Starting phenix.real_space_refine
on Thu Mar  6 01:19:24 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xpe_22286/03_2025/6xpe_22286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xpe_22286/03_2025/6xpe_22286.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6xpe_22286/03_2025/6xpe_22286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xpe_22286/03_2025/6xpe_22286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xpe_22286/03_2025/6xpe_22286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xpe_22286/03_2025/6xpe_22286.cif"
  }
  resolution = 4.1
  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=   0.001 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 144 atoms to isotropic.
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      8      6.06       5
     S      32      5.16       5
     C    2806      2.51       5
     N     692      2.21       5
     O     754      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 4292
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2142
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 268}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "A"
      Number of atoms: 2142
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 277, 2142
          Classifications: {'peptide': 277}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 8, 'TRANS': 268}
          Chain breaks: 5
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 5
          Unresolved non-hydrogen dihedrals: 3
          Planarities with less than four sites: {'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 4
    Chain: "B"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Unusual residues: {' ZN': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "A"
      Number of atoms: 5
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 5
          Unusual residues: {' ZN': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   2158  SG  CYS A  53      34.917  42.485  22.387  1.00140.11           S
  ATOM   2079  SG  CYS B 361      36.563  50.333  26.866  1.00135.63           S
  ATOM   2104  SG  CYS B 364      39.360  48.066  24.716  1.00130.17           S
  ATOM     16  SG  CYS B  53      39.783  23.915  22.387  1.00140.11           S
  ATOM   4221  SG  CYS A 361      38.137  16.067  26.866  1.00135.63           S
  ATOM   4246  SG  CYS A 364      35.340  18.334  24.716  1.00130.17           S

  Time building chain proxies: 3.89, per 1000 atoms: 0.91
  Number of scatterers: 4292
  At special positions: 0
  Unit cell: (75.53, 67.23, 101.26, 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      8     29.99
     S      32     16.00
     O     754      8.00
     N     692      7.00
     C    2806      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 1.49
  Conformation dependent library (CDL) restraints added in 825.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A 401 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  52 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 361 "
        pdb="ZN    ZN A 401 " - pdb=" SG  CYS B 364 "
        pdb="ZN    ZN A 401 " - pdb=" NE2 HIS A  54 "
      pdb="  ZN A 402 "
        pdb="ZN    ZN A 402 " - pdb=" NE2 HIS A 301 "
        pdb="ZN    ZN A 402 " - pdb=" ND1 HIS A 318 "
        pdb="ZN    ZN A 402 " - pdb=" SG  CYS B  53 "
      pdb="  ZN A 403 "
        pdb="ZN    ZN A 403 " - pdb=" NE2 HIS B  52 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 361 "
        pdb="ZN    ZN A 403 " - pdb=" SG  CYS A 364 "
        pdb="ZN    ZN A 403 " - pdb=" NE2 HIS B  54 "
      pdb="  ZN A 404 "
        pdb="ZN    ZN A 404 " - pdb=" NE2 HIS A 137 "
        pdb="ZN    ZN A 404 " - pdb=" NE2 HIS A 345 "
      pdb="  ZN A 405 "
        pdb="ZN    ZN A 405 " - pdb=" NE2 HIS A 106 "
      pdb="  ZN B 401 "
        pdb="ZN    ZN B 401 " - pdb=" ND1 HIS B 318 "
        pdb="ZN    ZN B 401 " - pdb=" NE2 HIS B 301 "
        pdb="ZN    ZN B 401 " - pdb=" SG  CYS A  53 "
      pdb="  ZN B 402 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B 137 "
        pdb="ZN    ZN B 402 " - pdb=" NE2 HIS B 345 "
      pdb="  ZN B 403 "
        pdb="ZN    ZN B 403 " - pdb=" NE2 HIS B 106 "
      Number of angles added : 4


