Starting phenix.real_space_refine (version: 1.20rc4)
on Wed Dec  1 16:06:44 2021 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602_updated.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602.map
  Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602_ligands.cif

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602_ligands.cif"
    default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602_ligands.cif"
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602_updated.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d76_30602/12_2021/7d76_30602_updated.pdb"
  }
  resolution = 3.1
  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=  -0.000 sd=   0.009
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Convert atoms to be neutral
Process input model

  Symmetric amino acids flipped
    None
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib"
  Total number of atoms: 7015
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 1707
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 215, 1707
          Classifications: {'peptide': 215}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 4, 'TRANS': 210}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 2600
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 338, 2600
          Classifications: {'peptide': 338}
          Link IDs: {'PTRANS': 5, 'TRANS': 332}
    Chain: "G"
      Number of atoms: 429
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 56, 429
          Classifications: {'peptide': 56}
          Link IDs: {'PTRANS': 4, 'TRANS': 51}
    Chain: "R"
      Number of atoms: 2107
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 265, 2097
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 4, 'TRANS': 260}
      Conformer: "B"
        Number of residues, atoms: 265, 2097
          Classifications: {'peptide': 265}
          Link IDs: {'PTRANS': 4, 'TRANS': 260}
          bond proxies already assigned to first conformer: 2143
    Chain: "A"
      Number of atoms: 17
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 17
          Unusual residues: {'PLM': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'PLM:plan-1': 1}
          Unresolved non-hydrogen planarities: 1
    Chain: "R"
      Number of atoms: 155
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 155
          Unusual residues: {'PLM': 2, 'Y01': 1, 'CLR': 2, 'GXR': 1}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  AHIS R 309 " occ=0.50
      ... (18 atoms not shown)
      pdb=" NE2BHIS R 309 " occ=0.50
  Time building chain proxies: 5.33, per 1000 atoms: 0.76
  Number of scatterers: 7015
  At special positions: 0
  Unit cell: (79.092, 111.54, 111.54, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      46     16.00
     O    1273      8.00
     N    1174      7.00
     C    4521      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS R 338 " - pdb=" SG  CYS R 420 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.50
        Amimo 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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.78
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1628

