Starting phenix.real_space_refine (version: dev)
on Mon Feb 27 00:19:20 2023 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2023/7oi0_12916.pdb
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2023/7oi0_12916.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.76
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2023/7oi0_12916.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2023/7oi0_12916.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2023/7oi0_12916.pdb"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oi0_12916/02_2023/7oi0_12916.pdb"
  }
  resolution = 2.76
  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=   0.007 sd=   0.083
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Process input model

  Symmetric amino acids flipped
    Residue "D GLU   14": "OE1" <-> "OE2"
    Residue "D TYR   50": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "D GLU   68": "OE1" <-> "OE2"
    Residue "H GLU   90": "OE1" <-> "OE2"
    Residue "H GLU  123": "OE1" <-> "OE2"
    Residue "L GLU   69": "OE1" <-> "OE2"
    Residue "L GLU   75": "OE1" <-> "OE2"
    Residue "O GLU    5": "OE1" <-> "OE2"
    Residue "P PHE   32": "CD1" <-> "CD2" "CE1" <-> "CE2"
    Residue "P GLU   34": "OE1" <-> "OE2"
    Residue "T GLU   52": "OE1" <-> "OE2"
  Time to flip residues: 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib"
  Total number of atoms: 29255
  Number of models: 1
  Model: ""
    Number of chains: 17
    Chain: "D"
      Number of atoms: 1643
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 205, 1643
          Classifications: {'peptide': 205}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 6, 'TRANS': 198}
    Chain: "F"
      Number of atoms: 817
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 100, 817
          Classifications: {'peptide': 100}
          Link IDs: {'PTRANS': 4, 'TRANS': 95}
    Chain: "H"
      Number of atoms: 979
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 129, 979
          Classifications: {'peptide': 129}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 123}
    Chain: "K"
      Number of atoms: 702
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 702
          Classifications: {'peptide': 95}
          Link IDs: {'PTRANS': 3, 'TRANS': 91}
    Chain: "L"
      Number of atoms: 955
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 123, 955
          Classifications: {'peptide': 123}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 7, 'TRANS': 115}
    Chain: "O"
      Number of atoms: 716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 716
          Classifications: {'peptide': 88}
          Modifications used: {'COO': 1}
          Link IDs: {'TRANS': 87}
    Chain: "P"
      Number of atoms: 649
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 649
          Classifications: {'peptide': 82}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 79}
    Chain: "Q"
      Number of atoms: 648
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 648
          Classifications: {'peptide': 80}
          Link IDs: {'PTRANS': 2, 'TRANS': 77}
    Chain: "R"
      Number of atoms: 407
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 50, 407
          Classifications: {'peptide': 50}
          Link IDs: {'PTRANS': 2, 'TRANS': 47}
    Chain: "T"
      Number of atoms: 665
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 85, 665
          Classifications: {'peptide': 85}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 83}
    Chain: "A"
      Number of atoms: 20700
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 963, 20700
          Classifications: {'RNA': 963}
          Modifications used: {'rna2p_pur': 74, 'rna2p_pyr': 44, 'rna3p_pur': 487, 'rna3p_pyr': 358}
          Link IDs: {'rna2p': 118, 'rna3p': 844}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "L"
      Number of atoms: 4
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 4
          Classifications: {'water': 4}
          Link IDs: {None: 3}
    Chain: "P"
      Number of atoms: 18
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 18, 18
          Classifications: {'water': 18}
          Link IDs: {None: 17}
    Chain: "Q"
      Number of atoms: 3
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 3
          Classifications: {'water': 3}
          Link IDs: {None: 2}
    Chain: "T"
      Number of atoms: 6
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 6
          Classifications: {'water': 6}
          Link IDs: {None: 5}
    Chain: "A"
      Number of atoms: 337
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 337
          Classifications: {'water': 337}
          Link IDs: {None: 336}
  Time building chain proxies: 16.43, per 1000 atoms: 0.56
  Number of scatterers: 29255
  At special positions: 0
  Unit cell: (111.8, 155.66, 212.42, 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      30     16.00
     P     963     15.00
     O    8527      8.00
     N    5400      7.00
     C   14335      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: 18.36
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1930

