Starting phenix.real_space_refine
on Sun Oct 13 12:24:18 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/10_2024/8ouy_17205_trim.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/10_2024/8ouy_17205.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/10_2024/8ouy_17205.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/10_2024/8ouy_17205.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/10_2024/8ouy_17205_trim.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ouy_17205/10_2024/8ouy_17205_trim.cif"
  }
  resolution = 3.4
  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=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     P       8      5.49       5
     Mg      3      5.21       5
     S      50      5.16       5
     C    4608      2.51       5
     N    1268      2.21       5
     O    1378      1.98       5
     H    7380      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib"
  Total number of atoms: 14695
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1131
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 70, 1131
          Classifications: {'peptide': 70}
          Link IDs: {'PTRANS': 2, 'TRANS': 67}
    Chain: "B"
      Number of atoms: 4977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 313, 4977
          Classifications: {'peptide': 313}
          Link IDs: {'PTRANS': 10, 'TRANS': 302}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 4722
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 308, 4722
          Classifications: {'peptide': 308}
          Link IDs: {'PTRANS': 7, 'TRANS': 300}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 3773
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 234, 3773
          Classifications: {'peptide': 234}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 227}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 8.37, per 1000 atoms: 0.57
  Number of scatterers: 14695
  At special positions: 0
  Unit cell: (98.28, 104.76, 95.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     S      50     16.00
     P       8     15.00
     Mg      3     11.99
     O    1378      8.00
     N    1268      7.00
     C    4608      6.00
     H    7380      1.00
    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: 3.93
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1722

