Starting phenix.real_space_refine (version: 1.21rc1)
on Sun Apr 23 11:32:20 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/04_2023/7joa_22409.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/04_2023/7joa_22409.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/04_2023/7joa_22409.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/04_2023/7joa_22409.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/04_2023/7joa_22409.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7joa_22409/04_2023/7joa_22409.pdb"
  }
  resolution = 3.3
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
-------------------------------------------------------------------------------
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=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     290      5.49       5
     S      25      5.16       5
     C    8556      2.51       5
     N    2771      2.21       5
     O    3351      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A PHE   84": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C ARG   32": "NH1" <-> "NH2"
    Residue "C TYR   39": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "C GLU   64": "OE1" <-> "OE2"
    Residue "C ARG   71": "NH1" <-> "NH2"
    Residue "C GLU   91": "OE1" <-> "OE2"
    Residue "D ARG   33": "NH1" <-> "NH2"
    Residue "D TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D TYR   83": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "F ASP   24": "OD1" <-> "OD2"
    Residue "G ARG   32": "NH1" <-> "NH2"
    Residue "G TYR   39": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "G GLU   64": "OE1" <-> "OE2"
    Residue "G ARG   71": "NH1" <-> "NH2"
    Residue "G GLU   91": "OE1" <-> "OE2"
    Residue "H ARG   33": "NH1" <-> "NH2"
    Residue "H TYR   37": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "H TYR   83": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K ARG  222": "NH1" <-> "NH2"
    Residue "K PHE  251": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K GLU  276": "OE1" <-> "OE2"
    Residue "K GLU  302": "OE1" <-> "OE2"
    Residue "K GLU  303": "OE1" <-> "OE2"
    Residue "K GLU  411": "OE1" <-> "OE2"
    Residue "K PHE  428": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "K GLU  463": "OE1" <-> "OE2"
    Residue "K PHE  469": "CD1" <-> "CD2" "CE1" <-> "CE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib"
  Total number of atoms: 14994
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 810
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 810
          Classifications: {'peptide': 98}
          Link IDs: {'PTRANS': 4, 'TRANS': 93}
    Chain: "B"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 648
          Classifications: {'peptide': 81}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "C"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 801
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 97, 801
          Classifications: {'peptide': 97}
          Link IDs: {'PTRANS': 3, 'TRANS': 93}
    Chain: "F"
      Number of atoms: 683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 683
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "G"
      Number of atoms: 837
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 109, 837
          Classifications: {'peptide': 109}
          Link IDs: {'PTRANS': 5, 'TRANS': 103}
    Chain: "H"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 2990
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2990
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "J"
      Number of atoms: 2955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 145, 2955
          Classifications: {'DNA': 145}
          Link IDs: {'rna3p': 144}
    Chain: "K"
      Number of atoms: 2961
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 359, 2961
          Unusual residues: {' ZN': 1}
          Classifications: {'peptide': 358, 'undetermined': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 342, None: 1}
            Not linked:
              pdbres="ASP K 505 "
              pdbres=" ZN K 601 "

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM  13969  SG  CYS K 384      23.933  65.763  50.961  1.00 90.89           S
  ATOM  13975  SG  CYS K 385      24.055  69.257  48.730  1.00 83.30           S
  ATOM  14020  SG  CYS K 392      23.001  70.170  51.751  1.00 87.81           S

  Time building chain proxies: 7.50, per 1000 atoms: 0.50
  Number of scatterers: 14994
  At special positions: 0
  Unit cell: (150.15, 110.11, 116.48, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      25     16.00
     P     290     15.00
     O    3351      8.00
     N    2771      7.00
     C    8556      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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: 6.75
  Conformation dependent library (CDL) restraints added in 1.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN K 601 "
        pdb="ZN    ZN K 601 " - pdb=" SG  CYS K 385 "
        pdb="ZN    ZN K 601 " - pdb=" SG  CYS K 392 "
        pdb="ZN    ZN K 601 " - pdb=" NE2 HIS K 378 "
        pdb="ZN    ZN K 601 " - pdb=" SG  CYS K 384 "
      Number of angles added : 3