  Finding SS restraints...
    Secondary structure from input PDB file:
      31 helices and 11 sheets defined
      39.9% alpha, 15.9% beta
      338 base pairs and 532 stacking pairs defined.
    Time for finding SS restraints: 12.98
  Creating SS restraints...
    Processing helix  chain 'D' and resid 6 through 14
      removed outlier: 3.928A  pdb=" N   LEU D  10 " --> pdb=" O   PRO D   6 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   SER D  11 " --> pdb=" O   LYS D   7 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLU D  14 " --> pdb=" O   LEU D  10 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 48 through 65
    Processing helix  chain 'D' and resid 67 through 81
    Processing helix  chain 'D' and resid 84 through 95
    Processing helix  chain 'D' and resid 96 through 104
    Processing helix  chain 'D' and resid 109 through 119
    Processing helix  chain 'D' and resid 146 through 149
    Processing helix  chain 'D' and resid 151 through 160
      removed outlier: 3.603A  pdb=" N   GLU D 159 " --> pdb=" O   LYS D 155 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   LEU D 160 " --> pdb=" O   ALA D 156 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 195 through 203
      removed outlier: 4.030A  pdb=" N   ILE D 199 " --> pdb=" O   ASN D 195 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 14 through 16
      No H-bonds generated for 'chain 'F' and resid 14 through 16'
    Processing helix  chain 'F' and resid 17 through 32
    Processing helix  chain 'F' and resid 50 through 54
      removed outlier: 3.640A  pdb=" N   LYS F  53 " --> pdb=" O   PRO F  50 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU F  54 " --> pdb=" O   ILE F  51 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'F' and resid 50 through 54'
    Processing helix  chain 'F' and resid 69 through 81
      removed outlier: 4.153A  pdb=" N   GLU F  73 " --> pdb=" O   GLU F  69 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   LEU F  74 " --> pdb=" O   VAL F  70 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 4 through 19
      removed outlier: 3.694A  pdb=" N   MET H   9 " --> pdb=" O   PRO H   5 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 29 through 42
    Processing helix  chain 'H' and resid 87 through 91
    Processing helix  chain 'H' and resid 111 through 119
    Processing helix  chain 'K' and resid 58 through 72
    Processing helix  chain 'K' and resid 91 through 101
    Processing helix  chain 'L' and resid 2 through 9
    Processing helix  chain 'O' and resid 3 through 14
    Processing helix  chain 'O' and resid 23 through 46
      removed outlier: 4.111A  pdb=" N   ALA O  43 " --> pdb=" O   GLN O  39 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   GLU O  44 " --> pdb=" O   GLY O  40 " (cutoff:3.500A)
      removed outlier: 4.133A  pdb=" N   HIS O  45 " --> pdb=" O   HIS O  41 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 49 through 73
      removed outlier: 3.678A  pdb=" N   ARG O  53 " --> pdb=" O   HIS O  49 " (cutoff:3.500A)
      removed outlier: 4.613A  pdb=" N   GLY O  54 " --> pdb=" O   HIS O  50 " (cutoff:3.500A)
      removed outlier: 3.709A  pdb=" N   LEU O  55 " --> pdb=" O   SER O  51 " (cutoff:3.500A)
    Processing helix  chain 'O' and resid 73 through 84
      removed outlier: 5.012A  pdb=" N   GLU O  82 " --> pdb=" O   THR O  78 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 53 through 63
      removed outlier: 3.845A  pdb=" N   ILE P  57 " --> pdb=" O   ASP P  53 " (cutoff:3.500A)
    Processing helix  chain 'P' and resid 68 through 82
    Processing helix  chain 'R' and resid 25 through 32
      removed outlier: 3.662A  pdb=" N   LYS R  29 " --> pdb=" O   ALA R  26 " (cutoff:3.500A)
      removed outlier: 5.355A  pdb=" N   ASN R  30 " --> pdb=" O   THR R  27 " (cutoff:3.500A)
    Processing helix  chain 'R' and resid 49 through 64
    Processing helix  chain 'T' and resid 3 through 39
    Processing helix  chain 'T' and resid 42 through 63
      Proline residue:  T  55  - end of helix
    Processing helix  chain 'T' and resid 67 through 86
    Processing sheet with id=AA1, first strand: chain 'D' and resid 127 through 128
    Processing sheet with id=AA2, first strand: chain 'F' and resid 2 through 3
    Processing sheet with id=AA3, first strand: chain 'F' and resid 40 through 46
      removed outlier: 3.736A  pdb=" N   GLU F  40 " --> pdb=" O   LEU F  61 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   LEU F  61 " --> pdb=" O   GLU F  40 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   TYR F  59 " --> pdb=" O   TRP F  42 " (cutoff:3.500A)
      removed outlier: 4.147A  pdb=" N   ARG F  44 " --> pdb=" O   ALA F  57 " (cutoff:3.500A)
      removed outlier: 4.987A  pdb=" N   ALA F  57 " --> pdb=" O   ARG F  44 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'H' and resid 23 through 24
    Processing sheet with id=AA5, first strand: chain 'H' and resid 50 through 51
    Processing sheet with id=AA6, first strand: chain 'H' and resid 75 through 76
    Processing sheet with id=AA7, first strand: chain 'H' and resid 75 through 76
      removed outlier: 6.900A  pdb=" N   VAL H 102 " --> pdb=" O   ILE H 125 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 40 through 45
      removed outlier: 6.645A  pdb=" N   ILE K  33 " --> pdb=" O   LEU K  41 " (cutoff:3.500A)
      removed outlier: 5.036A  pdb=" N   TRP K  43 " --> pdb=" O   VAL K  31 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   VAL K  31 " --> pdb=" O   TRP K  43 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 28 through 31
      removed outlier: 10.174A  pdb=" N   VAL L  92 " --> pdb=" O   GLU L  61 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   THR L  63 " --> pdb=" O   VAL L  92 " (cutoff:3.500A)
      removed outlier: 4.062A  pdb=" N   TYR L  94 " --> pdb=" O   THR L  63 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'P' and resid 50 through 51
      removed outlier: 4.865A  pdb=" N   VAL P  19 " --> pdb=" O   VAL P  36 " (cutoff:3.500A)
      removed outlier: 4.577A  pdb=" N   PHE P  38 " --> pdb=" O   TYR P  17 " (cutoff:3.500A)
      removed outlier: 6.668A  pdb=" N   TYR P  17 " --> pdb=" O   PHE P  38 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'Q' and resid 7 through 16
      removed outlier: 7.901A  pdb=" N   GLN Q   8 " --> pdb=" O   GLU Q  25 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   GLU Q  25 " --> pdb=" O   GLN Q   8 " (cutoff:3.500A)
      removed outlier: 6.287A  pdb=" N   VAL Q  21 " --> pdb=" O   VAL Q  12 " (cutoff:3.500A)
      removed outlier: 4.965A  pdb=" N   ASP Q  14 " --> pdb=" O   SER Q  19 " (cutoff:3.500A)
      removed outlier: 7.447A  pdb=" N   SER Q  19 " --> pdb=" O   ASP Q  14 " (cutoff:3.500A)
      removed outlier: 15.667A  pdb=" N   LYS Q  70 " --> pdb=" O   THR Q  40 " (cutoff:3.500A)
      removed outlier: 14.072A  pdb=" N   LYS Q  42 " --> pdb=" O   LYS Q  70 " (cutoff:3.500A)
      removed outlier: 9.785A  pdb=" N   TRP Q  72 " --> pdb=" O   LYS Q  42 " (cutoff:3.500A)
      removed outlier: 6.835A  pdb=" N   HIS Q  44 " --> pdb=" O   TRP Q  72 " (cutoff:3.500A)
      removed outlier: 7.683A  pdb=" N   LEU Q  74 " --> pdb=" O   HIS Q  44 " (cutoff:3.500A)
      removed outlier: 7.330A  pdb=" N   HIS Q  46 " --> pdb=" O   LEU Q  74 " (cutoff:3.500A)
      removed outlier: 8.720A  pdb=" N   ARG Q  76 " --> pdb=" O   HIS Q  46 " (cutoff:3.500A)
      removed outlier: 5.922A  pdb=" N   SER Q  71 " --> pdb=" O   CYS Q  63 " (cutoff:3.500A)
      removed outlier: 6.457A  pdb=" N   GLU Q  59 " --> pdb=" O   VAL Q  75 " (cutoff:3.500A)
      removed outlier: 4.801A  pdb=" N   VAL Q  77 " --> pdb=" O   VAL Q  57 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   VAL Q  57 " --> pdb=" O   VAL Q  77 " (cutoff:3.500A)