  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1080

  Finding SS restraints...
    Secondary structure from input PDB file:
      16 helices and 2 sheets defined
      62.5% alpha, 4.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.39
  Creating SS restraints...
    Processing helix  chain 'B' and resid 65 through 84
      removed outlier: 3.705A  pdb=" N   ALA B  70 " --> pdb=" O   GLU B  66 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS B  71 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER B  76 " --> pdb=" O   TRP B  72 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ALA B  77 " --> pdb=" O   LYS B  73 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 124
      removed outlier: 4.324A  pdb=" N   LEU B 115 " --> pdb=" O   LEU B 111 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   LEU B 116 " --> pdb=" O   THR B 112 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 138 through 168
      removed outlier: 3.682A  pdb=" N   LEU B 142 " --> pdb=" O   ARG B 138 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 176 through 196
      removed outlier: 3.741A  pdb=" N   ILE B 180 " --> pdb=" O   THR B 176 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL B 181 " --> pdb=" O   VAL B 177 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER B 182 " --> pdb=" O   MET B 178 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA B 185 " --> pdb=" O   VAL B 181 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA B 187 " --> pdb=" O   SER B 183 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU B 196 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 211 through 239
      removed outlier: 4.504A  pdb=" N   VAL B 219 " --> pdb=" O   ARG B 215 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL B 231 " --> pdb=" O   GLN B 227 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE B 237 " --> pdb=" O   ILE B 233 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 246 through 274
      removed outlier: 4.342A  pdb=" N   ILE B 250 " --> pdb=" O   ILE B 246 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE B 257 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER B 262 " --> pdb=" O   LEU B 258 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   THR B 265 " --> pdb=" O   ALA B 261 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   ILE B 266 " --> pdb=" O   SER B 262 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ASP B 269 " --> pdb=" O   THR B 265 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE B 272 " --> pdb=" O   LYS B 268 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU B 274 " --> pdb=" O   PHE B 270 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 284 through 293
      removed outlier: 3.550A  pdb=" N   LYS B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU B 289 " --> pdb=" O   SER B 285 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU B 290 " --> pdb=" O   GLY B 286 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 327 through 340
      removed outlier: 3.798A  pdb=" N   ARG B 331 " --> pdb=" O   SER B 327 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LYS B 336 " --> pdb=" O   ARG B 332 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 84
      removed outlier: 3.705A  pdb=" N   ALA A  70 " --> pdb=" O   GLU A  66 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   LYS A  71 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   SER A  76 " --> pdb=" O   TRP A  72 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ALA A  77 " --> pdb=" O   LYS A  73 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 124
      removed outlier: 3.821A  pdb=" N   LEU A 115 " --> pdb=" O   LEU A 111 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   LEU A 116 " --> pdb=" O   THR A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 168
      removed outlier: 3.682A  pdb=" N   LEU A 142 " --> pdb=" O   ARG A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 196
      removed outlier: 3.741A  pdb=" N   ILE A 180 " --> pdb=" O   THR A 176 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   VAL A 181 " --> pdb=" O   VAL A 177 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   SER A 182 " --> pdb=" O   MET A 178 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ALA A 185 " --> pdb=" O   VAL A 181 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA A 187 " --> pdb=" O   SER A 183 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   LEU A 196 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 211 through 239
      removed outlier: 4.504A  pdb=" N   VAL A 219 " --> pdb=" O   ARG A 215 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   VAL A 231 " --> pdb=" O   GLN A 227 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE A 237 " --> pdb=" O   ILE A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 246 through 274
      removed outlier: 4.342A  pdb=" N   ILE A 250 " --> pdb=" O   ILE A 246 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE A 257 " --> pdb=" O   PHE A 253 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   SER A 262 " --> pdb=" O   LEU A 258 " (cutoff:3.500A)
      removed outlier: 4.977A  pdb=" N   THR A 265 " --> pdb=" O   ALA A 261 " (cutoff:3.500A)
      removed outlier: 5.032A  pdb=" N   ILE A 266 " --> pdb=" O   SER A 262 " (cutoff:3.500A)
      removed outlier: 4.128A  pdb=" N   ASP A 269 " --> pdb=" O   THR A 265 " (cutoff:3.500A)
      removed outlier: 4.262A  pdb=" N   ILE A 272 " --> pdb=" O   LYS A 268 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   LEU A 274 " --> pdb=" O   PHE A 270 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 284 through 293
      removed outlier: 3.550A  pdb=" N   LYS A 288 " --> pdb=" O   TYR A 284 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLU A 289 " --> pdb=" O   SER A 285 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   LEU A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 327 through 340
      removed outlier: 3.798A  pdb=" N   ARG A 331 " --> pdb=" O   SER A 327 " (cutoff:3.500A)
      removed outlier: 4.550A  pdb=" N   LYS A 336 " --> pdb=" O   ARG A 332 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 301 through 307
      removed outlier: 5.011A  pdb=" N   SER B 302 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   HIS B 318 " --> pdb=" O   SER B 302 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 301 through 307
      removed outlier: 5.011A  pdb=" N   SER A 302 " --> pdb=" O   HIS A 318 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   HIS A 318 " --> pdb=" O   SER A 302 " (cutoff:3.500A)

