Starting phenix.real_space_refine
on Thu Jul 24 12:02:22 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7urd_26709/07_2025/7urd_26709.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7urd_26709/07_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_26709/07_2025/7urd_26709.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_2025/7urd_26709.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_2025/7urd_26709.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7urd_26709/07_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-5711/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: 4.34, per 1000 atoms: 0.78
  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: 2.13
  Conformation dependent library (CDL) restraints added in 883.6 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: 0.62
  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: 1.56

  Time building geometry restraints manager: 1.82 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:             1.390
  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:          0.230
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     19.190
  Find NCS groups from input model:        0.060
  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:15.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.440
-------------------------------------------------------------------------------
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      :  0.018   0.430   5714  Z= 0.878
  Angle     :  1.040  30.975   7785  Z= 0.425
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.11031 (  298)
  hydrogen bonds       : angle       6.14658 (  849)
  metal coordination   : bond        0.16255 (    4)
  metal coordination   : angle      21.12353 (    3)
  SS BOND              : bond        0.00203 (    5)
  SS BOND              : angle       0.55958 (   10)
  covalent geometry    : bond        0.01739 ( 5705)
  covalent geometry    : angle       0.95385 ( 7772)

*********************** 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  : 0.550 
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: 1.1724
  time to fit residues: 123.9386
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  : 0.629 
-------------------------------------------------------------------------------
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   5714  Z= 0.125
  Angle     :  1.095  32.247   7785  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03008 (  298)
  hydrogen bonds       : angle       4.40163 (  849)
  metal coordination   : bond        0.01002 (    4)
  metal coordination   : angle       1.20572 (    3)
  SS BOND              : bond        0.00289 (    5)
  SS BOND              : angle       0.53168 (   10)
  covalent geometry    : bond        0.00280 ( 5705)
  covalent geometry    : angle       1.09501 ( 7772)

*********************** 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  : 0.618 
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: 1.1856
  time to fit residues: 116.6377
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  : 0.618 
-------------------------------------------------------------------------------
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:    0.0980
   chunk 48 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   overall best weight:    0.7782

-------------------------------------------------------------------------------
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 = 0.3419 r_free = 0.3419 target = 0.127576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2981 r_free = 0.2981 target = 0.091530 restraints weight = 6267.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.2964 rms_B_bonded: 2.26
r_work: 0.2826 rms_B_bonded: 2.81 restraints_weight: 0.5000
r_work: 0.2686 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.2686
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   5714  Z= 0.129
  Angle     :  1.075  31.467   7785  Z= 0.405
  Chirality :  0.118   2.116    874
  Planarity :  0.004   0.040    924
  Dihedral  : 20.152 179.433   1059
  Min Nonbonded Distance : 2.605

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   0.018   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02803 (  298)
  hydrogen bonds       : angle       4.07795 (  849)
  metal coordination   : bond        0.00553 (    4)
  metal coordination   : angle       1.44507 (    3)
  SS BOND              : bond        0.00390 (    5)
  SS BOND              : angle       0.63989 (   10)
  covalent geometry    : bond        0.00296 ( 5705)
  covalent geometry    : angle       1.07506 ( 7772)

*********************** 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  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8208 (OUTLIER) cc_final: 0.7741 (ptt)
REVERT: A  109 MET cc_start: 0.6999 (mmt) cc_final: 0.6249 (mtm)
REVERT: A  112 MET cc_start: 0.7892 (mtp) cc_final: 0.7681 (mtp)
REVERT: A  124 ARG cc_start: 0.7572 (OUTLIER) cc_final: 0.7222 (mtm-85)
REVERT: A  142 ASP cc_start: 0.8492 (m-30) cc_final: 0.8286 (m-30)
REVERT: A  154 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7685 (mt-10)
REVERT: A  235 ARG cc_start: 0.7436 (mmt180) cc_final: 0.6673 (mtm180)
REVERT: A  375 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7807 (mtt-85)
REVERT: A  432 HIS cc_start: 0.7838 (t-90) cc_final: 0.7500 (t-170)
REVERT: L   81 ARG cc_start: 0.7869 (ptp90) cc_final: 0.7641 (ptp-170)
REVERT: H  101 GLN cc_start: 0.8218 (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: 1.2114
  time to fit residues: 112.7448
Evaluate side-chains
  84 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.567 
-------------------------------------------------------------------------------
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:    2.9990
   chunk 64 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9990
   chunk 44 optimal weight:    0.3980
   chunk 57 optimal weight:    3.9990
   chunk 20 optimal weight:    0.7980
   chunk 40 optimal weight:    1.9990
   chunk 8 optimal weight:    0.9980
   chunk 54 optimal weight:    0.6980
   chunk 26 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   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 = 0.3467 r_free = 0.3467 target = 0.129613 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.093072 restraints weight = 6274.261|
|-----------------------------------------------------------------------------|
r_work (start): 0.3009 rms_B_bonded: 2.34
r_work: 0.2873 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2735 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.2735
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8119
moved from start:          0.1749

