Starting phenix.real_space_refine
on Sun Nov 17 21:27:42 2024 by dcliebschner
===============================================================================

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

  Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/11_2024/6pwf_20507.cif
  Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/11_2024/6pwf_20507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.07
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/11_2024/6pwf_20507.map"
    default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/11_2024/6pwf_20507.map"
    model {
      file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/11_2024/6pwf_20507.cif"
    }
    default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6pwf_20507/11_2024/6pwf_20507.cif"
  }
  resolution = 4.07
  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=   0.005
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     292      5.49       5
     S      27      5.16       5
     C    8674      2.51       5
     N    2812      2.21       5
     O    3392      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib"
  Total number of atoms: 15197
  Number of models: 1
  Model: ""
    Number of chains: 11
    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: 671
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 88, 671
          Classifications: {'peptide': 88}
          Incomplete info: {'truncation_to_alanine': 8}
          Link IDs: {'PTRANS': 1, 'TRANS': 86}
          Unresolved non-hydrogen bonds: 37
          Unresolved non-hydrogen angles: 44
          Unresolved non-hydrogen dihedrals: 32
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 3, 'HIS:plan': 1}
          Unresolved non-hydrogen planarities: 20
    Chain: "C"
      Number of atoms: 798
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 104, 798
          Classifications: {'peptide': 104}
          Link IDs: {'PTRANS': 5, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 723
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 92, 723
          Classifications: {'peptide': 92}
          Link IDs: {'PTRANS': 2, 'TRANS': 89}
    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: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 807
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    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: 3011
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3011
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "J"
      Number of atoms: 2975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2975
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 3263
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 454, 3263
          Classifications: {'peptide': 454}
          Incomplete info: {'truncation_to_alanine': 118}
          Link IDs: {'PTRANS': 15, 'TRANS': 438}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 463
          Unresolved non-hydrogen angles: 580
          Unresolved non-hydrogen dihedrals: 379
          Unresolved non-hydrogen chiralities: 26
          Planarities with less than four sites: {'GLN:plan1': 14, 'HIS:plan': 4, 'TYR:plan': 1, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 14, 'PHE:plan': 4, 'GLU:plan': 17, 'ARG:plan': 10}
          Unresolved non-hydrogen planarities: 306
  Time building chain proxies: 9.19, per 1000 atoms: 0.60
  Number of scatterers: 15197
  At special positions: 0
  Unit cell: (111.72, 149.52, 115.92, 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      27     16.00
     P     292     15.00
     O    3392      8.00
     N    2812      7.00
     C    8674      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  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.71
  Conformation dependent library (CDL) restraints added in 1.4 seconds
  