    236 hydrogen bonds defined for protein.
    708 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: 1.11

  Time building geometry restraints manager: 1.43 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1298
        1.34 -     1.46: 834
        1.46 -     1.57: 2192
        1.57 -     1.69: 2
        1.69 -     1.81: 44
  Bond restraints: 4370
  Sorted by residual:
  bond pdb=" N   HIS B 106 "
       pdb=" CA  HIS B 106 "
    ideal  model  delta    sigma   weight residual
    1.459  1.397  0.062 1.20e-02 6.94e+03 2.68e+01
  bond pdb=" CA  PRO B 354 "
       pdb=" C   PRO B 354 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.065 1.42e-02 4.96e+03 2.08e+01
  bond pdb=" CA  PRO A 354 "
       pdb=" C   PRO A 354 "
    ideal  model  delta    sigma   weight residual
    1.520  1.584 -0.065 1.42e-02 4.96e+03 2.08e+01
  bond pdb=" CA  VAL A 355 "
       pdb=" C   VAL A 355 "
    ideal  model  delta    sigma   weight residual
    1.523  1.562 -0.039 1.27e-02 6.20e+03 9.57e+00
  bond pdb=" CA  VAL B 355 "
       pdb=" C   VAL B 355 "
    ideal  model  delta    sigma   weight residual
    1.523  1.562 -0.039 1.27e-02 6.20e+03 9.57e+00
  ... (remaining 4365 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.93: 5750
        1.93 -     3.87: 148
        3.87 -     5.80: 32
        5.80 -     7.74: 7
        7.74 -     9.67: 3
  Bond angle restraints: 5940
  Sorted by residual:
  angle pdb=" C   VAL A 355 "
        pdb=" N   ASP A 356 "
        pdb=" CA  ASP A 356 "
      ideal   model   delta    sigma   weight residual
     123.00  131.98   -8.98 1.38e+00 5.25e-01 4.24e+01
  angle pdb=" C   VAL B 355 "
        pdb=" N   ASP B 356 "
        pdb=" CA  ASP B 356 "
      ideal   model   delta    sigma   weight residual
     123.00  131.98   -8.98 1.38e+00 5.25e-01 4.24e+01
  angle pdb=" C   PHE A 114 "
        pdb=" N   LEU A 115 "
        pdb=" CA  LEU A 115 "
      ideal   model   delta    sigma   weight residual
     120.82  127.96   -7.14 1.50e+00 4.44e-01 2.26e+01
  angle pdb=" N   PHE A 114 "
        pdb=" CA  PHE A 114 "
        pdb=" C   PHE A 114 "
      ideal   model   delta    sigma   weight residual
     110.80  120.47   -9.67 2.13e+00 2.20e-01 2.06e+01
  angle pdb=" N   VAL B 355 "
        pdb=" CA  VAL B 355 "
        pdb=" C   VAL B 355 "
      ideal   model   delta    sigma   weight residual
     109.34  116.94   -7.60 2.08e+00 2.31e-01 1.33e+01
  ... (remaining 5935 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    11.89: 2155
       11.89 -    23.79: 264
       23.79 -    35.68: 120
       35.68 -    47.57: 41
       47.57 -    59.47: 10
  Dihedral angle restraints: 2590
    sinusoidal: 952
      harmonic: 1638
  Sorted by residual:
  dihedral pdb=" CA  LEU B 308 "
           pdb=" C   LEU B 308 "
           pdb=" N   THR B 309 "
           pdb=" CA  THR B 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.21  -29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  LEU A 308 "
           pdb=" C   LEU A 308 "
           pdb=" N   THR A 309 "
           pdb=" CA  THR A 309 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.21  -29.79     0      5.00e+00 4.00e-02 3.55e+01
  dihedral pdb=" CA  PRO A 354 "
           pdb=" C   PRO A 354 "
           pdb=" N   VAL A 355 "
           pdb=" CA  VAL A 355 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.06   23.94     0      5.00e+00 4.00e-02 2.29e+01
  ... (remaining 2587 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.067: 666
       0.067 -    0.135: 73
       0.135 -    0.202: 2
       0.202 -    0.269: 0
       0.269 -    0.337: 1
  Chirality restraints: 742
  Sorted by residual:
  chirality pdb=" CA  PHE A 114 "
            pdb=" N   PHE A 114 "
            pdb=" C   PHE A 114 "
            pdb=" CB  PHE A 114 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.17    0.34 2.00e-01 2.50e+01 2.83e+00
  chirality pdb=" CB  ILE B 305 "
            pdb=" CA  ILE B 305 "
            pdb=" CG1 ILE B 305 "
            pdb=" CG2 ILE B 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.83e-01
  chirality pdb=" CB  ILE A 305 "
            pdb=" CA  ILE A 305 "
            pdb=" CG1 ILE A 305 "
            pdb=" CG2 ILE A 305 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.51    0.14 2.00e-01 2.50e+01 4.83e-01
  ... (remaining 739 not shown)