  Finding SS restraints...
    Secondary structure from input PDB file:
      44 helices and 6 sheets defined
      51.1% alpha, 13.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.31
  Creating SS restraints...
    Processing helix  chain 'A' and resid 5 through 10
      removed outlier: 3.775A  pdb=" N   VAL A   9 " --> pdb=" O   LYS A   5 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   GLY A  10 " --> pdb=" O   LEU A   6 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 5 through 10'
    Processing helix  chain 'A' and resid 12 through 21
    Processing helix  chain 'A' and resid 26 through 32
    Processing helix  chain 'A' and resid 34 through 43
    Processing helix  chain 'A' and resid 45 through 58
    Processing helix  chain 'A' and resid 67 through 72
    Processing helix  chain 'B' and resid 20 through 30
    Processing helix  chain 'B' and resid 34 through 38
    Processing helix  chain 'B' and resid 42 through 50
      removed outlier: 3.992A  pdb=" N   LYS B  48 " --> pdb=" O   SER B  44 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   VAL B  50 " --> pdb=" O   LEU B  46 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 53 through 66
      removed outlier: 3.627A  pdb=" N   ARG B  65 " --> pdb=" O   LEU B  61 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 86 through 97
    Processing helix  chain 'B' and resid 104 through 111
    Processing helix  chain 'B' and resid 130 through 142
    Processing helix  chain 'B' and resid 145 through 149
    Processing helix  chain 'B' and resid 165 through 188
      removed outlier: 3.545A  pdb=" N   VAL B 169 " --> pdb=" O   MET B 165 " (cutoff:3.500A)
      removed outlier: 3.825A  pdb=" N   ILE B 183 " --> pdb=" O   HIS B 179 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ALA B 184 " --> pdb=" O   LEU B 180 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   GLU B 185 " --> pdb=" O   GLN B 181 " (cutoff:3.500A)
      removed outlier: 4.898A  pdb=" N   LYS B 186 " --> pdb=" O   LEU B 182 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   HIS B 187 " --> pdb=" O   ILE B 183 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 191 through 199
      removed outlier: 3.817A  pdb=" N   GLU B 197 " --> pdb=" O   ARG B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 200 through 206
    Processing helix  chain 'B' and resid 215 through 233
      Proline residue:  B 227  - end of helix
      removed outlier: 3.763A  pdb=" N   SER B 231 " --> pdb=" O   PRO B 227 " (cutoff:3.500A)
      removed outlier: 3.595A  pdb=" N   HIS B 233 " --> pdb=" O   PHE B 229 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 252 through 258
      removed outlier: 3.751A  pdb=" N   SER B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   ARG B 258 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 263 through 276
      removed outlier: 5.281A  pdb=" N   MET B 269 " --> pdb=" O   LEU B 265 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   ILE B 270 " --> pdb=" O   ALA B 266 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   HIS B 276 " --> pdb=" O   LEU B 272 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 302 through 308
      removed outlier: 3.683A  pdb=" N   GLY B 306 " --> pdb=" O   GLU B 303 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 13 through 23
      removed outlier: 4.297A  pdb=" N   LEU C  19 " --> pdb=" O   GLU C  15 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 27 through 34
    Processing helix  chain 'C' and resid 35 through 41
    Processing helix  chain 'C' and resid 46 through 61
    Processing helix  chain 'C' and resid 68 through 79
      removed outlier: 3.602A  pdb=" N   GLU C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   GLU C  74 " --> pdb=" O   ASP C  70 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 86 through 93
    Processing helix  chain 'C' and resid 112 through 127
    Processing helix  chain 'C' and resid 142 through 152
    Processing helix  chain 'C' and resid 156 through 165
    Processing helix  chain 'C' and resid 174 through 192
    Processing helix  chain 'C' and resid 212 through 216
    Processing helix  chain 'C' and resid 221 through 242
      removed outlier: 3.746A  pdb=" N   ALA C 225 " --> pdb=" O   ARG C 221 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   LEU C 241 " --> pdb=" O   LEU C 237 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 265 through 270
      removed outlier: 4.087A  pdb=" N   PHE C 270 " --> pdb=" O   ARG C 266 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 23 through 28
      removed outlier: 3.501A  pdb=" N   ILE D  27 " --> pdb=" O   SER D  23 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 67