    363 hydrogen bonds defined for protein.
    1023 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      840 hydrogen bonds
      1286 hydrogen bond angles
      0 basepair planarities
      338 basepair parallelities
      532 stacking parallelities
  Total time for adding SS restraints: 25.85

  Time building geometry restraints manager: 19.01 seconds

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

  Histogram of bond lengths:
        1.17 -     1.30: 2788
        1.30 -     1.43: 14063
        1.43 -     1.56: 12652
        1.56 -     1.68: 1924
        1.68 -     1.81: 51
  Bond restraints: 31478
  Sorted by residual:
  bond pdb=" CB  VAL P  20 "
       pdb=" CG2 VAL P  20 "
    ideal  model  delta    sigma   weight residual
    1.521  1.404  0.117 3.30e-02 9.18e+02 1.25e+01
  bond pdb=" C5    G A 108 "
       pdb=" C6    G A 108 "
    ideal  model  delta    sigma   weight residual
    1.419  1.350  0.069 2.00e-02 2.50e+03 1.20e+01
  bond pdb=" N   ILE T  66 "
       pdb=" CA  ILE T  66 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.036 1.11e-02 8.12e+03 1.03e+01
  bond pdb=" N9    A A 452 "
       pdb=" C4    A A 452 "
    ideal  model  delta    sigma   weight residual
    1.374  1.310  0.064 2.00e-02 2.50e+03 1.02e+01
  bond pdb=" CD2 HIS P   9 "
       pdb=" NE2 HIS P   9 "
    ideal  model  delta    sigma   weight residual
    1.374  1.339  0.035 1.10e-02 8.26e+03 9.97e+00
  ... (remaining 31473 not shown)