  Finding SS restraints...
  running ksdssp...
    Secondary structure from input PDB file:
      20 helices and 9 sheets defined
      39.7% alpha, 15.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 30
    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 209 through 216
      removed outlier: 5.172A  pdb=" N   HIS A 214 " --> pdb=" O   LYS A 210 " (cutoff:3.500A)
      removed outlier: 6.254A  pdb=" N   CYS A 215 " --> pdb=" O   LYS A 211 " (cutoff:3.500A)
      removed outlier: 4.623A  pdb=" N   PHE A 216 " --> pdb=" O   TRP A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 243 through 255
    Processing helix  chain 'A' and resid 272 through 281
      removed outlier: 4.262A  pdb=" N   LYS A 280 " --> pdb=" O   GLY A 276 " (cutoff:3.500A)
      removed outlier: 4.384A  pdb=" N   LYS A 281 " --> pdb=" O   GLU A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 297 through 311
      removed outlier: 4.414A  pdb=" N   LYS A 311 " --> pdb=" O   GLN A 307 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 350
    Processing helix  chain 'B' and resid 4 through 25
    Processing helix  chain 'B' and resid 30 through 36
      removed outlier: 5.468A  pdb=" N   ASN B  36 " --> pdb=" O   GLN B  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 8 through 23
    Processing helix  chain 'G' and resid 30 through 43
    Processing helix  chain 'G' and resid 45 through 47
      No H-bonds generated for 'chain 'G' and resid 45 through 47'
    Processing helix  chain 'R' and resid 264 through 296
    Processing helix  chain 'R' and resid 305 through 328
    Processing helix  chain 'R' and resid 335 through 367
      removed outlier: 3.672A  pdb=" N   ALA R 340 " --> pdb=" O   ALA R 336 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 378 through 400
      Proline residue:  R 390  - end of helix
      removed outlier: 3.675A  pdb=" N   ALA R 400 " --> pdb=" O   GLY R 396 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 429 through 434
    Processing helix  chain 'R' and resid 436 through 463
      removed outlier: 4.339A  pdb=" N   ARG R 462 " --> pdb=" O   PHE R 458 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ALA R 463 " --> pdb=" O   THR R 459 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 472 through 495
      removed outlier: 4.167A  pdb=" N   LEU R 477 " --> pdb=" O   ARG R 473 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   LEU R 485 " --> pdb=" O   GLY R 481 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TRP R 490 " --> pdb=" O   VAL R 486 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 503 through 524
      removed outlier: 3.687A  pdb=" N   ILE R 517 " --> pdb=" O   GLN R 513 " (cutoff:3.500A)
    Processing sheet with id=  A, first strand: chain 'A' and resid 264 through 267
      removed outlier: 3.920A  pdb=" N   ALA A 221 " --> pdb=" O   LYS A  35 " (cutoff:3.500A)
      removed outlier: 6.697A  pdb=" N   HIS A 196 " --> pdb=" O   VAL A  34 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   LEU A  36 " --> pdb=" O   HIS A 196 " (cutoff:3.500A)
      removed outlier: 6.244A  pdb=" N   ARG A 198 " --> pdb=" O   LEU A  36 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   LEU A  38 " --> pdb=" O   ARG A 198 " (cutoff:3.500A)
      removed outlier: 6.290A  pdb=" N   PHE A 200 " --> pdb=" O   LEU A  38 " (cutoff:3.500A)
    Processing sheet with id=  B, first strand: chain 'B' and resid 91 through 94
      removed outlier: 4.025A  pdb=" N   LYS B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   SER B  74 " --> pdb=" O   LYS B  78 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   LEU B  70 " --> pdb=" O   TRP B  82 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA B  60 " --> pdb=" O   ALA B  73 " (cutoff:3.500A)
    Processing sheet with id=  C, first strand: chain 'B' and resid 100 through 105
      removed outlier: 7.126A  pdb=" N   GLY B 115 " --> pdb=" O   MET B 101 " (cutoff:3.500A)
      removed outlier: 4.509A  pdb=" N   CYS B 103 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
      removed outlier: 6.602A  pdb=" N   ALA B 113 " --> pdb=" O   CYS B 103 " (cutoff:3.500A)
      removed outlier: 5.049A  pdb=" N   TYR B 105 " --> pdb=" O   TYR B 111 " (cutoff:3.500A)
      removed outlier: 7.162A  pdb=" N   TYR B 111 " --> pdb=" O   TYR B 105 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   ARG B 137 " --> pdb=" O   ILE B 123 " (cutoff:3.500A)
      removed outlier: 6.469A  pdb=" N   ASN B 125 " --> pdb=" O   VAL B 135 " (cutoff:3.500A)
      removed outlier: 6.484A  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: 6.851A  pdb=" N   SER B 160 " --> pdb=" O   SER B 147 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   CYS B 149 " --> pdb=" O   VAL B 158 " (cutoff:3.500A)
      removed outlier: 6.880A  pdb=" N   VAL B 158 " --> pdb=" O   CYS B 149 " (cutoff:3.500A)
      removed outlier: 4.998A  pdb=" N   PHE B 151 " --> pdb=" O   GLN B 156 " (cutoff:3.500A)
      removed outlier: 7.448A  pdb=" N   GLN B 156 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   ILE B 157 " --> pdb=" O   TRP B 169 " (cutoff:3.500A)
      removed outlier: 6.223A  pdb=" N   ASP B 170 " --> pdb=" O   GLN B 176 " (cutoff:3.500A)
      removed outlier: 6.593A  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: 6.721A  pdb=" N   GLY B 202 " --> pdb=" O   MET B 188 " (cutoff:3.500A)
      removed outlier: 4.543A  pdb=" N   LEU B 190 " --> pdb=" O   VAL B 200 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL B 200 " --> pdb=" O   LEU B 190 " (cutoff:3.500A)
      removed outlier: 5.248A  pdb=" N   LEU B 192 " --> pdb=" O   LEU B 198 " (cutoff:3.500A)
      removed outlier: 7.299A  pdb=" N   LEU B 198 " --> pdb=" O   LEU B 192 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   GLN B 220 " --> pdb=" O   LEU B 210 " (cutoff:3.500A)
      removed outlier: 6.149A  pdb=" N   ASP B 212 " --> pdb=" O   CYS B 218 " (cutoff:3.500A)
      removed outlier: 6.129A  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: 6.481A  pdb=" N   GLY B 244 " --> pdb=" O   ASN B 230 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   ILE B 232 " --> pdb=" O   ALA B 242 " (cutoff:3.500A)
      removed outlier: 6.920A  pdb=" N   ALA B 242 " --> pdb=" O   ILE B 232 " (cutoff:3.500A)
      removed outlier: 4.830A  pdb=" N   PHE B 234 " --> pdb=" O   ALA B 240 " (cutoff:3.500A)
      removed outlier: 6.889A  pdb=" N   ALA B 240 " --> pdb=" O   PHE B 234 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   MET B 262 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
      removed outlier: 6.373A  pdb=" N   ASP B 254 " --> pdb=" O   GLU B 260 " (cutoff:3.500A)
      removed outlier: 6.110A  pdb=" N   GLU B 260 " --> pdb=" O   ASP B 254 " (cutoff:3.500A)
    Processing sheet with id=  G, first strand: chain 'B' and resid 275 through 278
      removed outlier: 6.612A  pdb=" N   ASP B 298 " --> pdb=" O   ARG B 304 " (cutoff:3.500A)
      removed outlier: 6.767A  pdb=" N   ARG B 304 " --> pdb=" O   ASP B 298 " (cutoff:3.500A)
    Processing sheet with id=  H, first strand: chain 'B' and resid 327 through 329
      removed outlier: 3.577A  pdb=" N   LYS B 337 " --> pdb=" O   THR B 329 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   LEU B 336 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   ARG B  49 " --> pdb=" O   ILE B 338 " (cutoff:3.500A)
    Processing sheet with id=  I, first strand: chain 'R' and resid 406 through 408
      removed outlier: 3.662A  pdb=" N   LEU R 417 " --> pdb=" O   ILE R 408 " (cutoff:3.500A)

    323 hydrogen bonds defined for protein.
    943 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: 2.04

  Time building geometry restraints manager: 3.03 seconds

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

  Histogram of bond lengths:
        1.19 -     1.33: 1249
        1.33 -     1.46: 2695
        1.46 -     1.60: 3152
        1.60 -     1.73: 5
        1.73 -     1.87: 65
  Bond restraints: 7166
  Sorted by residual:
  bond pdb=" C19 GXR R 604 "
       pdb=" C22 GXR R 604 "
    ideal  model  delta    sigma   weight residual
    0.459  1.473 -1.014 2.00e-02 2.50e+03 2.57e+03
  bond pdb=" C18 GXR R 604 "
       pdb=" C21 GXR R 604 "
    ideal  model  delta    sigma   weight residual
    2.104  1.328  0.776 2.00e-02 2.50e+03 1.51e+03
  bond pdb=" C14 GXR R 604 "
       pdb=" C19 GXR R 604 "
    ideal  model  delta    sigma   weight residual
    1.939  1.335  0.604 2.00e-02 2.50e+03 9.12e+02
  bond pdb=" C13 GXR R 604 "
       pdb=" C14 GXR R 604 "
    ideal  model  delta    sigma   weight residual
    1.776  1.489  0.287 2.00e-02 2.50e+03 2.07e+02
  bond pdb=" C10 GXR R 604 "
       pdb=" C14 GXR R 604 "
    ideal  model  delta    sigma   weight residual
    1.262  1.504 -0.242 2.00e-02 2.50e+03 1.46e+02
  ... (remaining 7161 not shown)

  Histogram of bond angle deviations from ideal:
       99.14 -   106.13: 122
      106.13 -   113.11: 3993
      113.11 -   120.10: 2566
      120.10 -   127.09: 2956
      127.09 -   134.07: 76
  Bond angle restraints: 9713
  Sorted by residual:
  angle pdb=" C10 GXR R 604 "
        pdb=" C18 GXR R 604 "
        pdb=" C21 GXR R 604 "
      ideal   model   delta    sigma   weight residual
     106.52  120.41  -13.89 3.00e+00 1.11e-01 2.14e+01
  angle pdb=" C   ALA R 337 "
        pdb=" N   CYS R 338 "
        pdb=" CA  CYS R 338 "
      ideal   model   delta    sigma   weight residual
     121.94  112.94    9.00 2.00e+00 2.50e-01 2.02e+01
  angle pdb=" C18 GXR R 604 "
        pdb=" C10 GXR R 604 "
        pdb=" C4  GXR R 604 "
      ideal   model   delta    sigma   weight residual
      99.21  112.23  -13.02 3.00e+00 1.11e-01 1.88e+01
  angle pdb=" C18 GXR R 604 "
        pdb=" C21 GXR R 604 "
        pdb=" C22 GXR R 604 "
      ideal   model   delta    sigma   weight residual
     107.23  119.37  -12.14 3.00e+00 1.11e-01 1.64e+01
  angle pdb=" O1  PLM R 602 "
        pdb=" C1  PLM R 602 "
        pdb=" O2  PLM R 602 "
      ideal   model   delta    sigma   weight residual
     128.81  119.99    8.82 2.30e+00 1.88e-01 1.46e+01
  ... (remaining 9708 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.79: 3820
       18.79 -    37.59: 312
       37.59 -    56.38: 46
       56.38 -    75.17: 8
       75.17 -    93.97: 4
  Dihedral angle restraints: 4190
    sinusoidal: 1664
      harmonic: 2526
  Sorted by residual:
  dihedral pdb=" CB  CYS R 338 "
           pdb=" SG  CYS R 338 "
           pdb=" SG  CYS R 420 "
           pdb=" CB  CYS R 420 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  165.80  -72.80     1      1.00e+01 1.00e-02 6.76e+01
  dihedral pdb=" CA  CYS R 338 "
           pdb=" C   CYS R 338 "
           pdb=" N   TRP R 339 "
           pdb=" CA  TRP R 339 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.32   24.68     0      5.00e+00 4.00e-02 2.44e+01
  dihedral pdb=" CA  LYS A  54 "
           pdb=" C   LYS A  54 "
           pdb=" N   ILE A  55 "
           pdb=" CA  ILE A  55 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.78  -17.22     0      5.00e+00 4.00e-02 1.19e+01
  ... (remaining 4187 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.107: 1063
       0.107 -    0.215: 32
       0.215 -    0.322: 9
       0.322 -    0.429: 3
       0.429 -    0.537: 3
  Chirality restraints: 1110
  Sorted by residual:
  chirality pdb=" CBG Y01 R 601 "
            pdb=" CAQ Y01 R 601 "
            pdb=" CBD Y01 R 601 "
            pdb=" CBI Y01 R 601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.87    0.54 2.00e-01 2.50e+01 7.20e+00
  chirality pdb=" C4  GXR R 604 "
            pdb=" C10 GXR R 604 "
            pdb=" C3  GXR R 604 "
            pdb=" C9  GXR R 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.79    2.26    0.53 2.00e-01 2.50e+01 6.98e+00
  chirality pdb=" C1  GXR R 604 "
            pdb=" C2  GXR R 604 "
            pdb=" C5  GXR R 604 "
            pdb=" C7  GXR R 604 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.28   -2.81    0.52 2.00e-01 2.50e+01 6.83e+00
  ... (remaining 1107 not shown)

