Starting phenix.real_space_refine
on Wed Nov 15 13:00:11 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/11_2023/6pwe_20506.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/11_2023/6pwe_20506.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.95
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/11_2023/6pwe_20506.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/11_2023/6pwe_20506.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/11_2023/6pwe_20506.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwe_20506/11_2023/6pwe_20506.pdb"
  }
  resolution = 3.95
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
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: 5
    Type Number    sf(0)   Gaussians
     P     294      5.49       5
     S      14      5.16       5
     C    6576      2.51       5
     N    2231      2.21       5
     O    2808      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped
    Residue "A ARG   83": "NH1" <-> "NH2"
    Residue "A ARG  129": "NH1" <-> "NH2"
    Residue "E ARG   83": "NH1" <-> "NH2"
    Residue "E ARG  129": "NH1" <-> "NH2"
  Time to flip residues: 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/modules/chem_data/mon_lib"
  Total number of atoms: 11923
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "A"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "B"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 626
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "C"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 789
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "D"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 743
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 790
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 790
          Classifications: {'peptide': 96}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "F"
      Number of atoms: 626
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 79, 626
          Classifications: {'peptide': 79}
          Link IDs: {'PTRANS': 1, 'TRANS': 77}
    Chain: "G"
      Number of atoms: 789
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 789
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "H"
      Number of atoms: 743
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 743
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "I"
      Number of atoms: 3031
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 3031
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
    Chain: "J"
      Number of atoms: 2996
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 147, 2996
          Classifications: {'DNA': 147}
          Link IDs: {'rna3p': 146}
  Time building chain proxies: 6.30, per 1000 atoms: 0.53
  Number of scatterers: 11923
  At special positions: 0
  Unit cell: (108.36, 113.4, 120.96, 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)
     S      14     16.00
     P     294     15.00
     O    2808      8.00
     N    2231      7.00
     C    6576      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: 6.86
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1392