    Processing helix  chain 'D' and resid 68 through 72
    Processing helix  chain 'D' and resid 88 through 100
      removed outlier: 3.611A  pdb=" N   ILE D  95 " --> pdb=" O   ARG D  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 113
      removed outlier: 4.384A  pdb=" N   TYR D 110 " --> pdb=" O   GLU D 106 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 122 through 138
      removed outlier: 3.639A  pdb=" N   GLU D 134 " --> pdb=" O   LEU D 130 " (cutoff:3.500A)
      removed outlier: 5.247A  pdb=" N   SER D 135 " --> pdb=" O   TYR D 131 " (cutoff:3.500A)
      removed outlier: 4.199A  pdb=" N   MET D 136 " --> pdb=" O   SER D 132 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   PHE D 137 " --> pdb=" O   LEU D 133 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   CYS D 138 " --> pdb=" O   GLU D 134 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 154 through 162
      removed outlier: 3.570A  pdb=" N   VAL D 160 " --> pdb=" O   TRP D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 170
    Processing helix  chain 'D' and resid 170 through 187
      removed outlier: 3.590A  pdb=" N   LYS D 182 " --> pdb=" O   GLN D 178 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ASN D 185 " --> pdb=" O   GLU D 181 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 228 through 233
    Processing sheet with id=AA1, first strand: chain 'A' and resid 65 through 66
      removed outlier: 6.635A  pdb=" N   GLU B 154 " --> pdb=" O   ARG B 237 " (cutoff:3.500A)
      removed outlier: 5.979A  pdb=" N   VAL B 239 " --> pdb=" O   GLU B 154 " (cutoff:3.500A)
      removed outlier: 6.589A  pdb=" N   VAL B 156 " --> pdb=" O   VAL B 239 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   VAL B 241 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ILE B 158 " --> pdb=" O   VAL B 241 " (cutoff:3.500A)
      removed outlier: 6.558A  pdb=" N   THR B 121 " --> pdb=" O   LEU B 282 " (cutoff:3.500A)
      removed outlier: 6.879A  pdb=" N   ARG B 312 " --> pdb=" O   TYR B 327 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   HIS B 316 " --> pdb=" O   LEU B 323 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   VAL B 337 " --> pdb=" O   ALA B 324 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   CYS B 335 " --> pdb=" O   LEU B 326 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 340 through 342
    Processing sheet with id=AA3, first strand: chain 'C' and resid 66 through 67
      removed outlier: 7.522A  pdb=" N   LEU D 146 " --> pdb=" O   PHE D 192 " (cutoff:3.500A)
      removed outlier: 8.452A  pdb=" N   THR D 194 " --> pdb=" O   LEU D 146 " (cutoff:3.500A)
      removed outlier: 7.392A  pdb=" N   LEU D 148 " --> pdb=" O   THR D 194 " (cutoff:3.500A)
      removed outlier: 7.320A  pdb=" N   ILE D  43 " --> pdb=" O   HIS D 237 " (cutoff:3.500A)
      removed outlier: 8.687A  pdb=" N   MET D 239 " --> pdb=" O   ILE D  43 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   GLU D  45 " --> pdb=" O   MET D 239 " (cutoff:3.500A)
      removed outlier: 8.227A  pdb=" N   PHE D 241 " --> pdb=" O   GLU D  45 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   HIS D  47 " --> pdb=" O   PHE D 241 " (cutoff:3.500A)
      removed outlier: 9.305A  pdb=" N   LYS D 243 " --> pdb=" O   HIS D  47 " (cutoff:3.500A)
      removed outlier: 3.757A  pdb=" N   SER D 254 " --> pdb=" O   SER D 242 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   SER D 257 " --> pdb=" O   LYS D 266 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 81 through 82
    Processing sheet with id=AA5, first strand: chain 'C' and resid 167 through 171
      removed outlier: 6.812A  pdb=" N   LEU C 133 " --> pdb=" O   VAL C 204 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   ASP C 206 " --> pdb=" O   LEU C 133 " (cutoff:3.500A)
      removed outlier: 7.245A  pdb=" N   VAL C 135 " --> pdb=" O   ASP C 206 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   VAL C 203 " --> pdb=" O   ALA C 244 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   THR C 248 " --> pdb=" O   VAL C 205 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   THR C 103 " --> pdb=" O   VAL C 247 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   ASN C 249 " --> pdb=" O   THR C 103 " (cutoff:3.500A)
      removed outlier: 6.022A  pdb=" N   ILE C 105 " --> pdb=" O   ASN C 249 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR C 274 " --> pdb=" O   VAL C 102 " (cutoff:3.500A)
      removed outlier: 6.138A  pdb=" N   ARG C 275 " --> pdb=" O   ALA C 296 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 252 through 253