  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2118

  Finding SS restraints...
    Secondary structure from input PDB file:
      47 helices and 12 sheets defined
      63.2% alpha, 7.4% beta
      138 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 6.03
  Creating SS restraints...
    Processing helix  chain 'A' and resid 45 through 55
    Processing helix  chain 'A' and resid 63 through 76
      removed outlier: 3.659A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.526A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.544A  pdb=" N   ALA A 114 " --> pdb=" O   CYS A 110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.609A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.774A  pdb=" N   ILE B  34 " --> pdb=" O   THR B  30 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 76
      removed outlier: 4.119A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   ALA B  76 " --> pdb=" O   TYR B  72 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.529A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.848A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 27 through 37
    Processing helix  chain 'C' and resid 46 through 73
      removed outlier: 3.616A  pdb=" N   TYR C  50 " --> pdb=" O   GLY C  46 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.535A  pdb=" N   LEU C  83 " --> pdb=" O   ILE C  79 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 92 through 97
    Processing helix  chain 'D' and resid 37 through 49
      removed outlier: 3.643A  pdb=" N   GLN D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL D  48 " --> pdb=" O   VAL D  44 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.898A  pdb=" N   ASN D  84 " --> pdb=" O   LEU D  80 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.587A  pdb=" N   ILE D  94 " --> pdb=" O   THR D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 124
      removed outlier: 4.105A  pdb=" N   LYS D 108 " --> pdb=" O   GLY D 104 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   SER D 124 " --> pdb=" O   LYS D 120 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 45 through 55
    Processing helix  chain 'E' and resid 63 through 76
      removed outlier: 3.949A  pdb=" N   PHE E  67 " --> pdb=" O   ARG E  63 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 114
      removed outlier: 3.581A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA E 114 " --> pdb=" O   CYS E 110 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.702A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 25 through 29
    Processing helix  chain 'F' and resid 30 through 42
      removed outlier: 3.779A  pdb=" N   ILE F  34 " --> pdb=" O   THR F  30 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.188A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.763A  pdb=" N   ALA F  76 " --> pdb=" O   TYR F  72 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 92
      removed outlier: 3.587A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 27 through 37
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 3.617A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   ASN G  73 " --> pdb=" O   ALA G  69 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.535A  pdb=" N   LEU G  83 " --> pdb=" O   ILE G  79 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 92 through 97
    Processing helix  chain 'H' and resid 37 through 49
      removed outlier: 3.642A  pdb=" N   GLN H  47 " --> pdb=" O   LYS H  43 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL H  48 " --> pdb=" O   VAL H  44 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 55 through 84
      removed outlier: 3.898A  pdb=" N   ASN H  84 " --> pdb=" O   LEU H  80 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 90 through 102
      removed outlier: 3.585A  pdb=" N   ILE H  94 " --> pdb=" O   THR H  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 104 through 124
      removed outlier: 4.104A  pdb=" N   LYS H 108 " --> pdb=" O   GLY H 104 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   SER H 124 " --> pdb=" O   LYS H 120 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 149 through 185
      removed outlier: 3.797A  pdb=" N   ARG K 161 " --> pdb=" O   LEU K 157 " (cutoff:3.500A)
      removed outlier: 4.136A  pdb=" N   LYS K 162 " --> pdb=" O   ARG K 158 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   ASP K 163 " --> pdb=" O   LEU K 159 " (cutoff:3.500A)
      removed outlier: 4.753A  pdb=" N   GLU K 166 " --> pdb=" O   LYS K 162 " (cutoff:3.500A)
      removed outlier: 5.206A  pdb=" N   ALA K 167 " --> pdb=" O   ASP K 163 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 248 through 250
      No H-bonds generated for 'chain 'K' and resid 248 through 250'
    Processing helix  chain 'K' and resid 258 through 276
      removed outlier: 3.705A  pdb=" N   GLU K 276 " --> pdb=" O   GLU K 272 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 319 through 325
      removed outlier: 4.399A  pdb=" N   GLU K 324 " --> pdb=" O   SER K 321 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 332 through 342
      removed outlier: 4.377A  pdb=" N   VAL K 336 " --> pdb=" O   LEU K 332 " (cutoff:3.500A)
      removed outlier: 3.601A  pdb=" N   ARG K 337 " --> pdb=" O   GLY K 333 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 367 through 377
    Processing helix  chain 'K' and resid 393 through 412
    Processing helix  chain 'K' and resid 413 through 416
    Processing helix  chain 'K' and resid 419 through 434
      removed outlier: 3.847A  pdb=" N   VAL K 423 " --> pdb=" O   CYS K 419 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 436 through 443
      removed outlier: 4.038A  pdb=" N   ASP K 441 " --> pdb=" O   SER K 438 " (cutoff:3.500A)
      Proline residue:  K 442  - end of helix
    Processing helix  chain 'K' and resid 444 through 463
      removed outlier: 3.525A  pdb=" N   PHE K 455 " --> pdb=" O   LYS K 451 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 482 through 499
    Processing helix  chain 'K' and resid 500 through 505
      removed outlier: 5.995A  pdb=" N   ILE K 503 " --> pdb=" O   GLY K 500 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.193A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.598A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98
    Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43
      removed outlier: 8.193A  pdb=" N   ARG C  42 " --> pdb=" O   ILE D  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'C' and resid 101 through 102
      removed outlier: 6.953A  pdb=" N   THR C 101 " --> pdb=" O   TYR F  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84
      removed outlier: 7.526A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.500A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43
      removed outlier: 8.045A  pdb=" N   ARG G  42 " --> pdb=" O   ILE H  89 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'K' and resid 193 through 195
      removed outlier: 4.626A  pdb=" N   MET K 215 " --> pdb=" O   LEU K 195 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   PHE K 212 " --> pdb=" O   ASP K 307 " (cutoff:3.500A)
      removed outlier: 8.156A  pdb=" N   ILE K 309 " --> pdb=" O   PHE K 212 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL K 214 " --> pdb=" O   ILE K 309 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   ALA K 311 " --> pdb=" O   VAL K 214 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   PHE K 216 " --> pdb=" O   ALA K 311 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   GLU K 313 " --> pdb=" O   PHE K 216 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   LEU K 218 " --> pdb=" O   GLU K 313 " (cutoff:3.500A)
      removed outlier: 3.905A  pdb=" N   ASP K 281 " --> pdb=" O   ARG K 299 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'K' and resid 193 through 195
      removed outlier: 4.626A  pdb=" N   MET K 215 " --> pdb=" O   LEU K 195 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   PHE K 212 " --> pdb=" O   ASP K 307 " (cutoff:3.500A)
      removed outlier: 8.156A  pdb=" N   ILE K 309 " --> pdb=" O   PHE K 212 " (cutoff:3.500A)
      removed outlier: 6.689A  pdb=" N   VAL K 214 " --> pdb=" O   ILE K 309 " (cutoff:3.500A)
      removed outlier: 7.386A  pdb=" N   ALA K 311 " --> pdb=" O   VAL K 214 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   PHE K 216 " --> pdb=" O   ALA K 311 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   GLU K 313 " --> pdb=" O   PHE K 216 " (cutoff:3.500A)
      removed outlier: 6.153A  pdb=" N   LEU K 218 " --> pdb=" O   GLU K 313 " (cutoff:3.500A)
      removed outlier: 7.730A  pdb=" N   LEU K 310 " --> pdb=" O   PRO K 349 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'K' and resid 223 through 227
    Processing sheet with id=AB3, first strand: chain 'K' and resid 252 through 253

