Starting phenix.real_space_refine (version: dev)
on Sun Feb 19 01:23:24 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/02_2023/7na7_24267_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/02_2023/7na7_24267.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/02_2023/7na7_24267.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/02_2023/7na7_24267.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/02_2023/7na7_24267_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7na7_24267/02_2023/7na7_24267_updated.pdb"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.023
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
Process input model

  Symmetric amino acids flipped
    Residue "B GLU   10": "OE1" <-> "OE2"
    Residue "R TYR  106": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "R GLU  202": "OE1" <-> "OE2"
    Residue "L GLU    8": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 9036
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1752
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 1752
          Classifications: {'peptide': 217}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 214}
          Chain breaks: 2
    Chain: "B"
      Number of atoms: 2584
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 336, 2584
          Classifications: {'peptide': 336}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 330}
    Chain: "G"
      Number of atoms: 418
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 54, 418
          Classifications: {'peptide': 54}
          Link IDs: {'PTRANS': 4, 'TRANS': 49}
    Chain: "N"
      Number of atoms: 1784
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 232, 1784
          Classifications: {'peptide': 232}
          Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 221}
          Chain breaks: 1
    Chain: "R"
      Number of atoms: 2339
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 291, 2339
          Classifications: {'peptide': 291}
          Link IDs: {'PTRANS': 11, 'TRANS': 279}
          Chain breaks: 1
    Chain: "L"
      Number of atoms: 103
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 103
          Classifications: {'peptide': 12}
          Link IDs: {'PTRANS': 1, 'TRANS': 10}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Planarities with less than four sites: {'1IC:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 56
          Unusual residues: {'CLR': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 5.43, per 1000 atoms: 0.60
  Number of scatterers: 9036
  At special positions: 0
  Unit cell: (87.75, 120.25, 124.8, 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      62     16.00
     O    1662      8.00
     N    1526      7.00
     C    5786      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS N  22 " - pdb=" SG  CYS N  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS N 159 " - pdb=" SG  CYS N 229 " distance=2.04
    Simple disulfide: pdb=" SG  CYS R 116 " - pdb=" SG  CYS R 198 " 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: 3.27
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2238 Ramachandran restraints generated.
    1119 Oldfield, 0 Emsley, 1119 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
    Skipped
      Input volumes are d-peptide like
        pdb=" CB  1IC L   3 "
  Number of C-beta restraints generated:  2132