    338 hydrogen bonds defined for protein.
    942 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: 5.28

  Time building geometry restraints manager: 4.44 seconds

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

  Histogram of bond lengths:
        0.84 -     1.03: 7352
        1.03 -     1.23: 34
        1.23 -     1.42: 2983
        1.42 -     1.62: 4367
        1.62 -     1.81: 72
  Bond restraints: 14808
  Sorted by residual:
  bond pdb=" N   GLY C   2 "
       pdb=" CA  GLY C   2 "
    ideal  model  delta    sigma   weight residual
    1.451  1.491 -0.040 1.60e-02 3.91e+03 6.40e+00
  bond pdb=" N   GLY D  20 "
       pdb=" CA  GLY D  20 "
    ideal  model  delta    sigma   weight residual
    1.451  1.490 -0.039 1.60e-02 3.91e+03 6.08e+00
  bond pdb=" N   LYS A   4 "
       pdb=" CA  LYS A   4 "
    ideal  model  delta    sigma   weight residual
    1.458  1.490 -0.032 1.90e-02 2.77e+03 2.79e+00
  bond pdb=" N   GLY D  20 "
       pdb=" H   GLY D  20 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.29e+00
  bond pdb=" N   GLY C   2 "
       pdb=" H   GLY C   2 "
    ideal  model  delta    sigma   weight residual
    0.860  0.890 -0.030 2.00e-02 2.50e+03 2.25e+00
  ... (remaining 14803 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.72: 26780
       11.72 -    23.44: 0
       23.44 -    35.16: 0
       35.16 -    46.88: 0
       46.88 -    58.60: 1
  Bond angle restraints: 26781
  Sorted by residual:
  angle pdb=" C   MET B  10 "
        pdb=" N   GLN B  11 "
        pdb=" H   GLN B  11 "
      ideal   model   delta    sigma   weight residual
     123.68   65.08   58.60 3.00e+00 1.11e-01 3.82e+02
  angle pdb=" C3' ATP C 401 "
        pdb=" C4' ATP C 401 "
        pdb=" O4' ATP C 401 "
      ideal   model   delta    sigma   weight residual
     105.22  101.39    3.83 1.30e+00 5.94e-01 8.72e+00
  angle pdb=" C2' ATP C 401 "
        pdb=" C3' ATP C 401 "
        pdb=" O3' ATP C 401 "
      ideal   model   delta    sigma   weight residual
     111.83  105.17    6.66 2.67e+00 1.40e-01 6.23e+00
  angle pdb=" C3' ATP C 401 "
        pdb=" C2' ATP C 401 "
        pdb=" O2' ATP C 401 "
      ideal   model   delta    sigma   weight residual
     111.83  105.41    6.42 2.67e+00 1.40e-01 5.78e+00
  angle pdb=" C1' ATP D 302 "
        pdb=" C2' ATP D 302 "
        pdb=" O2' ATP D 302 "
      ideal   model   delta    sigma   weight residual
     110.58  103.86    6.72 2.79e+00 1.28e-01 5.78e+00
  ... (remaining 26776 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.12: 6589
       31.12 -    62.23: 292
       62.23 -    93.35: 33
       93.35 -   124.46: 1
      124.46 -   155.58: 2
  Dihedral angle restraints: 6917
    sinusoidal: 3881
      harmonic: 3036
  Sorted by residual:
  dihedral pdb=" C5' ADP B 401 "
           pdb=" O5' ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" O2A ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   95.58 -155.58     1      2.00e+01 2.50e-03 4.59e+01
  dihedral pdb=" O2A ADP B 401 "
           pdb=" O3A ADP B 401 "
           pdb=" PA  ADP B 401 "
           pdb=" PB  ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   88.76 -148.76     1      2.00e+01 2.50e-03 4.45e+01
  dihedral pdb=" O1B ADP B 401 "
           pdb=" O3A ADP B 401 "
           pdb=" PB  ADP B 401 "
           pdb=" PA  ADP B 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -176.52  116.52     1      2.00e+01 2.50e-03 3.47e+01
  ... (remaining 6914 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1057
       0.060 -    0.120: 102
       0.120 -    0.179: 12
       0.179 -    0.239: 1
       0.239 -    0.299: 5
  Chirality restraints: 1177
  Sorted by residual:
  chirality pdb=" C2' ATP D 302 "
            pdb=" C1' ATP D 302 "
            pdb=" C3' ATP D 302 "
            pdb=" O2' ATP D 302 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.98    0.30 2.00e-01 2.50e+01 2.24e+00
  chirality pdb=" C3' ATP C 401 "
            pdb=" C2' ATP C 401 "
            pdb=" C4' ATP C 401 "
            pdb=" O3' ATP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.93    0.29 2.00e-01 2.50e+01 2.11e+00
  chirality pdb=" C2' ATP C 401 "
            pdb=" C1' ATP C 401 "
            pdb=" C3' ATP C 401 "
            pdb=" O2' ATP C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.68   -2.97    0.29 2.00e-01 2.50e+01 2.10e+00
  ... (remaining 1174 not shown)

  Planarity restraints: 2148
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   MET B  10 "    0.092 2.00e-02 2.50e+03   2.32e-01 5.39e+02
        pdb=" N   GLN B  11 "   -0.399 2.00e-02 2.50e+03
        pdb=" CA  GLN B  11 "    0.135 2.00e-02 2.50e+03
        pdb=" H   GLN B  11 "    0.172 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE B 246 "    0.021 5.00e-02 4.00e+02   3.13e-02 1.57e+00
        pdb=" N   PRO B 247 "   -0.054 5.00e-02 4.00e+02
        pdb=" CA  PRO B 247 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO B 247 "    0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER D  37 "   -0.018 5.00e-02 4.00e+02   2.77e-02 1.23e+00
        pdb=" N   PRO D  38 "    0.048 5.00e-02 4.00e+02
        pdb=" CA  PRO D  38 "   -0.014 5.00e-02 4.00e+02
        pdb=" CD  PRO D  38 "   -0.016 5.00e-02 4.00e+02
  ... (remaining 2145 not shown)