  Finding SS restraints...
    Secondary structure from input PDB file:
      38 helices and 6 sheets defined
      59.4% alpha, 1.6% beta
      95 base pairs and 208 stacking pairs defined.
    Time for finding SS restraints: 5.09
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 50
    Processing helix  chain 'A' and resid 64 through 75
      removed outlier: 4.620A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 88 through 105
      removed outlier: 3.841A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.628A  pdb=" N   GLN A  93 " --> pdb=" O   VAL A  89 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU A  94 " --> pdb=" O   MET A  90 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 108 through 113
      removed outlier: 3.602A  pdb=" N   HIS A 113 " --> pdb=" O   LEU A 109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 128
      removed outlier: 3.589A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 24 through 29
      removed outlier: 3.516A  pdb=" N   GLN B  27 " --> pdb=" O   ASP B  24 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 30 through 39
      removed outlier: 3.533A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 63
      removed outlier: 4.463A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL B  60 " --> pdb=" O   GLY B  56 " (cutoff:3.500A)
      removed outlier: 4.039A  pdb=" N   PHE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 76
      removed outlier: 3.921A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 4.527A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   THR B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.853A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 21
      removed outlier: 3.699A  pdb=" N   ALA C  20 " --> pdb=" O   ARG C  16 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 33
      removed outlier: 3.888A  pdb=" N   LEU C  32 " --> pdb=" O   ARG C  28 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 72
      removed outlier: 3.700A  pdb=" N   ALA C  51 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   VAL C  53 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 3.873A  pdb=" N   GLU C  63 " --> pdb=" O   ALA C  59 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY C  66 " --> pdb=" O   LEU C  62 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN C  67 " --> pdb=" O   GLU C  63 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ALA C  68 " --> pdb=" O   LEU C  64 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 78 through 88
      removed outlier: 3.955A  pdb=" N   LEU C  82 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   GLN C  83 " --> pdb=" O   PRO C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 89 through 94
      removed outlier: 3.970A  pdb=" N   LYS C  94 " --> pdb=" O   GLU C  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 43
      removed outlier: 3.690A  pdb=" N   ILE D  38 " --> pdb=" O   TYR D  34 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LYS D  40 " --> pdb=" O   ILE D  36 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS D  43 " --> pdb=" O   TYR D  39 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 54 through 80
      removed outlier: 3.535A  pdb=" N   ASN D  60 " --> pdb=" O   MET D  56 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ALA D  72 " --> pdb=" O   GLU D  68 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   ARG D  76 " --> pdb=" O   ALA D  72 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR D  80 " --> pdb=" O   ARG D  76 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 94
      removed outlier: 3.699A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 117
      removed outlier: 3.602A  pdb=" N   VAL D 108 " --> pdb=" O   ALA D 104 " (cutoff:3.500A)
      removed outlier: 5.030A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 4.500A  pdb=" N   LYS D 113 " --> pdb=" O   SER D 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 50
    Processing helix  chain 'E' and resid 64 through 75
      removed outlier: 4.620A  pdb=" N   LEU E  70 " --> pdb=" O   PRO E  66 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   GLU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 88 through 105
      removed outlier: 3.842A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   GLN E  93 " --> pdb=" O   VAL E  89 " (cutoff:3.500A)
      removed outlier: 4.113A  pdb=" N   GLU E  94 " --> pdb=" O   MET E  90 " (cutoff:3.500A)
      removed outlier: 3.865A  pdb=" N   GLU E  97 " --> pdb=" O   GLN E  93 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 108 through 113
      removed outlier: 3.601A  pdb=" N   HIS E 113 " --> pdb=" O   LEU E 109 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 128
      removed outlier: 3.590A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.516A  pdb=" N   GLN F  27 " --> pdb=" O   ASP F  24 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 39
      removed outlier: 3.534A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 63
      removed outlier: 4.463A  pdb=" N   ARG F  55 " --> pdb=" O   TYR F  51 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 4.038A  pdb=" N   PHE F  61 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 76
      removed outlier: 3.921A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
      removed outlier: 4.525A  pdb=" N   TYR F  72 " --> pdb=" O   ASP F  68 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.854A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG F  92 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
      removed outlier: 3.968A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 16 through 21
      removed outlier: 3.698A  pdb=" N   ALA G  20 " --> pdb=" O   ARG G  16 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 33
      removed outlier: 3.888A  pdb=" N   LEU G  32 " --> pdb=" O   ARG G  28 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 45 through 72
      removed outlier: 3.701A  pdb=" N   ALA G  51 " --> pdb=" O   PRO G  47 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   VAL G  53 " --> pdb=" O   TYR G  49 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   GLU G  63 " --> pdb=" O   ALA G  59 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   GLY G  66 " --> pdb=" O   LEU G  62 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   ASN G  67 " --> pdb=" O   GLU G  63 " (cutoff:3.500A)
      removed outlier: 3.619A  pdb=" N   ALA G  68 " --> pdb=" O   LEU G  64 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 78 through 88
      removed outlier: 3.955A  pdb=" N   LEU G  82 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   GLN G  83 " --> pdb=" O   PRO G  79 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 89 through 94
      removed outlier: 3.970A  pdb=" N   LYS G  94 " --> pdb=" O   GLU G  90 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 43
      removed outlier: 3.689A  pdb=" N   ILE H  38 " --> pdb=" O   TYR H  34 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   LYS H  40 " --> pdb=" O   ILE H  36 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LYS H  43 " --> pdb=" O   TYR H  39 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 54 through 80
      removed outlier: 3.535A  pdb=" N   ASN H  60 " --> pdb=" O   MET H  56 " (cutoff:3.500A)
      removed outlier: 4.647A  pdb=" N   ALA H  72 " --> pdb=" O   GLU H  68 " (cutoff:3.500A)
      removed outlier: 3.971A  pdb=" N   ARG H  76 " --> pdb=" O   ALA H  72 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   TYR H  80 " --> pdb=" O   ARG H  76 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 94
      removed outlier: 3.699A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 117
      removed outlier: 3.602A  pdb=" N   VAL H 108 " --> pdb=" O   ALA H 104 " (cutoff:3.500A)
      removed outlier: 5.029A  pdb=" N   SER H 109 " --> pdb=" O   LYS H 105 " (cutoff:3.500A)
      removed outlier: 4.501A  pdb=" N   LYS H 113 " --> pdb=" O   SER H 109 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.787A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 41 through 42
      removed outlier: 7.109A  pdb=" N   ARG C  41 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 76 through 77
    Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.536A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'G' and resid 41 through 42
      removed outlier: 7.395A  pdb=" N   ARG G  41 " --> pdb=" O   ILE H  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'G' and resid 76 through 77