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2268

  Finding SS restraints...
    Secondary structure from input PDB file:
      67 helices and 8 sheets defined
      53.5% alpha, 3.6% beta
      79 base pairs and 216 stacking pairs defined.
    Time for finding SS restraints: 5.77
  Creating SS restraints...
    Processing helix  chain 'A' and resid 50 through 55
    Processing helix  chain 'A' and resid 63 through 75
      removed outlier: 3.900A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 78
      No H-bonds generated for 'chain 'A' and resid 76 through 78'
    Processing helix  chain 'A' and resid 88 through 112
      removed outlier: 3.589A  pdb=" N   LEU A  92 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   ALA A  95 " --> pdb=" O   ALA A  91 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLU A  97 " --> pdb=" O   GLN A  93 " (cutoff:3.500A)
      removed outlier: 4.052A  pdb=" N   ALA A  98 " --> pdb=" O   GLU A  94 " (cutoff:3.500A)
      removed outlier: 4.032A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   ASN A 108 " --> pdb=" O   PHE A 104 " (cutoff:3.500A)
      removed outlier: 4.822A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 4.166A  pdb=" N   CYS A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 115
      No H-bonds generated for 'chain 'A' and resid 113 through 115'
    Processing helix  chain 'A' and resid 120 through 133
      removed outlier: 3.701A  pdb=" N   LEU A 126 " --> pdb=" O   LYS A 122 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ARG A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE A 130 " --> pdb=" O   LEU A 126 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   ARG A 131 " --> pdb=" O   ALA A 127 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLU A 133 " --> pdb=" O   ARG A 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
      removed outlier: 4.105A  pdb=" N   ILE B  29 " --> pdb=" O   ILE B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 31 through 41
      removed outlier: 3.853A  pdb=" N   LEU B  37 " --> pdb=" O   ALA B  33 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   ARG B  40 " --> pdb=" O   ARG B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 49 through 62
      removed outlier: 4.014A  pdb=" N   GLU B  53 " --> pdb=" O   LEU B  49 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 3.938A  pdb=" N   LYS B  59 " --> pdb=" O   ARG B  55 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   PHE B  61 " --> pdb=" O   VAL B  57 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 66 through 76
      removed outlier: 3.647A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 4.394A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 4.080A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 28 through 35
      removed outlier: 3.813A  pdb=" N   ARG C  34 " --> pdb=" O   HIS C  30 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 67
      removed outlier: 3.565A  pdb=" N   ALA C  51 " --> pdb=" O   PRO C  47 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU C  55 " --> pdb=" O   ALA C  51 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   LEU C  62 " --> pdb=" O   ALA C  58 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 68 through 70
      No H-bonds generated for 'chain 'C' and resid 68 through 70'
    Processing helix  chain 'C' and resid 78 through 87
      removed outlier: 3.947A  pdb=" N   LEU C  82 " --> pdb=" O   ILE C  78 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   GLN C  83 " --> pdb=" O   PRO C  79 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 91 through 96
      removed outlier: 3.757A  pdb=" N   LEU C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 37 through 46
      removed outlier: 3.650A  pdb=" N   VAL D  45 " --> pdb=" O   VAL D  41 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 53 through 61
      removed outlier: 3.620A  pdb=" N   MET D  59 " --> pdb=" O   ALA D  55 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 81
      removed outlier: 4.794A  pdb=" N   ALA D  72 " --> pdb=" O   GLU D  68 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ARG D  76 " --> pdb=" O   ALA D  72 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   ASN D  81 " --> pdb=" O   LEU D  77 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 97
      removed outlier: 3.780A  pdb=" N   THR D  93 " --> pdb=" O   ARG D  89 " (cutoff:3.500A)
      removed outlier: 4.298A  pdb=" N   ALA D  94 " --> pdb=" O   GLU D  90 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 119
      removed outlier: 4.127A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   LYS D 113 " --> pdb=" O   SER D 109 " (cutoff:3.500A)
      removed outlier: 4.191A  pdb=" N   ALA D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
      removed outlier: 3.546A  pdb=" N   THR D 116 " --> pdb=" O   THR D 112 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   LYS D 117 " --> pdb=" O   LYS D 113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 50 through 55
    Processing helix  chain 'E' and resid 63 through 75
      removed outlier: 3.900A  pdb=" N   GLU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 76 through 78
      No H-bonds generated for 'chain 'E' and resid 76 through 78'
    Processing helix  chain 'E' and resid 88 through 112
      removed outlier: 3.590A  pdb=" N   LEU E  92 " --> pdb=" O   ALA E  88 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA E  95 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLU E  97 " --> pdb=" O   GLN E  93 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   ALA E  98 " --> pdb=" O   GLU E  94 " (cutoff:3.500A)
      removed outlier: 4.033A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ASN E 108 " --> pdb=" O   PHE E 104 " (cutoff:3.500A)
      removed outlier: 4.823A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 4.165A  pdb=" N   CYS E 110 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 113 through 115
      No H-bonds generated for 'chain 'E' and resid 113 through 115'
    Processing helix  chain 'E' and resid 120 through 133
      removed outlier: 3.701A  pdb=" N   LEU E 126 " --> pdb=" O   LYS E 122 " (cutoff:3.500A)
      removed outlier: 3.980A  pdb=" N   ARG E 129 " --> pdb=" O   GLN E 125 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   ILE E 130 " --> pdb=" O   LEU E 126 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   ARG E 131 " --> pdb=" O   ALA E 127 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLU E 133 " --> pdb=" O   ARG E 129 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 31 through 41
      removed outlier: 3.881A  pdb=" N   LEU F  37 " --> pdb=" O   ALA F  33 " (cutoff:3.500A)
      removed outlier: 3.812A  pdb=" N   ARG F  40 " --> pdb=" O   ARG F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 54
      removed outlier: 3.744A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 54 through 62
      removed outlier: 4.353A  pdb=" N   VAL F  60 " --> pdb=" O   GLY F  56 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   PHE F  61 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 66 through 76
      removed outlier: 3.737A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
      removed outlier: 4.237A  pdb=" N   TYR F  72 " --> pdb=" O   ASP F  68 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 82 through 93
      removed outlier: 3.894A  pdb=" N   VAL F  86 " --> pdb=" O   THR F  82 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG F  92 " --> pdb=" O   TYR F  88 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 28 through 36
      removed outlier: 4.300A  pdb=" N   ARG G  34 " --> pdb=" O   HIS G  30 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 57
      removed outlier: 3.857A  pdb=" N   ALA G  52 " --> pdb=" O   VAL G  48 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   VAL G  53 " --> pdb=" O   TYR G  49 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLU G  55 " --> pdb=" O   ALA G  51 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 60 through 65
    Processing helix  chain 'G' and resid 66 through 68
      No H-bonds generated for 'chain 'G' and resid 66 through 68'
    Processing helix  chain 'G' and resid 78 through 89
      removed outlier: 3.885A  pdb=" N   LEU G  82 " --> pdb=" O   ILE G  78 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   GLN G  83 " --> pdb=" O   PRO G  79 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ASN G  88 " --> pdb=" O   LEU G  84 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ASP G  89 " --> pdb=" O   ALA G  85 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 90 through 96
      removed outlier: 3.782A  pdb=" N   LYS G  94 " --> pdb=" O   GLU G  90 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LEU G  95 " --> pdb=" O   GLU G  91 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 36 through 46
      removed outlier: 3.698A  pdb=" N   GLN H  44 " --> pdb=" O   LYS H  40 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 52 through 82
      removed outlier: 3.898A  pdb=" N   SER H  57 " --> pdb=" O   SER H  53 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ILE H  58 " --> pdb=" O   LYS H  54 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   SER H  61 " --> pdb=" O   SER H  57 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   VAL H  63 " --> pdb=" O   MET H  59 " (cutoff:3.500A)
      removed outlier: 3.762A  pdb=" N   ASN H  64 " --> pdb=" O   ASN H  60 " (cutoff:3.500A)
      removed outlier: 4.646A  pdb=" N   ASP H  65 " --> pdb=" O   SER H  61 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ARG H  69 " --> pdb=" O   ASP H  65 " (cutoff:3.500A)
      removed outlier: 4.507A  pdb=" N   ALA H  72 " --> pdb=" O   GLU H  68 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLU H  73 " --> pdb=" O   ARG H  69 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   ARG H  76 " --> pdb=" O   ALA H  72 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   HIS H  79 " --> pdb=" O   SER H  75 " (cutoff:3.500A)
      removed outlier: 4.029A  pdb=" N   TYR H  80 " --> pdb=" O   ARG H  76 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASN H  81 " --> pdb=" O   LEU H  77 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 103 through 112
      removed outlier: 3.561A  pdb=" N   VAL H 108 " --> pdb=" O   ALA H 104 " (cutoff:3.500A)
      removed outlier: 4.746A  pdb=" N   SER H 109 " --> pdb=" O   LYS H 105 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 112 through 120
      removed outlier: 4.705A  pdb=" N   TYR H 118 " --> pdb=" O   ALA H 114 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   SER H 120 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 186 through 191
    Processing helix  chain 'K' and resid 193 through 203
      removed outlier: 3.787A  pdb=" N   SER K 198 " --> pdb=" O   ASN K 194 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   LEU K 199 " --> pdb=" O   TRP K 195 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   ASN K 202 " --> pdb=" O   SER K 198 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   GLY K 203 " --> pdb=" O   LEU K 199 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 217 through 225
      removed outlier: 3.894A  pdb=" N   SER K 222 " --> pdb=" O   LEU K 218 " (cutoff:3.500A)
      removed outlier: 4.924A  pdb=" N   PHE K 223 " --> pdb=" O   GLN K 219 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 225 through 230
      removed outlier: 4.228A  pdb=" N   HIS K 229 " --> pdb=" O   GLY K 225 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE K 230 " --> pdb=" O   TYR K 226 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 225 through 230'
