Starting phenix.real_space_refine
on Fri Dec  8 14:27:16 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/12_2023/8ia7_35297_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/12_2023/8ia7_35297.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/12_2023/8ia7_35297.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/12_2023/8ia7_35297.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/12_2023/8ia7_35297_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ia7_35297/12_2023/8ia7_35297_updated.pdb"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


Starting job
===============================================================================
-------------------------------------------------------------------------------
Citation:
*********
Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams
PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography.
Acta Cryst. D74:531-544.

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.006
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: 4
    Type Number    sf(0)   Gaussians
     S      59      5.16       5
     C    5489      2.51       5
     N    1473      2.21       5
     O    1565      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "R ARG  201": "NH1" <-> "NH2"
    Residue "R ARG  333": "NH1" <-> "NH2"
    Residue "R ARG  396": "NH1" <-> "NH2"
    Residue "R PHE  397": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  403": "OE1" <-> "OE2"
    Residue "B ARG   68": "NH1" <-> "NH2"
    Residue "B ARG  134": "NH1" <-> "NH2"
    Residue "B ARG  137": "NH1" <-> "NH2"
    Residue "B ARG  256": "NH1" <-> "NH2"
    Residue "E PHE   27": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "E ARG  148": "NH1" <-> "NH2"
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU   14": "OE1" <-> "OE2"
    Residue "A ARG   15": "NH1" <-> "NH2"
    Residue "A ARG   24": "NH1" <-> "NH2"
    Residue "A ARG   32": "NH1" <-> "NH2"
    Residue "A GLU   43": "OE1" <-> "OE2"
    Residue "A ARG  208": "NH1" <-> "NH2"
    Residue "A GLU  215": "OE1" <-> "OE2"
    Residue "A GLU  228": "OE1" <-> "OE2"
    Residue "A GLU  243": "OE1" <-> "OE2"
    Residue "A GLU  244": "OE1" <-> "OE2"
    Residue "A ARG  250": "NH1" <-> "NH2"
    Residue "A ARG  294": "NH1" <-> "NH2"
    Residue "A GLU  301": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib"
  Total number of atoms: 8586
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "R"
      Number of atoms: 2159
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2159
          Classifications: {'peptide': 276}
          Link IDs: {'PTRANS': 13, 'TRANS': 262}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2471
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2471
          Classifications: {'peptide': 338}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
          Unresolved non-hydrogen bonds: 132
          Unresolved non-hydrogen angles: 162
          Unresolved non-hydrogen dihedrals: 106
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 6, 'ASN:plan1': 1, 'HIS:plan': 1, 'PHE:plan': 1, 'GLU:plan': 4, 'ARG:plan': 7}
          Unresolved non-hydrogen planarities: 99
    Chain: "C"
      Number of atoms: 353
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 51, 353
          Classifications: {'peptide': 51}
          Incomplete info: {'truncation_to_alanine': 11}
          Link IDs: {'PTRANS': 4, 'TRANS': 46}
          Unresolved non-hydrogen bonds: 41
          Unresolved non-hydrogen angles: 48
          Unresolved non-hydrogen dihedrals: 34
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 2, 'ARG:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "E"
      Number of atoms: 1723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1723
          Classifications: {'peptide': 231}
          Incomplete info: {'truncation_to_alanine': 16}
          Link IDs: {'PTRANS': 10, 'TRANS': 220}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 67
          Unresolved non-hydrogen dihedrals: 41
          Unresolved non-hydrogen chiralities: 4
          Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 7, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 37
    Chain: "A"
      Number of atoms: 1802
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1802
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 213}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 78
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 78
          Unusual residues: {'NH2': 1}
          Classifications: {'peptide': 8, 'undetermined': 1}
          Link IDs: {'NH2_CTERM': 1, 'TRANS': 7}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'TYS:plan-2': 1}
          Unresolved non-hydrogen planarities: 1
  Time building chain proxies: 5.08, per 1000 atoms: 0.59
  Number of scatterers: 8586
  At special positions: 0
  Unit cell: (114.582, 114.582, 123.708, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      59     16.00
     O    1565      8.00
     N    1473      7.00
     C    5489      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 127 " - pdb=" SG  CYS R 205 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 147 " - pdb=" SG  CYS E 217 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amino acid           : False - 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: 3.48
  Conformation dependent library (CDL) restraints added in 1.8 seconds
  