    206 hydrogen bonds defined for protein.
    600 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      225 hydrogen bonds
      438 hydrogen bond angles
      0 basepair planarities
      95 basepair parallelities
      208 stacking parallelities
  Total time for adding SS restraints: 3.59

  Time building geometry restraints manager: 7.26 seconds

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

  Histogram of bond lengths:
        1.21 -     1.32: 1843
        1.32 -     1.44: 4466
        1.44 -     1.56: 5815
        1.56 -     1.68: 586
        1.68 -     1.80: 26
  Bond restraints: 12736
  Sorted by residual:
  bond pdb=" C3'  DG I  20 "
       pdb=" O3'  DG I  20 "
    ideal  model  delta    sigma   weight residual
    1.422  1.482 -0.060 3.00e-02 1.11e+03 3.98e+00
  bond pdb=" CB  PRO A  66 "
       pdb=" CG  PRO A  66 "
    ideal  model  delta    sigma   weight residual
    1.492  1.404  0.088 5.00e-02 4.00e+02 3.09e+00
  bond pdb=" CB  PRO E  66 "
       pdb=" CG  PRO E  66 "
    ideal  model  delta    sigma   weight residual
    1.492  1.404  0.088 5.00e-02 4.00e+02 3.06e+00
  bond pdb=" C3'  DC I  52 "
       pdb=" O3'  DC I  52 "
    ideal  model  delta    sigma   weight residual
    1.422  1.472 -0.050 3.00e-02 1.11e+03 2.82e+00
  bond pdb=" C3'  DG I  38 "
       pdb=" O3'  DG I  38 "
    ideal  model  delta    sigma   weight residual
    1.422  1.373  0.049 3.00e-02 1.11e+03 2.68e+00
  ... (remaining 12731 not shown)