  Planarity restraints: 706
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA B 105 "   -0.021 2.00e-02 2.50e+03   4.31e-02 1.86e+01
        pdb=" C   ALA B 105 "    0.075 2.00e-02 2.50e+03
        pdb=" O   ALA B 105 "   -0.029 2.00e-02 2.50e+03
        pdb=" N   HIS B 106 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 106 "   -0.019 2.00e-02 2.50e+03   2.17e-02 7.08e+00
        pdb=" CG  HIS B 106 "    0.019 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 106 "   -0.003 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 106 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 106 "    0.014 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 106 "   -0.036 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASP B 248 "   -0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO B 249 "    0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO B 249 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO B 249 "   -0.020 5.00e-02 4.00e+02
  ... (remaining 703 not shown)

  Histogram of nonbonded interaction distances:
        1.49 -     2.17: 9
        2.17 -     2.86: 1745
        2.86 -     3.54: 6492
        3.54 -     4.22: 9384
        4.22 -     4.90: 15752
  Nonbonded interactions: 33382
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.492 2.230
  nonbonded pdb=" OD2 ASP B 224 "
            pdb="ZN    ZN B 403 "
     model   vdw
     1.514 2.230
  nonbonded pdb=" OD1 ASP B 224 "
            pdb="ZN    ZN B 403 "
     model   vdw
     1.590 2.230
  nonbonded pdb=" CG  ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.615 2.460
  nonbonded pdb=" OD1 ASP A 224 "
            pdb="ZN    ZN A 405 "
     model   vdw
     1.619 2.230
  ... (remaining 33377 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 52 through 369 or resid 401 through 403))
  selection = chain 'B'
}

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 group one per residue
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:             15.330
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     17.730
  Find NCS groups from input model:        0.210
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.360
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   36.920
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8339
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      :  0.006   0.065   4370  Z= 0.410
  Angle     :  0.819   9.670   5940  Z= 0.461
  Chirality :  0.044   0.337    742
  Planarity :  0.004   0.043    706
  Dihedral  : 14.302  59.467   1510
  Min Nonbonded Distance : 1.492

Molprobity Statistics.
  All-atom Clashscore : 20.11
  Ramachandran Plot:
    Outliers :  1.32 %
    Allowed  : 10.57 %
    Favored  : 88.11 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.08 %
    Favored  : 85.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -5.36 (0.30), residues: 530
  helix: -3.29 (0.21), residues: 332
  sheet: -4.09 (0.59), residues: 44
  loop : -3.38 (0.51), residues: 154

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 122 
 HIS   0.025   0.002   HIS B 106 
 PHE   0.012   0.001   PHE B 218 
 TYR   0.007   0.001   TYR B 160 
 ARG   0.002   0.000   ARG B 131 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 69
  time to evaluate  : 0.525 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 GLN cc_start: 0.9142 (tp40) cc_final: 0.8608 (tm-30)
REVERT: B  310 MET cc_start: 0.7366 (mmm) cc_final: 0.7068 (mtp)
REVERT: A  227 GLN cc_start: 0.9131 (tp40) cc_final: 0.8593 (tm-30)
REVERT: A  310 MET cc_start: 0.7360 (mmm) cc_final: 0.7074 (mtp)
  outliers start: 10
  outliers final: 2
  residues processed: 75
  average time/residue: 0.2725
  time to fit residues: 25.9249
Evaluate side-chains
  52 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 50
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   chunk 13 optimal weight:    6.9990
   chunk 27 optimal weight:    6.9990
   chunk 21 optimal weight:    5.9990
   chunk 42 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 25 optimal weight:    6.9990
   chunk 31 optimal weight:    0.0870
   chunk 49 optimal weight:    0.8980
   overall best weight:    2.9964