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2096

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      24 helices and 14 sheets defined
      32.1% alpha, 21.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.65
  Creating SS restraints...
    Processing helix  chain 'R' and resid 55 through 81
    Processing helix  chain 'R' and resid 88 through 107
      removed outlier: 4.018A  pdb=" N   PHE R  92 " --> pdb=" O   VAL R  88 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 109 through 116
      Proline residue:  R 114  - end of helix
    Processing helix  chain 'R' and resid 123 through 157
      removed outlier: 3.567A  pdb=" N   SER R 139 " --> pdb=" O   GLY R 135 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 159 through 163
    Processing helix  chain 'R' and resid 168 through 191
      removed outlier: 4.004A  pdb=" N   VAL R 187 " --> pdb=" O   GLY R 183 " (cutoff:3.500A)
      Proline residue:  R 188  - end of helix
    Processing helix  chain 'R' and resid 215 through 226
    Processing helix  chain 'R' and resid 228 through 247
    Processing helix  chain 'R' and resid 325 through 359
      Proline residue:  R 348  - end of helix
    Processing helix  chain 'R' and resid 361 through 366
    Processing helix  chain 'R' and resid 371 through 390
      removed outlier: 3.981A  pdb=" N   SER R 382 " --> pdb=" O   LEU R 378 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ALA R 383 " --> pdb=" O   SER R 379 " (cutoff:3.500A)
      removed outlier: 3.854A  pdb=" N   CYS R 384 " --> pdb=" O   TYR R 380 " (cutoff:3.500A)
      Proline residue:  R 387  - end of helix
    Processing helix  chain 'R' and resid 396 through 402
      removed outlier: 3.616A  pdb=" N   CYS R 401 " --> pdb=" O   ARG R 398 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 4 through 24
      removed outlier: 3.665A  pdb=" N   ARG B   8 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 33
      No H-bonds generated for 'chain 'B' and resid 30 through 33'
    Processing helix  chain 'C' and resid 13 through 23
    Processing helix  chain 'C' and resid 30 through 43
    Processing helix  chain 'E' and resid 29 through 31
      No H-bonds generated for 'chain 'E' and resid 29 through 31'
    Processing helix  chain 'A' and resid 7 through 32
      removed outlier: 3.901A  pdb=" N   ALA A  11 " --> pdb=" O   ALA A   7 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 55
    Processing helix  chain 'A' and resid 211 through 213
      No H-bonds generated for 'chain 'A' and resid 211 through 213'
    Processing helix  chain 'A' and resid 241 through 253
    Processing helix  chain 'A' and resid 270 through 276
    Processing helix  chain 'A' and resid 298 through 308
    Processing helix  chain 'A' and resid 330 through 349
    Processing sheet with id=  A, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.735A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.364A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.069A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.309A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.953A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.966A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.456A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.158A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 6.335A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.404A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 146 through 151
      removed outlier: 7.055A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.340A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.019A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   THR B 178 " --> pdb=" O   LEU B 168 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.481A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.957A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.678A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 4.098A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.598A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.550A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.844A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.392A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 5.153A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.361A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.909A  pdb=" N   SER B 245 " --> pdb=" O   THR B 249 " (cutoff:3.500A)
      removed outlier: 4.726A  pdb=" N   THR B 249 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   CYS B 250 " --> pdb=" O   TYR B 264 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.845A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 276 through 278
      removed outlier: 3.586A  pdb=" N   GLY B 306 " --> pdb=" O   VAL B 296 " (cutoff:3.500A)
      removed outlier: 6.124A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.445A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 47 through 51
      removed outlier: 6.817A  pdb=" N   ILE B 338 " --> pdb=" O   ARG B  48 " (cutoff:3.500A)
      removed outlier: 4.888A  pdb=" N   THR B  50 " --> pdb=" O   LEU B 336 " (cutoff:3.500A)
      removed outlier: 6.774A  pdb=" N   LEU B 336 " --> pdb=" O   THR B  50 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'E' and resid 3 through 7
    Processing sheet with id=  I, first strand: chain 'E' and resid 10 through 12
    Processing sheet with id=  J, first strand: chain 'E' and resid 95 through 99
      removed outlier: 5.878A  pdb=" N   ARG E  38 " --> pdb=" O   TRP E  47 " (cutoff:3.500A)
      removed outlier: 5.282A  pdb=" N   TRP E  47 " --> pdb=" O   ARG E  38 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'E' and resid 134 through 136
      removed outlier: 6.575A  pdb=" N   LYS E 232 " --> pdb=" O   VAL E 135 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=  K
    Processing sheet with id=  L, first strand: chain 'E' and resid 143 through 148
    Processing sheet with id=  M, first strand: chain 'E' and resid 213 through 219
      removed outlier: 3.538A  pdb=" N   ILE E 177 " --> pdb=" O   TRP E 164 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU E 166 " --> pdb=" O   LEU E 175 " (cutoff:3.500A)
      removed outlier: 5.844A  pdb=" N   LEU E 175 " --> pdb=" O   LEU E 166 " (cutoff:3.500A)
    Processing sheet with id=  N, first strand: chain 'A' and resid 262 through 268
      removed outlier: 4.200A  pdb=" N   SER A 219 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 223 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 4.231A  pdb=" N   VAL A 200 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   GLY A  40 " --> pdb=" O   VAL A 200 " (cutoff:3.500A)

    382 hydrogen bonds defined for protein.
    1101 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: 2.38

  Time building geometry restraints manager: 3.78 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: 1743
        1.33 -     1.45: 2110
        1.45 -     1.57: 4826
        1.57 -     1.69: 1
        1.69 -     1.82: 87
  Bond restraints: 8767
  Sorted by residual:
  bond pdb=" C   PHE L   8 "
       pdb=" N   NH2 L   9 "
    ideal  model  delta    sigma   weight residual
    2.329  1.328  1.001 1.40e-02 5.10e+03 5.11e+03
  bond pdb=" O2  TYS L   2 "
       pdb=" S   TYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.461  1.632 -0.171 2.00e-02 2.50e+03 7.35e+01
  bond pdb=" OH  TYS L   2 "
       pdb=" S   TYS L   2 "
    ideal  model  delta    sigma   weight residual
    1.679  1.534  0.145 2.00e-02 2.50e+03 5.29e+01
  bond pdb=" C   ALA R 352 "
       pdb=" O   ALA R 352 "
    ideal  model  delta    sigma   weight residual
    1.237  1.207  0.030 1.17e-02 7.31e+03 6.49e+00
  bond pdb=" CA  ASN R 353 "
       pdb=" C   ASN R 353 "
    ideal  model  delta    sigma   weight residual
    1.523  1.494  0.029 1.30e-02 5.92e+03 4.97e+00
  ... (remaining 8762 not shown)

  Histogram of bond angle deviations from ideal:
       99.16 -   106.13: 178
      106.13 -   113.09: 4797
      113.09 -   120.06: 2914
      120.06 -   127.03: 3921
      127.03 -   133.99: 102
  Bond angle restraints: 11912
  Sorted by residual:
  angle pdb=" N   THR R 193 "
        pdb=" CA  THR R 193 "
        pdb=" C   THR R 193 "
      ideal   model   delta    sigma   weight residual
     108.56  118.68  -10.12 1.74e+00 3.30e-01 3.38e+01
  angle pdb=" CA  TYR R 189 "
        pdb=" C   TYR R 189 "
        pdb=" N   PRO R 190 "
      ideal   model   delta    sigma   weight residual
     120.58  116.55    4.03 7.40e-01 1.83e+00 2.97e+01
  angle pdb=" N   TYR E 161 "
        pdb=" CA  TYR E 161 "
        pdb=" C   TYR E 161 "
      ideal   model   delta    sigma   weight residual
     108.52  116.46   -7.94 1.74e+00 3.30e-01 2.08e+01
  angle pdb=" C   TYR R 189 "
        pdb=" N   PRO R 190 "
        pdb=" CA  PRO R 190 "
      ideal   model   delta    sigma   weight residual
     119.05  123.92   -4.87 1.11e+00 8.12e-01 1.93e+01
  angle pdb=" N   ASP L   7 "
        pdb=" CA  ASP L   7 "
        pdb=" C   ASP L   7 "
      ideal   model   delta    sigma   weight residual
     110.80  119.96   -9.16 2.13e+00 2.20e-01 1.85e+01
  ... (remaining 11907 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.74: 4728
       17.74 -    35.49: 393
       35.49 -    53.23: 48
       53.23 -    70.97: 4
       70.97 -    88.71: 1
  Dihedral angle restraints: 5174
    sinusoidal: 1924
      harmonic: 3250
  Sorted by residual:
  dihedral pdb=" CA  TYR E 223 "
           pdb=" C   TYR E 223 "
           pdb=" N   PRO E 224 "
           pdb=" CA  PRO E 224 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  137.63   42.37     0      5.00e+00 4.00e-02 7.18e+01
  dihedral pdb=" CA  LEU R 203 "
           pdb=" C   LEU R 203 "
           pdb=" N   GLN R 204 "
           pdb=" CA  GLN R 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.25   26.75     0      5.00e+00 4.00e-02 2.86e+01
  dihedral pdb=" CA  ASP A 313 "
           pdb=" C   ASP A 313 "
           pdb=" N   SER A 314 "
           pdb=" CA  SER A 314 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.55   20.45     0      5.00e+00 4.00e-02 1.67e+01
  ... (remaining 5171 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.070: 1227
       0.070 -    0.139: 141
       0.139 -    0.209: 5
       0.209 -    0.278: 2
       0.278 -    0.348: 1
  Chirality restraints: 1376
  Sorted by residual:
  chirality pdb=" CA  ASP L   7 "
            pdb=" N   ASP L   7 "
            pdb=" C   ASP L   7 "
            pdb=" CB  ASP L   7 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.03e+00
  chirality pdb=" CA  THR R 193 "
            pdb=" N   THR R 193 "
            pdb=" C   THR R 193 "
            pdb=" CB  THR R 193 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.26    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CA  PHE L   8 "
            pdb=" N   PHE L   8 "
            pdb=" C   PHE L   8 "
            pdb=" CB  PHE L   8 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.52e+00
  ... (remaining 1373 not shown)

  Planarity restraints: 1501
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TYR E 223 "   -0.041 5.00e-02 4.00e+02   6.24e-02 6.23e+00
        pdb=" N   PRO E 224 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO E 224 "   -0.032 5.00e-02 4.00e+02
        pdb=" CD  PRO E 224 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO R 188 "   -0.008 2.00e-02 2.50e+03   1.64e-02 2.68e+00
        pdb=" C   PRO R 188 "    0.028 2.00e-02 2.50e+03
        pdb=" O   PRO R 188 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   TYR R 189 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ARG E 179 "    0.007 2.00e-02 2.50e+03   1.42e-02 2.00e+00
        pdb=" C   ARG E 179 "   -0.024 2.00e-02 2.50e+03
        pdb=" O   ARG E 179 "    0.009 2.00e-02 2.50e+03
        pdb=" N   MET E 180 "    0.008 2.00e-02 2.50e+03
  ... (remaining 1498 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 799
        2.74 -     3.28: 8305
        3.28 -     3.82: 13620
        3.82 -     4.36: 16238
        4.36 -     4.90: 28947
  Nonbonded interactions: 67909
  Sorted by model distance:
  nonbonded pdb=" O   SER E 194 "
            pdb=" OG1 THR E 201 "
     model   vdw
     2.202 2.440
  nonbonded pdb=" O   ILE B  58 "
            pdb=" OG  SER B 316 "
     model   vdw
     2.224 2.440
  nonbonded pdb=" O   ARG B  68 "
            pdb=" OG  SER B  84 "
     model   vdw
     2.262 2.440
  nonbonded pdb=" O   SER E 106 "
            pdb=" OG  SER E 106 "
     model   vdw
     2.280 2.440
  nonbonded pdb=" OH  TYR R 189 "
            pdb=" OD2 ASP L   7 "
     model   vdw
     2.286 2.440
  ... (remaining 67904 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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:             0.320
  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:          2.120
  Check model and map are aligned:         0.150
  Set scattering table:                    0.100
  Process input model:                     27.550
  Find NCS groups from input model:        0.230
  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:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7494
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      :  0.011   1.001   8767  Z= 0.425
  Angle     :  0.727  10.122  11912  Z= 0.434
  Chirality :  0.045   0.348   1376
  Planarity :  0.004   0.062   1501
  Dihedral  : 12.552  88.713   3072
  Min Nonbonded Distance : 2.202

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.18 %
    Allowed  :  5.00 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.23 (0.23), residues: 1101
  helix:  0.12 (0.26), residues: 357
  sheet: -1.07 (0.31), residues: 251
  loop : -2.99 (0.24), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP R 346 
   HIS   0.005   0.001   HIS B 183 
   PHE   0.012   0.001   PHE A  49 
   TYR   0.015   0.001   TYR E  94 
   ARG   0.003   0.000   ARG A  32 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 181
  time to evaluate  : 1.020 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 181
  average time/residue: 0.2132
  time to fit residues: 52.6503
Evaluate side-chains
  144 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 144
  time to evaluate  : 0.989 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.3643
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 92 optimal weight:    0.5980
   chunk 82 optimal weight:    9.9990
   chunk 45 optimal weight:    0.9990
   chunk 28 optimal weight:    5.9990
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    0.5980
   chunk 85 optimal weight:   30.0000
   chunk 33 optimal weight:    0.0980
   chunk 51 optimal weight:    7.9990
   chunk 63 optimal weight:    0.9980
   chunk 98 optimal weight:    4.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
R  72 ASN
R 204 GLN
R 353 ASN
B  32 GLN
E 167 GLN
A 293 GLN
A 311 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7493
moved from start:          0.1060

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   8767  Z= 0.155
  Angle     :  0.546   7.542  11912  Z= 0.275
  Chirality :  0.042   0.274   1376
  Planarity :  0.003   0.050   1501
  Dihedral  :  4.505  41.142   1220
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.81 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.15 %
    Favored  : 86.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.06 (0.25), residues: 1101
  helix:  1.51 (0.28), residues: 361
  sheet: -0.72 (0.31), residues: 257
  loop : -2.51 (0.25), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP R 346 
   HIS   0.003   0.001   HIS B 311 
   PHE   0.016   0.001   PHE L   8 
   TYR   0.013   0.001   TYR R 192 
   ARG   0.002   0.000   ARG R 396 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 141
  time to evaluate  : 1.012 
Fit side-chains
  outliers start: 14
  outliers final: 9
  residues processed: 147
  average time/residue: 0.2197
  time to fit residues: 44.1196
Evaluate side-chains
  137 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 128
  time to evaluate  : 1.017 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.0832
  time to fit residues: 2.8193
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 55 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 82 optimal weight:    0.7980
   chunk 67 optimal weight:    0.4980
   chunk 27 optimal weight:   20.0000
   chunk 99 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0060
   chunk 88 optimal weight:    4.9990
   chunk 98 optimal weight:    5.9990
   chunk 33 optimal weight:    0.6980
   chunk 79 optimal weight:    9.9990
   overall best weight:    0.7998

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN
R 204 GLN
B 176 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7497
moved from start:          0.1376

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   8767  Z= 0.157
  Angle     :  0.537   8.193  11912  Z= 0.268
  Chirality :  0.042   0.183   1376
  Planarity :  0.003   0.048   1501
  Dihedral  :  4.319  39.888   1220
  Min Nonbonded Distance : 2.211

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.54 %
    Favored  : 95.37 %
  Rotamer:
    Outliers :  1.34 %
    Allowed  : 14.05 %
    Favored  : 84.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    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: -0.43 (0.26), residues: 1101
  helix:  2.09 (0.28), residues: 362
  sheet: -0.44 (0.31), residues: 264
  loop : -2.19 (0.26), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.010   0.001   TRP R 346 
   HIS   0.003   0.001   HIS B 183 
   PHE   0.012   0.001   PHE B 253 
   TYR   0.030   0.001   TYR R 192 
   ARG   0.001   0.000   ARG B 137 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 134
  time to evaluate  : 1.027 
Fit side-chains
  outliers start: 12
  outliers final: 5
  residues processed: 142
  average time/residue: 0.2056
  time to fit residues: 40.8335
Evaluate side-chains
  132 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 127
  time to evaluate  : 0.995 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0891
  time to fit residues: 2.1572
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 97 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 51 optimal weight:    0.2980
   chunk 10 optimal weight:    0.5980
   chunk 47 optimal weight:    0.8980
   chunk 66 optimal weight:    6.9990
   chunk 99 optimal weight:    5.9990
   chunk 105 optimal weight:    0.8980
   chunk 94 optimal weight:    0.6980
   chunk 28 optimal weight:    5.9990
   chunk 87 optimal weight:    6.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7483
moved from start:          0.1594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   8767  Z= 0.141
  Angle     :  0.519   8.261  11912  Z= 0.259
  Chirality :  0.041   0.167   1376
  Planarity :  0.003   0.044   1501
  Dihedral  :  4.152  38.732   1220
  Min Nonbonded Distance : 2.200

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 14.27 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    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: -0.05 (0.26), residues: 1101
  helix:  2.36 (0.28), residues: 364
  sheet: -0.26 (0.31), residues: 262
  loop : -1.90 (0.27), residues: 475

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP R 346 
   HIS   0.003   0.001   HIS B 183 
   PHE   0.010   0.001   PHE A  49 
   TYR   0.014   0.001   TYR R 192 
   ARG   0.003   0.000   ARG B 304 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 138
  time to evaluate  : 1.102 
Fit side-chains
  outliers start: 14
  outliers final: 10
  residues processed: 143
  average time/residue: 0.2193
  time to fit residues: 43.4011
Evaluate side-chains
  135 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 125
  time to evaluate  : 1.016 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 0
  residues processed: 10
  average time/residue: 0.0831
  time to fit residues: 2.9469
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 59 optimal weight:   10.0000
   chunk 1 optimal weight:    0.9990
   chunk 78 optimal weight:    0.8980
   chunk 43 optimal weight:    6.9990
   chunk 89 optimal weight:    2.9990
   chunk 72 optimal weight:    6.9990
   chunk 0 optimal weight:    5.9990
   chunk 53 optimal weight:    6.9990
   chunk 94 optimal weight:    2.9990
   chunk 26 optimal weight:    0.0970
   chunk 35 optimal weight:    0.5980
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7503
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   8767  Z= 0.181
  Angle     :  0.537   8.798  11912  Z= 0.270
  Chirality :  0.042   0.177   1376
  Planarity :  0.003   0.043   1501
  Dihedral  :  4.206  38.416   1220
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 6.47
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.18 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  1.90 %
    Allowed  : 14.72 %
    Favored  : 83.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    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: -0.05 (0.26), residues: 1101
  helix:  2.33 (0.28), residues: 366
  sheet: -0.15 (0.32), residues: 255
  loop : -1.95 (0.27), residues: 480

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.009   0.001   TRP B  82 
   HIS   0.004   0.001   HIS B 183 
   PHE   0.011   0.001   PHE B 253 
   TYR   0.016   0.001   TYR A 229 
   ARG   0.002   0.000   ARG B 304 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 1.026 
Fit side-chains
  outliers start: 17
  outliers final: 11
  residues processed: 145
  average time/residue: 0.2250
  time to fit residues: 44.7762
Evaluate side-chains
  142 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 131
  time to evaluate  : 0.983 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0837
  time to fit residues: 3.0411
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 20 optimal weight:    4.9990
   chunk 61 optimal weight:    0.0070
   chunk 26 optimal weight:    3.9990
   chunk 105 optimal weight:    3.9990
   chunk 87 optimal weight:    8.9990
   chunk 48 optimal weight:    9.9990
   chunk 8 optimal weight:    0.7980
   chunk 34 optimal weight:    0.7980
   chunk 55 optimal weight:    5.9990
   chunk 101 optimal weight:    4.9990
   overall best weight:    1.5202

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7528
moved from start:          0.1774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8767  Z= 0.219
  Angle     :  0.554   9.286  11912  Z= 0.280
  Chirality :  0.042   0.159   1376
  Planarity :  0.003   0.044   1501
  Dihedral  :  4.314  39.914   1220
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 6.95
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.18 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 15.27 %
    Favored  : 83.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    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: -0.01 (0.26), residues: 1101
  helix:  2.47 (0.28), residues: 357
  sheet: -0.13 (0.32), residues: 255
  loop : -1.93 (0.27), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  63 
   HIS   0.004   0.001   HIS B 183 
   PHE   0.012   0.001   PHE B 253 
   TYR   0.012   0.001   TYR A 289 
   ARG   0.003   0.000   ARG R 356 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  143 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 135
  time to evaluate  : 1.032 
Fit side-chains
  outliers start: 8
  outliers final: 7
  residues processed: 136
  average time/residue: 0.2205
  time to fit residues: 41.6775
Evaluate side-chains
  139 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 132
  time to evaluate  : 1.046 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0846
  time to fit residues: 2.5755
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 11 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 59 optimal weight:    5.9990
   chunk 88 optimal weight:    3.9990
   chunk 58 optimal weight:    0.7980
   chunk 105 optimal weight:    4.9990
   chunk 65 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 48 optimal weight:    9.9990
   chunk 41 optimal weight:    1.9990
   overall best weight:    1.5586

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN
B 176 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7531
moved from start:          0.1819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   8767  Z= 0.221
  Angle     :  0.555   8.488  11912  Z= 0.279
  Chirality :  0.042   0.158   1376
  Planarity :  0.003   0.043   1501
  Dihedral  :  4.347  39.404   1220
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 7.18
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.63 %
    Favored  : 94.28 %
  Rotamer:
    Outliers :  0.89 %
    Allowed  : 16.61 %
    Favored  : 82.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    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:  0.02 (0.26), residues: 1101
  helix:  2.46 (0.28), residues: 357
  sheet: -0.10 (0.32), residues: 260
  loop : -1.91 (0.27), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.011   0.001   TRP B  63 
   HIS   0.003   0.001   HIS B 183 
   PHE   0.011   0.001   PHE B 253 
   TYR   0.012   0.001   TYR A 289 
   ARG   0.002   0.000   ARG B 137 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 133
  time to evaluate  : 1.094 
Fit side-chains
  outliers start: 8
  outliers final: 4
  residues processed: 137
  average time/residue: 0.2164
  time to fit residues: 40.8955
Evaluate side-chains
  134 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 0.924 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1007
  time to fit residues: 1.9847
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 109
   random chunks:
   chunk 62 optimal weight:    0.3980
   chunk 31 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 66 optimal weight:   10.0000
   chunk 71 optimal weight:    3.9990
   chunk 51 optimal weight:    3.9990
   chunk 9 optimal weight:    0.7980
   chunk 82 optimal weight:    4.9990
   chunk 95 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   chunk 91 optimal weight:    3.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
R 161 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7553
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   8767  Z= 0.271
  Angle     :  0.583   8.212  11912  Z= 0.294
  Chirality :  0.043   0.173   1376
  Planarity :  0.003   0.045   1501
  Dihedral  :  4.489  41.676   1220
  Min Nonbonded Distance : 2.141

Molprobity Statistics.
  All-atom Clashscore : 7.65
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.81 %
    Favored  : 94.10 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  : 17.95 %
    Favored  : 81.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 2.70 %
    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: -0.06 (0.26), residues: 1101
  helix:  2.27 (0.28), residues: 360
  sheet: -0.13 (0.32), residues: 260
  loop : -1.89 (0.27), residues: 481

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
   TRP   0.013   0.001   TRP B  63 
   HIS   0.004   0.001   HIS B 183 
   PHE   0.012   0.001   PHE B 253 
   TYR   0.012   0.001   TYR A 289 
   ARG   0.002   0.000   ARG B 137 

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

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

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2202 Ramachandran restraints generated.
    1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 129
  time to evaluate  : 1.139 
Fit side-chains
  outliers start: 9
  outliers final: 7
  residues processed: 132
  average time/residue: 0.2625
  time to fit residues: 48.0204
Evaluate side-chains
  134 residues out of total 959 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 127
  time to evaluate  : 0.972 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0813
  time to fit residues: 2.4002
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Traceback (most recent call last):
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in <module>
    run_program(real_space_refine.Program)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/iotbx/cli_parser.py", line 931, in run_program
    task.run()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/programs/real_space_refine.py", line 191, in run
    log         = self.logger)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__
    log                   = log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 297, in __init__
    self.caller(self.refine_xyz)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 312, in caller
    func()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 673, in refine_xyz
    self.minimization_no_ncs()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 737, in minimization_no_ncs
    log                         = self.log)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__
    gradients_method            = gradients_method)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine
    rms_angles_limit = rms_angles_limit)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__
    weight     = weight)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine
    states_collector                = self.states_accumulator)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__
    exception_handling_params=lbfgs_exception_handling_params)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run
    line_search)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus
    f, g = target_evaluator.compute_functional_and_gradients()
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients
    compute_gradients=True)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1479, in energies_sites
    flags=flags, sites_cart=sites_cart, site_labels=site_labels)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1381, in pair_proxies
    check_bonded_distance_cutoff(sites_frac=sites_frac)
  File "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1262, in check_bonded_distance_cutoff
    raise RuntimeError(msg)
RuntimeError: Bond distance > max_reasonable_bond_distance: 70.9227 > 50:
  distance: 44 - 49:  35.610
  distance: 49 - 50:  21.633
  distance: 50 - 51:  57.751
  distance: 50 - 53:  41.174
  distance: 51 - 52:  52.928
  distance: 51 - 57:   3.777
  distance: 53 - 54:  11.479
  distance: 54 - 55:  40.080
  distance: 54 - 56:  40.024
  distance: 57 - 58:  39.227
  distance: 58 - 59:  70.012
  distance: 58 - 61:  40.102
  distance: 61 - 62:  41.388
  distance: 62 - 63:   8.580
  distance: 62 - 64:  31.520
  distance: 63 - 65:  36.268
  distance: 64 - 66:  39.753
  distance: 66 - 67:  39.526
  distance: 69 - 70:  39.221
  distance: 70 - 71:  39.524
  distance: 70 - 73:  17.455
  distance: 71 - 72:  31.627
  distance: 71 - 80:  50.852
  distance: 73 - 74:  46.588
  distance: 74 - 76:  56.489
  distance: 76 - 78:  56.622
  distance: 80 - 86:  54.321
  distance: 81 - 82:  40.666
  distance: 81 - 84:  41.035
  distance: 84 - 85:  10.116
  distance: 85 - 86:  31.218
  distance: 87 - 88:  40.508
  distance: 88 - 89:  39.714
  distance: 88 - 91:  40.583
  distance: 89 - 90:   4.785
  distance: 89 - 96:   7.493
  distance: 93 - 94:  56.026
  distance: 93 - 95:  40.991
  distance: 96 - 97:  52.519
  distance: 98 - 99:  40.542
  distance: 98 - 108:  40.289
  distance: 100 - 101:   9.446
  distance: 101 - 102:   8.993
  distance: 101 - 103:  50.354
  distance: 102 - 104:  38.239
  distance: 103 - 105:  38.773
  distance: 104 - 106:  35.437
  distance: 105 - 106:  67.335
  distance: 106 - 107:  40.053
  distance: 108 - 109:  39.050
  distance: 109 - 110:  21.144
  distance: 109 - 112:  41.469
  distance: 110 - 111:  20.097
  distance: 110 - 116:  40.007
  distance: 112 - 113:  39.056
  distance: 113 - 114:  39.898
  distance: 113 - 115:  11.903
  distance: 116 - 117:  22.126
  distance: 117 - 118:  19.332
  distance: 118 - 120:   9.647
  distance: 120 - 121:  30.925
  distance: 120 - 126:  29.239
  distance: 121 - 122:  11.537
  distance: 121 - 124:  11.101
  distance: 122 - 123:   4.712
  distance: 122 - 127:  35.078
  distance: 124 - 125:  16.809
  distance: 125 - 126:  41.357
  distance: 127 - 128:   6.562
  distance: 128 - 129:  33.678
  distance: 128 - 131:   6.428
  distance: 129 - 136:  34.882
  distance: 131 - 132:  40.578
  distance: 132 - 133:  40.210