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      29 helices and 12 sheets defined
      34.3% alpha, 21.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.16
  Creating SS restraints...
    Processing helix  chain 'A' and resid 9 through 31
    Processing helix  chain 'A' and resid 46 through 48
      No H-bonds generated for 'chain 'A' and resid 46 through 48'
    Processing helix  chain 'A' and resid 208 through 210
      No H-bonds generated for 'chain 'A' and resid 208 through 210'
    Processing helix  chain 'A' and resid 212 through 215
    Processing helix  chain 'A' and resid 227 through 230
      removed outlier: 4.069A  pdb=" N   TYR A 230 " --> pdb=" O   LEU A 227 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 227 through 230'
    Processing helix  chain 'A' and resid 242 through 254
    Processing helix  chain 'A' and resid 271 through 280
      removed outlier: 3.699A  pdb=" N   GLU A 275 " --> pdb=" O   LYS A 271 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   GLU A 276 " --> pdb=" O   ASP A 272 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 285
      No H-bonds generated for 'chain 'A' and resid 283 through 285'
    Processing helix  chain 'A' and resid 296 through 308
    Processing helix  chain 'A' and resid 328 through 351
    Processing helix  chain 'B' and resid 8 through 21
      removed outlier: 3.545A  pdb=" N   GLU B  12 " --> pdb=" O   ARG B   8 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ASN B  16 " --> pdb=" O   GLU B  12 " (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 'G' and resid 10 through 23
    Processing helix  chain 'G' and resid 30 through 43
      removed outlier: 4.444A  pdb=" N   ASP G  36 " --> pdb=" O   LYS G  32 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   LEU G  37 " --> pdb=" O   ALA G  33 " (cutoff:3.500A)
    Processing helix  chain 'N' and resid 29 through 31
      No H-bonds generated for 'chain 'N' and resid 29 through 31'
    Processing helix  chain 'N' and resid 88 through 90
      No H-bonds generated for 'chain 'N' and resid 88 through 90'
    Processing helix  chain 'R' and resid 40 through 70
      removed outlier: 4.142A  pdb=" N   ALA R  44 " --> pdb=" O   ALA R  40 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   GLY R  45 " --> pdb=" O   PRO R  41 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 72 through 74
      No H-bonds generated for 'chain 'R' and resid 72 through 74'
    Processing helix  chain 'R' and resid 77 through 94
    Processing helix  chain 'R' and resid 96 through 104
    Processing helix  chain 'R' and resid 113 through 146
      removed outlier: 3.713A  pdb=" N   GLN R 120 " --> pdb=" O   CYS R 116 " (cutoff:3.500A)
      removed outlier: 3.992A  pdb=" N   SER R 123 " --> pdb=" O   PHE R 119 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   TYR R 128 " --> pdb=" O   GLU R 124 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 148 through 154
      removed outlier: 3.607A  pdb=" N   VAL R 153 " --> pdb=" O   LEU R 149 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 157 through 178
      removed outlier: 3.570A  pdb=" N   LEU R 162 " --> pdb=" O   GLY R 158 " (cutoff:3.500A)
      removed outlier: 3.955A  pdb=" N   VAL R 163 " --> pdb=" O   ARG R 159 " (cutoff:3.500A)
      Proline residue:  R 177  - end of helix
    Processing helix  chain 'R' and resid 192 through 195
      No H-bonds generated for 'chain 'R' and resid 192 through 195'
    Processing helix  chain 'R' and resid 202 through 206
    Processing helix  chain 'R' and resid 209 through 242
      removed outlier: 3.512A  pdb=" N   SER R 218 " --> pdb=" O   VAL R 214 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE R 219 " --> pdb=" O   TRP R 215 " (cutoff:3.500A)
      removed outlier: 4.369A  pdb=" N   PHE R 220 " --> pdb=" O   VAL R 216 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   PHE R 221 " --> pdb=" O   SER R 217 " (cutoff:3.500A)
      Proline residue:  R 224  - end of helix
    Processing helix  chain 'R' and resid 256 through 289
      Proline residue:  R 278  - end of helix
    Processing helix  chain 'R' and resid 296 through 324
      removed outlier: 3.629A  pdb=" N   GLN R 302 " --> pdb=" O   ALA R 298 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ALA R 316 " --> pdb=" O   PHE R 312 " (cutoff:3.500A)
      Proline residue:  R 320  - end of helix
    Processing helix  chain 'R' and resid 328 through 337
    Processing sheet with id=  A, first strand: chain 'A' and resid 319 through 323
      removed outlier: 6.741A  pdb=" N   ILE A 264 " --> pdb=" O   TYR A 320 " (cutoff:3.500A)
      removed outlier: 7.821A  pdb=" N   HIS A 322 " --> pdb=" O   ILE A 264 " (cutoff:3.500A)
      removed outlier: 6.458A  pdb=" N   LEU A 266 " --> pdb=" O   HIS A 322 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ALA A 220 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 58 through 63
      removed outlier: 6.667A  pdb=" N   ALA B  73 " --> pdb=" O   TYR B  59 " (cutoff:3.500A)
      removed outlier: 4.408A  pdb=" N   MET B  61 " --> pdb=" O   VAL B  71 " (cutoff:3.500A)
      removed outlier: 6.698A  pdb=" N   VAL B  71 " --> pdb=" O   MET B  61 " (cutoff:3.500A)
      removed outlier: 5.119A  pdb=" N   TRP B  63 " --> pdb=" O   LEU B  69 " (cutoff:3.500A)
      removed outlier: 7.241A  pdb=" N   LEU B  69 " --> pdb=" O   TRP B  63 " (cutoff:3.500A)
      removed outlier: 3.770A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 4.592A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 6.427A  pdb=" N   ASP B  83 " --> pdb=" O   LYS B  89 " (cutoff:3.500A)
      removed outlier: 5.945A  pdb=" N   LYS B  89 " --> pdb=" O   ASP B  83 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 6.733A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.339A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.188A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 5.976A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 5.957A  pdb=" N   VAL B 135 " --> pdb=" O   ASN B 125 " (cutoff:3.500A)
    Processing sheet with id=  D, first strand: chain 'B' and resid 146 through 151
      removed outlier: 6.718A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.666A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 5.057A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.557A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   THR B 165 " --> pdb=" O   SER B 161 " (cutoff:3.500A)
      removed outlier: 6.571A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.158A  pdb=" N   GLN B 176 " --> pdb=" O   ASP B 170 " (cutoff:3.500A)
    Processing sheet with id=  E, first strand: chain 'B' and resid 187 through 192
      removed outlier: 6.659A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.327A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.085A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.231A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.347A  pdb=" N   CYS B 218 " --> pdb=" O   ASP B 212 " (cutoff:3.500A)
    Processing sheet with id=  F, first strand: chain 'B' and resid 229 through 234
      removed outlier: 6.493A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.375A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.680A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.899A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 7.080A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.649A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.044A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 273 through 278
      removed outlier: 6.370A  pdb=" N   GLY B 288 " --> pdb=" O   THR B 274 " (cutoff:3.500A)
      removed outlier: 4.246A  pdb=" N   VAL B 276 " --> pdb=" O   LEU B 286 " (cutoff:3.500A)
      removed outlier: 6.687A  pdb=" N   LEU B 286 " --> pdb=" O   VAL B 276 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   PHE B 278 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
      removed outlier: 7.025A  pdb=" N   LEU B 284 " --> pdb=" O   PHE B 278 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.100A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 317 through 320
      removed outlier: 3.587A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'N' and resid 3 through 7
    Processing sheet with id=  J, first strand: chain 'N' and resid 115 through 117
      removed outlier: 5.793A  pdb=" N   ARG N  38 " --> pdb=" O   TRP N  47 " (cutoff:3.500A)
      removed outlier: 5.065A  pdb=" N   TRP N  47 " --> pdb=" O   ARG N  38 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   ALA N  40 " --> pdb=" O   LEU N  45 " (cutoff:3.500A)
      removed outlier: 6.743A  pdb=" N   LEU N  45 " --> pdb=" O   ALA N  40 " (cutoff:3.500A)
    Processing sheet with id=  K, first strand: chain 'N' and resid 146 through 148
      removed outlier: 6.511A  pdb=" N   LYS N 244 " --> pdb=" O   VAL N 147 " (cutoff:3.500A)
      removed outlier: 6.091A  pdb=" N   LEU N 178 " --> pdb=" O   LEU N 187 " (cutoff:3.500A)
      removed outlier: 5.466A  pdb=" N   LEU N 187 " --> pdb=" O   LEU N 178 " (cutoff:3.500A)
    Processing sheet with id=  L, first strand: chain 'N' and resid 155 through 160

    397 hydrogen bonds defined for protein.
    1131 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: 2.82

  Time building geometry restraints manager: 3.44 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 1446
        1.30 -     1.43: 2481
        1.43 -     1.56: 5218
        1.56 -     1.69: 0
        1.69 -     1.82: 88
  Bond restraints: 9233
  Sorted by residual:
  bond pdb=" CA  SER N 106 "
       pdb=" CB  SER N 106 "
    ideal  model  delta    sigma   weight residual
    1.531  1.449  0.082 1.22e-02 6.72e+03 4.51e+01
  bond pdb=" C   PRO N 107 "
       pdb=" O   PRO N 107 "
    ideal  model  delta    sigma   weight residual
    1.234  1.169  0.064 1.14e-02 7.69e+03 3.17e+01
  bond pdb=" CA  SER N 105 "
       pdb=" CB  SER N 105 "
    ideal  model  delta    sigma   weight residual
    1.529  1.447  0.082 1.61e-02 3.86e+03 2.62e+01
  bond pdb=" C   LEU N 174 "
       pdb=" O   LEU N 174 "
    ideal  model  delta    sigma   weight residual
    1.236  1.177  0.058 1.14e-02 7.69e+03 2.62e+01
  bond pdb=" C   TYR N 175 "
       pdb=" O   TYR N 175 "
    ideal  model  delta    sigma   weight residual
    1.234  1.185  0.048 1.17e-02 7.31e+03 1.71e+01
  ... (remaining 9228 not shown)

  Histogram of bond angle deviations from ideal:
       97.37 -   104.73: 143
      104.73 -   112.10: 4547
      112.10 -   119.46: 3234
      119.46 -   126.82: 4466
      126.82 -   134.18: 117
  Bond angle restraints: 12507
  Sorted by residual:
  angle pdb=" C   1IC L   3 "
        pdb=" CA  1IC L   3 "
        pdb=" CB  1IC L   3 "
      ideal   model   delta    sigma   weight residual
     110.50  126.38  -15.88 1.50e+00 4.44e-01 1.12e+02
  angle pdb=" C   GLN R 302 "
        pdb=" CA  GLN R 302 "
        pdb=" CB  GLN R 302 "
      ideal   model   delta    sigma   weight residual
     110.63  126.91  -16.28 1.85e+00 2.92e-01 7.75e+01
  angle pdb=" N   GLU A   8 "
        pdb=" CA  GLU A   8 "
        pdb=" C   GLU A   8 "
      ideal   model   delta    sigma   weight residual
     112.92  103.28    9.64 1.23e+00 6.61e-01 6.14e+01
  angle pdb=" C   ARG N 191 "
        pdb=" CA  ARG N 191 "
        pdb=" CB  ARG N 191 "
      ideal   model   delta    sigma   weight residual
     111.80  122.64  -10.84 1.46e+00 4.69e-01 5.51e+01
  angle pdb=" N   LEU R 103 "
        pdb=" CA  LEU R 103 "
        pdb=" C   LEU R 103 "
      ideal   model   delta    sigma   weight residual
     113.01  105.72    7.29 1.20e+00 6.94e-01 3.69e+01
  ... (remaining 12502 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.26: 5155
       22.26 -    44.51: 273
       44.51 -    66.77: 23
       66.77 -    89.03: 5
       89.03 -   111.28: 1
  Dihedral angle restraints: 5457
    sinusoidal: 2154
      harmonic: 3303
  Sorted by residual:
  dihedral pdb=" C   GLN R 302 "
           pdb=" N   GLN R 302 "
           pdb=" CA  GLN R 302 "
           pdb=" CB  GLN R 302 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -141.66   19.06     0      2.50e+00 1.60e-01 5.81e+01
  dihedral pdb=" C   ARG N 191 "
           pdb=" N   ARG N 191 "
           pdb=" CA  ARG N 191 "
           pdb=" CB  ARG N 191 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -140.00   17.40     0      2.50e+00 1.60e-01 4.84e+01
  dihedral pdb=" C   ASN R 305 "
           pdb=" N   ASN R 305 "
           pdb=" CA  ASN R 305 "
           pdb=" CB  ASN R 305 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -137.94   15.34     0      2.50e+00 1.60e-01 3.76e+01
  ... (remaining 5454 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    1.166: 1416
       1.166 -    2.333: 0
       2.333 -    3.499: 0
       3.499 -    4.665: 0
       4.665 -    5.831: 2
  Chirality restraints: 1418
  Sorted by residual:
  chirality pdb=" C13 CLR R 402 "
            pdb=" C12 CLR R 402 "
            pdb=" C14 CLR R 402 "
            pdb=" C17 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.93    2.90   -5.83 2.00e-01 2.50e+01 8.50e+02
  chirality pdb=" C17 CLR R 402 "
            pdb=" C13 CLR R 402 "
            pdb=" C16 CLR R 402 "
            pdb=" C20 CLR R 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55   -2.63    5.18 2.00e-01 2.50e+01 6.72e+02
  chirality pdb=" CA  1IC L   3 "
            pdb=" N   1IC L   3 "
            pdb=" C   1IC L   3 "
            pdb=" CB  1IC L   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.84   -0.65 2.00e-01 2.50e+01 1.04e+01
  ... (remaining 1415 not shown)

  Planarity restraints: 1566
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU N 174 "    0.026 2.00e-02 2.50e+03   5.27e-02 2.78e+01
        pdb=" C   LEU N 174 "   -0.091 2.00e-02 2.50e+03
        pdb=" O   LEU N 174 "    0.035 2.00e-02 2.50e+03
        pdb=" N   TYR N 175 "    0.031 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A   6 "   -0.022 2.00e-02 2.50e+03   4.36e-02 1.90e+01
        pdb=" C   SER A   6 "    0.075 2.00e-02 2.50e+03
        pdb=" O   SER A   6 "   -0.028 2.00e-02 2.50e+03
        pdb=" N   ALA A   7 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL N 147 "   -0.047 5.00e-02 4.00e+02   7.10e-02 8.06e+00
        pdb=" N   PRO N 148 "    0.123 5.00e-02 4.00e+02
        pdb=" CA  PRO N 148 "   -0.037 5.00e-02 4.00e+02
        pdb=" CD  PRO N 148 "   -0.039 5.00e-02 4.00e+02
  ... (remaining 1563 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 573
        2.72 -     3.27: 8769
        3.27 -     3.81: 15027
        3.81 -     4.36: 19489
        4.36 -     4.90: 33272
  Nonbonded interactions: 77130
  Sorted by model distance:
  nonbonded pdb=" OG1 THR R  76 "
            pdb=" OD1 ASN R  79 "
     model   vdw
     2.178 2.440
  nonbonded pdb=" O   GLY R  57 "
            pdb=" ND2 ASN R  61 "
     model   vdw
     2.250 2.520
  nonbonded pdb=" O   MET G  38 "
            pdb=" OE1 GLU G  42 "
     model   vdw
     2.277 3.040
  nonbonded pdb=" O   PRO R 192 "
            pdb=" OD1 ASN R 196 "
     model   vdw
     2.284 3.040
  nonbonded pdb=" O   PHE N  32 "
            pdb=" NH2 ARG N  72 "
     model   vdw
     2.322 2.520
  ... (remaining 77125 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
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    5786      2.51       5
     N    1526      2.21       5
     O    1662      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
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:                  0.010
  Normalize map: mean=0, sd=1:             4.730
  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:          14.310
  Check model and map are aligned:         0.130
  Process input model:                     26.170
  Find NCS groups from input model:        0.290
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Set scattering table:                    0.090
  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:13.970
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   59.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7541
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      :  0.006   0.082   9233  Z= 0.402
  Angle     :  1.043  16.282  12507  Z= 0.655
  Chirality :  0.218   5.831   1418
  Planarity :  0.006   0.071   1566
  Dihedral  : 12.925 111.283   3316
  Min Nonbonded Distance : 2.178

Molprobity Statistics.
  All-atom Clashscore : 7.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.61 %
    Favored  : 98.39 %
  Rotamer Outliers :  0.61 %
  Cbeta Deviations :  0.47 %
  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 (0.23), residues: 1119
  helix:  0.86 (0.26), residues: 388
  sheet:  0.67 (0.28), residues: 298
  loop : -0.62 (0.26), residues: 433

*********************** 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
  243 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 237
  time to evaluate  : 0.968 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 0
  residues processed: 241
  average time/residue: 1.0952
  time to fit residues: 283.1903
Evaluate side-chains
  204 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 1.148 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.4984
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    1.9990
   chunk 84 optimal weight:    1.9990
   chunk 47 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   chunk 57 optimal weight:    0.0970
   chunk 45 optimal weight:    0.6980
   chunk 87 optimal weight:    0.8980
   chunk 33 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 65 optimal weight:    0.7980
   chunk 101 optimal weight:    0.5980
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
** A 331 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  16 ASN
B 175 GLN
B 230 ASN
** B 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN
N 142 GLN
N 179 GLN
N 183 GLN
R 120 GLN
R 302 GLN
R 319 ASN
L   9 HIS

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7710
moved from start:          0.2109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.032   9233  Z= 0.244
  Angle     :  0.769  31.648  12507  Z= 0.356
  Chirality :  0.065   1.833   1418
  Planarity :  0.004   0.052   1566
  Dihedral  :  5.089  35.914   1263
  Min Nonbonded Distance : 2.245

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer Outliers :  2.55 %
  Cbeta Deviations :  0.09 %
  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:  0.60 (0.24), residues: 1119
  helix:  1.15 (0.26), residues: 399
  sheet:  0.76 (0.28), residues: 303
  loop : -0.52 (0.28), residues: 417

*********************** 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
  244 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 25
    poor density    : 219
  time to evaluate  : 1.043 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 25
  outliers final: 11
  residues processed: 230
  average time/residue: 1.1602
  time to fit residues: 285.3976
Evaluate side-chains
  217 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 206
  time to evaluate  : 1.071 
Switching outliers to nearest non-outliers
  outliers start: 11
  outliers final: 7
  residues processed: 5
  average time/residue: 0.1242
  time to fit residues: 2.4487
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 56 optimal weight:    0.5980
   chunk 31 optimal weight:    0.3980
   chunk 84 optimal weight:    2.9990
   chunk 69 optimal weight:    0.3980
   chunk 28 optimal weight:    0.9980
   chunk 101 optimal weight:    0.5980
   chunk 110 optimal weight:    0.8980
   chunk 90 optimal weight:    0.7980
   chunk 34 optimal weight:    2.9990
   chunk 81 optimal weight:    1.9990
   chunk 100 optimal weight:    0.4980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
** A 322 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 155 ASN
B 156 GLN
B 293 ASN
B 295 ASN
** B 340 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  17 GLN
** G  59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
N  82 GLN
N 142 GLN
N 179 GLN
L   9 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.2929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.050   9233  Z= 0.220
  Angle     :  0.729  30.565  12507  Z= 0.329
  Chirality :  0.064   1.799   1418
  Planarity :  0.004   0.048   1566
  Dihedral  :  4.792  42.867   1263
  Min Nonbonded Distance : 2.199

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.70 %
    Favored  : 98.30 %
  Rotamer Outliers :  2.96 %
  Cbeta Deviations :  0.09 %
  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:  0.67 (0.24), residues: 1119
  helix:  1.29 (0.26), residues: 392
  sheet:  0.66 (0.28), residues: 299
  loop : -0.42 (0.28), residues: 428

*********************** 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
  252 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 223
  time to evaluate  : 1.081 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 29
  outliers final: 12
  residues processed: 236
  average time/residue: 1.1132
  time to fit residues: 281.6173
Evaluate side-chains
  220 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 208
  time to evaluate  : 1.058 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 7
  residues processed: 5
  average time/residue: 0.4011
  time to fit residues: 3.8656
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 76 optimal weight:    0.0770
   chunk 52 optimal weight:    0.0770
   chunk 11 optimal weight:    0.0270
   chunk 48 optimal weight:    1.9990
   chunk 68 optimal weight:    0.8980
   chunk 102 optimal weight:    0.8980
   chunk 108 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 96 optimal weight:    0.2980
   chunk 29 optimal weight:    1.9990
   chunk 90 optimal weight:    0.9980
   overall best weight:    0.2554

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  17 GLN
B 155 ASN
B 156 GLN
B 220 GLN
B 239 ASN
B 295 ASN
B 340 ASN
G  59 ASN
** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.3248

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9233  Z= 0.149
  Angle     :  0.692  31.800  12507  Z= 0.304
  Chirality :  0.062   1.780   1418
  Planarity :  0.003   0.049   1566
  Dihedral  :  4.648  35.746   1263
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 8.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.43 %
    Favored  : 98.57 %
  Rotamer Outliers :  2.75 %
  Cbeta Deviations :  0.09 %
  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:  0.90 (0.25), residues: 1119
  helix:  1.62 (0.27), residues: 387
  sheet:  0.69 (0.27), residues: 304
  loop : -0.35 (0.29), residues: 428

*********************** 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
  231 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 27
    poor density    : 204
  time to evaluate  : 1.035 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 27
  outliers final: 15
  residues processed: 216
  average time/residue: 1.1550
  time to fit residues: 267.4911
Evaluate side-chains
  214 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 199
  time to evaluate  : 1.012 
Switching outliers to nearest non-outliers
  outliers start: 15
  outliers final: 8
  residues processed: 7
  average time/residue: 0.6409
  time to fit residues: 6.5376
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 61 optimal weight:    0.4980
   chunk 1 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 92 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9980
   chunk 0 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 97 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A  22 ASN
A 331 ASN
B  17 GLN
B 239 ASN
B 295 ASN
G  59 ASN
** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN
R 186 HIS
R 302 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.3524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.045   9233  Z= 0.298
  Angle     :  0.751  30.662  12507  Z= 0.339
  Chirality :  0.065   1.843   1418
  Planarity :  0.004   0.056   1566
  Dihedral  :  4.845  25.562   1263
  Min Nonbonded Distance : 2.185

Molprobity Statistics.
  All-atom Clashscore : 8.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer Outliers :  3.77 %
  Cbeta Deviations :  0.09 %
  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:  0.79 (0.25), residues: 1119
  helix:  1.55 (0.27), residues: 381
  sheet:  0.57 (0.28), residues: 300
  loop : -0.35 (0.29), residues: 438

*********************** 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
  232 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 37
    poor density    : 195
  time to evaluate  : 1.005 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 37
  outliers final: 23
  residues processed: 213
  average time/residue: 1.1555
  time to fit residues: 263.3994
Evaluate side-chains
  217 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 194
  time to evaluate  : 0.966 
Switching outliers to nearest non-outliers
  outliers start: 23
  outliers final: 13
  residues processed: 10
  average time/residue: 0.4334
  time to fit residues: 6.3966
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 97 optimal weight:    2.9990
   chunk 21 optimal weight:    0.5980
   chunk 63 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 108 optimal weight:    0.9980
   chunk 89 optimal weight:    0.7980
   chunk 50 optimal weight:    0.7980
   chunk 9 optimal weight:    0.7980
   chunk 35 optimal weight:    0.9990
   chunk 56 optimal weight:    0.7980
   chunk 104 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  17 GLN
B  44 GLN
B 156 GLN
B 239 ASN
B 293 ASN
B 340 ASN
G  59 ASN
** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7791
moved from start:          0.3739

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.036   9233  Z= 0.296
  Angle     :  0.741  30.574  12507  Z= 0.336
  Chirality :  0.066   1.860   1418
  Planarity :  0.004   0.057   1566
  Dihedral  :  4.854  27.594   1263
  Min Nonbonded Distance : 2.146

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer Outliers :  4.08 %
  Cbeta Deviations :  0.09 %
  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:  0.68 (0.25), residues: 1119
  helix:  1.43 (0.27), residues: 382
  sheet:  0.52 (0.28), residues: 298
  loop : -0.38 (0.29), residues: 439

*********************** 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
  235 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 40
    poor density    : 195
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
  outliers start: 40
  outliers final: 21
  residues processed: 217
  average time/residue: 1.0109
  time to fit residues: 237.0245
Evaluate side-chains
  217 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 196
  time to evaluate  : 1.084 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 14
  residues processed: 7
  average time/residue: 0.3941
  time to fit residues: 4.7794
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 61 optimal weight:    1.9990
   chunk 79 optimal weight:    0.4980
   chunk 91 optimal weight:    0.8980
   chunk 60 optimal weight:    0.7980
   chunk 107 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9980
   chunk 65 optimal weight:    0.7980
   chunk 49 optimal weight:    1.9990
   chunk 66 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0670
   overall best weight:    0.6118

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  17 GLN
B  44 GLN
B 156 GLN
B 239 ASN
G  59 ASN
** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7786
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9233  Z= 0.255
  Angle     :  0.730  30.494  12507  Z= 0.328
  Chirality :  0.065   1.868   1418
  Planarity :  0.004   0.057   1566
  Dihedral  :  4.757  22.668   1263
  Min Nonbonded Distance : 2.143

Molprobity Statistics.
  All-atom Clashscore : 8.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer Outliers :  3.98 %
  Cbeta Deviations :  0.09 %
  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:  0.69 (0.25), residues: 1119
  helix:  1.42 (0.27), residues: 382
  sheet:  0.54 (0.28), residues: 302
  loop : -0.38 (0.30), residues: 435

*********************** 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
  232 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 39
    poor density    : 193
  time to evaluate  : 1.024 
Fit side-chains
   revert: symmetry clash
  outliers start: 39
  outliers final: 26
  residues processed: 213
  average time/residue: 1.0860
  time to fit residues: 248.3102
Evaluate side-chains
  217 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 191
  time to evaluate  : 0.972 
Switching outliers to nearest non-outliers
  outliers start: 26
  outliers final: 16
  residues processed: 10
  average time/residue: 0.6877
  time to fit residues: 9.0429
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 21 optimal weight:    0.0050
   chunk 20 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 73 optimal weight:    0.6980
   chunk 53 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 84 optimal weight:    1.9990
   chunk 98 optimal weight:    0.8980
   chunk 103 optimal weight:    0.5980
   overall best weight:    0.5594

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  17 GLN
B 156 GLN
B 239 ASN
B 340 ASN
G  59 ASN
** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7782
moved from start:          0.3901

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.033   9233  Z= 0.238
  Angle     :  0.723  30.418  12507  Z= 0.324
  Chirality :  0.065   1.877   1418
  Planarity :  0.004   0.058   1566
  Dihedral  :  4.759  26.151   1263
  Min Nonbonded Distance : 2.150

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.14 %
    Favored  : 97.86 %
  Rotamer Outliers :  3.26 %
  Cbeta Deviations :  0.09 %
  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:  0.69 (0.25), residues: 1119
  helix:  1.45 (0.27), residues: 382
  sheet:  0.54 (0.28), residues: 302
  loop : -0.42 (0.30), residues: 435

*********************** 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
  226 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 32
    poor density    : 194
  time to evaluate  : 1.048 
Fit side-chains
   revert: symmetry clash
  outliers start: 32
  outliers final: 21
  residues processed: 211
  average time/residue: 1.1571
  time to fit residues: 263.2044
Evaluate side-chains
  214 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 21
    poor density    : 193
  time to evaluate  : 1.043 
Switching outliers to nearest non-outliers
  outliers start: 21
  outliers final: 15
  residues processed: 6
  average time/residue: 0.4321
  time to fit residues: 4.5132
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 94 optimal weight:    0.1980
   chunk 100 optimal weight:    0.6980
   chunk 103 optimal weight:    0.5980
   chunk 60 optimal weight:    0.7980
   chunk 43 optimal weight:    4.9990
   chunk 78 optimal weight:    1.9990
   chunk 30 optimal weight:    0.5980
   chunk 90 optimal weight:    0.5980
   chunk 95 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 106 optimal weight:    0.1980
   overall best weight:    0.4380

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  17 GLN
B 156 GLN
B 239 ASN
G  59 ASN
** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN
R 186 HIS
L   9 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7771
moved from start:          0.3953

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9233  Z= 0.199
  Angle     :  0.711  30.334  12507  Z= 0.316
  Chirality :  0.065   1.886   1418
  Planarity :  0.004   0.058   1566
  Dihedral  :  4.678  22.869   1263
  Min Nonbonded Distance : 2.168

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.23 %
    Favored  : 97.77 %
  Rotamer Outliers :  2.85 %
  Cbeta Deviations :  0.09 %
  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:  0.70 (0.25), residues: 1119
  helix:  1.49 (0.27), residues: 383
  sheet:  0.48 (0.28), residues: 302
  loop : -0.39 (0.30), residues: 434

*********************** 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
  226 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 28
    poor density    : 198
  time to evaluate  : 1.120 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 18
  residues processed: 215
  average time/residue: 1.1626
  time to fit residues: 268.0435
Evaluate side-chains
  210 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 192
  time to evaluate  : 1.051 
Switching outliers to nearest non-outliers
  outliers start: 18
  outliers final: 14
  residues processed: 4
  average time/residue: 0.3762
  time to fit residues: 3.3320
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 50 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 111 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   chunk 88 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 68 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   chunk 70 optimal weight:    0.9990
   chunk 94 optimal weight:    2.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  17 GLN
B 239 ASN
N  82 GLN
** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7795
moved from start:          0.4010

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9233  Z= 0.333
  Angle     :  0.759  30.355  12507  Z= 0.344
  Chirality :  0.067   1.886   1418
  Planarity :  0.004   0.062   1566
  Dihedral  :  4.922  22.553   1263
  Min Nonbonded Distance : 2.127

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer Outliers :  2.65 %
  Cbeta Deviations :  0.09 %
  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:  1.19 (0.27), residues: 387
  sheet:  0.38 (0.28), residues: 298
  loop : -0.38 (0.29), residues: 434

********************** 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
  218 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 0.896 
Fit side-chains
   revert: symmetry clash
  outliers start: 26
  outliers final: 16
  residues processed: 209
  average time/residue: 1.0921
  time to fit residues: 245.2085
Evaluate side-chains
  208 residues out of total 981 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 192
  time to evaluate  : 1.032 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 14
  residues processed: 2
  average time/residue: 0.9352
  time to fit residues: 3.4627
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 112
   random chunks:
   chunk 27 optimal weight:    1.9990
   chunk 81 optimal weight:    0.9980
   chunk 13 optimal weight:    0.3980
   chunk 24 optimal weight:    0.6980
   chunk 88 optimal weight:    0.5980
   chunk 37 optimal weight:    1.9990
   chunk 91 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 78 optimal weight:    0.6980
   chunk 5 optimal weight:    3.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 331 ASN
B  17 GLN
B 239 ASN
N  82 GLN
** N 142 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
N 179 GLN
R 186 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.121157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.109073 restraints weight = 12631.486|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 1.48
r_work: 0.3338 rms_B_bonded: 1.97 restraints_weight: 0.5000
r_work: 0.3211 rms_B_bonded: 3.52 restraints_weight: 0.2500
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8176
moved from start:          0.4055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.034   9233  Z= 0.272
  Angle     :  0.740  30.264  12507  Z= 0.334
  Chirality :  0.066   1.895   1418
  Planarity :  0.004   0.061   1566
  Dihedral  :  4.908  23.657   1263
  Min Nonbonded Distance : 2.128

Molprobity Statistics.
  All-atom Clashscore : 9.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer Outliers :  2.24 %
  Cbeta Deviations :  0.09 %
  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:  0.49 (0.25), residues: 1119
  helix:  1.22 (0.27), residues: 383
  sheet:  0.49 (0.29), residues: 284
  loop : -0.48 (0.29), residues: 452

===============================================================================
Job complete
usr+sys time: 4380.89 seconds
wall clock time: 78 minutes 37.94 seconds (4717.94 seconds total)