  Histogram of bond angle deviations from ideal:
       97.63 -   104.68: 1204
      104.68 -   111.72: 6543
      111.72 -   118.77: 3699
      118.77 -   125.81: 6055
      125.81 -   132.85: 960
  Bond angle restraints: 18461
  Sorted by residual:
  angle pdb=" C   ARG H  30 "
        pdb=" N   LYS H  31 "
        pdb=" CA  LYS H  31 "
      ideal   model   delta    sigma   weight residual
     121.54  130.25   -8.71 1.91e+00 2.74e-01 2.08e+01
  angle pdb=" C   ARG D  30 "
        pdb=" N   LYS D  31 "
        pdb=" CA  LYS D  31 "
      ideal   model   delta    sigma   weight residual
     121.54  130.24   -8.70 1.91e+00 2.74e-01 2.07e+01
  angle pdb=" N   LYS D  31 "
        pdb=" CA  LYS D  31 "
        pdb=" CB  LYS D  31 "
      ideal   model   delta    sigma   weight residual
     110.49  117.07   -6.58 1.69e+00 3.50e-01 1.52e+01
  angle pdb=" N   LYS H  31 "
        pdb=" CA  LYS H  31 "
        pdb=" CB  LYS H  31 "
      ideal   model   delta    sigma   weight residual
     110.49  117.03   -6.54 1.69e+00 3.50e-01 1.50e+01
  angle pdb=" C   ALA C 102 "
        pdb=" N   GLN C 103 "
        pdb=" CA  GLN C 103 "
      ideal   model   delta    sigma   weight residual
     122.46  127.42   -4.96 1.41e+00 5.03e-01 1.24e+01
  ... (remaining 18456 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.76: 5217
       31.76 -    63.52: 1378
       63.52 -    95.29: 44
       95.29 -   127.05: 0
      127.05 -   158.81: 3
  Dihedral angle restraints: 6642
    sinusoidal: 4484
      harmonic: 2158
  Sorted by residual:
  dihedral pdb=" CA  LYS D  29 "
           pdb=" C   LYS D  29 "
           pdb=" N   ARG D  30 "
           pdb=" CA  ARG D  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -127.05  -52.95     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  LYS H  29 "
           pdb=" C   LYS H  29 "
           pdb=" N   ARG H  30 "
           pdb=" CA  ARG H  30 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -127.10  -52.90     0      5.00e+00 4.00e-02 1.12e+02
  dihedral pdb=" CA  ARG D  30 "
           pdb=" C   ARG D  30 "
           pdb=" N   LYS D  31 "
           pdb=" CA  LYS D  31 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  140.19   39.81     0      5.00e+00 4.00e-02 6.34e+01
  ... (remaining 6639 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 1265
       0.044 -    0.088: 667
       0.088 -    0.133: 129
       0.133 -    0.177: 27
       0.177 -    0.221: 10
  Chirality restraints: 2098
  Sorted by residual:
  chirality pdb=" CB  VAL G 106 "
            pdb=" CA  VAL G 106 "
            pdb=" CG1 VAL G 106 "
            pdb=" CG2 VAL G 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.22e+00
  chirality pdb=" CB  VAL C 106 "
            pdb=" CA  VAL C 106 "
            pdb=" CG1 VAL C 106 "
            pdb=" CG2 VAL C 106 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.20e+00
  chirality pdb=" CB  VAL C  99 "
            pdb=" CA  VAL C  99 "
            pdb=" CG1 VAL C  99 "
            pdb=" CG2 VAL C  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.41   -0.22 2.00e-01 2.50e+01 1.19e+00
  ... (remaining 2095 not shown)

  Planarity restraints: 1318
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A  65 "   -0.046 5.00e-02 4.00e+02   6.89e-02 7.60e+00
        pdb=" N   PRO A  66 "    0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO A  66 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO A  66 "   -0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU E  65 "    0.046 5.00e-02 4.00e+02   6.88e-02 7.58e+00
        pdb=" N   PRO E  66 "   -0.119 5.00e-02 4.00e+02
        pdb=" CA  PRO E  66 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO E  66 "    0.038 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY H 101 "    0.012 2.00e-02 2.50e+03   2.48e-02 6.15e+00
        pdb=" C   GLY H 101 "   -0.043 2.00e-02 2.50e+03
        pdb=" O   GLY H 101 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLU H 102 "    0.015 2.00e-02 2.50e+03
  ... (remaining 1315 not shown)

  Histogram of nonbonded interaction distances:
        2.26 -     2.79: 2734
        2.79 -     3.32: 10074
        3.32 -     3.85: 22518
        3.85 -     4.37: 26262
        4.37 -     4.90: 37230
  Nonbonded interactions: 98818
  Sorted by model distance:
  nonbonded pdb=" OH  TYR D  37 "
            pdb=" OP1  DG J  48 "
     model   vdw
     2.264 2.440
  nonbonded pdb=" OH  TYR H  37 "
            pdb=" OP1  DG I  48 "
     model   vdw
     2.281 2.440
  nonbonded pdb=" O   TYR F  51 "
            pdb=" NH1 ARG F  55 "
     model   vdw
     2.317 2.520
  nonbonded pdb=" O   TYR B  51 "
            pdb=" NH1 ARG B  55 "
     model   vdw
     2.318 2.520
  nonbonded pdb=" N2   DG I  21 "
            pdb=" O2   DC J -21 "
     model   vdw
     2.330 2.496
  ... (remaining 98813 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'
  selection = chain 'E'
}
ncs_group {
  reference = chain 'B'
  selection = chain 'F'
}
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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.820
  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:          7.590
  Check model and map are aligned:         0.160
  Set scattering table:                    0.110
  Process input model:                     37.480
  Find NCS groups from input model:        0.400
  Set up NCS constraints:                  0.050
  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:2.640
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   50.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
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      :  0.010   0.088  12736  Z= 0.556
  Angle     :  0.929   8.715  18461  Z= 0.526
  Chirality :  0.053   0.221   2098
  Planarity :  0.007   0.069   1318
  Dihedral  : 27.266 158.809   5250
  Min Nonbonded Distance : 2.264