  Histogram of bond angle deviations from ideal:
       96.68 -   104.80: 4486
      104.80 -   112.92: 18953
      112.92 -   121.04: 14899
      121.04 -   129.16: 7869
      129.16 -   137.28: 1089
  Bond angle restraints: 47296
  Sorted by residual:
  angle pdb=" C4'   G A 416 "
        pdb=" C3'   G A 416 "
        pdb=" O3'   G A 416 "
      ideal   model   delta    sigma   weight residual
     113.00  125.61  -12.61 1.50e+00 4.44e-01 7.07e+01
  angle pdb=" O2'   G A 416 "
        pdb=" C2'   G A 416 "
        pdb=" C1'   G A 416 "
      ideal   model   delta    sigma   weight residual
     108.40   97.74   10.66 1.50e+00 4.44e-01 5.05e+01
  angle pdb=" C4'   A A 465 "
        pdb=" C3'   A A 465 "
        pdb=" O3'   A A 465 "
      ideal   model   delta    sigma   weight residual
     113.00  123.41  -10.41 1.50e+00 4.44e-01 4.82e+01
  angle pdb=" C4'   A A 415 "
        pdb=" C3'   A A 415 "
        pdb=" O3'   A A 415 "
      ideal   model   delta    sigma   weight residual
     113.00  121.46   -8.46 1.50e+00 4.44e-01 3.18e+01
  angle pdb=" O4'   A A 182 "
        pdb=" C1'   A A 182 "
        pdb=" N9    A A 182 "
      ideal   model   delta    sigma   weight residual
     108.20  116.16   -7.96 1.50e+00 4.44e-01 2.82e+01
  ... (remaining 47291 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.35: 15843
       35.35 -    70.70: 779
       70.70 -   106.05: 69
      106.05 -   141.39: 7
      141.39 -   176.74: 11
  Dihedral angle restraints: 16709
    sinusoidal: 13723
      harmonic: 2986
  Sorted by residual:
  dihedral pdb=" O4'   U A 610 "
           pdb=" C1'   U A 610 "
           pdb=" N1    U A 610 "
           pdb=" C2    U A 610 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -160.00    5.95 -165.95     1      1.50e+01 4.44e-03 8.41e+01
  dihedral pdb=" O4'   U A 365 "
           pdb=" C1'   U A 365 "
           pdb=" N1    U A 365 "
           pdb=" C2    U A 365 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.60  149.40     1      1.50e+01 4.44e-03 7.94e+01
  dihedral pdb=" O4'   C A 754 "
           pdb=" C1'   C A 754 "
           pdb=" N1    C A 754 "
           pdb=" C2    C A 754 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   50.65  149.35     1      1.50e+01 4.44e-03 7.94e+01
  ... (remaining 16706 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.138: 5788
       0.138 -    0.275: 254
       0.275 -    0.413: 13
       0.413 -    0.551: 0
       0.551 -    0.689: 1
  Chirality restraints: 6056
  Sorted by residual:
  chirality pdb=" C3'   A A 465 "
            pdb=" C4'   A A 465 "
            pdb=" O3'   A A 465 "
            pdb=" C2'   A A 465 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -1.79   -0.69 2.00e-01 2.50e+01 1.19e+01
  chirality pdb=" CB  VAL P  20 "
            pdb=" CA  VAL P  20 "
            pdb=" CG1 VAL P  20 "
            pdb=" CG2 VAL P  20 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.24   -0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CB  ILE L  66 "
            pdb=" CA  ILE L  66 "
            pdb=" CG1 ILE L  66 "
            pdb=" CG2 ILE L  66 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.27    0.37 2.00e-01 2.50e+01 3.44e+00
  ... (remaining 6053 not shown)