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

Flipped N/Q/H residues before XYZ refinement:
B 211 ASN
** B 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 211 ASN
** A 301 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.085124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.068993 restraints weight = 13145.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.070822 restraints weight = 7884.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.072100 restraints weight = 5575.983|
|-----------------------------------------------------------------------------|
r_work (final): 0.3278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.2825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.026   4370  Z= 0.224
  Angle     :  0.627   5.721   5940  Z= 0.326
  Chirality :  0.043   0.229    742
  Planarity :  0.005   0.036    706
  Dihedral  :  4.898  26.792    572
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.28 %
    Favored  : 94.72 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.79 %
    Favored  : 95.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.72 (0.36), residues: 530
  helix: -1.09 (0.27), residues: 342
  sheet: -2.98 (0.69), residues: 42
  loop : -2.83 (0.56), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 122 
 HIS   0.009   0.001   HIS B 106 
 PHE   0.016   0.002   PHE A 114 
 TYR   0.007   0.001   TYR B  67 
 ARG   0.002   0.000   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.572 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  227 GLN cc_start: 0.8887 (tp40) cc_final: 0.8664 (tm-30)
REVERT: A  140 GLU cc_start: 0.8614 (mt-10) cc_final: 0.8298 (mt-10)
REVERT: A  227 GLN cc_start: 0.8906 (tp40) cc_final: 0.8649 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 69
  average time/residue: 0.1743
  time to fit residues: 16.6753
Evaluate side-chains
  42 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 25 optimal weight:    9.9990
   chunk 36 optimal weight:   20.0000
   chunk 53 optimal weight:    8.9990
   chunk 34 optimal weight:    2.9990
   chunk 43 optimal weight:    6.9990
   chunk 14 optimal weight:    0.9990
   chunk 21 optimal weight:    6.9990
   chunk 10 optimal weight:    9.9990
   chunk 32 optimal weight:    0.0770
   chunk 42 optimal weight:    5.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    3.2146

-------------------------------------------------------------------------------
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 = 0.3548 r_free = 0.3548 target = 0.085506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.069554 restraints weight = 13011.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.071428 restraints weight = 7617.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3266 r_free = 0.3266 target = 0.072731 restraints weight = 5337.307|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.3695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4370  Z= 0.225
  Angle     :  0.612   6.539   5940  Z= 0.313
  Chirality :  0.042   0.173    742
  Planarity :  0.004   0.039    706
  Dihedral  :  4.630  23.988    572
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 11.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.83 %
    Favored  : 94.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.63 (0.37), residues: 530
  helix: -0.14 (0.28), residues: 342
  sheet: -2.32 (0.65), residues: 48
  loop : -2.77 (0.56), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 122 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.022   0.002   PHE B 114 
 TYR   0.017   0.002   TYR B  69 
 ARG   0.002   0.000   ARG B 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  74 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ILE cc_start: 0.8985 (mt) cc_final: 0.8635 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 74
  average time/residue: 0.1894
  time to fit residues: 18.5813
Evaluate side-chains
  50 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 50
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 48 optimal weight:    5.9990
   chunk 25 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 14 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    6.9990
   chunk 42 optimal weight:    0.0370
   chunk 2 optimal weight:   20.0000
   chunk 33 optimal weight:    0.4980
   chunk 16 optimal weight:    6.9990
   overall best weight:    2.1064

-------------------------------------------------------------------------------
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 = 0.3598 r_free = 0.3598 target = 0.088061 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3253 r_free = 0.3253 target = 0.072201 restraints weight = 13059.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.073959 restraints weight = 7798.230|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.075200 restraints weight = 5626.568|
|-----------------------------------------------------------------------------|
r_work (final): 0.3329
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.4274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   4370  Z= 0.174
  Angle     :  0.561   6.973   5940  Z= 0.289
  Chirality :  0.040   0.137    742
  Planarity :  0.005   0.041    706
  Dihedral  :  4.481  23.898    572
  Min Nonbonded Distance : 2.094