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5714  Z= 0.128
  Angle     :  1.072  31.619   7785  Z= 0.403
  Chirality :  0.118   2.115    874
  Planarity :  0.004   0.039    924
  Dihedral  : 20.106 179.904   1059
  Min Nonbonded Distance : 2.607

Molprobity Statistics.
  All-atom Clashscore : 4.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  2.60 %
    Allowed  : 15.25 %
    Favored  : 82.15 %
  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:  0.63 (0.34), residues: 666
  helix:  1.64 (0.29), residues: 329
  sheet: -0.49 (0.44), residues: 127
  loop : -0.88 (0.46), residues: 210

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   0.014   0.001   PHE A 403 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02709 (  298)
  hydrogen bonds       : angle       3.96908 (  849)
  metal coordination   : bond        0.00570 (    4)
  metal coordination   : angle       1.26128 (    3)
  SS BOND              : bond        0.00318 (    5)
  SS BOND              : angle       0.71647 (   10)
  covalent geometry    : bond        0.00293 ( 5705)
  covalent geometry    : angle       1.07257 ( 7772)

*********************** 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
  98 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 83
  time to evaluate  : 0.592 
Fit side-chains
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7691 (ptt)
REVERT: A  109 MET cc_start: 0.6969 (mmt) cc_final: 0.6250 (mtm)
REVERT: A  112 MET cc_start: 0.7768 (mtp) cc_final: 0.7405 (mtt)
REVERT: A  124 ARG cc_start: 0.7575 (OUTLIER) cc_final: 0.7087 (mtt-85)
REVERT: A  154 GLU cc_start: 0.8020 (OUTLIER) cc_final: 0.7685 (mt-10)
REVERT: A  235 ARG cc_start: 0.7306 (mmt180) cc_final: 0.6592 (mtm180)
REVERT: A  375 ARG cc_start: 0.8129 (OUTLIER) cc_final: 0.7827 (mtt-85)
REVERT: A  432 HIS cc_start: 0.7840 (t-90) cc_final: 0.7501 (t-170)
REVERT: L   89 THR cc_start: 0.8853 (p) cc_final: 0.8157 (m)
REVERT: H   29 GLU cc_start: 0.6744 (mm-30) cc_final: 0.6543 (mt-10)
REVERT: H  101 GLN cc_start: 0.8168 (tt0) cc_final: 0.7920 (tt0)
REVERT: H  119 TYR cc_start: 0.6752 (t80) cc_final: 0.6450 (t80)
  outliers start: 15
  outliers final: 3
  residues processed: 92
  average time/residue: 1.3762
  time to fit residues: 132.4215
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  : 0.686 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 26 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   chunk 40 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 19 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    4.9990
   chunk 60 optimal weight:    0.4980
   chunk 22 optimal weight:    1.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.128620 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3008 r_free = 0.3008 target = 0.092036 restraints weight = 6287.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.2989 rms_B_bonded: 2.34
r_work: 0.2851 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1828

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5714  Z= 0.148
  Angle     :  1.078  31.749   7785  Z= 0.406
  Chirality :  0.118   2.112    874
  Planarity :  0.004   0.040    924
  Dihedral  : 20.108 179.720   1059
  Min Nonbonded Distance : 2.606

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.90 %
    Favored  : 96.10 %
  Rotamer:
    Outliers :  1.39 %
    Allowed  : 16.81 %
    Favored  : 81.80 %
  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:  0.79 (0.34), residues: 666
  helix:  1.76 (0.29), residues: 329
  sheet: -0.30 (0.45), residues: 127
  loop : -0.86 (0.46), residues: 210

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 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02812 (  298)
  hydrogen bonds       : angle       3.93470 (  849)
  metal coordination   : bond        0.00807 (    4)
  metal coordination   : angle       1.57417 (    3)
  SS BOND              : bond        0.00250 (    5)
  SS BOND              : angle       0.68857 (   10)
  covalent geometry    : bond        0.00347 ( 5705)
  covalent geometry    : angle       1.07783 ( 7772)

*********************** 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
  94 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 86
  time to evaluate  : 0.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 MET cc_start: 0.8222 (OUTLIER) cc_final: 0.7696 (ptt)
REVERT: A  109 MET cc_start: 0.7002 (mmt) cc_final: 0.6276 (mtm)
REVERT: A  112 MET cc_start: 0.7774 (mtp) cc_final: 0.7445 (mtt)
REVERT: A  124 ARG cc_start: 0.7554 (OUTLIER) cc_final: 0.7233 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7715 (mt-10)
REVERT: A  235 ARG cc_start: 0.7330 (mmt180) cc_final: 0.6611 (mtm180)
REVERT: A  432 HIS cc_start: 0.7804 (t-90) cc_final: 0.7366 (t70)
REVERT: L   89 THR cc_start: 0.8837 (p) cc_final: 0.8162 (m)
REVERT: H  101 GLN cc_start: 0.8200 (tt0) cc_final: 0.7953 (tt0)
REVERT: H  119 TYR cc_start: 0.6835 (t80) cc_final: 0.6462 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 88
  average time/residue: 1.1979
  time to fit residues: 110.4753
Evaluate side-chains
  91 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 85
  time to evaluate  : 0.602 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 59 optimal weight:    0.3980
   chunk 31 optimal weight:    0.5980
   chunk 65 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 39 optimal weight:    0.5980
   chunk 45 optimal weight:    4.9990
   chunk 24 optimal weight:    0.9980
   chunk 35 optimal weight:    3.9990
   chunk 27 optimal weight:    0.0870
   chunk 3 optimal weight:    0.7980
   chunk 26 optimal weight:    0.0270
   overall best weight:    0.3416

-------------------------------------------------------------------------------
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 = 0.133019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.096624 restraints weight = 6141.206|
|-----------------------------------------------------------------------------|
r_work (start): 0.3059 rms_B_bonded: 2.32
r_work: 0.2924 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2785 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2785
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8071
moved from start:          0.2135

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5714  Z= 0.089
  Angle     :  1.054  31.459   7785  Z= 0.390
  Chirality :  0.118   2.106    874
  Planarity :  0.004   0.039    924
  Dihedral  : 19.953 179.790   1059
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.45 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  1.73 %
    Allowed  : 16.98 %
    Favored  : 81.28 %
  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:  1.05 (0.34), residues: 666
  helix:  1.99 (0.29), residues: 331
  sheet: -0.25 (0.45), residues: 126
  loop : -0.78 (0.45), residues: 209

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   0.009   0.001   PHE A  67 
 TYR   0.016   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02332 (  298)
  hydrogen bonds       : angle       3.64978 (  849)
  metal coordination   : bond        0.00288 (    4)
  metal coordination   : angle       1.34781 (    3)
  SS BOND              : bond        0.00261 (    5)
  SS BOND              : angle       0.77114 (   10)
  covalent geometry    : bond        0.00189 ( 5705)
  covalent geometry    : angle       1.05437 ( 7772)