  Planarity restraints: 2401
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C A 335 "   -0.069 2.00e-02 2.50e+03   3.65e-02 3.00e+01
        pdb=" N1    C A 335 "    0.080 2.00e-02 2.50e+03
        pdb=" C2    C A 335 "    0.002 2.00e-02 2.50e+03
        pdb=" O2    C A 335 "    0.008 2.00e-02 2.50e+03
        pdb=" N3    C A 335 "   -0.008 2.00e-02 2.50e+03
        pdb=" C4    C A 335 "   -0.005 2.00e-02 2.50e+03
        pdb=" N4    C A 335 "   -0.018 2.00e-02 2.50e+03
        pdb=" C5    C A 335 "   -0.006 2.00e-02 2.50e+03
        pdb=" C6    C A 335 "    0.018 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A A 181 "   -0.069 2.00e-02 2.50e+03   3.16e-02 2.75e+01
        pdb=" N9    A A 181 "    0.072 2.00e-02 2.50e+03
        pdb=" C8    A A 181 "    0.012 2.00e-02 2.50e+03
        pdb=" N7    A A 181 "   -0.013 2.00e-02 2.50e+03
        pdb=" C5    A A 181 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    A A 181 "   -0.011 2.00e-02 2.50e+03
        pdb=" N6    A A 181 "   -0.009 2.00e-02 2.50e+03
        pdb=" N1    A A 181 "   -0.014 2.00e-02 2.50e+03
        pdb=" C2    A A 181 "    0.009 2.00e-02 2.50e+03
        pdb=" N3    A A 181 "    0.009 2.00e-02 2.50e+03
        pdb=" C4    A A 181 "    0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U A 438 "    0.064 2.00e-02 2.50e+03   3.21e-02 2.32e+01
        pdb=" N1    U A 438 "   -0.063 2.00e-02 2.50e+03
        pdb=" C2    U A 438 "   -0.014 2.00e-02 2.50e+03
        pdb=" O2    U A 438 "   -0.009 2.00e-02 2.50e+03
        pdb=" N3    U A 438 "    0.015 2.00e-02 2.50e+03
        pdb=" C4    U A 438 "    0.008 2.00e-02 2.50e+03
        pdb=" O4    U A 438 "    0.014 2.00e-02 2.50e+03
        pdb=" C5    U A 438 "    0.004 2.00e-02 2.50e+03
        pdb=" C6    U A 438 "   -0.020 2.00e-02 2.50e+03
  ... (remaining 2398 not shown)

  Histogram of nonbonded interaction distances:
        1.98 -     2.56: 729
        2.56 -     3.15: 23322
        3.15 -     3.73: 63512
        3.73 -     4.32: 87681
        4.32 -     4.90: 112427
  Nonbonded interactions: 287671
  Sorted by model distance:
  nonbonded pdb=" N2    G A 444 "
            pdb=" O2    C A 490 "
     model   vdw
     1.977 2.496
  nonbonded pdb=" N2    G A 457 "
            pdb=" O2    C A 475 "
     model   vdw
     1.982 2.496
  nonbonded pdb=" O6    G A 410 "
            pdb=" O2'   U A 429 "
     model   vdw
     1.983 2.440
  nonbonded pdb=" O2    C A 658 "
            pdb=" N2    G A 748 "
     model   vdw
     2.021 2.496
  nonbonded pdb=" OD1 ASP D  98 "
            pdb=" N   ASN D  99 "
     model   vdw
     2.025 2.520
  ... (remaining 287666 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     963      5.49       5
     S      30      5.16       5
     C   14335      2.51       5
     N    5400      2.21       5
     O    8527      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             3.790
  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:             0.030
  Extract box with map and model:          19.500
  Check model and map are aligned:         0.390
  Process input model:                     101.540
  Find NCS groups from input model:        0.560
  Set up NCS constraints:                  0.090
  Set refine NCS operators:                0.000
  Set scattering table:                    0.270
  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:13.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:  139.540
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7471
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      :  0.014   0.117  31478  Z= 0.836
  Angle     :  1.079  12.609  47296  Z= 0.566
  Chirality :  0.063   0.689   6056
  Planarity :  0.007   0.062   2401
  Dihedral  : 17.048 176.743  14779
  Min Nonbonded Distance : 1.977

Molprobity Statistics.
  All-atom Clashscore : 23.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.23 %
    Favored  : 89.77 %
  Rotamer Outliers :  0.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.50 (0.24), residues: 1017
  helix: -0.71 (0.26), residues: 379
  sheet: -2.44 (0.38), residues: 147
  loop : -2.14 (0.26), residues: 491

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 2
    poor density    : 113
  time to evaluate  : 1.531 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 2
  outliers final: 3
  residues processed: 115
  average time/residue: 1.5334
  time to fit residues: 206.5317
Evaluate side-chains
  105 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 3
    poor density    : 102
  time to evaluate  : 1.482 
Switching outliers to nearest non-outliers
  outliers start: 3
  outliers final: 3
  residues processed: 2
  average time/residue: 0.3959
  time to fit residues: 3.0524
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 165 optimal weight:   10.0000
   chunk 148 optimal weight:    0.6980
   chunk 82 optimal weight:    1.9990
   chunk 50 optimal weight:   50.0000
   chunk 100 optimal weight:   30.0000
   chunk 79 optimal weight:    7.9990
   chunk 153 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 93 optimal weight:    0.7980
   chunk 114 optimal weight:    0.6980
   chunk 177 optimal weight:   50.0000
   overall best weight:    0.9582

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

Flipped N/Q/H residues before XYZ refinement:
D  99 ASN
** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F   3 HIS
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
L   4 ASN
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** O  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7303
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.042  31478  Z= 0.189
  Angle     :  0.631  10.355  47296  Z= 0.323
  Chirality :  0.036   0.287   6056
  Planarity :  0.005   0.054   2401
  Dihedral  : 16.111 177.295  12712
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 16.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer Outliers :  1.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.46 (0.25), residues: 1017
  helix:  0.57 (0.26), residues: 379
  sheet: -2.03 (0.38), residues: 155
  loop : -1.86 (0.27), residues: 483

