: 89
  average time/residue: 1.3059
  time to fit residues: 121.5433
Evaluate side-chains
  85 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.665 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  375 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 61 optimal weight:    1.9990
   chunk 64 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 57 optimal weight:    2.9990
   chunk 20 optimal weight:    0.4980
   chunk 40 optimal weight:    0.6980
   chunk 8 optimal weight:    0.9990
   chunk 54 optimal weight:    0.5980
   chunk 26 optimal weight:    0.3980
   chunk 4 optimal weight:    0.9990
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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 = 0.3486 r_free = 0.3486 target = 0.131173 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3045 r_free = 0.3045 target = 0.094432 restraints weight = 6250.201|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 2.34
r_work: 0.2896 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2758 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
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      :  0.002   0.023   5705  Z= 0.154
  Angle     :  1.064  31.583   7772  Z= 0.397
  Chirality :  0.118   2.116    874
  Planarity :  0.004   0.039    924
  Dihedral  : 20.061 179.972   1059
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 14.73 %
    Favored  : 82.67 %
  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:  0.67 (0.34), residues: 666
  helix:  1.69 (0.29), residues: 331
  sheet: -0.56 (0.44), residues: 127
  loop : -0.87 (0.46), residues: 208

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  74 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.012   0.001   PHE A 403 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8191 (OUTLIER) cc_final: 0.7654 (ptt)
REVERT: A  109 MET cc_start: 0.6964 (mmt) cc_final: 0.6246 (mtm)
REVERT: A  112 MET cc_start: 0.7797 (mtp) cc_final: 0.7422 (mtt)
REVERT: A  124 ARG cc_start: 0.7544 (OUTLIER) cc_final: 0.7080 (mtt-85)
REVERT: A  154 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7649 (mt-10)
REVERT: A  235 ARG cc_start: 0.7306 (mmt180) cc_final: 0.6577 (mtm180)
REVERT: A  375 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7839 (mtt-85)
REVERT: A  432 HIS cc_start: 0.7833 (t-90) cc_final: 0.7476 (t-170)
REVERT: L   89 THR cc_start: 0.8842 (p) cc_final: 0.8192 (m)
REVERT: H  101 GLN cc_start: 0.8159 (tt0) cc_final: 0.7853 (tt0)
REVERT: H  119 TYR cc_start: 0.6720 (t80) cc_final: 0.6373 (t80)
  outliers start: 15
  outliers final: 3
  residues processed: 94
  average time/residue: 1.1713
  time to fit residues: 115.2229
Evaluate side-chains
  83 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 76
  time to evaluate  : 0.540 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  375 ARG
Chi-restraints excluded: chain A residue  388 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 35 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 40 optimal weight:    0.8980
   chunk 49 optimal weight:    0.2980
   chunk 19 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9984

-------------------------------------------------------------------------------
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 = 0.3456 r_free = 0.3456 target = 0.128749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.092027 restraints weight = 6269.600|
|-----------------------------------------------------------------------------|
r_work (start): 0.2994 rms_B_bonded: 2.34
r_work: 0.2856 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2718 rms_B_bonded: 4.50 restraints_weight: 0.2500
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8137
moved from start:          0.1861

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5705  Z= 0.229
  Angle     :  1.079  31.359   7772  Z= 0.407
  Chirality :  0.118   2.109    874
  Planarity :  0.004   0.039    924
  Dihedral  : 20.097 179.564   1059
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.64 %
    Favored  : 81.98 %
  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:  0.80 (0.34), residues: 666
  helix:  1.74 (0.29), residues: 330
  sheet: -0.26 (0.45), residues: 127
  loop : -0.84 (0.46), residues: 209