    507 hydrogen bonds defined for protein.
    1470 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      356 hydrogen bonds
      712 hydrogen bond angles
      0 basepair planarities
      138 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 6.88

  Time building geometry restraints manager: 7.15 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2781
        1.33 -     1.45: 4959
        1.45 -     1.57: 7503
        1.57 -     1.69: 578
        1.69 -     1.81: 40
  Bond restraints: 15861
  Sorted by residual:
  bond pdb=" CA  GLN A  55 "
       pdb=" C   GLN A  55 "
    ideal  model  delta    sigma   weight residual
    1.524  1.471  0.052 2.25e-02 1.98e+03 5.37e+00
  bond pdb=" C4'  DG J -49 "
       pdb=" C3'  DG J -49 "
    ideal  model  delta    sigma   weight residual
    1.523  1.496  0.027 2.00e-02 2.50e+03 1.88e+00
  bond pdb=" C3'  DG I  27 "
       pdb=" O3'  DG I  27 "
    ideal  model  delta    sigma   weight residual
    1.422  1.381  0.041 3.00e-02 1.11e+03 1.87e+00
  bond pdb=" CG  ARG F  39 "
       pdb=" CD  ARG F  39 "
    ideal  model  delta    sigma   weight residual
    1.520  1.479  0.041 3.00e-02 1.11e+03 1.84e+00
  bond pdb=" CB  VAL F  43 "
       pdb=" CG2 VAL F  43 "
    ideal  model  delta    sigma   weight residual
    1.521  1.477  0.044 3.30e-02 9.18e+02 1.79e+00
  ... (remaining 15856 not shown)