  Histogram of nonbonded interaction distances:
        1.51 -     2.13: 340
        2.13 -     2.75: 26698
        2.75 -     3.37: 39756
        3.37 -     3.98: 50200
        3.98 -     4.60: 79939
  Nonbonded interactions: 196933
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU D 164 "
            pdb=" H   GLU D 164 "
     model   vdw
     1.513 2.450
  nonbonded pdb=" HG1 THR C 209 "
            pdb=" OD1 ASN C 249 "
     model   vdw
     1.625 2.450
  nonbonded pdb=" OD1 ASP C 279 "
            pdb=" H   THR C 280 "
     model   vdw
     1.631 2.450
  nonbonded pdb=" O   LEU D  58 "
            pdb=" HG1 THR D  62 "
     model   vdw
     1.636 2.450
  nonbonded pdb=" OE1 GLU D  28 "
            pdb=" H   ASN D  30 "
     model   vdw
     1.636 2.450
  ... (remaining 196928 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.380
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.180
  Extract box with map and model:          0.590
  Check model and map are aligned:         0.120
  Set scattering table:                    0.150
  Process input model:                     34.700
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.040
  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:2.850
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.120
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
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      :  0.002   0.040   7428  Z= 0.163
  Angle     :  0.523   6.715  10043  Z= 0.264
  Chirality :  0.042   0.299   1177
  Planarity :  0.003   0.031   1257
  Dihedral  : 17.648 155.580   2809
  Min Nonbonded Distance : 1.811

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 14.45 %
    Favored  : 85.55 %
  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: -0.78 (0.28), residues: 907
  helix:  0.06 (0.27), residues: 407
  sheet: -1.02 (0.41), residues: 153
  loop : -0.79 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 317 
 HIS   0.003   0.001   HIS D 237 
 PHE   0.007   0.001   PHE B 199 
 TYR   0.010   0.001   TYR C  72 
 ARG   0.002   0.000   ARG C  55 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 803 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.635 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   32 PHE cc_start: 0.7807 (m-10) cc_final: 0.7538 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 100
  average time/residue: 0.4769
  time to fit residues: 64.2432
Evaluate side-chains
  100 residues out of total 803 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 1.430 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    3.9990
   chunk 23 optimal weight:    0.8980
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    1.9990
   chunk 71 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 43 optimal weight:    0.6980
   chunk 53 optimal weight:    0.0170
   chunk 82 optimal weight:    1.9990
   overall best weight:    0.9222

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

Flipped N/Q/H residues before XYZ refinement:
** C 249 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.0944

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7428  Z= 0.218
  Angle     :  0.532   6.205  10043  Z= 0.279
  Chirality :  0.039   0.137   1177
  Planarity :  0.004   0.031   1257
  Dihedral  : 10.497 166.297   1069
  Min Nonbonded Distance : 1.748

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.07 %
    Favored  : 94.93 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 13.82 %
    Favored  : 85.18 %
  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: -0.59 (0.28), residues: 907
  helix:  0.32 (0.25), residues: 428
  sheet: -1.02 (0.40), residues: 152
  loop : -0.83 (0.36), residues: 327

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C 268 
 HIS   0.005   0.001   HIS B  95 
 PHE   0.011   0.001   PHE B 346 
 TYR   0.012   0.001   TYR C  72 
 ARG   0.004   0.000   ARG C 232 

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

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

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1814 Ramachandran restraints generated.
    907 Oldfield, 0 Emsley, 907 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 803 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 104
  time to evaluate  : 1.464 
Fit side-chains
   revert: symmetry clash
REVERT: B  192 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7744 (m-70)
REVERT: C   23 HIS cc_start: 0.4878 (m90) cc_final: 0.4405 (m170)
REVERT: D   32 PHE cc_start: 0.7862 (m-80) cc_final: 0.7595 (m-10)
  outliers start: 8
  outliers final: 5
  residues processed: 109
  average time/residue: 0.4794
  time to fit residues: 70.9327
Evaluate side-chains
  104 residues out of total 803 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 1.200 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  192 HIS
Chi-restraints excluded: chain B residue  196 LEU
Chi-restraints excluded: chain B residue  198 ASP
Chi-restraints excluded: chain B residue  220 LEU
Chi-restraints excluded: chain C residue  307 GLU
Chi-restraints excluded: chain D residue  111 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 45 optimal weight:    0.7980
   chunk 25 optimal weight:    2.9990
   chunk 68 optimal weight:    2.9990
   chunk 56 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 89 optimal weight:    0.0970
   chunk 73 optimal weight:    0.5980
   chunk 28 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
B  11 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7715
moved from start:          0.1256
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: