Starting phenix.real_space_refine
on Fri Aug 22 18:12:50 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8unq_42413/08_2025/8unq_42413.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8unq_42413/08_2025/8unq_42413.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8unq_42413/08_2025/8unq_42413.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8unq_42413/08_2025/8unq_42413.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8unq_42413/08_2025/8unq_42413.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8unq_42413/08_2025/8unq_42413.cif"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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=   0.025
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      40      5.16       5
     C    4289      2.51       5
     N    1161      2.21       5
     O    1194      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6687
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1770
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 239, 1758
          Classifications: {'peptide': 239}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 62}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 235
          Unresolved non-hydrogen angles: 286
          Unresolved non-hydrogen dihedrals: 187
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 8, 'ASN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 162
      Conformer: "B"
        Number of residues, atoms: 239, 1758
          Classifications: {'peptide': 239}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 62}
          Link IDs: {'PTRANS': 6, 'TRANS': 232}
          Chain breaks: 2
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 235
          Unresolved non-hydrogen angles: 286
          Unresolved non-hydrogen dihedrals: 187
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'GLU:plan': 18, 'ASP:plan': 10, 'GLN:plan1': 2, 'ARG:plan': 8, 'ASN:plan1': 2, 'PHE:plan': 1}
          Unresolved non-hydrogen planarities: 162
          bond proxies already assigned to first conformer: 1778
    Chain: "B"
      Number of atoms: 2412
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 334, 2412
          Classifications: {'peptide': 334}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 44}
          Link IDs: {'PTRANS': 5, 'TRANS': 328}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 157
          Unresolved non-hydrogen angles: 193
          Unresolved non-hydrogen dihedrals: 121
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 12, 'GLN:plan1': 5, 'ARG:plan': 7, 'ASN:plan1': 3}
          Unresolved non-hydrogen planarities: 120
    Chain: "G"
      Number of atoms: 343
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 55, 343
          Classifications: {'peptide': 55}
          Incomplete info: {'truncation_to_alanine': 24}
          Link IDs: {'PTRANS': 4, 'TRANS': 50}
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 83
          Unresolved non-hydrogen angles: 99
          Unresolved non-hydrogen dihedrals: 69
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 40
    Chain: "R"
      Number of atoms: 2114
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 287, 2114
          Classifications: {'peptide': 287}
          Incomplete info: {'truncation_to_alanine': 55}
          Link IDs: {'PTRANS': 7, 'TRANS': 279}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 202
          Unresolved non-hydrogen angles: 251
          Unresolved non-hydrogen dihedrals: 164
          Unresolved non-hydrogen chiralities: 13
          Planarities with less than four sites: {'ASP:plan': 5, 'GLU:plan': 10, 'TRP:plan': 1, 'GLN:plan1': 6, 'ASN:plan1': 3, 'ARG:plan': 3, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 122
    Chain: "A"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 32
          Unusual residues: {'GTP': 1}
          Classifications: {'undetermined': 1}
    Chain: "R"
      Number of atoms: 16
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 16
          Unusual residues: {'G1I': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR A 360 " occ=0.51
      ... (22 atoms not shown)
      pdb=" OH BTYR A 360 " occ=0.49
  Time building chain proxies: 1.55, per 1000 atoms: 0.23
  Number of scatterers: 6687
  At special positions: 0
  Unit cell: (85.9023, 135.361, 98.0501, 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)
     S      40     16.00
     P       3     15.00
     O    1194      8.00
     N    1161      7.00
     C    4289      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 106 " - pdb=" SG  CYS R 191 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R 184 " - pdb=" SG  CYS R 190 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.34
  Conformation dependent library (CDL) restraints added in 289.2 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1738

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 8 sheets defined
      48.4% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.20
  Creating SS restraints...
    Processing helix  chain 'A' and resid 10 through 40
      removed outlier: 3.565A  pdb=" N   GLU A  21 " --> pdb=" O   LYS A  17 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   ALA A  22 " --> pdb=" O   ALA A  18 " (cutoff:3.500A)
      removed outlier: 3.906A  pdb=" N   VAL A  36 " --> pdb=" O   LYS A  32 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR A  40 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 52 through 62
      removed outlier: 3.517A  pdb=" N   MET A  60 " --> pdb=" O   ILE A  56 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 239
      removed outlier: 3.582A  pdb=" N   GLN A 236 " --> pdb=" O   LYS A 233 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASN A 239 " --> pdb=" O   GLN A 236 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 264 through 278
    Processing helix  chain 'A' and resid 293 through 302
      removed outlier: 3.730A  pdb=" N   LEU A 297 " --> pdb=" O   LYS A 293 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA A 298 " --> pdb=" O   GLN A 294 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 307 through 312
      removed outlier: 4.143A  pdb=" N   TYR A 311 " --> pdb=" O   LYS A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 313 through 318
      removed outlier: 3.542A  pdb=" N   ALA A 316 " --> pdb=" O   PRO A 313 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG A 317 " --> pdb=" O   GLU A 314 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 331 through 352
      removed outlier: 3.568A  pdb=" N   PHE A 345 " --> pdb=" O   ILE A 341 " (cutoff:3.500A)
      removed outlier: 4.241A  pdb=" N   ILE A 348 " --> pdb=" O   GLU A 344 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   SER A 352 " --> pdb=" O   ILE A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 391
      removed outlier: 3.518A  pdb=" N   PHE A 376 " --> pdb=" O   ILE A 372 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   TYR A 391 " --> pdb=" O   HIS A 387 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 26
    Processing helix  chain 'B' and resid 29 through 34
      removed outlier: 3.702A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 9 through 24
      removed outlier: 3.507A  pdb=" N   LYS G  20 " --> pdb=" O   VAL G  16 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   MET G  21 " --> pdb=" O   GLU G  17 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.578A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   HIS G  44 " --> pdb=" O   TYR G  40 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 30 through 61
      removed outlier: 3.525A  pdb=" N   GLY R  50 " --> pdb=" O   ALA R  46 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   ASN R  51 " --> pdb=" O   ILE R  47 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE R  61 " --> pdb=" O   ALA R  57 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 67 through 97
      removed outlier: 4.266A  pdb=" N   PHE R  71 " --> pdb=" O   VAL R  67 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   ILE R  72 " --> pdb=" O   THR R  68 " (cutoff:3.500A)
      removed outlier: 4.560A  pdb=" N   VAL R  87 " --> pdb=" O   GLY R  83 " (cutoff:3.500A)
      Proline residue:  R  88  - end of helix
    Processing helix  chain 'R' and resid 102 through 137
      removed outlier: 4.114A  pdb=" N   ILE R 121 " --> pdb=" O   VAL R 117 " (cutoff:3.500A)
      removed outlier: 4.245A  pdb=" N   GLU R 122 " --> pdb=" O   THR R 118 " (cutoff:3.500A)
      removed outlier: 4.159A  pdb=" N   THR R 123 " --> pdb=" O   ALA R 119 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   LEU R 124 " --> pdb=" O   SER R 120 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 140 through 145
    Processing helix  chain 'R' and resid 146 through 163
      removed outlier: 3.891A  pdb=" N   ARG R 151 " --> pdb=" O   LYS R 147 " (cutoff:3.500A)
      removed outlier: 3.928A  pdb=" N   VAL R 152 " --> pdb=" O   ASN R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 166 through 171
    Processing helix  chain 'R' and resid 172 through 175
    Processing helix  chain 'R' and resid 178 through 187
    Processing helix  chain 'R' and resid 196 through 208
      removed outlier: 3.771A  pdb=" N   SER R 204 " --> pdb=" O   ALA R 200 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 209 through 238
      removed outlier: 3.831A  pdb=" N   VAL R 213 " --> pdb=" O   TYR R 209 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ILE R 214 " --> pdb=" O   VAL R 210 " (cutoff:3.500A)
      removed outlier: 4.091A  pdb=" N   MET R 215 " --> pdb=" O   PRO R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 269 through 287
      removed outlier: 3.747A  pdb=" N   PHE R 282 " --> pdb=" O   ILE R 278 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 288 through 299
      removed outlier: 4.541A  pdb=" N   ILE R 294 " --> pdb=" O   PHE R 290 " (cutoff:3.500A)
      removed outlier: 3.929A  pdb=" N   VAL R 297 " --> pdb=" O   ASN R 293 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   GLN R 299 " --> pdb=" O   VAL R 295 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 304 through 317
      removed outlier: 3.596A  pdb=" N   VAL R 317 " --> pdb=" O   TRP R 313 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 318 through 320
      No H-bonds generated for 'chain 'R' and resid 318 through 320'
    Processing helix  chain 'R' and resid 321 through 327
    Processing helix  chain 'R' and resid 329 through 339
      removed outlier: 3.521A  pdb=" N   LEU R 339 " --> pdb=" O   ALA R 335 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214
      removed outlier: 3.677A  pdb=" N   PHE A 212 " --> pdb=" O   PHE A 219 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   ARG A  42 " --> pdb=" O   ALA A 243 " (cutoff:3.500A)
      removed outlier: 8.262A  pdb=" N   ILE A 245 " --> pdb=" O   ARG A  42 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU A  44 " --> pdb=" O   ILE A 245 " (cutoff:3.500A)
      removed outlier: 7.752A  pdb=" N   VAL A 247 " --> pdb=" O   LEU A  44 " (cutoff:3.500A)
      removed outlier: 6.909A  pdb=" N   LEU A  46 " --> pdb=" O   VAL A 247 " (cutoff:3.500A)
      removed outlier: 9.096A  pdb=" N   ALA A 249 " --> pdb=" O   LEU A  46 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   ILE A 244 " --> pdb=" O   ILE A 288 " (cutoff:3.500A)
      removed outlier: 7.475A  pdb=" N   PHE A 290 " --> pdb=" O   ILE A 244 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   PHE A 246 " --> pdb=" O   PHE A 290 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   ASN A 292 " --> pdb=" O   PHE A 246 " (cutoff:3.500A)
      removed outlier: 6.516A  pdb=" N   VAL A 248 " --> pdb=" O   ASN A 292 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.619A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
      removed outlier: 3.655A  pdb=" N   GLY B 330 " --> pdb=" O   CYS B 317 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 4.193A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.935A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.724A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.134A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.225A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   GLY B 116 " --> pdb=" O   ILE B 120 " (cutoff:3.500A)
      removed outlier: 5.517A  pdb=" N   ILE B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 5.864A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.349A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.042A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.642A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.882A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.488A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.110A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.287A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.715A  pdb=" N   PHE B 199 " --> pdb=" O   TRP B 211 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.708A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.739A  pdb=" N   LEU B 210 " --> pdb=" O   ARG B 219 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 229 through 232
      removed outlier: 3.512A  pdb=" N   ALA B 231 " --> pdb=" O   GLY B 244 " (cutoff:3.500A)
      removed outlier: 3.792A  pdb=" N   PHE B 241 " --> pdb=" O   PHE B 253 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 277
      removed outlier: 3.827A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   LEU B 285 " --> pdb=" O   TRP B 297 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)

    356 hydrogen bonds defined for protein.
    1032 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: 0.94

  Time building geometry restraints manager: 0.46 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 1418
        1.33 -     1.45: 1637
        1.45 -     1.58: 3717
        1.58 -     1.70: 5
        1.70 -     1.82: 54
  Bond restraints: 6831
  Sorted by residual:
  bond pdb=" CA  SER A  51 "
       pdb=" CB  SER A  51 "
    ideal  model  delta    sigma   weight residual
    1.528  1.473  0.055 1.59e-02 3.96e+03 1.20e+01
  bond pdb=" N   GLU A  50 "
       pdb=" CA  GLU A  50 "
    ideal  model  delta    sigma   weight residual
    1.459  1.500 -0.042 1.32e-02 5.74e+03 9.94e+00
  bond pdb=" CA  ALA R 271 "
       pdb=" CB  ALA R 271 "
    ideal  model  delta    sigma   weight residual
    1.529  1.483  0.046 1.55e-02 4.16e+03 8.65e+00
  bond pdb=" N   LYS A  58 "
       pdb=" CA  LYS A  58 "
    ideal  model  delta    sigma   weight residual
    1.459  1.493 -0.034 1.17e-02 7.31e+03 8.53e+00
  bond pdb=" CA  SER A  54 "
       pdb=" CB  SER A  54 "
    ideal  model  delta    sigma   weight residual
    1.528  1.485  0.044 1.56e-02 4.11e+03 7.88e+00
  ... (remaining 6826 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 9109
        2.30 -     4.60: 209
        4.60 -     6.91: 19
        6.91 -     9.21: 7
        9.21 -    11.51: 4
  Bond angle restraints: 9348
  Sorted by residual:
  angle pdb=" N   ALA G  12 "
        pdb=" CA  ALA G  12 "
        pdb=" C   ALA G  12 "
      ideal   model   delta    sigma   weight residual
     111.28  104.30    6.98 1.09e+00 8.42e-01 4.10e+01
  angle pdb=" N   LEU G  19 "
        pdb=" CA  LEU G  19 "
        pdb=" C   LEU G  19 "
      ideal   model   delta    sigma   weight residual
     111.28  105.10    6.18 1.09e+00 8.42e-01 3.22e+01
  angle pdb=" N   ILE G   9 "
        pdb=" CA  ILE G   9 "
        pdb=" C   ILE G   9 "
      ideal   model   delta    sigma   weight residual
     110.62  105.19    5.43 1.02e+00 9.61e-01 2.84e+01
  angle pdb=" N   LEU B   7 "
        pdb=" CA  LEU B   7 "
        pdb=" C   LEU B   7 "
      ideal   model   delta    sigma   weight residual
     111.28  106.36    4.92 1.09e+00 8.42e-01 2.04e+01
  angle pdb=" N   LEU B   4 "
        pdb=" CA  LEU B   4 "
        pdb=" C   LEU B   4 "
      ideal   model   delta    sigma   weight residual
     111.28  106.37    4.91 1.09e+00 8.42e-01 2.03e+01
  ... (remaining 9343 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.64: 3857
       31.64 -    63.29: 90
       63.29 -    94.93: 3
       94.93 -   126.57: 1
      126.57 -   158.21: 1
  Dihedral angle restraints: 3952
    sinusoidal: 1276
      harmonic: 2676
  Sorted by residual:
  dihedral pdb=" CB  CYS R 184 "
           pdb=" SG  CYS R 184 "
           pdb=" SG  CYS R 190 "
           pdb=" CB  CYS R 190 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  154.11  -61.11     1      1.00e+01 1.00e-02 4.96e+01
  dihedral pdb=" C5' GTP A 401 "
           pdb=" O5' GTP A 401 "
           pdb=" PA  GTP A 401 "
           pdb=" O3A GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27 -132.52 -158.21     1      2.00e+01 2.50e-03 4.63e+01
  dihedral pdb=" C8  GTP A 401 "
           pdb=" C1' GTP A 401 "
           pdb=" N9  GTP A 401 "
           pdb=" O4' GTP A 401 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59   -5.32  109.91     1      2.00e+01 2.50e-03 3.22e+01
  ... (remaining 3949 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 810
       0.044 -    0.089: 212
       0.089 -    0.133: 75
       0.133 -    0.177: 14
       0.177 -    0.222: 8
  Chirality restraints: 1119
  Sorted by residual:
  chirality pdb=" CA  VAL A 256 "
            pdb=" N   VAL A 256 "
            pdb=" C   VAL A 256 "
            pdb=" CB  VAL A 256 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.66   -0.22 2.00e-01 2.50e+01 1.23e+00
  chirality pdb=" CA  ILE G   9 "
            pdb=" N   ILE G   9 "
            pdb=" C   ILE G   9 "
            pdb=" CB  ILE G   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.65   -0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  LEU B   7 "
            pdb=" N   LEU B   7 "
            pdb=" C   LEU B   7 "
            pdb=" CB  LEU B   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.21 2.00e-01 2.50e+01 1.15e+00
  ... (remaining 1116 not shown)

  Planarity restraints: 1172
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  17 "   -0.012 2.00e-02 2.50e+03   2.35e-02 5.53e+00
        pdb=" C   LYS A  17 "    0.041 2.00e-02 2.50e+03
        pdb=" O   LYS A  17 "   -0.015 2.00e-02 2.50e+03
        pdb=" N   ALA A  18 "   -0.014 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LYS A  53 "   -0.011 2.00e-02 2.50e+03   2.18e-02 4.73e+00
        pdb=" C   LYS A  53 "    0.038 2.00e-02 2.50e+03
        pdb=" O   LYS A  53 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   SER A  54 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B   7 "   -0.010 2.00e-02 2.50e+03   2.09e-02 4.36e+00
        pdb=" C   LEU B   7 "    0.036 2.00e-02 2.50e+03
        pdb=" O   LEU B   7 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   ARG B   8 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 1169 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 804
        2.75 -     3.29: 6422
        3.29 -     3.83: 10435
        3.83 -     4.36: 11471
        4.36 -     4.90: 21280
  Nonbonded interactions: 50412
  Sorted by model distance:
  nonbonded pdb=" O   GLN B  75 "
            pdb=" OG  SER B  98 "
     model   vdw
     2.218 3.040
  nonbonded pdb=" OG1 THR B  86 "
            pdb=" OD1 ASN B  88 "
     model   vdw
     2.242 3.040
  nonbonded pdb=" OH  TYR R 326 "
            pdb=" O   HOH R 601 "
     model   vdw
     2.350 3.040
  nonbonded pdb=" OD1 ASN A 292 "
            pdb=" N   LYS A 293 "
     model   vdw
     2.352 3.120
  nonbonded pdb=" OD1 ASP A 295 "
            pdb=" N   LEU A 296 "
     model   vdw
     2.352 3.120
  ... (remaining 50407 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=0.49 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:             2.190
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     6.350
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.020
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
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      :  0.004   0.055   6833  Z= 0.303
  Angle     :  0.766  11.509   9352  Z= 0.506
  Chirality :  0.049   0.222   1119
  Planarity :  0.004   0.051   1172
  Dihedral  : 13.493 158.212   2208
  Min Nonbonded Distance : 2.218

Molprobity Statistics.
  All-atom Clashscore : 3.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Rotamer:
    Outliers :  0.33 %
    Allowed  :  0.99 %
    Favored  : 98.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (0.29), residues: 902
  helix:  2.20 (0.27), residues: 397
  sheet:  0.32 (0.42), residues: 166
  loop : -0.87 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG R 175 
 TYR   0.007   0.001   TYR B  59 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.006   0.001   TRP R 105 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00445 ( 6831)
  covalent geometry    : angle       0.76578 ( 9348)
  SS BOND              : bond        0.00166 (    2)
  SS BOND              : angle       0.91142 (    4)
  hydrogen bonds       : bond        0.20167 (  356)
  hydrogen bonds       : angle       6.78438 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 110
  time to evaluate  : 0.237 
Fit side-chains
REVERT: B   78 LYS cc_start: 0.8439 (ttmm) cc_final: 0.8173 (mttp)
REVERT: G   38 MET cc_start: 0.8235 (tpp) cc_final: 0.7914 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 111
  average time/residue: 0.0775
  time to fit residues: 11.3766
Evaluate side-chains
  88 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  269 HIS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 49 optimal weight:    0.0970
   chunk 53 optimal weight:    6.9990
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 38 optimal weight:    4.9990
   chunk 61 optimal weight:   20.0000
   chunk 45 optimal weight:    0.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.3685 r_free = 0.3685 target = 0.131111 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.105169 restraints weight = 41717.351|
|-----------------------------------------------------------------------------|
r_work (start): 0.3352 rms_B_bonded: 5.14
r_work (final): 0.3352
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3352
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3352 r_free = 0.3352    target_work(ls_wunit_k1) = 0.104         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3352
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8267
moved from start:          0.1141

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   6833  Z= 0.115
  Angle     :  0.486   6.864   9352  Z= 0.263
  Chirality :  0.041   0.152   1119
  Planarity :  0.003   0.037   1172
  Dihedral  :  7.421 147.301   1007
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  9.36 %
    Favored  : 90.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.29 (0.29), residues: 902
  helix:  2.31 (0.27), residues: 407
  sheet:  0.43 (0.42), residues: 167
  loop : -0.80 (0.33), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  42 
 TYR   0.010   0.001   TYR A 339 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.005   0.001   TRP A 277 
 HIS   0.005   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6831)
  covalent geometry    : angle       0.48429 ( 9348)
  SS BOND              : bond        0.00669 (    2)
  SS BOND              : angle       2.26098 (    4)
  hydrogen bonds       : bond        0.04587 (  356)
  hydrogen bonds       : angle       4.69529 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 96
  time to evaluate  : 0.260 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.7898 (m-80) cc_final: 0.7633 (m-80)
REVERT: G   38 MET cc_start: 0.7849 (tpp) cc_final: 0.7488 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 97
  average time/residue: 0.0817
  time to fit residues: 10.5635
Evaluate side-chains
  89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 88
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 27 optimal weight:    3.9990
   chunk 85 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 50 optimal weight:    0.9980
   chunk 48 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9980
   chunk 42 optimal weight:    0.8980
   chunk 24 optimal weight:   10.0000
   chunk 64 optimal weight:    5.9990
   chunk 30 optimal weight:    3.9990
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 294 GLN
B  75 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.130239 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.104473 restraints weight = 31015.996|
|-----------------------------------------------------------------------------|
r_work (start): 0.3351 rms_B_bonded: 4.71
r_work: 0.3179 rms_B_bonded: 4.78 restraints_weight: 0.5000
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3166
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8420
moved from start:          0.1490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6833  Z= 0.110
  Angle     :  0.455   6.327   9352  Z= 0.245
  Chirality :  0.040   0.152   1119
  Planarity :  0.003   0.036   1172
  Dihedral  :  7.164 146.456   1005
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 2.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.33 %
    Favored  : 98.67 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 10.84 %
    Favored  : 88.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.29), residues: 902
  helix:  2.65 (0.27), residues: 401
  sheet:  0.32 (0.42), residues: 160
  loop : -0.79 (0.33), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.011   0.001   TYR R 308 
 PHE   0.011   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B 339 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 ( 6831)
  covalent geometry    : angle       0.45283 ( 9348)
  SS BOND              : bond        0.00160 (    2)
  SS BOND              : angle       2.19597 (    4)
  hydrogen bonds       : bond        0.04134 (  356)
  hydrogen bonds       : angle       4.20333 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.272 
Fit side-chains
REVERT: G   38 MET cc_start: 0.8520 (tpp) cc_final: 0.8210 (mtp)
  outliers start: 3
  outliers final: 2
  residues processed: 94
  average time/residue: 0.0793
  time to fit residues: 10.0268
Evaluate side-chains
  90 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 27 optimal weight:    4.9990
   chunk 77 optimal weight:    2.9990
   chunk 67 optimal weight:    1.9990
   chunk 9 optimal weight:    2.9990
   chunk 50 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 70 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 3 optimal weight:    2.9990
   chunk 21 optimal weight:    0.1980
   chunk 65 optimal weight:    0.9990
   overall best weight:    1.0384

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

Flipped N/Q/H residues before XYZ refinement:
** R  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.129046 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.102669 restraints weight = 34841.833|
|-----------------------------------------------------------------------------|
r_work (start): 0.3319 rms_B_bonded: 4.97
r_work: 0.3146 rms_B_bonded: 4.95 restraints_weight: 0.5000
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3139
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3139 r_free = 0.3139    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3139
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.021   6833  Z= 0.121
  Angle     :  0.464   6.505   9352  Z= 0.249
  Chirality :  0.040   0.149   1119
  Planarity :  0.003   0.037   1172
  Dihedral  :  7.114 145.257   1005
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.66 %
    Favored  : 87.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.29), residues: 902
  helix:  2.62 (0.27), residues: 406
  sheet:  0.15 (0.41), residues: 162
  loop : -0.65 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.012   0.001   TYR R 308 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.006   0.001   TRP A 277 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00274 ( 6831)
  covalent geometry    : angle       0.46305 ( 9348)
  SS BOND              : bond        0.00109 (    2)
  SS BOND              : angle       1.46200 (    4)
  hydrogen bonds       : bond        0.04204 (  356)
  hydrogen bonds       : angle       4.11753 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 91
  time to evaluate  : 0.257 
Fit side-chains
REVERT: B   59 TYR cc_start: 0.8591 (m-80) cc_final: 0.6955 (m-80)
REVERT: G   38 MET cc_start: 0.8568 (tpp) cc_final: 0.8227 (mtp)
  outliers start: 8
  outliers final: 4
  residues processed: 97
  average time/residue: 0.0687
  time to fit residues: 8.8947
Evaluate side-chains
  91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 75 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   chunk 63 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 15 optimal weight:    0.0670
   chunk 74 optimal weight:    0.7980
   chunk 42 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 9 optimal weight:    0.9980
   chunk 35 optimal weight:    0.7980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
** A 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** R  51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.128082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.104434 restraints weight = 27059.345|
|-----------------------------------------------------------------------------|
r_work (start): 0.3260 rms_B_bonded: 3.84
r_work: 0.3114 rms_B_bonded: 4.29 restraints_weight: 0.5000
r_work (final): 0.3114
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3125
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3125 r_free = 0.3125    target_work(ls_wunit_k1) = 0.093         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3125
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040   6833  Z= 0.102
  Angle     :  0.446   6.339   9352  Z= 0.240
  Chirality :  0.039   0.143   1119
  Planarity :  0.003   0.037   1172
  Dihedral  :  7.048 145.262   1005
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 2.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.78 %
    Favored  : 98.22 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 12.64 %
    Favored  : 86.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.56 (0.29), residues: 902
  helix:  2.69 (0.27), residues: 406
  sheet:  0.21 (0.41), residues: 160
  loop : -0.64 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.009   0.001   TYR R 308 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.006   0.001   TRP B  63 
 HIS   0.004   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 6831)
  covalent geometry    : angle       0.44388 ( 9348)
  SS BOND              : bond        0.00145 (    2)
  SS BOND              : angle       2.07072 (    4)
  hydrogen bonds       : bond        0.03759 (  356)
  hydrogen bonds       : angle       4.01213 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 90
  time to evaluate  : 0.268 
Fit side-chains
REVERT: G   38 MET cc_start: 0.8508 (tpp) cc_final: 0.8159 (mtp)
  outliers start: 3
  outliers final: 3
  residues processed: 93
  average time/residue: 0.0956
  time to fit residues: 11.8101
Evaluate side-chains
  92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 89
  time to evaluate  : 0.270 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 16 optimal weight:    0.2980
   chunk 58 optimal weight:    2.9990
   chunk 63 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   chunk 43 optimal weight:    5.9990
   chunk 45 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0670
   chunk 71 optimal weight:    1.9990
   chunk 85 optimal weight:    0.0970
   overall best weight:    0.4316

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

Flipped N/Q/H residues before XYZ refinement:
B  75 GLN
R  51 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.129786 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.105291 restraints weight = 37678.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.3276 rms_B_bonded: 4.84
r_work (final): 0.3276
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3275
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3275 r_free = 0.3275    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3275
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8237
moved from start:          0.1858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   6833  Z= 0.086
  Angle     :  0.424   6.366   9352  Z= 0.228
  Chirality :  0.039   0.139   1119
  Planarity :  0.003   0.036   1172
  Dihedral  :  6.925 145.898   1005
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 2.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.49 %
    Allowed  : 12.97 %
    Favored  : 86.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.67 (0.29), residues: 902
  helix:  2.78 (0.27), residues: 406
  sheet:  0.30 (0.42), residues: 160
  loop : -0.61 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 385 
 TYR   0.007   0.001   TYR R 308 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.006   0.001   TRP R 105 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00172 ( 6831)
  covalent geometry    : angle       0.42253 ( 9348)
  SS BOND              : bond        0.00257 (    2)
  SS BOND              : angle       1.84669 (    4)
  hydrogen bonds       : bond        0.03179 (  356)
  hydrogen bonds       : angle       3.85166 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 91
  time to evaluate  : 0.186 
Fit side-chains
REVERT: A  295 ASP cc_start: 0.8522 (p0) cc_final: 0.8315 (p0)
REVERT: G   38 MET cc_start: 0.7815 (tpp) cc_final: 0.7455 (mtp)
  outliers start: 3
  outliers final: 3
  residues processed: 93
  average time/residue: 0.0855
  time to fit residues: 10.5285
Evaluate side-chains
  95 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 0.262 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   63 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 62 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 84 optimal weight:    1.9990
   chunk 61 optimal weight:    6.9990
   chunk 5 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   chunk 23 optimal weight:   30.0000
   chunk 26 optimal weight:    8.9990
   chunk 77 optimal weight:    2.9990
   chunk 49 optimal weight:    7.9990
   chunk 0 optimal weight:   30.0000
   overall best weight:    1.5384

-------------------------------------------------------------------------------
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 = 0.3546 r_free = 0.3546 target = 0.124229 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.099631 restraints weight = 41541.726|
|-----------------------------------------------------------------------------|
r_work (start): 0.3190 rms_B_bonded: 4.91
r_work (final): 0.3190
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.098         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8335
moved from start:          0.1920

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6833  Z= 0.162
  Angle     :  0.505   6.404   9352  Z= 0.272
  Chirality :  0.041   0.152   1119
  Planarity :  0.003   0.038   1172
  Dihedral  :  7.160 143.044   1005
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 3.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.11 %
    Favored  : 97.89 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.64 %
    Favored  : 86.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.29), residues: 902
  helix:  2.66 (0.27), residues: 412
  sheet:  0.04 (0.42), residues: 162
  loop : -0.64 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.015   0.001   TYR R 308 
 PHE   0.018   0.001   PHE B 241 
 TRP   0.005   0.001   TRP B 339 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 6831)
  covalent geometry    : angle       0.50394 ( 9348)
  SS BOND              : bond        0.00245 (    2)
  SS BOND              : angle       1.79612 (    4)
  hydrogen bonds       : bond        0.04769 (  356)
  hydrogen bonds       : angle       4.11391 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 89
  time to evaluate  : 0.273 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8562 (OUTLIER) cc_final: 0.7441 (t80)
REVERT: G   38 MET cc_start: 0.7837 (tpp) cc_final: 0.7423 (mtp)
REVERT: R  231 GLN cc_start: 0.8610 (tm-30) cc_final: 0.8317 (tm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 94
  average time/residue: 0.1025
  time to fit residues: 12.4654
Evaluate side-chains
  93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.268 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   63 ARG
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  203 SER
Chi-restraints excluded: chain R residue  295 VAL
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 66 optimal weight:    0.9980
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    0.6980
   chunk 23 optimal weight:   30.0000
   chunk 64 optimal weight:    6.9990
   chunk 88 optimal weight:    0.9990
   chunk 35 optimal weight:    2.9990
   chunk 55 optimal weight:    0.6980
   chunk 56 optimal weight:    1.9990
   chunk 6 optimal weight:    3.9990
   chunk 77 optimal weight:    4.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
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 = 0.3563 r_free = 0.3563 target = 0.125409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3225 r_free = 0.3225 target = 0.100385 restraints weight = 34195.874|
|-----------------------------------------------------------------------------|
r_work (start): 0.3203 rms_B_bonded: 4.52
r_work: 0.3043 rms_B_bonded: 4.82 restraints_weight: 0.5000
r_work (final): 0.3043
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3049
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3049 r_free = 0.3049    target_work(ls_wunit_k1) = 0.088         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3049
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8447
moved from start:          0.1958

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   6833  Z= 0.124
  Angle     :  0.469   6.309   9352  Z= 0.252
  Chirality :  0.040   0.144   1119
  Planarity :  0.003   0.037   1172
  Dihedral  :  7.074 142.639   1005
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 2.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 12.48 %
    Favored  : 86.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.49 (0.30), residues: 902
  helix:  2.67 (0.27), residues: 410
  sheet: -0.03 (0.42), residues: 162
  loop : -0.67 (0.34), residues: 330

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG R 175 
 TYR   0.011   0.001   TYR R 308 
 PHE   0.013   0.001   PHE B 241 
 TRP   0.005   0.001   TRP B  63 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 6831)
  covalent geometry    : angle       0.46757 ( 9348)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       1.64588 (    4)
  hydrogen bonds       : bond        0.04190 (  356)
  hydrogen bonds       : angle       4.04181 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 87
  time to evaluate  : 0.223 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8773 (OUTLIER) cc_final: 0.7485 (t80)
REVERT: G   38 MET cc_start: 0.8543 (tpp) cc_final: 0.8183 (mtp)
  outliers start: 7
  outliers final: 6
  residues processed: 91
  average time/residue: 0.0892
  time to fit residues: 10.6116
Evaluate side-chains
  92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 85
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   63 ARG
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 21 optimal weight:    0.0000
   chunk 37 optimal weight:    3.9990
   chunk 64 optimal weight:    6.9990
   chunk 76 optimal weight:    3.9990
   chunk 40 optimal weight:    5.9990
   chunk 28 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 42 optimal weight:    1.9990
   chunk 81 optimal weight:    3.9990
   chunk 23 optimal weight:   30.0000
   chunk 71 optimal weight:    0.9990
   overall best weight:    1.7992

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

Flipped N/Q/H residues before XYZ refinement:
R 172 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.122542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.097491 restraints weight = 36265.497|
|-----------------------------------------------------------------------------|
r_work (start): 0.3160 rms_B_bonded: 4.53
r_work: 0.3002 rms_B_bonded: 4.80 restraints_weight: 0.5000
r_work (final): 0.3002
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3005
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.48   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3005 r_free = 0.3005    target_work(ls_wunit_k1) = 0.086         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3005
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.2068

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   6833  Z= 0.183
  Angle     :  0.525   6.366   9352  Z= 0.283
  Chirality :  0.042   0.151   1119
  Planarity :  0.003   0.039   1172
  Dihedral  :  7.255 140.262   1005
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 2.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.34 %
    Favored  : 97.66 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 12.48 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.27 (0.29), residues: 902
  helix:  2.53 (0.26), residues: 412
  sheet: -0.25 (0.41), residues: 162
  loop : -0.79 (0.34), residues: 328

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG R 175 
 TYR   0.016   0.001   TYR A 339 
 PHE   0.018   0.001   PHE B 241 
 TRP   0.006   0.001   TRP B  63 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00440 ( 6831)
  covalent geometry    : angle       0.52388 ( 9348)
  SS BOND              : bond        0.00230 (    2)
  SS BOND              : angle       1.78784 (    4)
  hydrogen bonds       : bond        0.05146 (  356)
  hydrogen bonds       : angle       4.24813 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.208 
Fit side-chains
REVERT: B  234 PHE cc_start: 0.8828 (OUTLIER) cc_final: 0.7618 (t80)
REVERT: G   38 MET cc_start: 0.8606 (tpp) cc_final: 0.8215 (mtp)
REVERT: R  231 GLN cc_start: 0.8868 (tm-30) cc_final: 0.8616 (tm-30)
  outliers start: 8
  outliers final: 7
  residues processed: 90
  average time/residue: 0.0714
  time to fit residues: 8.5849
Evaluate side-chains
  92 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 84
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  234 PHE
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   63 ARG
Chi-restraints excluded: chain R residue  161 SER
Chi-restraints excluded: chain R residue  203 SER
Chi-restraints excluded: chain R residue  272 LEU
Chi-restraints excluded: chain R residue  314 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 71 optimal weight:    0.5980
   chunk 29 optimal weight:    4.9990
   chunk 28 optimal weight:    3.9990
   chunk 70 optimal weight:    0.8980
   chunk 52 optimal weight:    0.8980
   chunk 50 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0060
   chunk 4 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 57 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   overall best weight:    0.6796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.126172 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3244 r_free = 0.3244 target = 0.101544 restraints weight = 34428.242|
|-----------------------------------------------------------------------------|
r_work (start): 0.3221 rms_B_bonded: 4.41
r_work: 0.3063 rms_B_bonded: 4.75 restraints_weight: 0.5000
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.47   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3069 r_free = 0.3069    target_work(ls_wunit_k1) = 0.090         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8427
moved from start:          0.2033

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6833  Z= 0.101
  Angle     :  0.451   6.241   9352  Z= 0.243
  Chirality :  0.039   0.140   1119
  Planarity :  0.003   0.039   1172
  Dihedral  :  7.096 141.871   1005
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 2.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.56 %
    Favored  : 98.44 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 13.14 %
    Favored  : 86.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.43 (0.29), residues: 902
  helix:  2.66 (0.27), residues: 410
  sheet: -0.09 (0.42), residues: 160
  loop : -0.73 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.011   0.001   TYR B  59 
 PHE   0.011   0.001   PHE A 212 
 TRP   0.007   0.001   TRP R 105 
 HIS   0.008   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 6831)
  covalent geometry    : angle       0.45021 ( 9348)
  SS BOND              : bond        0.00135 (    2)
  SS BOND              : angle       1.53281 (    4)
  hydrogen bonds       : bond        0.03703 (  356)
  hydrogen bonds       : angle       3.99873 ( 1032)

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

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

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1804 Ramachandran restraints generated.
    902 Oldfield, 0 Emsley, 902 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.187 
Fit side-chains
REVERT: G   38 MET cc_start: 0.8553 (tpp) cc_final: 0.8191 (mtp)
REVERT: R  231 GLN cc_start: 0.8783 (tm-30) cc_final: 0.8406 (tm-30)
  outliers start: 4
  outliers final: 4
  residues processed: 89
  average time/residue: 0.0824
  time to fit residues: 9.5008
Evaluate side-chains
  89 residues out of total 792 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  243 THR
Chi-restraints excluded: chain B residue  327 VAL
Chi-restraints excluded: chain R residue   63 ARG
Chi-restraints excluded: chain R residue  272 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 89
   random chunks:
   chunk 59 optimal weight:    0.8980
   chunk 4 optimal weight:    8.9990
   chunk 34 optimal weight:    0.8980
   chunk 81 optimal weight:    0.6980
   chunk 12 optimal weight:    0.0040
   chunk 56 optimal weight:    0.2980
   chunk 88 optimal weight:    0.9990
   chunk 3 optimal weight:    5.9990
   chunk 71 optimal weight:    1.9990
   chunk 86 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   overall best weight:    0.5392

-------------------------------------------------------------------------------
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 = 0.3593 r_free = 0.3593 target = 0.127735 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.102764 restraints weight = 34220.564|
|-----------------------------------------------------------------------------|
r_work (start): 0.3243 rms_B_bonded: 4.57
r_work: 0.3084 rms_B_bonded: 4.87 restraints_weight: 0.5000
r_work (final): 0.3084
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3084
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3084 r_free = 0.3084    target_work(ls_wunit_k1) = 0.091         |
| occupancies: max = 1.00  min = 0.49   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3084
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8407
moved from start:          0.2066

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   6833  Z= 0.091
  Angle     :  0.448   8.993   9352  Z= 0.236
  Chirality :  0.039   0.139   1119
  Planarity :  0.003   0.037   1172
  Dihedral  :  6.975 142.613   1005
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 2.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.89 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  0.66 %
    Allowed  : 13.46 %
    Favored  : 85.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.52 (0.30), residues: 902
  helix:  2.80 (0.26), residues: 404
  sheet: -0.04 (0.41), residues: 165
  loop : -0.74 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 385 
 TYR   0.009   0.001   TYR A 339 
 PHE   0.012   0.001   PHE A 212 
 TRP   0.007   0.001   TRP R 105 
 HIS   0.007   0.001   HIS A 220 

Details of bonding type rmsd
  covalent geometry    : bond        0.00191 ( 6831)
  covalent geometry    : angle       0.44656 ( 9348)
  SS BOND              : bond        0.00191 (    2)
  SS BOND              : angle       1.47087 (    4)
  hydrogen bonds       : bond        0.03403 (  356)
  hydrogen bonds       : angle       3.88893 ( 1032)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1543.68 seconds
wall clock time: 27 minutes 4.11 seconds (1624.11 seconds total)