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H  66 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.016   0.001   PHE A 403 
 TYR   0.018   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 183 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.6980 (mmt) cc_final: 0.6237 (mtm)
REVERT: A  112 MET cc_start: 0.7783 (mtp) cc_final: 0.7570 (mtp)
REVERT: A  124 ARG cc_start: 0.7522 (OUTLIER) cc_final: 0.7214 (mtm-85)
REVERT: A  142 ASP cc_start: 0.8213 (m-30) cc_final: 0.8008 (m-30)
REVERT: A  154 GLU cc_start: 0.8065 (OUTLIER) cc_final: 0.7725 (mt-10)
REVERT: A  235 ARG cc_start: 0.7336 (mmt180) cc_final: 0.6605 (mtm180)
REVERT: A  432 HIS cc_start: 0.7817 (t-90) cc_final: 0.7349 (t70)
REVERT: L   89 THR cc_start: 0.8840 (p) cc_final: 0.8151 (m)
REVERT: H   29 GLU cc_start: 0.6852 (mt-10) cc_final: 0.5828 (mm-30)
REVERT: H  101 GLN cc_start: 0.8108 (tt0) cc_final: 0.7827 (tt0)
REVERT: H  119 TYR cc_start: 0.6819 (t80) cc_final: 0.6431 (t80)
  outliers start: 8
  outliers final: 4
  residues processed: 86
  average time/residue: 1.1928
  time to fit residues: 107.3842
Evaluate side-chains
  90 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 84
  time to evaluate  : 0.613 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  111 GLU
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  388 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 59 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   chunk 65 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 39 optimal weight:    0.7980
   chunk 45 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 27 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.130537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.094301 restraints weight = 6153.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.3031 rms_B_bonded: 2.30
r_work: 0.2895 rms_B_bonded: 2.83 restraints_weight: 0.5000
r_work: 0.2759 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2759
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8090
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5705  Z= 0.166
  Angle     :  1.066  31.316   7772  Z= 0.397
  Chirality :  0.118   2.108    874
  Planarity :  0.004   0.039    924
  Dihedral  : 20.017 179.653   1059
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 16.98 %
    Favored  : 80.76 %
  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:  0.96 (0.34), residues: 666
  helix:  1.93 (0.29), residues: 331
  sheet: -0.29 (0.45), residues: 128
  loop : -0.84 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A  74 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.012   0.001   PHE A 403 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.557 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8192 (OUTLIER) cc_final: 0.7662 (ptt)
REVERT: A  109 MET cc_start: 0.6979 (mmt) cc_final: 0.6225 (mtm)
REVERT: A  112 MET cc_start: 0.7745 (mtp) cc_final: 0.7341 (mtt)
REVERT: A  122 LYS cc_start: 0.8157 (tttm) cc_final: 0.7924 (tttp)
REVERT: A  124 ARG cc_start: 0.7467 (OUTLIER) cc_final: 0.7162 (mtm-85)
REVERT: A  142 ASP cc_start: 0.8124 (m-30) cc_final: 0.7876 (m-30)
REVERT: A  154 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7673 (mt-10)
REVERT: A  235 ARG cc_start: 0.7302 (mmt180) cc_final: 0.6603 (mtm180)
REVERT: A  338 PHE cc_start: 0.7358 (t80) cc_final: 0.6308 (m-80)
REVERT: A  432 HIS cc_start: 0.7773 (t-90) cc_final: 0.7357 (t70)
REVERT: L   89 THR cc_start: 0.8795 (p) cc_final: 0.8194 (m)
REVERT: H   30 LEU cc_start: 0.8559 (OUTLIER) cc_final: 0.8182 (tm)
REVERT: H  101 GLN cc_start: 0.8050 (tt0) cc_final: 0.7751 (tt0)
REVERT: H  119 TYR cc_start: 0.6847 (t80) cc_final: 0.6390 (t80)
  outliers start: 13
  outliers final: 3
  residues processed: 89
  average time/residue: 1.2340
  time to fit residues: 114.8161
Evaluate side-chains
  86 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 79
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain H residue   30 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 57 optimal weight:    0.6980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.5980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0970
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    0.8980
   chunk 25 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   overall best weight:    0.5978

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.131003 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.094562 restraints weight = 6210.655|
|-----------------------------------------------------------------------------|
r_work (start): 0.3049 rms_B_bonded: 2.34
r_work: 0.2914 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.2150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5705  Z= 0.162
  Angle     :  1.064  31.388   7772  Z= 0.396
  Chirality :  0.118   2.107    874
  Planarity :  0.004   0.040    924
  Dihedral  : 19.990 179.564   1059
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.33 %
    Favored  : 80.59 %
  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:  1.08 (0.34), residues: 666
  helix:  2.01 (0.29), residues: 331
  sheet: -0.16 (0.46), residues: 128
  loop : -0.78 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 128 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.012   0.001   PHE A 403 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.541 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.7528 (OUTLIER) cc_final: 0.7271 (tm-30)
REVERT: A   72 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7629 (ptt)
REVERT: A  109 MET cc_start: 0.6936 (mmt) cc_final: 0.6156 (mtm)
REVERT: A  124 ARG cc_start: 0.7427 (OUTLIER) cc_final: 0.7115 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7692 (mt-10)
REVERT: A  235 ARG cc_start: 0.7322 (mmt180) cc_final: 0.6597 (mtm180)
REVERT: A  432 HIS cc_start: 0.7807 (t-90) cc_final: 0.7292 (t-170)
REVERT: L   85 SER cc_start: 0.8267 (t) cc_final: 0.8024 (p)
REVERT: L   89 THR cc_start: 0.8788 (p) cc_final: 0.8229 (m)
REVERT: H   74 TYR cc_start: 0.7827 (OUTLIER) cc_final: 0.6996 (p90)
REVERT: H  101 GLN cc_start: 0.8063 (tt0) cc_final: 0.7857 (tt0)
REVERT: H  119 TYR cc_start: 0.6852 (t80) cc_final: 0.6388 (t80)
  outliers start: 12
  outliers final: 4
  residues processed: 86
  average time/residue: 1.2322
  time to fit residues: 110.8710
Evaluate side-chains
  87 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain H residue   74 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 9 optimal weight:    1.9990
   chunk 44 optimal weight:    0.7980
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    2.9990
   chunk 52 optimal weight:    3.9990
   chunk 18 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 42 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.129778 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.093350 restraints weight = 6148.373|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.33
r_work: 0.2878 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2106

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5705  Z= 0.189
  Angle     :  1.070  31.476   7772  Z= 0.401
  Chirality :  0.118   2.104    874
  Planarity :  0.004   0.039    924
  Dihedral  : 20.003 179.768   1059
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 17.85 %
    Favored  : 80.07 %
  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:  1.10 (0.34), residues: 666
  helix:  1.97 (0.29), residues: 331
  sheet: -0.05 (0.46), residues: 129
  loop : -0.76 (0.45), residues: 206

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 128 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.013   0.001   PHE A 403 
 TYR   0.018   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 183 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.543 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   27 ASP cc_start: 0.7813 (OUTLIER) cc_final: 0.7582 (m-30)
REVERT: A   72 MET cc_start: 0.8187 (OUTLIER) cc_final: 0.7633 (ptt)
REVERT: A  109 MET cc_start: 0.6980 (mmt) cc_final: 0.6238 (mtp)
REVERT: A  112 MET cc_start: 0.7891 (mtp) cc_final: 0.7513 (mtt)
REVERT: A  124 ARG cc_start: 0.7383 (OUTLIER) cc_final: 0.7076 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7725 (mt-10)
REVERT: A  235 ARG cc_start: 0.7334 (mmt180) cc_final: 0.6583 (mtm180)
REVERT: A  258 GLU cc_start: 0.7836 (tt0) cc_final: 0.7464 (tt0)
REVERT: A  432 HIS cc_start: 0.7808 (t-90) cc_final: 0.7491 (t-90)
REVERT: L   23 HIS cc_start: 0.8221 (m-70) cc_final: 0.7884 (m-70)
REVERT: L   85 SER cc_start: 0.8269 (t) cc_final: 0.8024 (p)
REVERT: L   89 THR cc_start: 0.8813 (p) cc_final: 0.8271 (m)
REVERT: H   30 LEU cc_start: 0.8377 (OUTLIER) cc_final: 0.7891 (tm)
REVERT: H   74 TYR cc_start: 0.7883 (OUTLIER) cc_final: 0.6929 (p90)
REVERT: H  101 GLN cc_start: 0.8099 (tt0) cc_final: 0.7893 (tt0)
REVERT: H  119 TYR cc_start: 0.6897 (t80) cc_final: 0.6582 (t80)
  outliers start: 12
  outliers final: 4
  residues processed: 85
  average time/residue: 1.2324
  time to fit residues: 109.4496
Evaluate side-chains
  90 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 ASP
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain A residue  388 LEU
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain H residue   30 LEU
Chi-restraints excluded: chain H residue   74 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 32 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 31 optimal weight:    0.5980
   chunk 54 optimal weight:    0.0570
   chunk 13 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   chunk 60 optimal weight:    0.0020
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   overall best weight:    0.3706

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.132672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.096269 restraints weight = 6195.342|
|-----------------------------------------------------------------------------|
r_work (start): 0.3055 rms_B_bonded: 2.34
r_work: 0.2918 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2776 rms_B_bonded: 4.59 restraints_weight: 0.2500
r_work (final): 0.2776
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8050
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5705  Z= 0.128
  Angle     :  1.058  31.295   7772  Z= 0.392
  Chirality :  0.117   2.097    874
  Planarity :  0.004   0.041    924
  Dihedral  : 19.939 179.705   1059
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 18.02 %
    Favored  : 80.07 %
  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:  1.26 (0.34), residues: 666
  helix:  2.11 (0.29), residues: 331
  sheet:  0.02 (0.46), residues: 128
  loop : -0.69 (0.45), residues: 207

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 128 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.012   0.001   PHE A  62 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 82
  time to evaluate  : 0.640 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.7495 (OUTLIER) cc_final: 0.7260 (tm-30)
REVERT: A   72 MET cc_start: 0.8149 (OUTLIER) cc_final: 0.7536 (ptt)
REVERT: A  109 MET cc_start: 0.6911 (mmt) cc_final: 0.6190 (mtm)
REVERT: A  112 MET cc_start: 0.7791 (mtp) cc_final: 0.7403 (mtt)
REVERT: A  124 ARG cc_start: 0.7308 (OUTLIER) cc_final: 0.7033 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8002 (OUTLIER) cc_final: 0.7677 (mt-10)
REVERT: A  186 SER cc_start: 0.8631 (OUTLIER) cc_final: 0.8322 (p)
REVERT: A  235 ARG cc_start: 0.7336 (mmt180) cc_final: 0.6559 (mtm180)
REVERT: A  298 THR cc_start: 0.8567 (t) cc_final: 0.8043 (p)
REVERT: A  432 HIS cc_start: 0.7786 (t-90) cc_final: 0.7435 (t-170)
REVERT: L   23 HIS cc_start: 0.8098 (m-70) cc_final: 0.7615 (m-70)
REVERT: L   85 SER cc_start: 0.8235 (t) cc_final: 0.8032 (p)
REVERT: L   89 THR cc_start: 0.8810 (p) cc_final: 0.8377 (m)
REVERT: H   30 LEU cc_start: 0.8341 (OUTLIER) cc_final: 0.7863 (tm)
REVERT: H   74 TYR cc_start: 0.7792 (OUTLIER) cc_final: 0.7055 (p90)
REVERT: H  119 TYR cc_start: 0.6812 (t80) cc_final: 0.6467 (t80)
  outliers start: 11
  outliers final: 1
  residues processed: 86
  average time/residue: 1.1812
  time to fit residues: 106.5709
Evaluate side-chains
  87 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.541 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain H residue   30 LEU
Chi-restraints excluded: chain H residue   74 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 36 optimal weight:    4.9990
   chunk 7 optimal weight:    0.6980
   chunk 12 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 34 optimal weight:    0.1980
   chunk 13 optimal weight:    0.5980
   chunk 23 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0030
   chunk 63 optimal weight:    4.9990
   chunk 50 optimal weight:    0.4980
   chunk 59 optimal weight:    0.8980
   overall best weight:    0.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.133107 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.096658 restraints weight = 6206.542|
|-----------------------------------------------------------------------------|
r_work (start): 0.3081 rms_B_bonded: 2.35
r_work: 0.2947 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2809 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.2809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8058
moved from start:          0.2360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5705  Z= 0.132
  Angle     :  1.061  31.384   7772  Z= 0.394
  Chirality :  0.117   2.097    874
  Planarity :  0.003   0.041    924
  Dihedral  : 19.920 179.802   1059
  Min Nonbonded Distance : 2.605

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 19.24 %
    Favored  : 79.38 %
  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:  1.35 (0.34), residues: 666
  helix:  2.16 (0.29), residues: 331
  sheet: -0.03 (0.45), residues: 136
  loop : -0.54 (0.47), residues: 199

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 128 
 HIS   0.003   0.001   HIS A  53 
 PHE   0.010   0.001   PHE A 403 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 362 

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

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

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1332 Ramachandran restraints generated.
    666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 83
  time to evaluate  : 0.676 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.7493 (OUTLIER) cc_final: 0.7244 (tm-30)
REVERT: A   72 MET cc_start: 0.8155 (OUTLIER) cc_final: 0.7543 (ptt)
REVERT: A  109 MET cc_start: 0.6931 (mmt) cc_final: 0.6213 (mtm)
REVERT: A  112 MET cc_start: 0.7797 (mtp) cc_final: 0.7380 (mtt)
REVERT: A  124 ARG cc_start: 0.7315 (OUTLIER) cc_final: 0.7032 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.7689 (mt-10)
REVERT: A  186 SER cc_start: 0.8621 (OUTLIER) cc_final: 0.8321 (p)
REVERT: A  235 ARG cc_start: 0.7329 (mmt180) cc_final: 0.6602 (mtm180)
REVERT: A  385 ARG cc_start: 0.8186 (mtm-85) cc_final: 0.7487 (mtm-85)
REVERT: A  432 HIS cc_start: 0.7775 (t-90) cc_final: 0.7417 (t-170)
REVERT: L   23 HIS cc_start: 0.8092 (m-70) cc_final: 0.7610 (m-70)
REVERT: L   89 THR cc_start: 0.8765 (p) cc_final: 0.8425 (m)
REVERT: H   30 LEU cc_start: 0.8293 (OUTLIER) cc_final: 0.7829 (tm)
REVERT: H   44 SER cc_start: 0.7538 (t) cc_final: 0.7215 (m)
REVERT: H   74 TYR cc_start: 0.7758 (OUTLIER) cc_final: 0.7054 (p90)
REVERT: H  119 TYR cc_start: 0.6815 (t80) cc_final: 0.6480 (t80)
  outliers start: 8
  outliers final: 1
  residues processed: 86
  average time/residue: 1.2217
  time to fit residues: 109.9832
Evaluate side-chains
  85 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 77
  time to evaluate  : 0.702 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
Chi-restraints excluded: chain A residue   72 MET
Chi-restraints excluded: chain A residue  124 ARG
Chi-restraints excluded: chain A residue  154 GLU
Chi-restraints excluded: chain A residue  186 SER
Chi-restraints excluded: chain L residue   92 SER
Chi-restraints excluded: chain H residue   30 LEU
Chi-restraints excluded: chain H residue   74 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 34 optimal weight:    0.4980
   chunk 50 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 59 optimal weight:    3.9990
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 52 optimal weight:    3.9990
   chunk 44 optimal weight:    0.6980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.130761 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.094219 restraints weight = 6275.986|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.35
r_work: 0.2901 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2763 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
moved from start:          0.2258

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5705  Z= 0.194
  Angle     :  1.074  31.558   7772  Z= 0.402
  Chirality :  0.118   2.098    874
  Planarity :  0.004   0.040    924
  Dihedral  : 19.962 179.968   1059
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 19.41 %
    Favored  : 78.68 %
  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:  1.31 (0.34), residues: 666
  helix:  2.10 (0.29), residues: 331
  sheet: -0.01 (0.45), residues: 137
  loop : -0.55 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP H 128 
 HIS   0.003   0.001   HIS A 336 
 PHE   0.015   0.001   PHE A  62 
 TYR   0.018   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 360 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4378.78 seconds
wall clock time: 75 minutes 10.76 seconds (4510.76 seconds total)