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.16 (0.37), residues: 530
  helix:  0.29 (0.29), residues: 342
  sheet: -1.97 (0.70), residues: 48
  loop : -2.87 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 122 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.012   0.002   PHE A 119 
 TYR   0.012   0.001   TYR B 284 
 ARG   0.008   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 LEU cc_start: 0.8915 (tp) cc_final: 0.8668 (tp)
REVERT: B  275 MET cc_start: 0.8613 (mmm) cc_final: 0.8224 (mmt)
REVERT: B  309 THR cc_start: 0.8142 (p) cc_final: 0.7920 (p)
REVERT: B  340 LYS cc_start: 0.9353 (ptmt) cc_final: 0.9058 (pttm)
REVERT: B  365 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7691 (tm-30)
REVERT: A  109 ILE cc_start: 0.8985 (mt) cc_final: 0.8648 (tp)
REVERT: A  309 THR cc_start: 0.8169 (p) cc_final: 0.7963 (p)
REVERT: A  340 LYS cc_start: 0.9348 (ptmt) cc_final: 0.9055 (pttm)
REVERT: A  365 GLU cc_start: 0.8206 (tm-30) cc_final: 0.7695 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.1376
  time to fit residues: 15.1563
Evaluate side-chains
  53 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 53
  time to evaluate  : 0.453 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 42 optimal weight:   10.0000
   chunk 3 optimal weight:    9.9990
   chunk 13 optimal weight:    6.9990
   chunk 1 optimal weight:    1.9990
   chunk 25 optimal weight:    6.9990
   chunk 52 optimal weight:    7.9990
   chunk 24 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 46 optimal weight:    3.9990
   chunk 4 optimal weight:    4.9990
   chunk 53 optimal weight:    0.0770
   overall best weight:    3.2146

-------------------------------------------------------------------------------
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 = 0.3594 r_free = 0.3594 target = 0.088073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.071964 restraints weight = 13152.255|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.073741 restraints weight = 7904.760|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.075030 restraints weight = 5627.959|
|-----------------------------------------------------------------------------|
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8241
moved from start:          0.4628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.025   4370  Z= 0.224
  Angle     :  0.609   6.675   5940  Z= 0.313
  Chirality :  0.042   0.242    742
  Planarity :  0.004   0.038    706
  Dihedral  :  4.423  22.597    572
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.09 %
    Favored  : 94.91 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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 (0.37), residues: 530
  helix:  0.38 (0.29), residues: 342
  sheet: -1.60 (0.73), residues: 46
  loop : -2.95 (0.50), residues: 142

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 152 
 HIS   0.004   0.001   HIS A 220 
 PHE   0.024   0.002   PHE B 342 
 TYR   0.013   0.001   TYR B  69 
 ARG   0.006   0.001   ARG B 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 73
  time to evaluate  : 0.473 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  275 MET cc_start: 0.8678 (mmm) cc_final: 0.8364 (mmt)
REVERT: A  109 ILE cc_start: 0.9002 (mt) cc_final: 0.8665 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 73
  average time/residue: 0.1424
  time to fit residues: 13.8141
Evaluate side-chains
  48 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 48
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 53 optimal weight:    4.9990
   chunk 37 optimal weight:    6.9990
   chunk 13 optimal weight:    3.9990
   chunk 50 optimal weight:    6.9990
   chunk 14 optimal weight:    3.9990
   chunk 23 optimal weight:   20.0000
   chunk 7 optimal weight:    0.9990
   chunk 1 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 44 optimal weight:    7.9990
   chunk 39 optimal weight:   20.0000
   overall best weight:    2.9990

-------------------------------------------------------------------------------
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 = 0.3607 r_free = 0.3607 target = 0.088633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.072097 restraints weight = 13063.418|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.074027 restraints weight = 7707.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.075212 restraints weight = 5463.200|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8247
moved from start:          0.4781

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4370  Z= 0.215
  Angle     :  0.583   6.100   5940  Z= 0.298
  Chirality :  0.041   0.188    742
  Planarity :  0.004   0.037    706
  Dihedral  :  4.410  24.409    572
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 9.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.91 %
    Favored  : 95.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.87 (0.38), residues: 530
  helix:  0.45 (0.29), residues: 348
  sheet: -1.42 (0.75), residues: 46
  loop : -2.86 (0.51), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.020   0.002   PHE B 342 
 TYR   0.013   0.001   TYR B  69 
 ARG   0.008   0.001   ARG B 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.508 
Fit side-chains
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8766 (t) cc_final: 0.8227 (p)
REVERT: B  275 MET cc_start: 0.8724 (mmm) cc_final: 0.8382 (mmt)
REVERT: A   75 CYS cc_start: 0.8766 (t) cc_final: 0.8246 (p)
REVERT: A  109 ILE cc_start: 0.9103 (mt) cc_final: 0.8764 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.1228
  time to fit residues: 11.8463
Evaluate side-chains
  47 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 10 optimal weight:    7.9990
   chunk 28 optimal weight:    5.9990
   chunk 9 optimal weight:    7.9990
   chunk 21 optimal weight:    6.9990
   chunk 26 optimal weight:   10.0000
   chunk 20 optimal weight:    6.9990
   chunk 36 optimal weight:    9.9990
   chunk 2 optimal weight:    8.9990
   chunk 47 optimal weight:    0.3980
   chunk 0 optimal weight:   30.0000
   overall best weight:    4.8788

