Starting phenix.real_space_refine
on Sun Apr 27 03:23:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6xpe_22286/04_2025/6xpe_22286.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6xpe_22286/04_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_22286/04_2025/6xpe_22286.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6xpe_22286/04_2025/6xpe_22286.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6xpe_22286/04_2025/6xpe_22286.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6xpe_22286/04_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-5669/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: 3.15, per 1000 atoms: 0.73
  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: 1.01
  Conformation dependent library (CDL) restraints added in 472.9 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: 0.36
  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: 0.93

  Time building geometry restraints manager: 1.22 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:             0.410
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     14.730
  Find NCS groups from input model:        0.120
  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:2.750
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.280
-------------------------------------------------------------------------------
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      :  0.021   0.575   4390  Z= 0.670
  Angle     :  0.912  21.804   5944  Z= 0.467
  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 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.30609 (  236)
  hydrogen bonds       : angle      10.60469 (  708)
  metal coordination   : bond        0.29794 (   20)
  metal coordination   : angle      15.50205 (    4)
  covalent geometry    : bond        0.00626 ( 4370)
  covalent geometry    : angle       0.81930 ( 5940)

*********************** 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  : 0.521 
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: 0.1874
  time to fit residues: 17.4102
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  : 0.474 
-------------------------------------------------------------------------------
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:    6.9990
   chunk 22 optimal weight:    8.9990
   chunk 13 optimal weight:    6.9990
   chunk 27 optimal weight:   10.0000
   chunk 21 optimal weight:    6.9990
   chunk 42 optimal weight:    8.9990
   chunk 16 optimal weight:    8.9990
   chunk 25 optimal weight:   20.0000
   chunk 31 optimal weight:    5.9990
   chunk 49 optimal weight:    8.9990
   overall best weight:    5.9990

-------------------------------------------------------------------------------
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 = 0.3507 r_free = 0.3507 target = 0.082731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.066534 restraints weight = 13156.601|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.068260 restraints weight = 8131.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.069431 restraints weight = 5911.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3206
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.2788

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.034   4390  Z= 0.238
  Angle     :  0.713   6.973   5944  Z= 0.367
  Chirality :  0.046   0.239    742
  Planarity :  0.005   0.037    706
  Dihedral  :  5.159  27.984    572
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 11.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  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: -3.09 (0.35), residues: 530
  helix: -1.37 (0.26), residues: 340
  sheet: -3.17 (0.66), residues: 42
  loop : -2.95 (0.54), residues: 148

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 122 
 HIS   0.004   0.001   HIS A 197 
 PHE   0.015   0.002   PHE A 114 
 TYR   0.010   0.001   TYR B  67 
 ARG   0.003   0.001   ARG A 331 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05332 (  236)
  hydrogen bonds       : angle       5.10267 (  708)
  metal coordination   : bond        0.01215 (   20)
  metal coordination   : angle       1.73806 (    4)
  covalent geometry    : bond        0.00536 ( 4370)
  covalent geometry    : angle       0.71145 ( 5940)

*********************** 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
  68 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  140 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8387 (mt-10)
REVERT: B  289 GLU cc_start: 0.8866 (pp20) cc_final: 0.8171 (pp20)
REVERT: B  310 MET cc_start: 0.7162 (mmm) cc_final: 0.6920 (mtp)
REVERT: B  333 GLU cc_start: 0.8495 (tp30) cc_final: 0.8185 (tp30)
REVERT: A  140 GLU cc_start: 0.8748 (mt-10) cc_final: 0.8373 (mt-10)
REVERT: A  289 GLU cc_start: 0.8852 (pp20) cc_final: 0.8148 (pp20)
REVERT: A  310 MET cc_start: 0.7170 (mmm) cc_final: 0.6925 (mtp)
REVERT: A  333 GLU cc_start: 0.8495 (tp30) cc_final: 0.8190 (tp30)
  outliers start: 0
  outliers final: 0
  residues processed: 68
  average time/residue: 0.1198
  time to fit residues: 11.3905
Evaluate side-chains
  43 residues out of total 482 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 43
  time to evaluate  : 0.489 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/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-5669/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/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-5669/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-5669/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-5669/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-5669/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: 54.7795 > 50:
  distance: 101 - 106:  26.590
  distance: 106 - 107:  10.624
  distance: 107 - 108:  39.318
  distance: 107 - 110:  21.438
  distance: 108 - 109:  14.349
  distance: 108 - 115:   4.188
  distance: 110 - 111:  11.496
  distance: 111 - 112:  41.052
  distance: 112 - 113:  23.095
  distance: 112 - 114:  16.283
  distance: 115 - 116:  31.195
  distance: 116 - 117:   6.848
  distance: 116 - 119:  12.563
  distance: 117 - 118:   8.165
  distance: 117 - 123:  17.592
  distance: 119 - 120:  13.785
  distance: 120 - 121:  43.513
  distance: 121 - 122:  45.424
  distance: 123 - 124:  18.223
  distance: 124 - 125:  28.737
  distance: 124 - 127:   8.005
  distance: 125 - 126:  23.630
  distance: 125 - 132:  31.473
  distance: 127 - 128:  33.437
  distance: 128 - 129:   6.482
  distance: 129 - 130:   9.768
  distance: 129 - 131:   3.029
  distance: 132 - 133:  14.383
  distance: 133 - 134:  24.350
  distance: 133 - 136:  21.605
  distance: 134 - 135:  11.822
  distance: 134 - 138:  12.544
  distance: 136 - 137:  21.312
  distance: 138 - 139:  13.592
  distance: 138 - 144:  15.179
  distance: 139 - 140:  22.139
  distance: 139 - 142:  20.300
  distance: 140 - 141:  12.106
  distance: 140 - 145:  12.475
  distance: 142 - 143:  16.835
  distance: 143 - 144:  24.969
  distance: 145 - 146:  22.317
  distance: 146 - 147:  23.507
  distance: 146 - 149:  19.535
  distance: 147 - 148:  11.633
  distance: 147 - 152:  17.781
  distance: 149 - 150:   5.114
  distance: 149 - 151:  35.007
  distance: 152 - 153:  12.193
  distance: 153 - 154:  23.417
  distance: 153 - 156:  10.201
  distance: 154 - 155:  25.268
  distance: 154 - 160:  27.343
  distance: 156 - 157:   7.741
  distance: 157 - 158:  19.486
  distance: 157 - 159:   5.138
  distance: 160 - 161:  14.475
  distance: 161 - 162:  14.369
  distance: 161 - 164:   6.890
  distance: 162 - 163:  13.995
  distance: 162 - 169:  14.070
  distance: 164 - 165:  26.573
  distance: 165 - 166:  13.087
  distance: 166 - 167:  16.992
  distance: 166 - 168:  20.684
  distance: 169 - 170:   8.825
  distance: 170 - 171:  11.410
  distance: 170 - 173:   5.029
  distance: 173 - 174:  10.432
  distance: 174 - 175:   7.683
  distance: 174 - 176:   7.715
  distance: 177 - 178:   7.339
  distance: 178 - 179:   8.674
  distance: 178 - 181:   9.216
  distance: 179 - 180:  10.815
  distance: 179 - 183:  12.402
  distance: 181 - 182:   6.564
  distance: 182 - 208:  12.064