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 15
    poor density    : 114
  time to evaluate  : 1.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 15
  outliers final: 5
  residues processed: 122
  average time/residue: 1.5053
  time to fit residues: 216.2451
Evaluate side-chains
  107 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 1.572 
Switching outliers to nearest non-outliers
  outliers start: 5
  outliers final: 2
  residues processed: 3
  average time/residue: 0.6632
  time to fit residues: 4.4305
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 55 optimal weight:    0.0270
   chunk 148 optimal weight:    4.9990
   chunk 121 optimal weight:    3.9990
   chunk 49 optimal weight:   30.0000
   chunk 178 optimal weight:   50.0000
   chunk 192 optimal weight:   50.0000
   chunk 158 optimal weight:    8.9990
   chunk 176 optimal weight:   30.0000
   chunk 60 optimal weight:    2.9990
   chunk 143 optimal weight:    4.9990
   overall best weight:    3.0046

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  95 HIS
** O  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7404
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.058  31478  Z= 0.389
  Angle     :  0.710  11.211  47296  Z= 0.358
  Chirality :  0.041   0.290   6056
  Planarity :  0.006   0.048   2401
  Dihedral  : 16.110 177.358  12712
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 16.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer Outliers :  2.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -1.27 (0.26), residues: 1017
  helix:  0.77 (0.26), residues: 380
  sheet: -2.10 (0.41), residues: 146
  loop : -1.75 (0.27), residues: 491

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 22
    poor density    : 99
  time to evaluate  : 1.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 22
  outliers final: 7
  residues processed: 112
  average time/residue: 1.4991
  time to fit residues: 197.8881
Evaluate side-chains
  102 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 1.619 
Switching outliers to nearest non-outliers
  outliers start: 7
  outliers final: 3
  residues processed: 4
  average time/residue: 0.4135
  time to fit residues: 4.3327
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 176 optimal weight:   30.0000
   chunk 134 optimal weight:    2.9990
   chunk 92 optimal weight:    0.7980
   chunk 19 optimal weight:    8.9990
   chunk 85 optimal weight:    0.4980
   chunk 119 optimal weight:    3.9990
   chunk 178 optimal weight:   50.0000
   chunk 189 optimal weight:   10.0000
   chunk 93 optimal weight:    0.9990
   chunk 169 optimal weight:   50.0000
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.4586

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 139 ASN
** D 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  72 ASN
L  95 HIS
** O  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.041  31478  Z= 0.214
  Angle     :  0.593  11.660  47296  Z= 0.301
  Chirality :  0.034   0.241   6056
  Planarity :  0.004   0.049   2401
  Dihedral  : 15.658 177.764  12712
  Min Nonbonded Distance : 2.038

Molprobity Statistics.
  All-atom Clashscore : 15.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Rotamer Outliers :  3.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.95 (0.26), residues: 1017
  helix:  1.15 (0.26), residues: 386
  sheet: -1.95 (0.38), residues: 170
  loop : -1.66 (0.28), residues: 461

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 105
  time to evaluate  : 1.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 10
  residues processed: 123
  average time/residue: 1.5394
  time to fit residues: 223.1115
Evaluate side-chains
  111 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 1.511 
Switching outliers to nearest non-outliers
  outliers start: 10
  outliers final: 5
  residues processed: 5
  average time/residue: 0.6201
  time to fit residues: 6.0618
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 157 optimal weight:    7.9990
   chunk 107 optimal weight:   20.0000
   chunk 2 optimal weight:    0.2980
   chunk 141 optimal weight:    7.9990
   chunk 78 optimal weight:    0.8980
   chunk 161 optimal weight:    3.9990
   chunk 130 optimal weight:    3.9990
   chunk 0 optimal weight:    6.9990
   chunk 96 optimal weight:    0.5980
   chunk 170 optimal weight:   50.0000
   chunk 47 optimal weight:   10.0000
   overall best weight:    1.9584

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 151 GLN
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  63 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  72 ASN
** O  45 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** Q   8 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7356
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.004   0.039  31478  Z= 0.268
  Angle     :  0.621  12.288  47296  Z= 0.314
  Chirality :  0.036   0.248   6056
  Planarity :  0.005   0.044   2401
  Dihedral  : 15.644 177.836  12712
  Min Nonbonded Distance : 2.041

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.37 %
    Favored  : 92.63 %
  Rotamer Outliers :  2.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.87 (0.26), residues: 1017
  helix:  1.21 (0.26), residues: 383
  sheet: -2.02 (0.40), residues: 153
  loop : -1.57 (0.27), residues: 481