  Histogram of bond angle deviations from ideal:
       98.21 -   105.36: 1398
      105.36 -   112.51: 8810
      112.51 -   119.66: 5273
      119.66 -   126.81: 6341
      126.81 -   133.96: 812
  Bond angle restraints: 22634
  Sorted by residual:
  angle pdb=" N   TRP K 431 "
        pdb=" CA  TRP K 431 "
        pdb=" CB  TRP K 431 "
      ideal   model   delta    sigma   weight residual
     110.28  116.47   -6.19 1.55e+00 4.16e-01 1.60e+01
  angle pdb=" C   TYR A  54 "
        pdb=" N   GLN A  55 "
        pdb=" CA  GLN A  55 "
      ideal   model   delta    sigma   weight residual
     122.55  114.52    8.03 2.03e+00 2.43e-01 1.57e+01
  angle pdb=" C   PHE E 104 "
        pdb=" N   GLU E 105 "
        pdb=" CA  GLU E 105 "
      ideal   model   delta    sigma   weight residual
     120.29  115.67    4.62 1.42e+00 4.96e-01 1.06e+01
  angle pdb=" CB  MET A  90 "
        pdb=" CG  MET A  90 "
        pdb=" SD  MET A  90 "
      ideal   model   delta    sigma   weight residual
     112.70  120.60   -7.90 3.00e+00 1.11e-01 6.93e+00
  angle pdb=" C   ARG K 461 "
        pdb=" N   THR K 462 "
        pdb=" CA  THR K 462 "
      ideal   model   delta    sigma   weight residual
     122.38  117.80    4.58 1.81e+00 3.05e-01 6.39e+00
  ... (remaining 22629 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    33.59: 7098
       33.59 -    67.18: 1458
       67.18 -   100.77: 34
      100.77 -   134.35: 0
      134.35 -   167.94: 1
  Dihedral angle restraints: 8591
    sinusoidal: 5316
      harmonic: 3275
  Sorted by residual:
  dihedral pdb=" CA  ASN K 377 "
           pdb=" C   ASN K 377 "
           pdb=" N   HIS K 378 "
           pdb=" CA  HIS K 378 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.69  -20.31     0      5.00e+00 4.00e-02 1.65e+01
  dihedral pdb=" CA  HIS D  49 "
           pdb=" C   HIS D  49 "
           pdb=" N   PRO D  50 "
           pdb=" CA  PRO D  50 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.73  -20.27     0      5.00e+00 4.00e-02 1.64e+01
  dihedral pdb=" CA  HIS H  49 "
           pdb=" C   HIS H  49 "
           pdb=" N   PRO H  50 "
           pdb=" CA  PRO H  50 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -159.75  -20.25     0      5.00e+00 4.00e-02 1.64e+01
  ... (remaining 8588 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.073: 2318
       0.073 -    0.146: 223
       0.146 -    0.219: 5
       0.219 -    0.292: 0
       0.292 -    0.365: 1
  Chirality restraints: 2547
  Sorted by residual:
  chirality pdb=" CB  ILE K 427 "
            pdb=" CA  ILE K 427 "
            pdb=" CG1 ILE K 427 "
            pdb=" CG2 ILE K 427 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.33e+00
  chirality pdb=" CB  ILE K 269 "
            pdb=" CA  ILE K 269 "
            pdb=" CG1 ILE K 269 "
            pdb=" CG2 ILE K 269 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.45    0.20 2.00e-01 2.50e+01 9.52e-01
  chirality pdb=" CA  PHE E 104 "
            pdb=" N   PHE E 104 "
            pdb=" C   PHE E 104 "
            pdb=" CB  PHE E 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.62e-01
  ... (remaining 2544 not shown)

  Planarity restraints: 1861
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP K 431 "    0.041 2.00e-02 2.50e+03   4.25e-02 4.52e+01
        pdb=" CG  TRP K 431 "   -0.111 2.00e-02 2.50e+03
        pdb=" CD1 TRP K 431 "    0.061 2.00e-02 2.50e+03
        pdb=" CD2 TRP K 431 "   -0.004 2.00e-02 2.50e+03
        pdb=" NE1 TRP K 431 "   -0.009 2.00e-02 2.50e+03
        pdb=" CE2 TRP K 431 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP K 431 "    0.008 2.00e-02 2.50e+03
        pdb=" CZ2 TRP K 431 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP K 431 "    0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP K 431 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA K 454 "    0.016 2.00e-02 2.50e+03   3.10e-02 9.64e+00
        pdb=" C   ALA K 454 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   ALA K 454 "    0.020 2.00e-02 2.50e+03
        pdb=" N   PHE K 455 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER K 446 "    0.015 2.00e-02 2.50e+03   3.01e-02 9.06e+00
        pdb=" C   SER K 446 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   SER K 446 "    0.020 2.00e-02 2.50e+03
        pdb=" N   SER K 447 "    0.018 2.00e-02 2.50e+03
  ... (remaining 1858 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.74: 1970
        2.74 -     3.28: 13642
        3.28 -     3.82: 26254
        3.82 -     4.36: 30171
        4.36 -     4.90: 45898
  Nonbonded interactions: 117935
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU C  92 "
            pdb=" NH1 ARG K 241 "
     model   vdw
     2.206 2.520
  nonbonded pdb=" O   ARG E 129 "
            pdb=" NH1 ARG E 129 "
     model   vdw
     2.232 2.520
  nonbonded pdb=" OE2 GLU K 494 "
            pdb=" ND2 ASN K 498 "
     model   vdw
     2.241 2.520
  nonbonded pdb=" NH2 ARG K 394 "
            pdb=" OD1 ASP K 437 "
     model   vdw
     2.249 2.520
  nonbonded pdb=" O   ILE C  78 "
            pdb=" OG  SER D  55 "
     model   vdw
     2.252 2.440
  ... (remaining 117930 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 38 through 134)
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 21 through 101)
}
ncs_group {
  reference = chain 'C'
  selection = chain 'G'
}
ncs_group {
  reference = chain 'D'
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             2.130
  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:          8.450
  Check model and map are aligned:         0.200
  Set scattering table:                    0.110
  Process input model:                     46.390
  Find NCS groups from input model:        0.540
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.740
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   60.640
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7989
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      :  0.009   0.052  15861  Z= 0.521
  Angle     :  0.780   8.033  22634  Z= 0.464
  Chirality :  0.045   0.365   2547
  Planarity :  0.006   0.054   1861
  Dihedral  : 26.000 167.942   6473
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 6.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.50 %
    Favored  : 93.50 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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: -0.33 (0.24), residues: 1107
  helix:  0.88 (0.20), residues: 655
  sheet: -0.47 (0.64), residues: 57
  loop : -2.08 (0.28), residues: 395

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 240
  time to evaluate  : 1.254 
Fit side-chains
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 240
  average time/residue: 0.4393
  time to fit residues: 134.9635
Evaluate side-chains
  129 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 129
  time to evaluate  : 1.189 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6851
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    8.9990
   chunk 102 optimal weight:    3.9990
   chunk 56 optimal weight:    0.5980
   chunk 34 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 105 optimal weight:    0.1980
   chunk 40 optimal weight:    0.6980
   chunk 64 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 122 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
B  25 ASN
C  38 ASN
F  25 ASN
F  75 HIS
G  24 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8003
moved from start:          0.2338

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.070  15861  Z= 0.185
  Angle     :  0.552   6.124  22634  Z= 0.327
  Chirality :  0.035   0.129   2547
  Planarity :  0.004   0.050   1861
  Dihedral  : 29.283 170.506   4159
  Min Nonbonded Distance : 2.244

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer Outliers :  1.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.34 (0.25), residues: 1107
  helix:  2.41 (0.20), residues: 653
  sheet:  0.06 (0.65), residues: 59
  loop : -1.73 (0.28), residues: 395

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 151
  time to evaluate  : 1.398 
Fit side-chains
  outliers start: 16
  outliers final: 13
  residues processed: 160
  average time/residue: 0.4124
  time to fit residues: 89.1633
Evaluate side-chains
  131 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 118
  time to evaluate  : 1.250 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1841
  time to fit residues: 5.6278
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 68 optimal weight:    2.9990
   chunk 38 optimal weight:    2.9990
   chunk 102 optimal weight:    2.9990
   chunk 83 optimal weight:    5.9990
   chunk 33 optimal weight:    0.8980
   chunk 122 optimal weight:    2.9990
   chunk 132 optimal weight:    7.9990
   chunk 109 optimal weight:    4.9990
   chunk 121 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 98 optimal weight:    5.9990
   overall best weight:    2.1788

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
K 413 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8143
moved from start:          0.3313

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.039  15861  Z= 0.345
  Angle     :  0.640  11.099  22634  Z= 0.369
  Chirality :  0.040   0.145   2547
  Planarity :  0.005   0.049   1861
  Dihedral  : 29.562 176.119   4159
  Min Nonbonded Distance : 2.175

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.53 %
    Favored  : 97.47 %
  Rotamer Outliers :  0.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.18 (0.25), residues: 1107
  helix:  2.24 (0.20), residues: 660
  sheet:  0.15 (0.63), residues: 59
  loop : -1.82 (0.27), residues: 388

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 125
  time to evaluate  : 1.330 
Fit side-chains
  outliers start: 9
  outliers final: 4
  residues processed: 133
  average time/residue: 0.3801
  time to fit residues: 67.8172
Evaluate side-chains
  121 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 117
  time to evaluate  : 1.325 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1309
  time to fit residues: 2.6760
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 121 optimal weight:    7.9990
   chunk 92 optimal weight:    4.9990
   chunk 63 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9990
   chunk 58 optimal weight:    3.9990
   chunk 82 optimal weight:    4.9990
   chunk 123 optimal weight:   10.0000
   chunk 130 optimal weight:    1.9990
   chunk 64 optimal weight:    0.0870
   chunk 116 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9990
   overall best weight:    1.2166

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

Flipped N/Q/H residues before XYZ refinement:
D  63 ASN
E  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8094
moved from start:          0.3494

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15861  Z= 0.209
  Angle     :  0.545   8.879  22634  Z= 0.323
  Chirality :  0.035   0.135   2547
  Planarity :  0.004   0.038   1861
  Dihedral  : 29.260 175.990   4159
  Min Nonbonded Distance : 2.233

Molprobity Statistics.
  All-atom Clashscore : 5.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.90 %
    Favored  : 98.10 %
  Rotamer Outliers :  1.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.52 (0.25), residues: 1107
  helix:  2.47 (0.20), residues: 661
  sheet:  0.57 (0.68), residues: 52
  loop : -1.60 (0.27), residues: 394

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 120
  time to evaluate  : 1.362 
Fit side-chains
  outliers start: 10
  outliers final: 8
  residues processed: 124
  average time/residue: 0.3528
  time to fit residues: 60.3669
Evaluate side-chains
  118 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 110
  time to evaluate  : 1.359 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1282
  time to fit residues: 3.6606
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 108 optimal weight:    5.9990
   chunk 74 optimal weight:    5.9990
   chunk 1 optimal weight:    0.0270
   chunk 97 optimal weight:    4.9990
   chunk 53 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 90 optimal weight:    5.9990
   chunk 0 optimal weight:    3.9990
   chunk 66 optimal weight:    1.9990
   chunk 117 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0980
   overall best weight:    1.0042

-------------------------------------------------------------------------------
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: 0.8073
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15861  Z= 0.192
  Angle     :  0.526   7.832  22634  Z= 0.312
  Chirality :  0.034   0.136   2547
  Planarity :  0.004   0.039   1861
  Dihedral  : 29.158 176.295   4159
  Min Nonbonded Distance : 2.256

Molprobity Statistics.
  All-atom Clashscore : 6.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer Outliers :  0.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.80 (0.25), residues: 1107
  helix:  2.65 (0.20), residues: 662
  sheet:  0.73 (0.66), residues: 52
  loop : -1.43 (0.28), residues: 393

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 115
  time to evaluate  : 1.309 
Fit side-chains
  outliers start: 5
  outliers final: 4
  residues processed: 119
  average time/residue: 0.3751
  time to fit residues: 61.4886
Evaluate side-chains
  109 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 105
  time to evaluate  : 1.424 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1470
  time to fit residues: 2.8693
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 43 optimal weight:    0.3980
   chunk 117 optimal weight:    1.9990
   chunk 25 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 32 optimal weight:    0.0370
   chunk 130 optimal weight:   10.0000
   chunk 108 optimal weight:    3.9990
   chunk 60 optimal weight:    0.9980
   chunk 10 optimal weight:    1.9990
   chunk 68 optimal weight:    3.9990
   chunk 125 optimal weight:   10.0000
   overall best weight:    1.0862

-------------------------------------------------------------------------------
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: 0.8081
moved from start:          0.3863

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15861  Z= 0.197
  Angle     :  0.533  13.002  22634  Z= 0.313
  Chirality :  0.034   0.132   2547
  Planarity :  0.004   0.035   1861
  Dihedral  : 29.095 177.040   4159
  Min Nonbonded Distance : 2.265

Molprobity Statistics.
  All-atom Clashscore : 5.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.81 %
    Favored  : 98.19 %
  Rotamer Outliers :  0.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.87 (0.25), residues: 1107
  helix:  2.65 (0.20), residues: 665
  sheet:  0.94 (0.65), residues: 52
  loop : -1.35 (0.28), residues: 390

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 113
  time to evaluate  : 1.287 
Fit side-chains
   revert: symmetry clash
  outliers start: 4
  outliers final: 3
  residues processed: 115
  average time/residue: 0.3634
  time to fit residues: 57.3275
Evaluate side-chains
  112 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 109
  time to evaluate  : 1.379 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1311
  time to fit residues: 2.4725
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 14 optimal weight:    0.0010
   chunk 74 optimal weight:    5.9990
   chunk 95 optimal weight:    5.9990
   chunk 73 optimal weight:    5.9990
   chunk 109 optimal weight:    0.3980
   chunk 72 optimal weight:    7.9990
   chunk 130 optimal weight:    4.9990
   chunk 81 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9990
   chunk 80 optimal weight:    4.9990
   overall best weight:    2.2792

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

Flipped N/Q/H residues before XYZ refinement:
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8150
moved from start:          0.3991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.039  15861  Z= 0.330
  Angle     :  0.615   8.764  22634  Z= 0.356
  Chirality :  0.039   0.154   2547
  Planarity :  0.004   0.038   1861
  Dihedral  : 29.279 179.391   4159
  Min Nonbonded Distance : 2.248

Molprobity Statistics.
  All-atom Clashscore : 5.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.71 %
    Favored  : 97.29 %
  Rotamer Outliers :  0.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.56 (0.25), residues: 1107
  helix:  2.35 (0.20), residues: 666
  sheet:  1.00 (0.64), residues: 52
  loop : -1.41 (0.28), residues: 389

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 111
  time to evaluate  : 1.207 
Fit side-chains
  outliers start: 7
  outliers final: 4
  residues processed: 115
  average time/residue: 0.3623
  time to fit residues: 56.8285
Evaluate side-chains
  108 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 104
  time to evaluate  : 1.225 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1240
  time to fit residues: 2.5203
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 51 optimal weight:    0.6980
   chunk 77 optimal weight:    4.9990
   chunk 39 optimal weight:    0.5980
   chunk 25 optimal weight:    0.8980
   chunk 82 optimal weight:    4.9990
   chunk 88 optimal weight:    4.9990
   chunk 64 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 102 optimal weight:    0.1980
   chunk 118 optimal weight:    7.9990
   chunk 124 optimal weight:    0.7980
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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: 0.8050
moved from start:          0.4140

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15861  Z= 0.163
  Angle     :  0.515   8.982  22634  Z= 0.306
  Chirality :  0.034   0.124   2547
  Planarity :  0.004   0.034   1861
  Dihedral  : 28.995 176.990   4159
  Min Nonbonded Distance : 2.252

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer Outliers :  0.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.99 (0.25), residues: 1107
  helix:  2.71 (0.20), residues: 666
  sheet:  1.24 (0.64), residues: 52
  loop : -1.27 (0.28), residues: 389

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 1.321 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 116
  average time/residue: 0.3821
  time to fit residues: 60.6567
Evaluate side-chains
  106 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 106
  time to evaluate  : 1.315 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.6774
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:    0.5980
   chunk 121 optimal weight:   10.0000
   chunk 124 optimal weight:    9.9990
   chunk 72 optimal weight:    7.9990
   chunk 52 optimal weight:    0.9980
   chunk 95 optimal weight:    5.9990
   chunk 37 optimal weight:    0.5980
   chunk 109 optimal weight:    3.9990
   chunk 114 optimal weight:    7.9990
   chunk 120 optimal weight:    5.9990
   chunk 79 optimal weight:    5.9990
   overall best weight:    2.4384

