Starting phenix.real_space_refine
on Tue Feb 11 05:49:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xpe_22286/02_2025/6xpe_22286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xpe_22286/02_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_22286/02_2025/6xpe_22286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xpe_22286/02_2025/6xpe_22286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xpe_22286/02_2025/6xpe_22286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xpe_22286/02_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-5592/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: 3.22, per 1000 atoms: 0.75
  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: 1.20
  Conformation dependent library (CDL) restraints added in 536.8 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: 0.38
  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: 1.12

  Time building geometry restraints manager: 1.36 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:             0.360
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.190
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.390
  Find NCS groups from input model:        0.160
  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:2.960
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.190
-------------------------------------------------------------------------------
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  : 0.501 
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: 0.1884
  time to fit residues: 17.5422
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  : 0.648 
-------------------------------------------------------------------------------
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:   10.0000
   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:    8.9990
   overall best weight:    4.4166

-------------------------------------------------------------------------------
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 = 0.3527 r_free = 0.3527 target = 0.083867 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.067734 restraints weight = 13090.054|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3207 r_free = 0.3207 target = 0.069484 restraints weight = 7990.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.070701 restraints weight = 5752.539|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.2803

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= 0.275
  Angle     :  0.658   6.213   5940  Z= 0.341
  Chirality :  0.044   0.239    742
  Planarity :  0.005   0.037    706
  Dihedral  :  5.017  27.354    572
  Min Nonbonded Distance : 1.978

Molprobity Statistics.
  All-atom Clashscore : 10.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.46 %
    Favored  : 93.54 %
  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: -2.86 (0.36), residues: 530
  helix: -1.21 (0.26), residues: 342
  sheet: -3.04 (0.68), residues: 42
  loop : -2.82 (0.56), residues: 146

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 122 
 HIS   0.005   0.001   HIS B 106 
 PHE   0.018   0.002   PHE A 114 
 TYR   0.008   0.001   TYR B  67 
 ARG   0.003   0.001   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
  66 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  140 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8356 (mt-10)
REVERT: A  140 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8347 (mt-10)
  outliers start: 0
  outliers final: 0
  residues processed: 66
  average time/residue: 0.1103
  time to fit residues: 10.2685
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  : 0.485 
-------------------------------------------------------------------------------
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:   10.0000
   chunk 36 optimal weight:    0.7980
   chunk 53 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 43 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   chunk 21 optimal weight:    5.9990
   chunk 10 optimal weight:    6.9990
   chunk 32 optimal weight:    6.9990
   chunk 42 optimal weight:    5.9990
   chunk 22 optimal weight:    8.9990
   overall best weight:    3.3186

-------------------------------------------------------------------------------
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 = 0.3552 r_free = 0.3552 target = 0.085375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.069317 restraints weight = 12495.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.071129 restraints weight = 7488.830|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3267 r_free = 0.3267 target = 0.072334 restraints weight = 5306.609|
|-----------------------------------------------------------------------------|
r_work (final): 0.3267
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8286
moved from start:          0.3700

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= 0.230
  Angle     :  0.612   7.298   5940  Z= 0.312
  Chirality :  0.042   0.169    742
  Planarity :  0.004   0.040    706
  Dihedral  :  4.795  27.941    572
  Min Nonbonded Distance : 2.050

Molprobity Statistics.
  All-atom Clashscore : 11.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.85 %
    Favored  : 94.15 %
  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: -1.66 (0.37), residues: 530
  helix: -0.20 (0.28), residues: 342
  sheet: -2.34 (0.66), residues: 48
  loop : -2.64 (0.59), 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   0.020   0.002   PHE B 114 
 TYR   0.006   0.001   TYR B  67 
 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
  75 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  109 ILE cc_start: 0.9024 (mt) cc_final: 0.8652 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 75
  average time/residue: 0.1475
  time to fit residues: 14.3928
Evaluate side-chains
  49 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
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:    0.7980
   chunk 25 optimal weight:    6.9990
   chunk 52 optimal weight:    8.9990
   chunk 14 optimal weight:    2.9990
   chunk 11 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 42 optimal weight:   20.0000
   chunk 2 optimal weight:   10.0000
   chunk 33 optimal weight:    0.8980
   chunk 16 optimal weight:    7.9990
   overall best weight:    1.3386