-------------------------------------------------------------------------------
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 = 0.3569 r_free = 0.3569 target = 0.086468 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.069838 restraints weight = 12825.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.071598 restraints weight = 7787.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.072905 restraints weight = 5649.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3265
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8302
moved from start:          0.4792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4370  Z= 0.305
  Angle     :  0.693   7.786   5940  Z= 0.345
  Chirality :  0.043   0.158    742
  Planarity :  0.005   0.037    706
  Dihedral  :  4.570  24.192    572
  Min Nonbonded Distance : 1.832

Molprobity Statistics.
  All-atom Clashscore : 10.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.01 (0.38), residues: 530
  helix:  0.34 (0.29), residues: 344
  sheet: -1.28 (0.74), residues: 46
  loop : -2.91 (0.50), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 306 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.021   0.002   PHE B 342 
 TYR   0.009   0.001   TYR B  67 
 ARG   0.009   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.437 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8826 (t) cc_final: 0.8251 (p)
REVERT: B  275 MET cc_start: 0.8831 (mmm) cc_final: 0.8460 (mmt)
REVERT: A  109 ILE cc_start: 0.9042 (mt) cc_final: 0.8671 (tp)
REVERT: A  310 MET cc_start: 0.6835 (mmm) cc_final: 0.6590 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 67
  average time/residue: 0.1403
  time to fit residues: 12.4748
Evaluate side-chains
  42 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 42
  time to evaluate  : 0.471 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 8 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 50 optimal weight:   20.0000
   chunk 12 optimal weight:    6.9990
   chunk 2 optimal weight:   20.0000
   chunk 13 optimal weight:    6.9990
   chunk 43 optimal weight:    5.9990
   chunk 26 optimal weight:    2.9990
   chunk 45 optimal weight:   10.0000
   overall best weight:    4.1990

-------------------------------------------------------------------------------
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 = 0.3572 r_free = 0.3572 target = 0.086867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3205 r_free = 0.3205 target = 0.070313 restraints weight = 12597.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.072067 restraints weight = 7582.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.073346 restraints weight = 5508.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.4946

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.027   4370  Z= 0.271
  Angle     :  0.661   7.329   5940  Z= 0.332
  Chirality :  0.042   0.139    742
  Planarity :  0.004   0.036    706
  Dihedral  :  4.589  26.099    572
  Min Nonbonded Distance : 1.775

Molprobity Statistics.
  All-atom Clashscore : 10.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.38), residues: 530
  helix:  0.36 (0.29), residues: 346
  sheet: -1.23 (0.76), residues: 46
  loop : -2.76 (0.51), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 197 
 PHE   0.021   0.002   PHE B 342 
 TYR   0.015   0.001   TYR B  69 
 ARG   0.008   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.478 
Fit side-chains
REVERT: B   75 CYS cc_start: 0.8827 (t) cc_final: 0.8242 (p)
REVERT: B  275 MET cc_start: 0.8790 (mmm) cc_final: 0.8417 (mmt)
REVERT: A   75 CYS cc_start: 0.8794 (t) cc_final: 0.8219 (p)
REVERT: A  109 ILE cc_start: 0.9046 (mt) cc_final: 0.8744 (tp)
REVERT: A  310 MET cc_start: 0.6780 (mmm) cc_final: 0.6566 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1369
  time to fit residues: 12.0571
Evaluate side-chains
  45 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 26 optimal weight:   10.0000
   chunk 18 optimal weight:    2.9990
   chunk 25 optimal weight:    2.9990
   chunk 9 optimal weight:   10.0000
   chunk 11 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 36 optimal weight:    9.9990
   chunk 15 optimal weight:    3.9990
   chunk 39 optimal weight:    0.5980
   chunk 43 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   overall best weight:    2.2586

-------------------------------------------------------------------------------
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 = 0.3629 r_free = 0.3629 target = 0.089789 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.073380 restraints weight = 12693.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.075249 restraints weight = 7773.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.076357 restraints weight = 5602.703|
|-----------------------------------------------------------------------------|
r_work (final): 0.3330
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8226
moved from start:          0.5290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4370  Z= 0.192
  Angle     :  0.591   6.041   5940  Z= 0.296
  Chirality :  0.040   0.122    742
  Planarity :  0.004   0.040    706
  Dihedral  :  4.399  23.574    572
  Min Nonbonded Distance : 1.816