    Processing helix  chain 'K' and resid 242 through 244
      No H-bonds generated for 'chain 'K' and resid 242 through 244'
    Processing helix  chain 'K' and resid 245 through 257
      removed outlier: 3.816A  pdb=" N   TRP K 249 " --> pdb=" O   THR K 245 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   LYS K 250 " --> pdb=" O   LEU K 246 " (cutoff:3.500A)
      removed outlier: 4.373A  pdb=" N   ARG K 251 " --> pdb=" O   ASP K 247 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   GLU K 254 " --> pdb=" O   LYS K 250 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 268 through 273
      removed outlier: 4.197A  pdb=" N   HIS K 273 " --> pdb=" O   LYS K 269 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 273 through 278
      removed outlier: 3.676A  pdb=" N   ASP K 278 " --> pdb=" O   GLN K 274 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 291 through 297
      removed outlier: 4.032A  pdb=" N   LEU K 296 " --> pdb=" O   TYR K 292 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ARG K 297 " --> pdb=" O   GLU K 293 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 316 through 320
      removed outlier: 3.795A  pdb=" N   LYS K 319 " --> pdb=" O   HIS K 316 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   ASN K 320 " --> pdb=" O   ARG K 317 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 316 through 320'
    Processing helix  chain 'K' and resid 325 through 330
    Processing helix  chain 'K' and resid 349 through 360
      removed outlier: 3.743A  pdb=" N   TRP K 353 " --> pdb=" O   LEU K 349 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   LEU K 355 " --> pdb=" O   GLU K 351 " (cutoff:3.500A)
      removed outlier: 3.817A  pdb=" N   PHE K 358 " --> pdb=" O   ALA K 354 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LEU K 360 " --> pdb=" O   LEU K 356 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 363 through 368
      removed outlier: 4.109A  pdb=" N   ASP K 368 " --> pdb=" O   PHE K 364 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 370 through 374
      removed outlier: 3.738A  pdb=" N   PHE K 374 " --> pdb=" O   ASP K 371 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 388 through 393
    Processing helix  chain 'K' and resid 400 through 404
    Processing helix  chain 'K' and resid 430 through 436
    Processing helix  chain 'K' and resid 453 through 460
      removed outlier: 3.852A  pdb=" N   ARG K 460 " --> pdb=" O   VAL K 456 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 490 through 501
      removed outlier: 3.584A  pdb=" N   LEU K 494 " --> pdb=" O   LYS K 490 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   LYS K 496 " --> pdb=" O   ILE K 492 " (cutoff:3.500A)
      removed outlier: 5.324A  pdb=" N   LYS K 499 " --> pdb=" O   ASP K 495 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   ARG K 500 " --> pdb=" O   LYS K 496 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 514 through 526
      removed outlier: 3.729A  pdb=" N   LEU K 518 " --> pdb=" O   MET K 514 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ILE K 520 " --> pdb=" O   ARG K 516 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ASP K 523 " --> pdb=" O   ASP K 519 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   CYS K 525 " --> pdb=" O   LEU K 521 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 540 through 552
      removed outlier: 3.547A  pdb=" N   ILE K 545 " --> pdb=" O   HIS K 541 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   ALA K 547 " --> pdb=" O   ASP K 543 " (cutoff:3.500A)
      removed outlier: 4.070A  pdb=" N   GLU K 550 " --> pdb=" O   ALA K 546 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 590 through 595
    Processing helix  chain 'K' and resid 596 through 599
    Processing helix  chain 'K' and resid 619 through 630
    Processing helix  chain 'K' and resid 634 through 640
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.330A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119
      removed outlier: 3.788A  pdb=" N   ILE A 119 " --> pdb=" O   ARG B  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'C' and resid 41 through 42
      removed outlier: 6.875A  pdb=" N   ARG C  41 " --> pdb=" O   ILE D  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'C' and resid 76 through 77
    Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.965A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.654A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'K' and resid 207 through 209
      removed outlier: 5.972A  pdb=" N   GLU K 308 " --> pdb=" O   ASN K 336 " (cutoff:3.500A)
      removed outlier: 7.408A  pdb=" N   LEU K 338 " --> pdb=" O   GLU K 308 " (cutoff:3.500A)
      removed outlier: 5.961A  pdb=" N   ILE K 310 " --> pdb=" O   LEU K 338 " (cutoff:3.500A)
      removed outlier: 7.775A  pdb=" N   ILE K 340 " --> pdb=" O   ILE K 310 " (cutoff:3.500A)
      removed outlier: 6.292A  pdb=" N   ILE K 312 " --> pdb=" O   ILE K 340 " (cutoff:3.500A)
      removed outlier: 6.562A  pdb=" N   LEU K 238 " --> pdb=" O   ILE K 311 " (cutoff:3.500A)
      removed outlier: 7.745A  pdb=" N   ASP K 313 " --> pdb=" O   LEU K 238 " (cutoff:3.500A)
      removed outlier: 6.574A  pdb=" N   ALA K 240 " --> pdb=" O   ASP K 313 " (cutoff:3.500A)
      removed outlier: 7.283A  pdb=" N   HIS K 237 " --> pdb=" O   CYS K 288 " (cutoff:3.500A)
      removed outlier: 7.855A  pdb=" N   THR K 290 " --> pdb=" O   HIS K 237 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   VAL K 239 " --> pdb=" O   THR K 290 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'K' and resid 532 through 534
      removed outlier: 6.902A  pdb=" N   VAL K 508 " --> pdb=" O   PHE K 561 " (cutoff:3.500A)

    264 hydrogen bonds defined for protein.
    777 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      184 hydrogen bonds
      356 hydrogen bond angles
      0 basepair planarities
      79 basepair parallelities
      216 stacking parallelities
  Total time for adding SS restraints: 6.56

  Time building geometry restraints manager: 4.34 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2513
        1.33 -     1.45: 5206
        1.45 -     1.57: 7718
        1.57 -     1.69: 582
        1.69 -     1.81: 47
  Bond restraints: 16066
  Sorted by residual:
  bond pdb=" C1'  DA I -73 "
       pdb=" N9   DA I -73 "
    ideal  model  delta    sigma   weight residual
    1.460  1.405  0.055 2.00e-02 2.50e+03 7.47e+00
  bond pdb=" C3'  DG J  25 "
       pdb=" O3'  DG J  25 "
    ideal  model  delta    sigma   weight residual
    1.422  1.499 -0.077 3.00e-02 1.11e+03 6.53e+00
  bond pdb=" C3'  DG J -34 "
       pdb=" O3'  DG J -34 "
    ideal  model  delta    sigma   weight residual
    1.422  1.489 -0.067 3.00e-02 1.11e+03 4.94e+00
  bond pdb=" C3'  DA I  -3 "
       pdb=" O3'  DA I  -3 "
    ideal  model  delta    sigma   weight residual
    1.422  1.488 -0.066 3.00e-02 1.11e+03 4.87e+00
  bond pdb=" C3'  DG I  -8 "
       pdb=" O3'  DG I  -8 "
    ideal  model  delta    sigma   weight residual
    1.422  1.484 -0.062 3.00e-02 1.11e+03 4.29e+00
  ... (remaining 16061 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.55: 22354
        2.55 -     5.09: 558
        5.09 -     7.64: 72
        7.64 -    10.18: 11
       10.18 -    12.73: 1
  Bond angle restraints: 22996
  Sorted by residual:
  angle pdb=" C   ARG B  19 "
        pdb=" N   LYS B  20 "
        pdb=" CA  LYS B  20 "
      ideal   model   delta    sigma   weight residual
     120.79  129.01   -8.22 1.39e+00 5.18e-01 3.50e+01
  angle pdb=" N   VAL D  95 "
        pdb=" CA  VAL D  95 "
        pdb=" C   VAL D  95 "
      ideal   model   delta    sigma   weight residual
     113.42  107.02    6.40 1.17e+00 7.31e-01 2.99e+01
  angle pdb=" N   VAL H  95 "
        pdb=" CA  VAL H  95 "
        pdb=" C   VAL H  95 "
      ideal   model   delta    sigma   weight residual
     112.96  107.50    5.46 1.00e+00 1.00e+00 2.98e+01
  angle pdb=" CA  ILE C  78 "
        pdb=" C   ILE C  78 "
        pdb=" N   PRO C  79 "
      ideal   model   delta    sigma   weight residual
     117.57  122.21   -4.64 1.01e+00 9.80e-01 2.11e+01
  angle pdb=" C   LEU K 345 "
        pdb=" N   GLN K 346 "
        pdb=" CA  GLN K 346 "
      ideal   model   delta    sigma   weight residual
     120.90  126.75   -5.85 1.41e+00 5.03e-01 1.72e+01
  ... (remaining 22991 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.28: 7439
       35.28 -    70.56: 1390
       70.56 -   105.83: 49
      105.83 -   141.11: 2
      141.11 -   176.39: 8
  Dihedral angle restraints: 8888
    sinusoidal: 5378
      harmonic: 3510
  Sorted by residual:
  dihedral pdb=" CA  LYS H  31 "
           pdb=" C   LYS H  31 "
           pdb=" N   GLU H  32 "
           pdb=" CA  GLU H  32 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  146.87   33.13     0      5.00e+00 4.00e-02 4.39e+01
  dihedral pdb=" CA  HIS K 465 "
           pdb=" C   HIS K 465 "
           pdb=" N   PRO K 466 "
           pdb=" CA  PRO K 466 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.58  -29.42     0      5.00e+00 4.00e-02 3.46e+01
  dihedral pdb=" CA  ALA K 369 "
           pdb=" C   ALA K 369 "
           pdb=" N   PHE K 370 "
           pdb=" CA  PHE K 370 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  150.82   29.18     0      5.00e+00 4.00e-02 3.41e+01
  ... (remaining 8885 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.063: 2012
       0.063 -    0.126: 545
       0.126 -    0.189: 76
       0.189 -    0.253: 6
       0.253 -    0.316: 1
  Chirality restraints: 2640
  Sorted by residual:
  chirality pdb=" CB  ILE K 310 "
            pdb=" CA  ILE K 310 "
            pdb=" CG1 ILE K 310 "
            pdb=" CG2 ILE K 310 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.33    0.32 2.00e-01 2.50e+01 2.49e+00
  chirality pdb=" CG  LEU H  99 "
            pdb=" CB  LEU H  99 "
            pdb=" CD1 LEU H  99 "
            pdb=" CD2 LEU H  99 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.36   -0.23 2.00e-01 2.50e+01 1.29e+00
  chirality pdb=" C3'  DA I  -3 "
            pdb=" C4'  DA I  -3 "
            pdb=" O3'  DA I  -3 "
            pdb=" C2'  DA I  -3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.66   -2.43   -0.23 2.00e-01 2.50e+01 1.28e+00
  ... (remaining 2637 not shown)

  Planarity restraints: 1909
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PRO K 476 "   -0.057 5.00e-02 4.00e+02   8.49e-02 1.15e+01
        pdb=" N   PRO K 477 "    0.147 5.00e-02 4.00e+02
        pdb=" CA  PRO K 477 "   -0.042 5.00e-02 4.00e+02
        pdb=" CD  PRO K 477 "   -0.048 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU K 360 "    0.050 5.00e-02 4.00e+02   7.53e-02 9.08e+00
        pdb=" N   PRO K 361 "   -0.130 5.00e-02 4.00e+02
        pdb=" CA  PRO K 361 "    0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO K 361 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG K 393 "   -0.044 5.00e-02 4.00e+02   6.68e-02 7.14e+00
        pdb=" N   PRO K 394 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO K 394 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO K 394 "   -0.038 5.00e-02 4.00e+02
  ... (remaining 1906 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.63: 268
        2.63 -     3.20: 12437
        3.20 -     3.77: 25605
        3.77 -     4.33: 33907
        4.33 -     4.90: 49504
  Nonbonded interactions: 121721
  Sorted by model distance:
  nonbonded pdb=" OP1  DA J  23 "
            pdb=" ND2 ASN K 588 "
     model   vdw
     2.066 3.120
  nonbonded pdb=" OD2 ASP D  65 "
            pdb=" OH  TYR F  98 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" O   TYR C  38 "
            pdb=" OG  SER D  75 "
     model   vdw
     2.288 3.040
  nonbonded pdb=" OD1 ASP K 536 "
            pdb=" OG1 THR K 539 "
     model   vdw
     2.289 3.040
  nonbonded pdb=" N2   DG I -21 "
            pdb=" O2   DC J  22 "
     model   vdw
     2.295 3.120
  ... (remaining 121716 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'E'
}
ncs_group {
  reference = (chain 'B' and resid 24 through 102)
  selection = chain 'F'
}
ncs_group {
  reference = chain 'C'
  selection = (chain 'G' and resid 14 through 117)
}
ncs_group {
  reference = chain 'D'
  selection = (chain 'H' and resid 30 through 121)
}

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:             1.570
  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:             0.020
  Extract box with map and model:          0.600
  Check model and map are aligned:         0.100
  Set scattering table:                    0.120
  Process input model:                     39.860
  Find NCS groups from input model:        0.310
  Set up NCS constraints:                  0.070
  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:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   45.660
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7373
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.009   0.085  16066  Z= 0.535
  Angle     :  1.013  12.731  22996  Z= 0.570
  Chirality :  0.056   0.316   2640
  Planarity :  0.008   0.085   1909
  Dihedral  : 26.976 176.386   6620
  Min Nonbonded Distance : 2.066

Molprobity Statistics.
  All-atom Clashscore : 6.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.76 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  3.52 %
    Favored  : 96.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.09 %

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: -6.10 (0.16), residues: 1188
  helix: -4.62 (0.09), residues: 644
  sheet: -2.34 (0.67), residues: 48
  loop : -3.19 (0.23), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.004   TRP K 427 
 HIS   0.011   0.003   HIS K 389 
 PHE   0.035   0.005   PHE K 613 
 TYR   0.040   0.004   TYR K 583 
 ARG   0.017   0.002   ARG B  40 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  278 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 277
  time to evaluate  : 1.248 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B   47 SER cc_start: 0.8384 (t) cc_final: 0.8070 (t)
REVERT: E   87 SER cc_start: 0.9233 (p) cc_final: 0.8877 (t)
REVERT: H   54 LYS cc_start: 0.9011 (tttp) cc_final: 0.8449 (tptt)
REVERT: K  221 ILE cc_start: 0.6890 (mt) cc_final: 0.6682 (mt)
REVERT: K  294 MET cc_start: 0.8923 (mmp) cc_final: 0.8238 (mmt)
REVERT: K  631 LEU cc_start: 0.7781 (mt) cc_final: 0.7399 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 277
  average time/residue: 0.3830
  time to fit residues: 141.5055
Evaluate side-chains
  158 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 121 optimal weight:    5.9990
   chunk 109 optimal weight:    0.7980
   chunk 60 optimal weight:    1.9990
   chunk 37 optimal weight:    3.9990
   chunk 73 optimal weight:    7.9990
   chunk 58 optimal weight:    2.9990
   chunk 112 optimal weight:    4.9990
   chunk 43 optimal weight:    3.9990
   chunk 68 optimal weight:    2.9990
   chunk 84 optimal weight:   10.0000
   chunk 130 optimal weight:    5.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  37 ASN
D  64 ASN
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  68 GLN
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G  72 ASN
** G  83 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  64 ASN
K 219 GLN
** K 237 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 389 HIS
K 513 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7352
moved from start:          0.2774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.051  16066  Z= 0.275
  Angle     :  0.710   6.037  22996  Z= 0.411
  Chirality :  0.043   0.218   2640
  Planarity :  0.006   0.063   1909
  Dihedral  : 31.517 177.355   4513
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  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: -4.90 (0.20), residues: 1188
  helix: -3.63 (0.14), residues: 655
  sheet: -1.92 (0.78), residues: 46
  loop : -2.60 (0.27), residues: 487

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP K 256 
 HIS   0.005   0.001   HIS F  75 
 PHE   0.016   0.002   PHE K 332 
 TYR   0.020   0.002   TYR D  80 
 ARG   0.005   0.001   ARG E  72 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 230
  time to evaluate  : 1.213 
Fit side-chains
REVERT: C   37 ASN cc_start: 0.8523 (m110) cc_final: 0.8123 (m110)
REVERT: C   83 GLN cc_start: 0.7615 (tp-100) cc_final: 0.7340 (tp40)
REVERT: C   88 ASN cc_start: 0.7257 (t0) cc_final: 0.6995 (t0)
REVERT: D   41 VAL cc_start: 0.8939 (p) cc_final: 0.8682 (t)
REVERT: D  119 THR cc_start: 0.6625 (p) cc_final: 0.6264 (t)
REVERT: H   68 GLU cc_start: 0.8118 (tm-30) cc_final: 0.7889 (tp30)
REVERT: K  256 TRP cc_start: 0.6316 (m100) cc_final: 0.6061 (m100)
REVERT: K  294 MET cc_start: 0.8809 (mmp) cc_final: 0.8483 (mmt)
REVERT: K  355 LEU cc_start: 0.8423 (mm) cc_final: 0.8217 (mm)
REVERT: K  396 LEU cc_start: 0.6310 (tp) cc_final: 0.5462 (pp)
REVERT: K  506 SER cc_start: 0.8571 (m) cc_final: 0.8187 (p)
REVERT: K  631 LEU cc_start: 0.8008 (mt) cc_final: 0.7621 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 230
  average time/residue: 0.3094
  time to fit residues: 102.4030
Evaluate side-chains
  154 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.901 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 72 optimal weight:   10.0000
   chunk 40 optimal weight:    7.9990
   chunk 108 optimal weight:    0.0970
   chunk 89 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 131 optimal weight:    0.9990
   chunk 141 optimal weight:    9.9990
   chunk 116 optimal weight:    2.9990
   chunk 129 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 105 optimal weight:    1.9990
   overall best weight:    1.8186

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

Flipped N/Q/H residues before XYZ refinement:
A  68 GLN
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 237 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7317
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059  16066  Z= 0.221
  Angle     :  0.627   7.232  22996  Z= 0.363
  Chirality :  0.040   0.197   2640
  Planarity :  0.005   0.046   1909
  Dihedral  : 30.980 179.735   4513
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 9.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.82 %
    Favored  : 93.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  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: -4.18 (0.21), residues: 1188
  helix: -3.02 (0.16), residues: 649
  sheet: -1.73 (0.71), residues: 56
  loop : -2.29 (0.27), residues: 483

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP K 587 
 HIS   0.003   0.001   HIS K 600 
 PHE   0.013   0.002   PHE G  24 
 TYR   0.041   0.002   TYR D  80 
 ARG   0.008   0.001   ARG E  52 

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

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

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2376 Ramachandran restraints generated.
    1188 Oldfield, 0 Emsley, 1188 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
REVERT: C   37 ASN cc_start: 0.8461 (m110) cc_final: 0.8036 (m110)
REVERT: C   88 ASN cc_start: 0.7171 (t0) cc_final: 0.6909 (t0)
REVERT: G   63 GLU cc_start: 0.7218 (tp30) cc_final: 0.6921 (tt0)
REVERT: H   68 GLU cc_start: 0.8161 (tm-30) cc_final: 0.7737 (tp30)
REVERT: K  294 MET cc_start: 0.8776 (mmp) cc_final: 0.8413 (mmt)
REVERT: K  459 LEU cc_start: 0.7699 (mt) cc_final: 0.7159 (mp)
REVERT: K  460 ARG cc_start: 0.7987 (ttm-80) cc_final: 0.7467 (ttm-80)
REVERT: K  506 SER cc_start: 0.8529 (m) cc_final: 0.8107 (p)
REVERT: K  631 LEU cc_start: 0.8143 (mt) cc_final: 0.7697 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 203
  average time/residue: 0.3126
  time to fit residues: 92.5209
Evaluate side-chains
  154 residues out of total 1034 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 154
  time to evaluate  : 1.311 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 144
   random chunks:
   chunk 129 optimal weight:    2.9990
   chunk 98 optimal weight:    9.9990
   chunk 67 optimal weight:    6.9990
   chunk 14 optimal weight:    2.9990
   chunk 62 optimal weight:   10.0000
   chunk 87 optimal weight:    8.9990
   chunk 131 optimal weight:    2.9990
   chunk 139 optimal weight:    5.9990
   chunk 68 optimal weight:    3.9990
   chunk 124 optimal weight:    8.9990
   chunk 37 optimal weight:    0.0870
   overall best weight:    2.6166

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

Flipped N/Q/H residues before XYZ refinement:
D  81 ASN
** F  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.3778
Sorry: Reduce crashed with command 'molprobity.reduce  -quiet -trim -'.
Dumping stdin to file 'reduce_fail.pdb'.
Return code: -15
Dumping stderr: