Starting phenix.real_space_refine
on Tue Nov 14 14:13:48 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1a_35915/11_2023/8j1a_35915_neut.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1a_35915/11_2023/8j1a_35915.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.24
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1a_35915/11_2023/8j1a_35915.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1a_35915/11_2023/8j1a_35915.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1a_35915/11_2023/8j1a_35915_neut.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8j1a_35915/11_2023/8j1a_35915_neut.pdb"
  }
  resolution = 3.24
  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=   0.036
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    5640      2.51       5
     N    1528      2.21       5
     O    1618      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A GLU    8": "OE1" <-> "OE2"
    Residue "A GLU  276": "OE1" <-> "OE2"
    Residue "B GLU  172": "OE1" <-> "OE2"
    Residue "B ASP  290": "OD1" <-> "OD2"
    Residue "R ARG  176": "NH1" <-> "NH2"
    Residue "S GLU  220": "OE1" <-> "OE2"
    Residue "S GLU  234": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 8845
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 1759
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 219, 1759
          Classifications: {'peptide': 219}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 216}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 11
          Unresolved non-hydrogen dihedrals: 8
          Planarities with less than four sites: {'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 7
    Chain: "B"
      Number of atoms: 2591
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2591
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 5, 'TRANS': 331}
    Chain: "G"
      Number of atoms: 447
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 58, 447
          Classifications: {'peptide': 58}
          Link IDs: {'PTRANS': 4, 'TRANS': 53}
    Chain: "R"
      Number of atoms: 2300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2300
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 12, 'TRANS': 278}
          Chain breaks: 1
    Chain: "S"
      Number of atoms: 1748
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1748
          Classifications: {'peptide': 232}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 35
          Unresolved non-hydrogen angles: 43
          Unresolved non-hydrogen dihedrals: 27
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'GLU:plan': 5, 'ASP:plan': 2}
          Unresolved non-hydrogen planarities: 26
  Time building chain proxies: 5.12, per 1000 atoms: 0.58
  Number of scatterers: 8845
  At special positions: 0
  Unit cell: (88.992, 119.48, 124.424, 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    1618      8.00
     N    1528      7.00
     C    5640      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS R  11 " - pdb=" SG  CYS R 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS R  93 " - pdb=" SG  CYS R 168 " distance=2.03
    Simple disulfide: pdb=" SG  CYS S  22 " - pdb=" SG  CYS S  96 " distance=2.03

  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: 3.47
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2120

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 13 sheets defined
      39.7% alpha, 22.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.97
  Creating SS restraints...
    Processing helix  chain 'A' and resid 8 through 33
      removed outlier: 3.539A  pdb=" N   GLU A  33 " --> pdb=" O   LYS A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 41 through 44
    Processing helix  chain 'A' and resid 45 through 54
    Processing helix  chain 'A' and resid 211 through 216
    Processing helix  chain 'A' and resid 242 through 255
    Processing helix  chain 'A' and resid 256 through 260
      removed outlier: 3.980A  pdb=" N   THR A 260 " --> pdb=" O   LYS A 257 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 281
      removed outlier: 4.359A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
      removed outlier: 4.200A  pdb=" N   LYS A 279 " --> pdb=" O   GLU A 275 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 282 through 286
    Processing helix  chain 'A' and resid 295 through 309
    Processing helix  chain 'A' and resid 329 through 351
    Processing helix  chain 'B' and resid 5 through 26
    Processing helix  chain 'B' and resid 29 through 35
      removed outlier: 3.582A  pdb=" N   ILE B  33 " --> pdb=" O   THR B  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 24
      removed outlier: 3.627A  pdb=" N   ASN G  24 " --> pdb=" O   LYS G  20 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 29 through 44
      removed outlier: 3.625A  pdb=" N   ALA G  33 " --> pdb=" O   LYS G  29 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 48
    Processing helix  chain 'R' and resid 13 through 15
      No H-bonds generated for 'chain 'R' and resid 13 through 15'
    Processing helix  chain 'R' and resid 16 through 48
      removed outlier: 4.197A  pdb=" N   TYR R  21 " --> pdb=" O   LEU R  17 " (cutoff:3.500A)
      removed outlier: 4.423A  pdb=" N   VAL R  22 " --> pdb=" O   GLY R  18 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 52
    Processing helix  chain 'R' and resid 53 through 71
      removed outlier: 4.033A  pdb=" N   LEU R  58 " --> pdb=" O   ARG R  54 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   ILE R  59 " --> pdb=" O   PHE R  55 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR R  69 " --> pdb=" O   ALA R  65 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 74 through 82
    Processing helix  chain 'R' and resid 89 through 124
      removed outlier: 3.651A  pdb=" N   ARG R  94 " --> pdb=" O   ALA R  90 " (cutoff:3.500A)
      removed outlier: 3.861A  pdb=" N   VAL R  95 " --> pdb=" O   THR R  91 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 127 through 133
      removed outlier: 3.598A  pdb=" N   VAL R 131 " --> pdb=" O   LEU R 127 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 133 through 153
      removed outlier: 3.557A  pdb=" N   VAL R 138 " --> pdb=" O   ALA R 134 " (cutoff:3.500A)
      removed outlier: 3.988A  pdb=" N   TRP R 145 " --> pdb=" O   LEU R 141 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   PHE R 152 " --> pdb=" O   GLY R 148 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 154 through 159
      Proline residue:  R 157  - end of helix
      No H-bonds generated for 'chain 'R' and resid 154 through 159'
    Processing helix  chain 'R' and resid 175 through 215
      removed outlier: 3.734A  pdb=" N   TYR R 186 " --> pdb=" O   LEU R 182 " (cutoff:3.500A)
      removed outlier: 4.391A  pdb=" N   TYR R 198 " --> pdb=" O   VAL R 194 " (cutoff:3.500A)
      removed outlier: 4.180A  pdb=" N   CYS R 199 " --> pdb=" O   GLY R 195 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   TYR R 215 " --> pdb=" O   ALA R 211 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 316 through 342
      Proline residue:  R 334  - end of helix
    Processing helix  chain 'R' and resid 347 through 349
      No H-bonds generated for 'chain 'R' and resid 347 through 349'
    Processing helix  chain 'R' and resid 350 through 371
      removed outlier: 3.838A  pdb=" N   LEU R 354 " --> pdb=" O   VAL R 350 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   TRP R 360 " --> pdb=" O   ALA R 356 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   LEU R 361 " --> pdb=" O   ASN R 357 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ASN R 362 " --> pdb=" O   LEU R 358 " (cutoff:3.500A)
      removed outlier: 4.562A  pdb=" N   GLY R 363 " --> pdb=" O   THR R 359 " (cutoff:3.500A)
      Proline residue:  R 367  - end of helix
    Processing helix  chain 'R' and resid 374 through 387
    Processing helix  chain 'R' and resid 387 through 392
    Processing helix  chain 'S' and resid 28 through 32
    Processing helix  chain 'S' and resid 53 through 56
      removed outlier: 4.168A  pdb=" N   GLY S  56 " --> pdb=" O   SER S  53 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'S' and resid 53 through 56'
    Processing helix  chain 'S' and resid 87 through 91
    Processing sheet with id=AA1, first strand: chain 'A' and resid 185 through 190
      removed outlier: 6.951A  pdb=" N   LYS A  35 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 7.548A  pdb=" N   ILE A 222 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 5.956A  pdb=" N   LEU A  37 " --> pdb=" O   ILE A 222 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   CYS A 224 " --> pdb=" O   LEU A  37 " (cutoff:3.500A)
      removed outlier: 6.772A  pdb=" N   LEU A  39 " --> pdb=" O   CYS A 224 " (cutoff:3.500A)
      removed outlier: 8.897A  pdb=" N   ALA A 226 " --> pdb=" O   LEU A  39 " (cutoff:3.500A)
      removed outlier: 6.383A  pdb=" N   ILE A 221 " --> pdb=" O   ILE A 265 " (cutoff:3.500A)
      removed outlier: 7.149A  pdb=" N   PHE A 267 " --> pdb=" O   ILE A 221 " (cutoff:3.500A)
      removed outlier: 6.423A  pdb=" N   PHE A 223 " --> pdb=" O   PHE A 267 " (cutoff:3.500A)
      removed outlier: 7.550A  pdb=" N   ASN A 269 " --> pdb=" O   PHE A 223 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   VAL A 225 " --> pdb=" O   ASN A 269 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51
      removed outlier: 3.562A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63
      removed outlier: 3.650A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   HIS B  91 " --> pdb=" O   ILE B  81 " (cutoff:3.500A)
      removed outlier: 6.758A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.147A  pdb=" N   CYS B 121 " --> pdb=" O   GLU B 138 " (cutoff:3.500A)
      removed outlier: 4.434A  pdb=" N   GLU B 138 " --> pdb=" O   CYS B 121 " (cutoff:3.500A)
      removed outlier: 6.659A  pdb=" N   ILE B 123 " --> pdb=" O   SER B 136 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ARG B 134 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 150
      removed outlier: 6.782A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.755A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 7.142A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.628A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.240A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 5.789A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.818A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.303A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.794A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.245A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.319A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   SER B 207 " --> pdb=" O   ALA B 203 " (cutoff:3.500A)
      removed outlier: 6.554A  pdb=" N   ALA B 208 " --> pdb=" O   THR B 221 " (cutoff:3.500A)
      removed outlier: 4.484A  pdb=" N   THR B 221 " --> pdb=" O   ALA B 208 " (cutoff:3.500A)
      removed outlier: 6.719A  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 234
      removed outlier: 6.665A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.449A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.963A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278
      removed outlier: 3.739A  pdb=" N   SER B 275 " --> pdb=" O   GLY B 288 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   CYS B 294 " --> pdb=" O   LEU B 308 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.250A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'R' and resid 161 through 162
      removed outlier: 4.159A  pdb=" N   VAL R 162 " --> pdb=" O   THR R 167 " (cutoff:3.500A)
      removed outlier: 4.118A  pdb=" N   THR R 167 " --> pdb=" O   VAL R 162 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7
    Processing sheet with id=AB2, first strand: chain 'S' and resid 11 through 12
      removed outlier: 6.916A  pdb=" N   MET S  34 " --> pdb=" O   TYR S  50 " (cutoff:3.500A)
      removed outlier: 4.616A  pdb=" N   TYR S  50 " --> pdb=" O   MET S  34 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   TRP S  36 " --> pdb=" O   VAL S  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142
    Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148
      removed outlier: 6.486A  pdb=" N   LEU S 174 " --> pdb=" O   TYR S 190 " (cutoff:3.500A)
      removed outlier: 4.586A  pdb=" N   TYR S 190 " --> pdb=" O   LEU S 174 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   TRP S 176 " --> pdb=" O   LEU S 188 " (cutoff:3.500A)

    444 hydrogen bonds defined for protein.
    1242 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: 2.62

  Time building geometry restraints manager: 3.76 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 1552
        1.33 -     1.45: 2399
        1.45 -     1.57: 4996
        1.57 -     1.69: 0
        1.69 -     1.81: 82
  Bond restraints: 9029
  Sorted by residual:
  bond pdb=" C   TYR A 287 "
       pdb=" O   TYR A 287 "
    ideal  model  delta    sigma   weight residual
    1.244  1.203  0.041 1.00e-02 1.00e+04 1.69e+01
  bond pdb=" C   ASN G  59 "
       pdb=" N   PRO G  60 "
    ideal  model  delta    sigma   weight residual
    1.336  1.369 -0.034 9.80e-03 1.04e+04 1.17e+01
  bond pdb=" CA  ARG R 176 "
       pdb=" C   ARG R 176 "
    ideal  model  delta    sigma   weight residual
    1.524  1.564 -0.040 1.26e-02 6.30e+03 1.02e+01
  bond pdb=" C   ASP B 163 "
       pdb=" N   THR B 164 "
    ideal  model  delta    sigma   weight residual
    1.332  1.369 -0.037 1.24e-02 6.50e+03 9.02e+00
  bond pdb=" CA  SER B 331 "
       pdb=" C   SER B 331 "
    ideal  model  delta    sigma   weight residual
    1.524  1.489  0.035 1.35e-02 5.49e+03 6.82e+00
  ... (remaining 9024 not shown)

  Histogram of bond angle deviations from ideal:
      100.12 -   106.90: 204
      106.90 -   113.67: 5034
      113.67 -   120.45: 3415
      120.45 -   127.23: 3489
      127.23 -   134.00: 93
  Bond angle restraints: 12235
  Sorted by residual:
  angle pdb=" N   TYR R 332 "
        pdb=" CA  TYR R 332 "
        pdb=" C   TYR R 332 "
      ideal   model   delta    sigma   weight residual
     113.12  120.45   -7.33 1.25e+00 6.40e-01 3.43e+01
  angle pdb=" CA  ASP B 163 "
        pdb=" C   ASP B 163 "
        pdb=" O   ASP B 163 "
      ideal   model   delta    sigma   weight residual
     120.55  114.60    5.95 1.21e+00 6.83e-01 2.42e+01
  angle pdb=" N   GLU A 289 "
        pdb=" CA  GLU A 289 "
        pdb=" C   GLU A 289 "
      ideal   model   delta    sigma   weight residual
     110.97  105.99    4.98 1.09e+00 8.42e-01 2.08e+01
  angle pdb=" N   SER B 331 "
        pdb=" CA  SER B 331 "
        pdb=" CB  SER B 331 "
      ideal   model   delta    sigma   weight residual
     111.22  104.32    6.90 1.58e+00 4.01e-01 1.91e+01
  angle pdb=" N   SER A 293 "
        pdb=" CA  SER A 293 "
        pdb=" C   SER A 293 "
      ideal   model   delta    sigma   weight residual
     109.46  102.24    7.22 1.66e+00 3.63e-01 1.89e+01
  ... (remaining 12230 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.58: 4749
       17.58 -    35.16: 456
       35.16 -    52.74: 108
       52.74 -    70.32: 30
       70.32 -    87.90: 8
  Dihedral angle restraints: 5351
    sinusoidal: 2061
      harmonic: 3290
  Sorted by residual:
  dihedral pdb=" N   SER B 331 "
           pdb=" C   SER B 331 "
           pdb=" CA  SER B 331 "
           pdb=" CB  SER B 331 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  113.84    8.96     0      2.50e+00 1.60e-01 1.28e+01
  dihedral pdb=" CG  ARG B 214 "
           pdb=" CD  ARG B 214 "
           pdb=" NE  ARG B 214 "
           pdb=" CZ  ARG B 214 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00   40.06   49.94     2      1.50e+01 4.44e-03 1.25e+01
  dihedral pdb=" CA  ASP B 290 "
           pdb=" CB  ASP B 290 "
           pdb=" CG  ASP B 290 "
           pdb=" OD1 ASP B 290 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -90.91   60.91     1      2.00e+01 2.50e-03 1.23e+01
  ... (remaining 5348 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1174
       0.054 -    0.107: 180
       0.107 -    0.161: 35
       0.161 -    0.215: 6
       0.215 -    0.268: 4
  Chirality restraints: 1399
  Sorted by residual:
  chirality pdb=" CA  TYR R 332 "
            pdb=" N   TYR R 332 "
            pdb=" C   TYR R 332 "
            pdb=" CB  TYR R 332 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.80e+00
  chirality pdb=" CA  ARG R 176 "
            pdb=" N   ARG R 176 "
            pdb=" C   ARG R 176 "
            pdb=" CB  ARG R 176 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.26 2.00e-01 2.50e+01 1.63e+00
  chirality pdb=" CA  SER A 293 "
            pdb=" N   SER A 293 "
            pdb=" C   SER A 293 "
            pdb=" CB  SER A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.73   -0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1396 not shown)

  Planarity restraints: 1543
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN S  13 "    0.057 5.00e-02 4.00e+02   8.38e-02 1.12e+01
        pdb=" N   PRO S  14 "   -0.145 5.00e-02 4.00e+02
        pdb=" CA  PRO S  14 "    0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO S  14 "    0.046 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP B 333 "    0.016 2.00e-02 2.50e+03   3.26e-02 1.06e+01
        pdb=" C   ASP B 333 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ASP B 333 "    0.021 2.00e-02 2.50e+03
        pdb=" N   SER B 334 "    0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY R 175 "    0.014 2.00e-02 2.50e+03   2.78e-02 7.75e+00
        pdb=" C   GLY R 175 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   GLY R 175 "    0.018 2.00e-02 2.50e+03
        pdb=" N   ARG R 176 "    0.016 2.00e-02 2.50e+03
  ... (remaining 1540 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 82
        2.56 -     3.15: 7341
        3.15 -     3.73: 13430
        3.73 -     4.32: 18841
        4.32 -     4.90: 33050
  Nonbonded interactions: 72744
  Sorted by model distance:
  nonbonded pdb=" CD1 LEU R  98 "
            pdb=" CE3 TRP R 156 "
     model   vdw
     1.976 3.760
  nonbonded pdb=" CD2 LEU R  98 "
            pdb=" CE2 TYR R 159 "
     model   vdw
     2.136 3.760
  nonbonded pdb=" O   THR B  86 "
            pdb=" OG1 THR B  87 "
     model   vdw
     2.174 2.440
  nonbonded pdb=" CD1 LEU R  98 "
            pdb=" CZ3 TRP R 156 "
     model   vdw
     2.189 3.760
  nonbonded pdb=" OH  TYR R  12 "
            pdb=" OE2 GLU R  14 "
     model   vdw
     2.268 2.440
  ... (remaining 72739 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:             0.810
  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:          4.050
  Check model and map are aligned:         0.150
  Set scattering table:                    0.090
  Process input model:                     26.770
  Find NCS groups from input model:        0.250
  Set up NCS constraints:                  0.030
  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:             0.010
  Load rotamer database and sin/cos tables:2.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   34.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
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   0.058   9029  Z= 0.255
  Angle     :  0.615   7.584  12235  Z= 0.371
  Chirality :  0.044   0.268   1399
  Planarity :  0.005   0.084   1543
  Dihedral  : 15.324  87.901   3222
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 5.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 16.37 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.36 (0.26), residues: 1119
  helix:  1.87 (0.28), residues: 370
  sheet: -0.56 (0.30), residues: 287
  loop : -0.48 (0.30), residues: 462

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 100
  average time/residue: 0.2910
  time to fit residues: 37.9739
Evaluate side-chains
  95 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 92
  time to evaluate  : 1.028 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.2244
  time to fit residues: 2.2014
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   chunk 28 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0770
   chunk 44 optimal weight:    0.4980
   chunk 87 optimal weight:    0.0170
   chunk 33 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 64 optimal weight:    0.7980
   chunk 100 optimal weight:    7.9990
   overall best weight:    0.4176

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN
B  75 GLN
B 110 ASN
B 132 ASN
R 352 HIS
S  82 GLN
S 179 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.1091

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   9029  Z= 0.148
  Angle     :  0.501   6.080  12235  Z= 0.267
  Chirality :  0.040   0.148   1399
  Planarity :  0.004   0.048   1543
  Dihedral  :  3.933  23.003   1234
  Min Nonbonded Distance : 2.034

Molprobity Statistics.
  All-atom Clashscore : 4.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.41 %
    Allowed  : 16.05 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1119
  helix:  1.92 (0.27), residues: 383
  sheet: -0.37 (0.30), residues: 281
  loop : -0.36 (0.30), residues: 455

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.999 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 16
  residues processed: 121
  average time/residue: 0.2235
  time to fit residues: 37.4823
Evaluate side-chains
  111 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.912 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 0
  residues processed: 16
  average time/residue: 0.1145
  time to fit residues: 4.3211
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 56 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 83 optimal weight:    3.9990
   chunk 68 optimal weight:    0.5980
   chunk 27 optimal weight:    2.9990
   chunk 100 optimal weight:   10.0000
   chunk 109 optimal weight:    2.9990
   chunk 89 optimal weight:    0.0070
   chunk 34 optimal weight:    5.9990
   chunk 81 optimal weight:    2.9990
   chunk 99 optimal weight:    2.9990
   overall best weight:    1.3202

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 306 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7911
moved from start:          0.1225

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   9029  Z= 0.237
  Angle     :  0.512   6.661  12235  Z= 0.273
  Chirality :  0.041   0.144   1399
  Planarity :  0.003   0.036   1543
  Dihedral  :  3.940  20.720   1234
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 5.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.84 %
    Favored  : 96.16 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 17.10 %
    Favored  : 81.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.26), residues: 1119
  helix:  1.90 (0.27), residues: 380
  sheet: -0.38 (0.30), residues: 281
  loop : -0.37 (0.30), residues: 458

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 103
  time to evaluate  : 0.992 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 11
  residues processed: 118
  average time/residue: 0.2414
  time to fit residues: 38.8890
Evaluate side-chains
  104 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 93
  time to evaluate  : 0.924 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 0
  residues processed: 11
  average time/residue: 0.0837
  time to fit residues: 3.0966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 75 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 11 optimal weight:    1.9990
   chunk 48 optimal weight:    0.0030
   chunk 67 optimal weight:    2.9990
   chunk 101 optimal weight:    8.9990
   chunk 107 optimal weight:    1.9990
   chunk 96 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   chunk 89 optimal weight:    1.9990
   chunk 60 optimal weight:    9.9990
   overall best weight:    1.3396

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 306 GLN
B  75 GLN
** R  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  82 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.1440

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   9029  Z= 0.239
  Angle     :  0.528   8.731  12235  Z= 0.277
  Chirality :  0.041   0.151   1399
  Planarity :  0.003   0.038   1543
  Dihedral  :  3.990  18.250   1234
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 18.89 %
    Favored  : 79.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.48 (0.26), residues: 1119
  helix:  1.85 (0.27), residues: 380
  sheet: -0.47 (0.30), residues: 282
  loop : -0.38 (0.30), residues: 457

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 1.023 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 6
  residues processed: 110
  average time/residue: 0.2261
  time to fit residues: 34.6058
Evaluate side-chains
  101 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 95
  time to evaluate  : 1.017 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0835
  time to fit residues: 2.3877
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 79 optimal weight:    0.7980
   chunk 44 optimal weight:    0.9990
   chunk 91 optimal weight:    1.9990
   chunk 74 optimal weight:    7.9990
   chunk 0 optimal weight:    6.9990
   chunk 54 optimal weight:    4.9990
   chunk 96 optimal weight:   10.0000
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    0.8980
   chunk 21 optimal weight:   20.0000
   overall best weight:    1.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 269 ASN
A 306 GLN
B  32 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.1607

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   9029  Z= 0.217
  Angle     :  0.514   7.001  12235  Z= 0.269
  Chirality :  0.041   0.136   1399
  Planarity :  0.003   0.037   1543
  Dihedral  :  3.941  16.857   1234
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 6.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 19.62 %
    Favored  : 78.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.43 (0.26), residues: 1119
  helix:  1.84 (0.27), residues: 381
  sheet: -0.56 (0.30), residues: 279
  loop : -0.40 (0.29), residues: 459

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 105
  time to evaluate  : 1.003 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 14
  outliers final: 8
  residues processed: 114
  average time/residue: 0.2275
  time to fit residues: 35.8817
Evaluate side-chains
  105 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 97
  time to evaluate  : 1.099 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1497
  time to fit residues: 3.0862
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 62 optimal weight:    0.9990
   chunk 26 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 89 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 35 optimal weight:    1.9990
   chunk 56 optimal weight:    0.6980
   chunk 103 optimal weight:    2.9990
   chunk 12 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 269 ASN
A 306 GLN
B 142 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7902
moved from start:          0.1751

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9029  Z= 0.184
  Angle     :  0.504   8.404  12235  Z= 0.263
  Chirality :  0.040   0.132   1399
  Planarity :  0.003   0.039   1543
  Dihedral  :  3.862  16.668   1234
  Min Nonbonded Distance : 2.061

Molprobity Statistics.
  All-atom Clashscore : 6.41
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 21.09 %
    Favored  : 77.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.42 (0.25), residues: 1119
  helix:  1.84 (0.27), residues: 386
  sheet: -0.58 (0.31), residues: 279
  loop : -0.43 (0.29), residues: 454

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 96
  time to evaluate  : 1.013 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 105
  average time/residue: 0.2301
  time to fit residues: 33.6924
Evaluate side-chains
  100 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 95
  time to evaluate  : 0.950 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.0789
  time to fit residues: 2.0174
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 60 optimal weight:    7.9990
   chunk 90 optimal weight:    4.9990
   chunk 59 optimal weight:    8.9990
   chunk 106 optimal weight:    4.9990
   chunk 66 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9990
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    4.9990
   chunk 63 optimal weight:    0.2980
   chunk 32 optimal weight:    5.9990
   overall best weight:    1.6588

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 269 ASN
S  82 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7955
moved from start:          0.1818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   9029  Z= 0.282
  Angle     :  0.549   8.641  12235  Z= 0.285
  Chirality :  0.042   0.155   1399
  Planarity :  0.004   0.042   1543
  Dihedral  :  4.070  18.189   1234
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 7.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.38 %
    Favored  : 95.62 %
  Rotamer:
    Outliers :  1.15 %
    Allowed  : 21.83 %
    Favored  : 77.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.25), residues: 1119
  helix:  1.79 (0.27), residues: 384
  sheet: -0.73 (0.30), residues: 285
  loop : -0.48 (0.29), residues: 450

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 106
  time to evaluate  : 1.063 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 7
  residues processed: 113
  average time/residue: 0.2179
  time to fit residues: 34.5379
Evaluate side-chains
  109 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 102
  time to evaluate  : 1.048 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 0
  residues processed: 7
  average time/residue: 0.0880
  time to fit residues: 2.6044
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 21 optimal weight:   10.0000
   chunk 20 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 97 optimal weight:    8.9990
   chunk 102 optimal weight:    5.9990
   chunk 93 optimal weight:    0.5980
   chunk 99 optimal weight:    3.9990
   overall best weight:    1.1182

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 195 HIS
A 269 ASN
A 306 GLN
S  82 GLN
S 179 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.1909

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9029  Z= 0.211
  Angle     :  0.520   8.886  12235  Z= 0.271
  Chirality :  0.041   0.131   1399
  Planarity :  0.003   0.040   1543
  Dihedral  :  3.962  17.313   1234
  Min Nonbonded Distance : 2.060

Molprobity Statistics.
  All-atom Clashscore : 6.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.29 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  : 22.14 %
    Favored  : 77.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.32 (0.25), residues: 1119
  helix:  1.87 (0.27), residues: 380
  sheet: -0.74 (0.30), residues: 280
  loop : -0.49 (0.29), residues: 459

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 104
  time to evaluate  : 1.067 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 3
  residues processed: 106
  average time/residue: 0.2295
  time to fit residues: 33.8378
Evaluate side-chains
  104 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 101
  time to evaluate  : 0.978 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.0853
  time to fit residues: 1.9128
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 102 optimal weight:    5.9990
   chunk 60 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0980
   chunk 78 optimal weight:    0.7980
   chunk 30 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 65 optimal weight:    0.0070
   chunk 105 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.5800

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
A 269 ASN
A 306 GLN
B 230 ASN
S  39 GLN
S  82 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   9029  Z= 0.149
  Angle     :  0.492   8.940  12235  Z= 0.256
  Chirality :  0.040   0.132   1399
  Planarity :  0.003   0.041   1543
  Dihedral  :  3.783  16.573   1234
  Min Nonbonded Distance : 2.064

Molprobity Statistics.
  All-atom Clashscore : 6.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.42 %
    Allowed  : 22.04 %
    Favored  : 77.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.50 (0.25), residues: 1119
  helix:  2.01 (0.27), residues: 380
  sheet: -0.52 (0.31), residues: 273
  loop : -0.47 (0.28), residues: 466

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 110
  time to evaluate  : 1.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 1
  residues processed: 113
  average time/residue: 0.2393
  time to fit residues: 37.8493
Evaluate side-chains
  104 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.994 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0842
  time to fit residues: 1.4786
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 50 optimal weight:    4.9990
   chunk 73 optimal weight:    6.9990
   chunk 110 optimal weight:    1.9990
   chunk 101 optimal weight:    8.9990
   chunk 88 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 68 optimal weight:    0.6980
   chunk 53 optimal weight:    6.9990
   chunk 69 optimal weight:    0.6980
   chunk 93 optimal weight:    0.0170
   chunk 26 optimal weight:    4.9990
   overall best weight:    1.0822

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
S  82 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7907
moved from start:          0.2088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   9029  Z= 0.204
  Angle     :  0.515   9.173  12235  Z= 0.266
  Chirality :  0.041   0.133   1399
  Planarity :  0.003   0.043   1543
  Dihedral  :  3.822  16.843   1234
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 22.14 %
    Favored  : 77.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.25), residues: 1119
  helix:  1.95 (0.27), residues: 381
  sheet: -0.64 (0.30), residues: 285
  loop : -0.49 (0.29), residues: 453

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

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

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 103
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 1
  residues processed: 104
  average time/residue: 0.2229
  time to fit residues: 32.2777
Evaluate side-chains
  102 residues out of total 967 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 1.019 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0858
  time to fit residues: 1.5951
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 111
   random chunks:
   chunk 81 optimal weight:    0.8980
   chunk 13 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 88 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 11 optimal weight:    7.9990
   chunk 16 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 5 optimal weight:    0.8980
   chunk 63 optimal weight:    0.2980
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
A 188 HIS
** A 304 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
S  39 GLN
S  82 GLN
S 179 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3990 r_free = 0.3990 target = 0.179401 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.135244 restraints weight = 9553.654|
|-----------------------------------------------------------------------------|
r_work (start): 0.3478 rms_B_bonded: 2.06
r_work: 0.3269 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.3118 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3118
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7836
moved from start:          0.2168

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9029  Z= 0.171
  Angle     :  0.504   9.167  12235  Z= 0.260
  Chirality :  0.040   0.147   1399
  Planarity :  0.003   0.041   1543
  Dihedral  :  3.780  16.657   1234
  Min Nonbonded Distance : 2.063

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  : 22.35 %
    Favored  : 77.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.03 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.51 (0.25), residues: 1119
  helix:  2.03 (0.27), residues: 379
  sheet: -0.47 (0.31), residues: 278
  loop : -0.51 (0.29), residues: 462
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2183.25 seconds
wall clock time: 40 minutes 22.76 seconds (2422.76 seconds total)