*********************** 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
  100 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 90
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.7003 (mmt) cc_final: 0.6244 (mtm)
REVERT: A  112 MET cc_start: 0.7715 (mtp) cc_final: 0.7311 (mtt)
REVERT: A  122 LYS cc_start: 0.8112 (tttm) cc_final: 0.7910 (tttp)
REVERT: A  124 ARG cc_start: 0.7430 (OUTLIER) cc_final: 0.7154 (mtm-85)
REVERT: A  154 GLU cc_start: 0.7993 (OUTLIER) cc_final: 0.7671 (mt-10)
REVERT: A  186 SER cc_start: 0.8670 (OUTLIER) cc_final: 0.8410 (p)
REVERT: A  235 ARG cc_start: 0.7323 (mmt180) cc_final: 0.6606 (mtm180)
REVERT: A  298 THR cc_start: 0.8605 (t) cc_final: 0.8096 (p)
REVERT: A  432 HIS cc_start: 0.7760 (t-90) cc_final: 0.7478 (t-170)
REVERT: L   89 THR cc_start: 0.8843 (p) cc_final: 0.8344 (m)
REVERT: H  101 GLN cc_start: 0.8200 (tt0) cc_final: 0.7950 (tt0)
REVERT: H  119 TYR cc_start: 0.6820 (t80) cc_final: 0.6401 (t80)
  outliers start: 10
  outliers final: 0
  residues processed: 93
  average time/residue: 1.5463
  time to fit residues: 150.2856
Evaluate side-chains
  83 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 80
  time to evaluate  : 1.017 
-------------------------------------------------------------------------------
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
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 57 optimal weight:    0.8980
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    0.4980
   chunk 9 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0770
   chunk 41 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 25 optimal weight:    3.9990
   chunk 48 optimal weight:    1.9990
   chunk 36 optimal weight:    0.0030
   overall best weight:    0.4548

-------------------------------------------------------------------------------
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 = 0.3506 r_free = 0.3506 target = 0.132516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3065 r_free = 0.3065 target = 0.095877 restraints weight = 6169.059|
|-----------------------------------------------------------------------------|
r_work (start): 0.3072 rms_B_bonded: 2.35
r_work: 0.2938 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2800 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.2800
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8078
moved from start:          0.2243

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5714  Z= 0.097
  Angle     :  1.057  31.356   7785  Z= 0.391
  Chirality :  0.118   2.105    874
  Planarity :  0.003   0.039    924
  Dihedral  : 19.950 179.681   1059
  Min Nonbonded Distance : 2.587

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.21 %
    Allowed  : 17.85 %
    Favored  : 80.94 %
  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:  1.22 (0.34), residues: 666
  helix:  2.11 (0.29), residues: 331
  sheet: -0.21 (0.45), residues: 134
  loop : -0.61 (0.47), residues: 201

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   0.011   0.001   PHE A  62 
 TYR   0.016   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 124 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02384 (  298)
  hydrogen bonds       : angle       3.59240 (  849)
  metal coordination   : bond        0.00421 (    4)
  metal coordination   : angle       1.28472 (    3)
  SS BOND              : bond        0.00222 (    5)
  SS BOND              : angle       0.66401 (   10)
  covalent geometry    : bond        0.00213 ( 5705)
  covalent geometry    : angle       1.05712 ( 7772)

*********************** 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
  92 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.7518 (OUTLIER) cc_final: 0.7268 (tm-30)
REVERT: A  109 MET cc_start: 0.6999 (mmt) cc_final: 0.6239 (mtm)
REVERT: A  112 MET cc_start: 0.7813 (mtp) cc_final: 0.7428 (mtt)
REVERT: A  124 ARG cc_start: 0.7367 (OUTLIER) cc_final: 0.7075 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8016 (OUTLIER) cc_final: 0.7689 (mt-10)
REVERT: A  186 SER cc_start: 0.8669 (OUTLIER) cc_final: 0.8384 (p)
REVERT: A  235 ARG cc_start: 0.7377 (mmt180) cc_final: 0.6623 (mtm180)
REVERT: A  298 THR cc_start: 0.8592 (t) cc_final: 0.8080 (p)
REVERT: A  432 HIS cc_start: 0.7796 (t-90) cc_final: 0.7447 (t-170)
REVERT: L   23 HIS cc_start: 0.8174 (m-70) cc_final: 0.7784 (m-70)
REVERT: L   89 THR cc_start: 0.8798 (p) cc_final: 0.8331 (m)
REVERT: H   38 LYS cc_start: 0.8595 (tttt) cc_final: 0.8112 (tttm)
REVERT: H   74 TYR cc_start: 0.7815 (OUTLIER) cc_final: 0.7206 (p90)
REVERT: H  101 GLN cc_start: 0.8110 (tt0) cc_final: 0.7877 (tt0)
REVERT: H  119 TYR cc_start: 0.6789 (t80) cc_final: 0.6365 (t80)
  outliers start: 7
  outliers final: 1
  residues processed: 88
  average time/residue: 1.3318
  time to fit residues: 122.5737
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  : 0.590 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
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  319 LEU
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:    0.5980
   chunk 44 optimal weight:    0.8980
   chunk 60 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 52 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 5 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.8380