-------------------------------------------------------------------------------
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 = 0.3605 r_free = 0.3605 target = 0.088557 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3260 r_free = 0.3260 target = 0.072315 restraints weight = 13025.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3303 r_free = 0.3303 target = 0.074257 restraints weight = 7760.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.075443 restraints weight = 5486.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8209
moved from start:          0.4431

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4370  Z= 0.150
  Angle     :  0.538   6.349   5940  Z= 0.276
  Chirality :  0.040   0.134    742
  Planarity :  0.005   0.040    706
  Dihedral  :  4.464  26.257    572
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 8.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.72 %
    Favored  : 95.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.92 %
    Favored  : 97.08 %
  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: -0.82 (0.38), residues: 530
  helix:  0.49 (0.29), residues: 336
  sheet: -1.87 (0.71), residues: 48
  loop : -2.42 (0.53), residues: 146

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   0.010   0.002   PHE B 119 
 TYR   0.015   0.001   TYR B  69 
 ARG   0.009   0.001   ARG B 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
  80 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   75 CYS cc_start: 0.8753 (t) cc_final: 0.8233 (p)
REVERT: B  111 LEU cc_start: 0.8900 (tp) cc_final: 0.8663 (tp)
REVERT: B  275 MET cc_start: 0.8644 (mmm) cc_final: 0.8279 (mmt)
REVERT: B  365 GLU cc_start: 0.8222 (tm-30) cc_final: 0.7860 (tm-30)
REVERT: A   75 CYS cc_start: 0.8733 (t) cc_final: 0.8229 (p)
REVERT: A  109 ILE cc_start: 0.8997 (mt) cc_final: 0.8667 (tp)
REVERT: A  227 GLN cc_start: 0.8801 (tp40) cc_final: 0.8461 (tm-30)
REVERT: A  365 GLU cc_start: 0.8210 (tm-30) cc_final: 0.7857 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 80
  average time/residue: 0.1086
  time to fit residues: 12.2755
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  : 0.462 
-------------------------------------------------------------------------------
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:    0.4980
   chunk 3 optimal weight:    8.9990
   chunk 13 optimal weight:    2.9990
   chunk 1 optimal weight:    6.9990
   chunk 25 optimal weight:    8.9990
   chunk 52 optimal weight:    4.9990
   chunk 24 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 46 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    3.4988

-------------------------------------------------------------------------------
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 = 0.3576 r_free = 0.3576 target = 0.087154 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.071003 restraints weight = 13229.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3259 r_free = 0.3259 target = 0.072770 restraints weight = 7966.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.074089 restraints weight = 5746.939|
|-----------------------------------------------------------------------------|
r_work (final): 0.3285
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.4573

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= 0.236
  Angle     :  0.599   5.914   5940  Z= 0.309
  Chirality :  0.043   0.230    742
  Planarity :  0.004   0.038    706
  Dihedral  :  4.425  23.634    572
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 8.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.66 %
    Favored  : 94.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  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: -0.85 (0.37), residues: 530
  helix:  0.45 (0.29), residues: 340
  sheet: -1.41 (0.73), residues: 46
  loop : -2.65 (0.50), residues: 144

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B 152 
 HIS   0.003   0.001   HIS A 220 
 PHE   0.014   0.002   PHE B 342 
 TYR   0.010   0.001   TYR A 284 
 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
  76 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 76
  time to evaluate  : 0.540 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  111 LEU cc_start: 0.8910 (tp) cc_final: 0.8700 (tp)
REVERT: B  227 GLN cc_start: 0.8860 (tp40) cc_final: 0.8611 (tp40)
REVERT: B  275 MET cc_start: 0.8600 (mmm) cc_final: 0.8176 (mmt)
REVERT: B  310 MET cc_start: 0.7312 (mtt) cc_final: 0.7084 (mtm)
REVERT: B  365 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7645 (tm-30)
REVERT: A  109 ILE cc_start: 0.9016 (mt) cc_final: 0.8678 (tp)
REVERT: A  310 MET cc_start: 0.7326 (mtt) cc_final: 0.7080 (mtm)
REVERT: A  365 GLU cc_start: 0.8141 (tm-30) cc_final: 0.7646 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 76
  average time/residue: 0.1407
  time to fit residues: 14.0646
Evaluate side-chains
  49 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 61.9536 > 50:
  distance: 30 - 46:   3.100
  distance: 32 - 54:   7.693
  distance: 43 - 67:  11.501
  distance: 48 - 54:   4.198
  distance: 49 - 75:  23.410
  distance: 54 - 55:  10.351
  distance: 55 - 56:   8.910
  distance: 55 - 58:  16.069
  distance: 56 - 57:  10.093
  distance: 56 - 60:   8.006
  distance: 57 - 83:  31.918
  distance: 58 - 59:   7.814
  distance: 60 - 61:   6.889
  distance: 61 - 62:  14.734
  distance: 61 - 64:  15.871
  distance: 62 - 63:  24.684
  distance: 62 - 67:   6.562
  distance: 63 - 89:  13.246
  distance: 64 - 65:   8.583
  distance: 64 - 66:  11.893
  distance: 67 - 68:   5.502
  distance: 68 - 69:  25.480
  distance: 68 - 71:  15.073
  distance: 69 - 70:  12.086
  distance: 69 - 75:   8.083
  distance: 70 - 94:  20.175
  distance: 71 - 72:  36.338
  distance: 72 - 74:   3.842
  distance: 75 - 76:  28.839
  distance: 76 - 77:  20.733
  distance: 76 - 79:  15.960
  distance: 77 - 78:  12.342
  distance: 77 - 83:  23.276
  distance: 83 - 84:  37.753
  distance: 84 - 85:  38.099
  distance: 84 - 87:  34.996
  distance: 85 - 86:  22.458
  distance: 85 - 89:  22.863
  distance: 86 - 110:  23.968
  distance: 87 - 88:   9.097
  distance: 89 - 90:  26.616
  distance: 90 - 91:  27.311
  distance: 90 - 93:   8.470
  distance: 91 - 92:  14.595
  distance: 91 - 94:  26.191
  distance: 92 - 118:  34.311
  distance: 94 - 95:  31.093
  distance: 95 - 96:  33.319
  distance: 95 - 98:  18.513
  distance: 96 - 97:  15.298
  distance: 96 - 102:  12.030
  distance: 98 - 99:  32.210
  distance: 99 - 100:  36.028
  distance: 99 - 101:  30.789
  distance: 102 - 103:  15.952
  distance: 103 - 104:   6.085
  distance: 103 - 106:  13.742
  distance: 104 - 105:   8.500
  distance: 104 - 110:  18.029
  distance: 106 - 107:  17.796
  distance: 106 - 108:  17.093
  distance: 107 - 109:  22.096
  distance: 110 - 111:  16.156
  distance: 111 - 112:  12.742
  distance: 111 - 114:  12.532
  distance: 112 - 113:   9.931
  distance: 112 - 118:  20.106
  distance: 114 - 115:  21.852
  distance: 114 - 116:  15.434
  distance: 115 - 117:  19.336
  distance: 118 - 119:   3.807
  distance: 119 - 120:  18.559
  distance: 119 - 122:  11.483
  distance: 120 - 121:  13.400
  distance: 120 - 130:  29.585
  distance: 122 - 123:   3.369
  distance: 123 - 124:  30.263
  distance: 123 - 125:  16.893
  distance: 124 - 126:  25.691
  distance: 125 - 127:  25.692
  distance: 126 - 128:  15.797
  distance: 127 - 128:  27.739
  distance: 128 - 129:  15.172