  Planarity restraints: 1201
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 GXR R 604 "   -0.008 2.00e-02 2.50e+03   1.64e-01 3.35e+02
        pdb=" C13 GXR R 604 "   -0.183 2.00e-02 2.50e+03
        pdb=" C14 GXR R 604 "    0.194 2.00e-02 2.50e+03
        pdb=" C19 GXR R 604 "    0.175 2.00e-02 2.50e+03
        pdb=" C22 GXR R 604 "   -0.179 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 347 "    0.017 2.00e-02 2.50e+03   3.22e-02 1.04e+01
        pdb=" C   ASN A 347 "   -0.056 2.00e-02 2.50e+03
        pdb=" O   ASN A 347 "    0.021 2.00e-02 2.50e+03
        pdb=" N   LEU A 348 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 105 "    0.014 2.00e-02 2.50e+03   1.42e-02 4.05e+00
        pdb=" CG  TYR B 105 "   -0.035 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 105 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 105 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 105 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 105 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 105 "    0.001 2.00e-02 2.50e+03
        pdb=" OH  TYR B 105 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1198 not shown)

  Histogram of nonbonded interaction distances:
        2.17 -     2.71: 298
        2.71 -     3.26: 7080
        3.26 -     3.81: 10812
        3.81 -     4.35: 13848
        4.35 -     4.90: 23770
  Nonbonded interactions: 55808
  Sorted by model distance:
  nonbonded pdb=" OG  SER B 161 "
            pdb=" OD1 ASP B 163 "
     model   vdw
     2.167 2.440
  nonbonded pdb=" O   LYS B  57 "
            pdb=" OG  SER B  74 "
     model   vdw
     2.198 2.440
  nonbonded pdb=" O   ALA R 430 "
            pdb=" OG1 THR R 434 "
     model   vdw
     2.223 2.440
  nonbonded pdb=" OD1 ASP A 341 "
            pdb=" ND2 ASN R 472 "
     model   vdw
     2.226 2.520
  nonbonded pdb=" OE2 GLU A 187 "
            pdb=" NH1 ARG A 198 "
     model   vdw
     2.256 2.520
  ... (remaining 55803 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: 5
    Type Number    sf(0)   Gaussians
     S      46      5.16       5
     Cl      1      4.86       5
     C    4521      2.51       5
     N    1174      2.21       5
     O    1273      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=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Write .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:             0.290
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          2.020
  Check model and map are aligned:         0.110
  Convert atoms to be neutral:             0.060
  Process input model:                     22.980
  Find NCS groups from input model:        0.190
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Set scattering table:                    0.010
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.250
  Set ADP refinement strategy:             0.000
  Write .geo file:                         0.000
  Internal consistency checks:             0.000
  Total:   27.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
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      :  0.020   1.014   7166  Z= 1.138
  Angle     :  0.849  13.892   9713  Z= 0.422
  Chirality :  0.060   0.537   1110
  Planarity :  0.006   0.164   1201
  Dihedral  : 13.926  93.968   2559
  Min Nonbonded Distance : 2.167

Molprobity Statistics.
  All-atom Clashscore : 8.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.55 (0.26), residues: 867
  helix:  0.07 (0.26), residues: 351
  sheet: -3.13 (0.32), residues: 183
  loop : -2.68 (0.28), residues: 333

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 133
  time to evaluate  : 0.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 133
  average time/residue: 0.2365
  time to fit residues: 39.8250
Evaluate side-chains
  98 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.839 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0940
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.8980
   chunk 64 optimal weight:    0.7980
   chunk 35 optimal weight:    4.9990
   chunk 22 optimal weight:    8.9990
   chunk 43 optimal weight:    5.9990
   chunk 34 optimal weight:    0.0670
   chunk 66 optimal weight:    7.9990
   chunk 25 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 49 optimal weight:    0.9980
   chunk 77 optimal weight:    0.7980
   overall best weight:    0.7118

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
A 214 HIS
A 295 ASN
A 307 GLN
** B  16 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  54 HIS
B 311 HIS
R 266 HIS
R 346 HIS
R 362 HIS

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
moved from start:          0.1242

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.056   7166  Z= 0.179
  Angle     :  0.583   8.642   9713  Z= 0.288
  Chirality :  0.043   0.217   1110
  Planarity :  0.004   0.067   1201
  Dihedral  :  7.484 126.480   1022
  Min Nonbonded Distance : 2.213

Molprobity Statistics.
  All-atom Clashscore : 9.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer Outliers :  1.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.12 (0.28), residues: 867
  helix:  1.51 (0.27), residues: 352
  sheet: -2.43 (0.35), residues: 174
  loop : -2.23 (0.30), residues: 341

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 0.800 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 126
  average time/residue: 0.1878
  time to fit residues: 31.7577
Evaluate side-chains
  112 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 107
  time to evaluate  : 0.793 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1466
  time to fit residues: 2.0844
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 23 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 21 optimal weight:    8.9990
   chunk 77 optimal weight:    0.9980
   chunk 83 optimal weight:    2.9990
   chunk 68 optimal weight:    0.7980
   chunk 76 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 62 optimal weight:    0.3980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
A 312 ASN
B  16 ASN
R 266 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8005
moved from start:          0.1566

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7166  Z= 0.187
  Angle     :  0.562   9.468   9713  Z= 0.279
  Chirality :  0.042   0.211   1110
  Planarity :  0.004   0.061   1201
  Dihedral  :  7.102 122.258   1022
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer Outliers :  0.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.48 (0.29), residues: 867
  helix:  2.10 (0.28), residues: 352
  sheet: -2.16 (0.35), residues: 174
  loop : -1.93 (0.31), residues: 341

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 109
  time to evaluate  : 0.869 
Fit side-chains
   revert: symmetry clash
  outliers start: 6
  outliers final: 1
  residues processed: 111
  average time/residue: 0.1835
  time to fit residues: 27.9597
Evaluate side-chains
  101 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.817 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0998
  time to fit residues: 1.2917
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 76 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   chunk 40 optimal weight:    3.9990
   chunk 8 optimal weight:    0.4980
   chunk 36 optimal weight:    5.9990
   chunk 51 optimal weight:    0.0030
   chunk 77 optimal weight:    0.8980
   chunk 82 optimal weight:    0.7980
   chunk 73 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
R 266 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7983
moved from start:          0.1846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.002   0.067   7166  Z= 0.164
  Angle     :  0.530   8.759   9713  Z= 0.265
  Chirality :  0.041   0.200   1110
  Planarity :  0.004   0.092   1201
  Dihedral  :  6.839 121.023   1022
  Min Nonbonded Distance : 2.193

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.12 %
    Favored  : 96.88 %
  Rotamer Outliers :  2.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -0.03 (0.29), residues: 867
  helix:  2.46 (0.28), residues: 353
  sheet: -1.88 (0.36), residues: 174
  loop : -1.72 (0.32), residues: 340

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 109
  time to evaluate  : 0.886 
Fit side-chains
  outliers start: 15
  outliers final: 6
  residues processed: 120
  average time/residue: 0.1761
  time to fit residues: 29.3833
Evaluate side-chains
  113 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 107
  time to evaluate  : 0.850 
Switching outliers to nearest non-outliers
  outliers start: 6
  outliers final: 0
  residues processed: 6
  average time/residue: 0.0748
  time to fit residues: 1.9252
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 46 optimal weight:    6.9990
   chunk 1 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 70 optimal weight:    4.9990
   chunk 56 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 41 optimal weight:    9.9990
   chunk 73 optimal weight:    7.9990
   chunk 20 optimal weight:    0.6980
   chunk 27 optimal weight:    0.4980
   overall best weight:    2.1984

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

Flipped N/Q/H residues before XYZ refinement:
A 307 GLN
R 266 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1615

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.081   7166  Z= 0.344
  Angle     :  0.621   9.122   9713  Z= 0.312
  Chirality :  0.045   0.202   1110
  Planarity :  0.005   0.096   1201
  Dihedral  :  7.681 123.500   1022
  Min Nonbonded Distance : 2.156

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.86 %
    Favored  : 95.14 %
  Rotamer Outliers :  0.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.29), residues: 867
  helix:  2.29 (0.27), residues: 353
  sheet: -1.74 (0.37), residues: 173
  loop : -1.71 (0.32), residues: 341

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 104
  time to evaluate  : 0.788 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 109
  average time/residue: 0.1681
  time to fit residues: 25.6527
Evaluate side-chains
  102 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 98
  time to evaluate  : 0.852 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0740
  time to fit residues: 1.6789
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 73 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9990
   chunk 48 optimal weight:    2.9990
   chunk 20 optimal weight:    0.5980
   chunk 82 optimal weight:    3.9990
   chunk 68 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 6 optimal weight:    2.9990
   chunk 27 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 79 optimal weight:    9.9990
   overall best weight:    0.8986

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

Flipped N/Q/H residues before XYZ refinement:
A 194 ASN
R 266 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.089   7166  Z= 0.198
  Angle     :  0.565  10.217   9713  Z= 0.280
  Chirality :  0.042   0.200   1110
  Planarity :  0.004   0.095   1201
  Dihedral  :  7.216 122.006   1022
  Min Nonbonded Distance : 2.174

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.36 %
    Favored  : 96.64 %
  Rotamer Outliers :  1.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.21 (0.30), residues: 867
  helix:  2.54 (0.28), residues: 353
  sheet: -1.55 (0.37), residues: 178
  loop : -1.56 (0.34), residues: 336

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 106
  time to evaluate  : 0.862 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 112
  average time/residue: 0.1642
  time to fit residues: 26.0204
Evaluate side-chains
  109 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 0.815 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.0679
  time to fit residues: 1.6123
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    0.7980
   chunk 46 optimal weight:    0.4980
   chunk 60 optimal weight:    1.9990
   chunk 69 optimal weight:    0.6980
   chunk 45 optimal weight:    0.9990
   chunk 81 optimal weight:    2.9990
   chunk 51 optimal weight:    8.9990
   chunk 49 optimal weight:    0.1980
   chunk 37 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.5580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.2053

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.098   7166  Z= 0.200
  Angle     :  0.545   8.865   9713  Z= 0.275
  Chirality :  0.041   0.202   1110
  Planarity :  0.005   0.106   1201
  Dihedral  :  6.904 120.877   1022
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer Outliers :  0.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.35 (0.30), residues: 867
  helix:  2.73 (0.28), residues: 353
  sheet: -1.49 (0.37), residues: 175
  loop : -1.56 (0.33), residues: 339

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 109
  time to evaluate  : 0.772 
Fit side-chains
  outliers start: 5
  outliers final: 1
  residues processed: 113
  average time/residue: 0.1765
  time to fit residues: 27.4945
Evaluate side-chains
  103 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 102
  time to evaluate  : 0.856 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0675
  time to fit residues: 1.2403
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:    1.9990
   chunk 24 optimal weight:    8.9990
   chunk 16 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   chunk 55 optimal weight:    4.9990
   chunk 40 optimal weight:    4.9990
   chunk 7 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 74 optimal weight:    5.9990
   chunk 78 optimal weight:    0.6980
   overall best weight:    1.4584

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

Flipped N/Q/H residues before XYZ refinement:
R 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.115   7166  Z= 0.281
  Angle     :  0.591   9.237   9713  Z= 0.300
  Chirality :  0.043   0.190   1110
  Planarity :  0.005   0.120   1201
  Dihedral  :  7.239 121.735   1022
  Min Nonbonded Distance : 2.157

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer Outliers :  0.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.28 (0.30), residues: 867
  helix:  2.59 (0.28), residues: 354
  sheet: -1.50 (0.37), residues: 181
  loop : -1.52 (0.34), residues: 332

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 103
  time to evaluate  : 0.843 
Fit side-chains
  outliers start: 5
  outliers final: 2
  residues processed: 105
  average time/residue: 0.1991
  time to fit residues: 28.9501
Evaluate side-chains
  102 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 100
  time to evaluate  : 0.849 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0749
  time to fit residues: 1.3501
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    0.6980
   chunk 76 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 33 optimal weight:    2.9990
   chunk 59 optimal weight:    1.9990
   chunk 23 optimal weight:   20.0000
   chunk 68 optimal weight:    0.6980
   chunk 72 optimal weight:    0.8980
   chunk 50 optimal weight:    3.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7992
moved from start:          0.2118

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.150   7166  Z= 0.239
  Angle     :  0.584  10.077   9713  Z= 0.296
  Chirality :  0.042   0.198   1110
  Planarity :  0.005   0.125   1201
  Dihedral  :  7.046 120.937   1022
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 8.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.47 %
    Favored  : 96.53 %
  Rotamer Outliers :  0.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.44 (0.30), residues: 867
  helix:  2.65 (0.28), residues: 353
  sheet: -1.29 (0.38), residues: 173
  loop : -1.42 (0.34), residues: 341

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 103
  time to evaluate  : 0.841 
Fit side-chains
  outliers start: 3
  outliers final: 1
  residues processed: 103
  average time/residue: 0.1763
  time to fit residues: 25.2983
Evaluate side-chains
  102 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 101
  time to evaluate  : 0.793 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.0717
  time to fit residues: 1.2156
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 56 optimal weight:    9.9990
   chunk 84 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9980
   chunk 7 optimal weight:    4.9990
   chunk 52 optimal weight:    0.7980
   chunk 41 optimal weight:    8.9990
   chunk 53 optimal weight:    2.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
R 266 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.2140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.161   7166  Z= 0.258
  Angle     :  0.616  14.453   9713  Z= 0.320
  Chirality :  0.042   0.196   1110
  Planarity :  0.006   0.139   1201
  Dihedral  :  7.061 120.623   1022
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  Rotamer Outliers :  0.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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:  0.44 (0.30), residues: 867
  helix:  2.70 (0.28), residues: 351
  sheet: -1.29 (0.37), residues: 181
  loop : -1.45 (0.35), residues: 335

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

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

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1734 Ramachandran restraints generated.
    867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 0.771 
Fit side-chains
  outliers start: 4
  outliers final: 2
  residues processed: 107
  average time/residue: 0.1815
  time to fit residues: 27.0067
Evaluate side-chains
  104 residues out of total 734 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 102
  time to evaluate  : 0.831 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.0727
  time to fit residues: 1.3983
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 20 optimal weight:    0.5980
   chunk 62 optimal weight:    4.9990
   chunk 9 optimal weight:    4.9990
   chunk 18 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 28 optimal weight:    1.9990
   chunk 69 optimal weight:    1.9990
   chunk 8 optimal weight:    2.9990
   chunk 12 optimal weight:    0.6980
   chunk 59 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   overall best weight:    1.2584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3953 r_free = 0.3953 target = 0.167712 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.123474 restraints weight = 20669.103|
|-----------------------------------------------------------------------------|
r_work (start): 0.3462 rms_B_bonded: 4.40
r_work: 0.3433 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work: 0.3409 rms_B_bonded: 3.96 restraints_weight: 0.2500
r_work: 0.3386 rms_B_bonded: 4.02 restraints_weight: 0.1250
r_work: 0.3362 rms_B_bonded: 4.17 restraints_weight: 0.0625
r_work: 0.3336 rms_B_bonded: 4.39 restraints_weight: 0.0312
r_work: 0.3308 rms_B_bonded: 4.69 restraints_weight: 0.0156
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3953
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3953 r_free = 0.3953    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3953 r_free = 0.3953    target_work(ls_wunit_k1) = 0.168         |
| occupancies: max = 1.00  min = 0.42   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3953
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8106
moved from start:          0.2092

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.164   7166  Z= 0.293
  Angle     :  0.633  15.058   9713  Z= 0.331
  Chirality :  0.043   0.192   1110
  Planarity :  0.006   0.143   1201
  Dihedral  :  7.224 121.369   1022
  Min Nonbonded Distance : 2.169

Molprobity Statistics.
  All-atom Clashscore : 8.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer Outliers :  0.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.41 (0.30), residues: 867
  helix:  2.61 (0.27), residues: 353
  sheet: -1.26 (0.37), residues: 181
  loop : -1.45 (0.35), residues: 333

===============================================================================
Job complete
usr+sys time: 1496.23 seconds
wall clock time: 27 minutes 58.81 seconds (1678.81 seconds total)