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 100
  time to evaluate  : 1.595 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 12
  residues processed: 115
  average time/residue: 1.4344
  time to fit residues: 196.1597
Evaluate side-chains
  109 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 1.598 
Switching outliers to nearest non-outliers
  outliers start: 12
  outliers final: 7
  residues processed: 5
  average time/residue: 1.0201
  time to fit residues: 8.3458
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 63 optimal weight:    0.0870
   chunk 170 optimal weight:   50.0000
   chunk 37 optimal weight:    5.9990
   chunk 111 optimal weight:    3.9990
   chunk 46 optimal weight:    5.9990
   chunk 189 optimal weight:   10.0000
   chunk 157 optimal weight:    7.9990
   chunk 87 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 62 optimal weight:    0.9980
   chunk 99 optimal weight:    0.6980
   overall best weight:    1.3562

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  72 ASN
L  95 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.2524

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.003   0.067  31478  Z= 0.205
  Angle     :  0.587  14.715  47296  Z= 0.298
  Chirality :  0.034   0.241   6056
  Planarity :  0.004   0.043   2401
  Dihedral  : 15.516 177.860  12712
  Min Nonbonded Distance : 2.048

Molprobity Statistics.
  All-atom Clashscore : 15.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer Outliers :  2.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.26), residues: 1017
  helix:  1.37 (0.26), residues: 383
  sheet: -1.99 (0.40), residues: 150
  loop : -1.43 (0.28), residues: 484

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 23
    poor density    : 103
  time to evaluate  : 1.604 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 23
  outliers final: 14
  residues processed: 122
  average time/residue: 1.3930
  time to fit residues: 201.1600
Evaluate side-chains
  113 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 1.643 
Switching outliers to nearest non-outliers
  outliers start: 14
  outliers final: 11
  residues processed: 3
  average time/residue: 0.3610
  time to fit residues: 3.5472
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 182 optimal weight:   10.0000
   chunk 21 optimal weight:    0.9990
   chunk 108 optimal weight:   10.0000
   chunk 138 optimal weight:    2.9990
   chunk 107 optimal weight:   20.0000
   chunk 159 optimal weight:    5.9990
   chunk 105 optimal weight:    2.9990
   chunk 188 optimal weight:   10.0000
   chunk 118 optimal weight:    3.9990
   chunk 115 optimal weight:   10.0000
   chunk 87 optimal weight:    4.9990
   overall best weight:    3.1990

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7403
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.052  31478  Z= 0.403
  Angle     :  0.700  14.303  47296  Z= 0.350
  Chirality :  0.040   0.259   6056
  Planarity :  0.006   0.101   2401
  Dihedral  : 15.753 177.301  12712
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 16.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer Outliers :  3.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.80 (0.26), residues: 1017
  helix:  1.17 (0.26), residues: 382
  sheet: -1.90 (0.41), residues: 150
  loop : -1.46 (0.28), residues: 485

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 29
    poor density    : 99
  time to evaluate  : 1.786 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 29
  outliers final: 16
  residues processed: 121
  average time/residue: 1.4842
  time to fit residues: 212.4592
Evaluate side-chains
  113 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.556 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 14
  residues processed: 3
  average time/residue: 0.3425
  time to fit residues: 3.4220
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 116 optimal weight:    3.9990
   chunk 75 optimal weight:    0.9990
   chunk 112 optimal weight:    2.9990
   chunk 56 optimal weight:    0.7980
   chunk 37 optimal weight:    5.9990
   chunk 36 optimal weight:    9.9990
   chunk 120 optimal weight:   10.0000
   chunk 128 optimal weight:    2.9990
   chunk 93 optimal weight:    2.9990
   chunk 17 optimal weight:    8.9990
   chunk 148 optimal weight:    3.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  72 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7365
moved from start:          0.2438

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.045  31478  Z= 0.292
  Angle     :  0.641  17.515  47296  Z= 0.322
  Chirality :  0.036   0.251   6056
  Planarity :  0.005   0.068   2401
  Dihedral  : 15.625 177.235  12712
  Min Nonbonded Distance : 2.035

Molprobity Statistics.
  All-atom Clashscore : 15.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer Outliers :  2.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.75 (0.26), residues: 1017
  helix:  1.25 (0.26), residues: 383
  sheet: -1.87 (0.40), residues: 154
  loop : -1.48 (0.28), residues: 480

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 24
    poor density    : 98
  time to evaluate  : 1.542 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 24
  outliers final: 16
  residues processed: 115
  average time/residue: 1.4721
  time to fit residues: 199.9400
Evaluate side-chains
  111 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 1.548 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 12
  residues processed: 4
  average time/residue: 0.3185
  time to fit residues: 3.8281
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 171 optimal weight:   30.0000
   chunk 180 optimal weight:   10.0000
   chunk 165 optimal weight:   10.0000
   chunk 176 optimal weight:   20.0000
   chunk 105 optimal weight:    2.9990
   chunk 76 optimal weight:    2.9990
   chunk 138 optimal weight:    1.9990
   chunk 54 optimal weight:    7.9990
   chunk 159 optimal weight:    5.9990
   chunk 166 optimal weight:   20.0000
   chunk 175 optimal weight:    6.9990
   overall best weight:    4.1990

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  17 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7434
moved from start:          0.2160

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.009   0.061  31478  Z= 0.515
  Angle     :  0.781  17.649  47296  Z= 0.387
  Chirality :  0.045   0.400   6056
  Planarity :  0.006   0.086   2401
  Dihedral  : 15.944 177.692  12712
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 17.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.36 %
    Favored  : 91.64 %
  Rotamer Outliers :  3.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.94 (0.26), residues: 1017
  helix:  1.02 (0.26), residues: 383
  sheet: -2.02 (0.39), residues: 160
  loop : -1.48 (0.28), residues: 474

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 26
    poor density    : 98
  time to evaluate  : 1.791 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 26
  outliers final: 16
  residues processed: 116
  average time/residue: 1.5278
  time to fit residues: 209.7490
Evaluate side-chains
  113 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 1.769 
Switching outliers to nearest non-outliers
  outliers start: 16
  outliers final: 11
  residues processed: 5
  average time/residue: 0.5817
  time to fit residues: 6.0838
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 115 optimal weight:   10.0000
   chunk 186 optimal weight:   10.0000
   chunk 113 optimal weight:    0.9990
   chunk 88 optimal weight:   30.0000
   chunk 129 optimal weight:    4.9990
   chunk 195 optimal weight:   30.0000
   chunk 179 optimal weight:   50.0000
   chunk 155 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0370
   chunk 120 optimal weight:   10.0000
   chunk 95 optimal weight:    0.0870
   overall best weight:    3.2244

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 197 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7410
moved from start:          0.2290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.007   0.053  31478  Z= 0.411
  Angle     :  0.725  22.446  47296  Z= 0.360
  Chirality :  0.041   0.362   6056
  Planarity :  0.006   0.076   2401
  Dihedral  : 15.831 177.742  12712
  Min Nonbonded Distance : 2.013

Molprobity Statistics.
  All-atom Clashscore : 16.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.06 %
    Favored  : 91.94 %
  Rotamer Outliers :  2.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.94 (0.26), residues: 1017
  helix:  1.07 (0.26), residues: 381
  sheet: -2.08 (0.38), residues: 154
  loop : -1.49 (0.28), residues: 482

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

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

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2034 Ramachandran restraints generated.
    1017 Oldfield, 0 Emsley, 1017 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 18
    poor density    : 100
  time to evaluate  : 1.599 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 18
  outliers final: 13
  residues processed: 113
  average time/residue: 1.4422
  time to fit residues: 192.9877
Evaluate side-chains
  112 residues out of total 858 non-(ALA, GLY, PRO) need fitting.
    rotamer outliers: 13
    poor density    : 99
  time to evaluate  : 1.609 
Switching outliers to nearest non-outliers
  outliers start: 13
  outliers final: 10
  residues processed: 4
  average time/residue: 0.3206
  time to fit residues: 3.8580
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 196
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 165 optimal weight:   20.0000
   chunk 47 optimal weight:    8.9990
   chunk 143 optimal weight:    4.9990
   chunk 22 optimal weight:    6.9990
   chunk 43 optimal weight:    1.9990
   chunk 155 optimal weight:   10.0000
   chunk 65 optimal weight:    5.9990
   chunk 159 optimal weight:    5.9990
   chunk 19 optimal weight:    0.0570
   chunk 28 optimal weight:    0.5980
   overall best weight:    2.3304

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

Flipped N/Q/H residues before XYZ refinement:
** D  99 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 197 HIS
F  81 ASN
** K 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** L  71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
L  72 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4400 r_free = 0.4400 target = 0.154502 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.131853 restraints weight = 50068.838|
|-----------------------------------------------------------------------------|
r_work (start): 0.4074 rms_B_bonded: 0.64
r_work: 0.3722 rms_B_bonded: 2.75 restraints_weight: 0.5000
r_work: 0.3666 rms_B_bonded: 3.51 restraints_weight: 0.2500
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd. rmsZ for bonds and angles.
  Bond      :  0.005   0.051  31478  Z= 0.312
  Angle     :  0.661  22.285  47296  Z= 0.332
  Chirality :  0.038   0.318   6056
  Planarity :  0.005   0.060   2401
  Dihedral  : 15.661 178.013  12712
  Min Nonbonded Distance : 2.023

Molprobity Statistics.
  All-atom Clashscore : 15.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.26 %
    Favored  : 91.74 %
  Rotamer Outliers :  1.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.10 %

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: -0.83 (0.26), residues: 1017
  helix:  1.14 (0.26), residues: 381
  sheet: -2.05 (0.39), residues: 149
  loop : -1.42 (0.28), residues: 487

===============================================================================
Job complete
usr+sys time: 5401.33 seconds
wall clock time: 100 minutes 51.07 seconds (6051.07 seconds total)