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  7.42 %
    Favored  : 92.31 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.56 %

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: -6.65 (0.18), residues: 728
  helix: -4.66 (0.11), residues: 440
  sheet:  None (None), residues: 0
  loop : -3.73 (0.27), residues: 288

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.961 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.3853
  time to fit residues: 125.8377
Evaluate side-chains
  163 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.886 
Switching outliers to nearest non-outliers
  outliers start: 0
  outliers final: 0
  residues processed: 0
  time to fit residues: 1.0452
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    6.9990
   chunk 74 optimal weight:    6.9990
   chunk 41 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 50 optimal weight:    1.9990
   chunk 39 optimal weight:    0.6980
   chunk 76 optimal weight:    5.9990
   chunk 29 optimal weight:    0.7980
   chunk 46 optimal weight:    8.9990
   chunk 57 optimal weight:    9.9990
   chunk 88 optimal weight:    6.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  23 GLN
D  60 ASN
D  64 ASN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  88 ASN
H  60 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7855
moved from start:          0.3019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043  12736  Z= 0.294
  Angle     :  0.695   7.764  18461  Z= 0.405
  Chirality :  0.040   0.188   2098
  Planarity :  0.006   0.048   1318
  Dihedral  : 31.530 161.380   3780
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 12.36
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.36 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 14.08 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.56 %

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: -5.00 (0.23), residues: 728
  helix: -3.16 (0.18), residues: 450
  sheet:  None (None), residues: 0
  loop : -3.36 (0.29), residues: 278

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 188
  time to evaluate  : 0.944 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 17
  residues processed: 202
  average time/residue: 0.2983
  time to fit residues: 80.6783
Evaluate side-chains
  165 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 148
  time to evaluate  : 0.924 
Switching outliers to nearest non-outliers
  outliers start: 17
  outliers final: 0
  residues processed: 17
  average time/residue: 0.1095
  time to fit residues: 4.5673
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 27 optimal weight:    3.9990
   chunk 74 optimal weight:    7.9990
   chunk 60 optimal weight:    5.9990
   chunk 24 optimal weight:    0.7980
   chunk 89 optimal weight:    6.9990
   chunk 96 optimal weight:   10.0000
   chunk 79 optimal weight:    5.9990
   chunk 88 optimal weight:    7.9990
   chunk 30 optimal weight:    3.9990
   chunk 71 optimal weight:    9.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  81 HIS
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  72 ASN
G 103 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7917
moved from start:          0.3862

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.054  12736  Z= 0.366
  Angle     :  0.699   6.509  18461  Z= 0.405
  Chirality :  0.040   0.177   2098
  Planarity :  0.005   0.039   1318
  Dihedral  : 31.579 164.432   3780
  Min Nonbonded Distance : 2.030

Molprobity Statistics.
  All-atom Clashscore : 14.09
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  7.28 %
    Favored  : 92.58 %
  Rotamer:
    Outliers :  3.56 %
    Allowed  : 15.70 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -4.17 (0.27), residues: 728
  helix: -2.43 (0.21), residues: 452
  sheet:  None (None), residues: 0
  loop : -3.16 (0.32), residues: 276

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  191 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 169
  time to evaluate  : 0.933 
Fit side-chains
   revert: symmetry clash
  outliers start: 22
  outliers final: 13
  residues processed: 184
  average time/residue: 0.2946
  time to fit residues: 72.6954
Evaluate side-chains
  165 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 152
  time to evaluate  : 0.784 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 0
  residues processed: 13
  average time/residue: 0.1081
  time to fit residues: 3.5676
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 88 optimal weight:    8.9990
   chunk 67 optimal weight:    4.9990
   chunk 46 optimal weight:    0.1980
   chunk 9 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 59 optimal weight:    0.9980
   chunk 89 optimal weight:    6.9990
   chunk 94 optimal weight:    8.9990
   chunk 84 optimal weight:   10.0000
   chunk 25 optimal weight:    6.9990
   chunk 78 optimal weight:    6.9990
   overall best weight:    2.0386

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  93 GLN
** G  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7852
moved from start:          0.4279

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  12736  Z= 0.246
  Angle     :  0.607   7.750  18461  Z= 0.357
  Chirality :  0.036   0.144   2098
  Planarity :  0.004   0.039   1318
  Dihedral  : 31.238 163.932   3780
  Min Nonbonded Distance : 2.059

Molprobity Statistics.
  All-atom Clashscore : 11.79
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.81 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  2.75 %
    Allowed  : 19.26 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -3.46 (0.28), residues: 728
  helix: -1.89 (0.23), residues: 450
  sheet:  None (None), residues: 0
  loop : -2.83 (0.33), residues: 278

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  183 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 17
    poor density    : 166
  time to evaluate  : 0.985 
Fit side-chains
   revert: symmetry clash
  outliers start: 17
  outliers final: 9
  residues processed: 179
  average time/residue: 0.3156
  time to fit residues: 76.6468
Evaluate side-chains
  159 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 9
    poor density    : 150
  time to evaluate  : 0.941 
Switching outliers to nearest non-outliers
  outliers start: 9
  outliers final: 0
  residues processed: 9
  average time/residue: 0.1005
  time to fit residues: 2.7362
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 53 optimal weight:    5.9990
   chunk 1 optimal weight:    0.3980
   chunk 70 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 80 optimal weight:   10.0000
   chunk 65 optimal weight:    3.9990
   chunk 0 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 85 optimal weight:    8.9990
   chunk 23 optimal weight:    8.9990
   chunk 31 optimal weight:    7.9990
   overall best weight:    2.6788

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  72 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7887
moved from start:          0.4509

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  12736  Z= 0.291
  Angle     :  0.635   7.680  18461  Z= 0.370
  Chirality :  0.037   0.133   2098
  Planarity :  0.005   0.042   1318
  Dihedral  : 31.314 164.170   3780
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 12.96
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  6.18 %
    Favored  : 93.68 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 20.87 %
    Favored  : 76.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -3.15 (0.29), residues: 728
  helix: -1.70 (0.23), residues: 452
  sheet:  None (None), residues: 0
  loop : -2.60 (0.34), residues: 276

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 157
  time to evaluate  : 0.918 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 16
  outliers final: 8
  residues processed: 166
  average time/residue: 0.2780
  time to fit residues: 63.0971
Evaluate side-chains
  154 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 8
    poor density    : 146
  time to evaluate  : 1.089 
Switching outliers to nearest non-outliers
  outliers start: 8
  outliers final: 0
  residues processed: 8
  average time/residue: 0.1055
  time to fit residues: 2.6345
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 85 optimal weight:    8.9990
   chunk 18 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 23 optimal weight:    9.9990
   chunk 94 optimal weight:   10.0000
   chunk 78 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 31 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 91 optimal weight:    7.9990
   overall best weight:    1.7990

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  72 ASN
G 103 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.4797

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  12736  Z= 0.231
  Angle     :  0.584   7.710  18461  Z= 0.344
  Chirality :  0.035   0.136   2098
  Planarity :  0.004   0.034   1318
  Dihedral  : 31.133 162.417   3780
  Min Nonbonded Distance : 2.074

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.40 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 22.17 %
    Favored  : 76.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -2.60 (0.29), residues: 728
  helix: -1.24 (0.24), residues: 450
  sheet:  None (None), residues: 0
  loop : -2.40 (0.35), residues: 278