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

Flipped N/Q/H residues before XYZ refinement:
C  24 GLN
D  47 GLN
** E  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8155
moved from start:          0.4177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.006   0.041  15861  Z= 0.353
  Angle     :  0.625   8.313  22634  Z= 0.361
  Chirality :  0.040   0.162   2547
  Planarity :  0.004   0.043   1861
  Dihedral  : 29.300 179.783   4159
  Min Nonbonded Distance : 2.215

Molprobity Statistics.
  All-atom Clashscore : 5.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer Outliers :  0.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.65 (0.25), residues: 1107
  helix:  2.41 (0.20), residues: 666
  sheet:  1.14 (0.65), residues: 52
  loop : -1.37 (0.28), residues: 389

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 1.287 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 108
  average time/residue: 0.3718
  time to fit residues: 55.0370
Evaluate side-chains
  104 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 1.309 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1362
  time to fit residues: 1.8261
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 128 optimal weight:    1.9990
   chunk 78 optimal weight:    4.9990
   chunk 60 optimal weight:    0.7980
   chunk 89 optimal weight:    5.9990
   chunk 134 optimal weight:    0.9980
   chunk 123 optimal weight:    7.9990
   chunk 107 optimal weight:    3.9990
   chunk 11 optimal weight:    1.9990
   chunk 82 optimal weight:    4.9990
   chunk 65 optimal weight:    0.6980
   chunk 85 optimal weight:    6.9990
   overall best weight:    1.2984

-------------------------------------------------------------------------------
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: 0.8126
moved from start:          0.4191

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.039  15861  Z= 0.222
  Angle     :  0.571   8.302  22634  Z= 0.337
  Chirality :  0.037   0.162   2547
  Planarity :  0.004   0.044   1861
  Dihedral  : 29.222 178.771   4159
  Min Nonbonded Distance : 2.219

Molprobity Statistics.
  All-atom Clashscore : 6.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer Outliers :  0.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  1.72 (0.25), residues: 1107
  helix:  2.47 (0.20), residues: 666
  sheet:  1.25 (0.66), residues: 52
  loop : -1.37 (0.28), residues: 389

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

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

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2214 Ramachandran restraints generated.
    1107 Oldfield, 0 Emsley, 1107 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 109
  time to evaluate  : 1.341 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 110
  average time/residue: 0.3980
  time to fit residues: 60.5112
Evaluate side-chains
  107 residues out of total 969 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 106
  time to evaluate  : 1.357 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1345
  time to fit residues: 1.9933
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 114 optimal weight:    0.0170
   chunk 32 optimal weight:    0.0030
   chunk 98 optimal weight:    5.9990
   chunk 15 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 44 optimal weight:    0.6980
   chunk 110 optimal weight:    0.9980
   chunk 13 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 94 optimal weight:    4.9990
   overall best weight:    0.4428

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

Flipped N/Q/H residues before XYZ refinement:
K 499 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.148779 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.108328 restraints weight = 23782.979|
|-----------------------------------------------------------------------------|
r_work (start): 0.3306 rms_B_bonded: 1.21
r_work: 0.3052 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2927 rms_B_bonded: 4.79 restraints_weight: 0.2500
r_work (final): 0.2927
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8393
moved from start:          0.4336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15861  Z= 0.153
  Angle     :  0.508   8.559  22634  Z= 0.302
  Chirality :  0.033   0.141   2547
  Planarity :  0.004   0.044   1861
  Dihedral  : 28.995 177.439   4159
  Min Nonbonded Distance : 2.232

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.63 %
    Favored  : 98.37 %
  Rotamer Outliers :  0.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.63 %
    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:  2.13 (0.25), residues: 1107
  helix:  2.77 (0.20), residues: 669
  sheet:  1.43 (0.67), residues: 52
  loop : -1.17 (0.28), residues: 386

===============================================================================
Job complete
usr+sys time: 2635.44 seconds
wall clock time: 48 minutes 33.61 seconds (2913.61 seconds total)