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.04 %
    Favored  : 93.96 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.72 (0.38), residues: 530
  helix:  0.47 (0.30), residues: 346
  sheet: -1.05 (0.80), residues: 46
  loop : -2.61 (0.50), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 152 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.013   0.002   PHE B 342 
 TYR   0.004   0.001   TYR B  67 
 ARG   0.009   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.487 
Fit side-chains
REVERT: B  275 MET cc_start: 0.8695 (mmm) cc_final: 0.8370 (mmt)
REVERT: A  109 ILE cc_start: 0.9109 (mt) cc_final: 0.8840 (tp)
REVERT: A  111 LEU cc_start: 0.8555 (tp) cc_final: 0.8347 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1339
  time to fit residues: 13.9125
Evaluate side-chains
  52 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 0 optimal weight:   30.0000
   chunk 46 optimal weight:    0.5980
   chunk 32 optimal weight:    0.9980
   chunk 20 optimal weight:    9.9990
   chunk 10 optimal weight:    7.9990
   chunk 24 optimal weight:    2.9990
   chunk 21 optimal weight:   10.0000
   chunk 5 optimal weight:    9.9990
   chunk 44 optimal weight:    4.9990
   chunk 31 optimal weight:    6.9990
   overall best weight:    2.9186

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

Flipped N/Q/H residues before XYZ refinement:
B 227 GLN
A 227 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.088632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3246 r_free = 0.3246 target = 0.072114 restraints weight = 12260.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.073948 restraints weight = 7470.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.075018 restraints weight = 5420.938|
|-----------------------------------------------------------------------------|
r_work (final): 0.3313
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.5268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4370  Z= 0.215
  Angle     :  0.627   5.942   5940  Z= 0.315
  Chirality :  0.041   0.120    742
  Planarity :  0.004   0.036    706
  Dihedral  :  4.431  24.211    572
  Min Nonbonded Distance : 1.784

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  :  0.00 %
    Favored  : 99.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.71 (0.38), residues: 530
  helix:  0.45 (0.30), residues: 346
  sheet: -1.00 (0.81), residues: 46
  loop : -2.52 (0.51), residues: 138

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 152 
 HIS   0.004   0.001   HIS B 345 
 PHE   0.019   0.002   PHE A 342 
 TYR   0.006   0.001   TYR B  67 
 ARG   0.009   0.001   ARG A 331 

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

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

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1060 Ramachandran restraints generated.
    530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  73 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.532 
Fit side-chains
REVERT: B  275 MET cc_start: 0.8735 (mmm) cc_final: 0.8366 (mmt)
REVERT: A  109 ILE cc_start: 0.9121 (mt) cc_final: 0.8851 (tp)
  outliers start: 2
  outliers final: 0
  residues processed: 71
  average time/residue: 0.1318
  time to fit residues: 12.5333
Evaluate side-chains
  52 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 54
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 28 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 27 optimal weight:    9.9990
   chunk 23 optimal weight:   10.0000
   chunk 44 optimal weight:    6.9990
   chunk 35 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:   10.0000
   chunk 37 optimal weight:    7.9990
   overall best weight:    4.5788

-------------------------------------------------------------------------------
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 = 0.3589 r_free = 0.3589 target = 0.087639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.070598 restraints weight = 12620.486|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3250 r_free = 0.3250 target = 0.072448 restraints weight = 7684.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.073572 restraints weight = 5567.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.3269
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8300
moved from start:          0.5167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.029   4370  Z= 0.291
  Angle     :  0.669   6.120   5940  Z= 0.336
  Chirality :  0.042   0.123    742
  Planarity :  0.005   0.035    706
  Dihedral  :  4.575  25.475    572
  Min Nonbonded Distance : 1.755

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.47 %
    Favored  : 94.53 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.21 %
    Favored  : 99.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.73 (0.39), residues: 530
  helix:  0.36 (0.29), residues: 350
  sheet: -1.05 (0.81), residues: 46
  loop : -2.37 (0.56), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 152 
 HIS   0.004   0.001   HIS B 197 
 PHE   0.017   0.002   PHE A 342 
 TYR   0.011   0.001   TYR B  69 
 ARG   0.009   0.001   ARG B 331 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1560.21 seconds
wall clock time: 28 minutes 57.86 seconds (1737.86 seconds total)