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 11
    poor density    : 152
  time to evaluate  : 0.852 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 11
  outliers final: 4
  residues processed: 158
  average time/residue: 0.2775
  time to fit residues: 60.0640
Evaluate side-chains
  146 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 142
  time to evaluate  : 0.970 
Switching outliers to nearest non-outliers
  outliers start: 4
  outliers final: 0
  residues processed: 4
  average time/residue: 0.1091
  time to fit residues: 1.9285
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 54 optimal weight:    0.8980
   chunk 69 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 79 optimal weight:    7.9990
   chunk 52 optimal weight:    5.9990
   chunk 94 optimal weight:   10.0000
   chunk 59 optimal weight:    0.9990
   chunk 57 optimal weight:    6.9990
   chunk 43 optimal weight:    0.5980
   chunk 58 optimal weight:    2.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
B  75 HIS
G  23 GLN
G  72 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5151

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12736  Z= 0.182
  Angle     :  0.561   9.373  18461  Z= 0.330
  Chirality :  0.033   0.142   2098
  Planarity :  0.004   0.034   1318
  Dihedral  : 30.915 159.904   3780
  Min Nonbonded Distance : 2.088

Molprobity Statistics.
  All-atom Clashscore : 11.05
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  4.12 %
    Favored  : 95.74 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 24.43 %
    Favored  : 74.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.42 %

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: -1.98 (0.30), residues: 728
  helix: -0.77 (0.24), residues: 456
  sheet:  None (None), residues: 0
  loop : -2.12 (0.35), residues: 272

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 6
    poor density    : 158
  time to evaluate  : 0.868 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 6
  outliers final: 1
  residues processed: 160
  average time/residue: 0.2972
  time to fit residues: 63.9118
Evaluate side-chains
  143 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 1
    poor density    : 142
  time to evaluate  : 0.887 
Switching outliers to nearest non-outliers
  outliers start: 1
  outliers final: 0
  residues processed: 1
  average time/residue: 0.1055
  time to fit residues: 1.2176
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 37 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 28 optimal weight:    3.9990
   chunk 18 optimal weight:    8.9990
   chunk 60 optimal weight:    0.0970
   chunk 64 optimal weight:    0.9980
   chunk 46 optimal weight:    7.9990
   chunk 8 optimal weight:    2.9990
   chunk 74 optimal weight:    8.9990
   chunk 85 optimal weight:   10.0000
   chunk 90 optimal weight:   10.0000
   overall best weight:    2.4184

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  23 GLN
G 103 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.5103

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.055  12736  Z= 0.273
  Angle     :  0.620  10.336  18461  Z= 0.357
  Chirality :  0.036   0.221   2098
  Planarity :  0.004   0.033   1318
  Dihedral  : 31.171 161.215   3780
  Min Nonbonded Distance : 2.072

Molprobity Statistics.
  All-atom Clashscore : 12.64
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  5.22 %
    Favored  : 94.51 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 25.57 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -2.08 (0.31), residues: 728
  helix: -0.90 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop : -2.08 (0.37), residues: 268

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 149
  time to evaluate  : 0.893 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 3
  residues processed: 156
  average time/residue: 0.2875
  time to fit residues: 60.7315
Evaluate side-chains
  142 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 139
  time to evaluate  : 0.892 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 0
  residues processed: 3
  average time/residue: 0.1045
  time to fit residues: 1.6362
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 88 optimal weight:    8.9990
   chunk 90 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 38 optimal weight:    2.9990
   chunk 69 optimal weight:    0.9990
   chunk 27 optimal weight:    0.5980
   chunk 79 optimal weight:    6.9990
   chunk 83 optimal weight:    8.9990
   chunk 87 optimal weight:    7.9990
   chunk 57 optimal weight:    0.9990
   overall best weight:    1.9188

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  25 ASN
G  23 GLN
G  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7820
moved from start:          0.5232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054  12736  Z= 0.242
  Angle     :  0.604  10.352  18461  Z= 0.349
  Chirality :  0.035   0.177   2098
  Planarity :  0.004   0.035   1318
  Dihedral  : 31.125 161.070   3780
  Min Nonbonded Distance : 2.087

Molprobity Statistics.
  All-atom Clashscore : 12.08
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.67 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 25.57 %
    Favored  : 72.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.28 %

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: -1.93 (0.31), residues: 728
  helix: -0.79 (0.24), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.99 (0.37), residues: 268

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 141
  time to evaluate  : 0.882 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 10
  outliers final: 5
  residues processed: 145
  average time/residue: 0.2838
  time to fit residues: 55.8390
Evaluate side-chains
  144 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 139
  time to evaluate  : 0.950 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 0
  residues processed: 5
  average time/residue: 0.1122
  time to fit residues: 2.1291
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 93 optimal weight:    7.9990
   chunk 56 optimal weight:    0.0470
   chunk 44 optimal weight:    1.9990
   chunk 64 optimal weight:    0.9980
   chunk 97 optimal weight:   10.0000
   chunk 89 optimal weight:    5.9990
   chunk 77 optimal weight:   10.0000
   chunk 8 optimal weight:    0.9990
   chunk 60 optimal weight:    8.9990
   chunk 47 optimal weight:    0.9990
   chunk 61 optimal weight:    0.7980
   overall best weight:    0.7682

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
G  23 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.5584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  12736  Z= 0.180
  Angle     :  0.568  10.647  18461  Z= 0.329
  Chirality :  0.033   0.134   2098
  Planarity :  0.003   0.035   1318
  Dihedral  : 30.788 158.999   3780
  Min Nonbonded Distance : 2.104

Molprobity Statistics.
  All-atom Clashscore : 10.58
  Ramachandran Plot:
    Outliers :  0.14 %
    Allowed  :  3.85 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  : 26.21 %
    Favored  : 73.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.25 (0.32), residues: 728
  helix: -0.23 (0.25), residues: 466
  sheet:  None (None), residues: 0
  loop : -1.81 (0.38), residues: 262

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

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

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1456 Ramachandran restraints generated.
    728 Oldfield, 0 Emsley, 728 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 4
    poor density    : 147
  time to evaluate  : 0.908 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 2
  residues processed: 147
  average time/residue: 0.3059
  time to fit residues: 60.7248
Evaluate side-chains
  140 residues out of total 618 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 138
  time to evaluate  : 0.970 
Switching outliers to nearest non-outliers
  outliers start: 2
  outliers final: 0
  residues processed: 2
  average time/residue: 0.1284
  time to fit residues: 1.5455
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 98
   random chunks:
   chunk 82 optimal weight:    7.9990
   chunk 23 optimal weight:    4.9990
   chunk 71 optimal weight:   10.0000
   chunk 11 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   chunk 77 optimal weight:   10.0000
   chunk 32 optimal weight:    3.9990
   chunk 79 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    0.6980
   chunk 68 optimal weight:    0.1980
   overall best weight:    2.1384

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

Flipped N/Q/H residues before XYZ refinement:
** A  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  25 ASN
** G  23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.134623 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.110884 restraints weight = 23609.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.112319 restraints weight = 15679.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.113241 restraints weight = 12217.166|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7796
moved from start:          0.5465

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12736  Z= 0.256
  Angle     :  0.613  11.139  18461  Z= 0.351
  Chirality :  0.035   0.131   2098
  Planarity :  0.004   0.033   1318
  Dihedral  : 31.012 160.876   3780
  Min Nonbonded Distance : 2.079

Molprobity Statistics.
  All-atom Clashscore : 12.59
  Ramachandran Plot:
    Outliers :  0.27 %
    Allowed  :  4.40 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 26.38 %
    Favored  : 72.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.14 %

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: -1.42 (0.32), residues: 728
  helix: -0.38 (0.25), residues: 460
  sheet:  None (None), residues: 0
  loop : -1.82 (0.38), residues: 268
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2133.31 seconds
wall clock time: 39 minutes 32.11 seconds (2372.11 seconds total)