-------------------------------------------------------------------------------
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 = 0.3476 r_free = 0.3476 target = 0.129948 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.093306 restraints weight = 6137.932|
|-----------------------------------------------------------------------------|
r_work (start): 0.3016 rms_B_bonded: 2.33
r_work: 0.2877 rms_B_bonded: 2.88 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8129
moved from start:          0.2145

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   5714  Z= 0.135
  Angle     :  1.073  31.483   7785  Z= 0.403
  Chirality :  0.118   2.103    874
  Planarity :  0.004   0.039    924
  Dihedral  : 19.996 179.730   1059
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 5.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 17.85 %
    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:  1.17 (0.34), residues: 666
  helix:  2.03 (0.29), residues: 331
  sheet: -0.15 (0.44), residues: 137
  loop : -0.64 (0.47), residues: 198

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   0.014   0.001   PHE A 403 
 TYR   0.018   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 360 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02668 (  298)
  hydrogen bonds       : angle       3.73257 (  849)
  metal coordination   : bond        0.00661 (    4)
  metal coordination   : angle       1.39962 (    3)
  SS BOND              : bond        0.00227 (    5)
  SS BOND              : angle       0.71687 (   10)
  covalent geometry    : bond        0.00313 ( 5705)
  covalent geometry    : angle       1.07364 ( 7772)

*********************** 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
  89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 80
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
REVERT: A  109 MET cc_start: 0.7037 (mmt) cc_final: 0.6261 (mtp)
REVERT: A  112 MET cc_start: 0.7780 (mtp) cc_final: 0.7352 (mtt)
REVERT: A  124 ARG cc_start: 0.7415 (OUTLIER) cc_final: 0.7101 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7738 (mt-10)
REVERT: A  235 ARG cc_start: 0.7392 (mmt180) cc_final: 0.6625 (mtm180)
REVERT: A  258 GLU cc_start: 0.7873 (tt0) cc_final: 0.7491 (tt0)
REVERT: A  432 HIS cc_start: 0.7820 (t-90) cc_final: 0.7507 (t-170)
REVERT: L   89 THR cc_start: 0.8826 (p) cc_final: 0.8293 (m)
REVERT: H   30 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8060 (tm)
REVERT: H   74 TYR cc_start: 0.7873 (OUTLIER) cc_final: 0.7196 (p90)
REVERT: H  119 TYR cc_start: 0.6896 (t80) cc_final: 0.6443 (t80)
  outliers start: 9
  outliers final: 4
  residues processed: 83
  average time/residue: 1.4742
  time to fit residues: 127.6013
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  : 0.595 
-------------------------------------------------------------------------------
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  186 SER
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  388 LEU
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:    0.7980
   chunk 29 optimal weight:    0.7980
   chunk 31 optimal weight:    0.6980
   chunk 54 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 49 optimal weight:    3.9990
   chunk 60 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 40 optimal weight:    0.7980
   chunk 10 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 = 0.3484 r_free = 0.3484 target = 0.130463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.093909 restraints weight = 6201.260|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 2.33
r_work: 0.2880 rms_B_bonded: 2.87 restraints_weight: 0.5000
r_work: 0.2740 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.2740
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8113
moved from start:          0.2216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5714  Z= 0.128
  Angle     :  1.073  31.441   7785  Z= 0.402
  Chirality :  0.118   2.102    874
  Planarity :  0.004   0.039    924
  Dihedral  : 19.989 179.653   1059
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 18.37 %
    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:  1.21 (0.34), residues: 666
  helix:  2.04 (0.29), residues: 331
  sheet: -0.15 (0.44), residues: 137
  loop : -0.56 (0.47), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP H 128 
 HIS   0.003   0.001   HIS A  94 
 PHE   0.013   0.001   PHE A 403 
 TYR   0.018   0.001   TYR A  83 
 ARG   0.001   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02656 (  298)
  hydrogen bonds       : angle       3.69808 (  849)
  metal coordination   : bond        0.00633 (    4)
  metal coordination   : angle       1.36849 (    3)
  SS BOND              : bond        0.00197 (    5)
  SS BOND              : angle       0.70353 (   10)
  covalent geometry    : bond        0.00296 ( 5705)
  covalent geometry    : angle       1.07313 ( 7772)

*********************** 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
  91 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 82
  time to evaluate  : 0.580 
Fit side-chains
   revert: symmetry clash
REVERT: A    7 GLN cc_start: 0.7501 (OUTLIER) cc_final: 0.7246 (tm-30)
REVERT: A  109 MET cc_start: 0.7004 (mmt) cc_final: 0.6238 (mtp)
REVERT: A  112 MET cc_start: 0.7763 (mtp) cc_final: 0.7403 (mtt)
REVERT: A  124 ARG cc_start: 0.7411 (OUTLIER) cc_final: 0.7113 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7724 (mt-10)
REVERT: A  235 ARG cc_start: 0.7354 (mmt180) cc_final: 0.6585 (mtm180)
REVERT: A  432 HIS cc_start: 0.7847 (t-90) cc_final: 0.7330 (t-170)
REVERT: L   89 THR cc_start: 0.8831 (p) cc_final: 0.8296 (m)
REVERT: H   30 LEU cc_start: 0.8338 (tt) cc_final: 0.7885 (tm)
REVERT: H   74 TYR cc_start: 0.7908 (OUTLIER) cc_final: 0.7134 (p90)
REVERT: H  119 TYR cc_start: 0.6916 (t80) cc_final: 0.6592 (t80)
  outliers start: 9
  outliers final: 4
  residues processed: 86
  average time/residue: 1.2023
  time to fit residues: 108.2389
Evaluate side-chains
  86 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.607 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
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  319 LEU
Chi-restraints excluded: chain A residue  388 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:    7.9990
   chunk 7 optimal weight:    0.0770
   chunk 12 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9990
   chunk 34 optimal weight:    0.1980
   chunk 13 optimal weight:    0.9980
   chunk 23 optimal weight:    0.3980
   chunk 17 optimal weight:    0.8980
   chunk 63 optimal weight:    3.9990
   chunk 50 optimal weight:    0.2980
   chunk 59 optimal weight:    0.7980
   overall best weight:    0.3538

-------------------------------------------------------------------------------
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 = 0.3528 r_free = 0.3528 target = 0.134249 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.097662 restraints weight = 6164.327|
|-----------------------------------------------------------------------------|
r_work (start): 0.3069 rms_B_bonded: 2.36
r_work: 0.2930 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2789 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2789
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8056
moved from start:          0.2470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   5714  Z= 0.093
  Angle     :  1.062  31.328   7785  Z= 0.394
  Chirality :  0.117   2.102    874
  Planarity :  0.003   0.040    924
  Dihedral  : 19.925 179.808   1059
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 5.12
  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:  2.18 (0.29), residues: 331
  sheet: -0.16 (0.44), residues: 136
  loop : -0.47 (0.48), 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   0.009   0.001   PHE A 403 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 362 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02412 (  298)
  hydrogen bonds       : angle       3.59004 (  849)
  metal coordination   : bond        0.00366 (    4)
  metal coordination   : angle       1.21310 (    3)
  SS BOND              : bond        0.00208 (    5)
  SS BOND              : angle       0.79887 (   10)
  covalent geometry    : bond        0.00200 ( 5705)
  covalent geometry    : angle       1.06227 ( 7772)

********************** 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
  89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.574 
Fit side-chains
REVERT: A    7 GLN cc_start: 0.7480 (OUTLIER) cc_final: 0.7230 (tm-30)
REVERT: A  109 MET cc_start: 0.6949 (mmt) cc_final: 0.6187 (mtm)
REVERT: A  112 MET cc_start: 0.7778 (mtp) cc_final: 0.7424 (mtt)
REVERT: A  124 ARG cc_start: 0.7321 (OUTLIER) cc_final: 0.7043 (mtm-85)
REVERT: A  154 GLU cc_start: 0.8007 (OUTLIER) cc_final: 0.7685 (mt-10)
REVERT: A  186 SER cc_start: 0.8622 (OUTLIER) cc_final: 0.8326 (p)
REVERT: A  235 ARG cc_start: 0.7326 (mmt180) cc_final: 0.6587 (mtm180)
REVERT: A  385 ARG cc_start: 0.8193 (mtm-85) cc_final: 0.7490 (mtm-85)
REVERT: A  432 HIS cc_start: 0.7782 (t-90) cc_final: 0.7470 (t-90)
REVERT: L   23 HIS cc_start: 0.8077 (m-70) cc_final: 0.7599 (m-70)
REVERT: L   89 THR cc_start: 0.8815 (p) cc_final: 0.8436 (m)
REVERT: H   30 LEU cc_start: 0.8314 (tt) cc_final: 0.7864 (tm)
REVERT: H   74 TYR cc_start: 0.7854 (OUTLIER) cc_final: 0.7169 (p90)
REVERT: H  119 TYR cc_start: 0.6759 (t80) cc_final: 0.6430 (t80)
  outliers start: 8
  outliers final: 3
  residues processed: 84
  average time/residue: 1.2085
  time to fit residues: 106.2549
Evaluate side-chains
  89 residues out of total 581 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue    7 GLN
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  186 SER
Chi-restraints excluded: chain A residue  319 LEU
Chi-restraints excluded: chain A residue  388 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:    0.5980
   chunk 50 optimal weight:    0.6980
   chunk 27 optimal weight:    0.8980
   chunk 59 optimal weight:    0.5980
   chunk 29 optimal weight:    0.8980
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 40 optimal weight:    0.8980
   chunk 52 optimal weight:    0.0670
   chunk 44 optimal weight:    0.9980
   overall best weight:    0.5718

-------------------------------------------------------------------------------
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 = 0.132554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3062 r_free = 0.3062 target = 0.095493 restraints weight = 6210.824|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.37
r_work: 0.2929 rms_B_bonded: 2.90 restraints_weight: 0.5000
r_work: 0.2790 rms_B_bonded: 4.57 restraints_weight: 0.2500
r_work (final): 0.2790
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
moved from start:          0.2506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.107   5714  Z= 0.123
  Angle     :  1.101  31.435   7785  Z= 0.418
  Chirality :  0.118   2.100    874
  Planarity :  0.004   0.039    924
  Dihedral  : 19.949 179.858   1059
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 5.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.60 %
    Favored  : 96.40 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 19.41 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 9.52 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  1.29 (0.34), residues: 666
  helix:  2.06 (0.29), residues: 337
  sheet: -0.15 (0.44), residues: 137
  loop : -0.48 (0.48), residues: 192

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   0.016   0.001   PHE A  62 
 TYR   0.017   0.001   TYR A  83 
 ARG   0.002   0.000   ARG A 183 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02591 (  298)
  hydrogen bonds       : angle       3.68514 (  849)
  metal coordination   : bond        0.00528 (    4)
  metal coordination   : angle       1.28898 (    3)
  SS BOND              : bond        0.01039 (    5)
  SS BOND              : angle       3.65640 (   10)
  covalent geometry    : bond        0.00300 ( 5705)
  covalent geometry    : angle       1.09393 ( 7772)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4779.25 seconds
wall clock time: 84 minutes 45.75 seconds (5085.75 seconds total)