Starting phenix.real_space_refine
on Sun Jun 15 03:52:15 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7xyf_33520/06_2025/7xyf_33520.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7xyf_33520/06_2025/7xyf_33520.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.3
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7xyf_33520/06_2025/7xyf_33520.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7xyf_33520/06_2025/7xyf_33520.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7xyf_33520/06_2025/7xyf_33520.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7xyf_33520/06_2025/7xyf_33520.cif"
  }
  resolution = 4.3
  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=   0.001 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Se     24      7.20       5
     P     292      5.49       5
     S      25      5.16       5
     C   10029      2.51       5
     N    3164      2.21       5
     O    3787      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 17321
  Number of models: 1
  Model: ""
    Number of chains: 11
    Chain: "A"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "B"
      Number of atoms: 646
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 81, 646
          Classifications: {'peptide': 81}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 79}
    Chain: "F"
      Number of atoms: 694
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 86, 694
          Classifications: {'peptide': 86}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 84}
    Chain: "C"
      Number of atoms: 812
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 812
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 5, 'TRANS': 100}
    Chain: "G"
      Number of atoms: 803
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 803
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "D"
      Number of atoms: 753
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 753
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "H"
      Number of atoms: 732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 732
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "J"
      Number of atoms: 3009
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 3009
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "I"
      Number of atoms: 2977
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 146, 2977
          Classifications: {'DNA': 146}
          Link IDs: {'rna3p': 145}
    Chain: "K"
      Number of atoms: 5281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 656, 5281
          Classifications: {'peptide': 656}
          Link IDs: {'PCIS': 2, 'PTRANS': 22, 'TRANS': 631}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Planarities with less than four sites: {'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 2
  Time building chain proxies: 10.02, per 1000 atoms: 0.58
  Number of scatterers: 17321
  At special positions: 0
  Unit cell: (134.16, 140.4, 135.2, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Se     24     33.99
     S      25     16.00
     P     292     15.00
     O    3787      8.00
     N    3164      7.00
     C   10029      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: 4.05
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2688

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 9 sheets defined
      61.9% alpha, 3.3% beta
      132 base pairs and 248 stacking pairs defined.
    Time for finding SS restraints: 8.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 44 through 57
      removed outlier: 3.590A  pdb=" N   ARG A  52 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   LYS A  56 " --> pdb=" O   ARG A  52 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.632A  pdb=" N   GLU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 114
      removed outlier: 4.091A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 3.899A  pdb=" N   LEU A 109 " --> pdb=" O   GLU A 105 " (cutoff:3.500A)
      removed outlier: 3.739A  pdb=" N   CYS A 110 " --> pdb=" O   ASP A 106 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 132
      removed outlier: 3.515A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLN A 125 " --> pdb=" O   PRO A 121 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 3.590A  pdb=" N   ARG E  52 " --> pdb=" O   LEU E  48 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 63 through 79
      removed outlier: 3.631A  pdb=" N   GLU E  73 " --> pdb=" O   ARG E  69 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 87 through 114
      removed outlier: 4.092A  pdb=" N   ASP E 106 " --> pdb=" O   GLY E 102 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   LEU E 109 " --> pdb=" O   GLU E 105 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   CYS E 110 " --> pdb=" O   ASP E 106 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 120 through 132
      removed outlier: 3.515A  pdb=" N   ILE E 124 " --> pdb=" O   MET E 120 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   ARG E 129 " --> pdb=" O   GLN E 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 42
      removed outlier: 3.624A  pdb=" N   ARG B  39 " --> pdb=" O   ARG B  35 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   ARG B  40 " --> pdb=" O   ARG B  36 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 50 through 76
      removed outlier: 3.980A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 4.395A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   ASN B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 4.230A  pdb=" N   ARG B  67 " --> pdb=" O   GLU B  63 " (cutoff:3.500A)
      removed outlier: 3.614A  pdb=" N   THR B  71 " --> pdb=" O   ARG B  67 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   TYR B  72 " --> pdb=" O   ASP B  68 " (cutoff:3.500A)
      removed outlier: 3.867A  pdb=" N   THR B  73 " --> pdb=" O   ALA B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 93
      removed outlier: 3.806A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   VAL B  87 " --> pdb=" O   ALA B  83 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   ARG B  92 " --> pdb=" O   TYR B  88 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   GLN B  93 " --> pdb=" O   ALA B  89 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 23 through 29
      removed outlier: 4.286A  pdb=" N   ILE F  26 " --> pdb=" O   ARG F  23 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
      removed outlier: 3.663A  pdb=" N   ARG F  39 " --> pdb=" O   ARG F  35 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   ARG F  40 " --> pdb=" O   ARG F  36 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.176A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   ASN F  64 " --> pdb=" O   VAL F  60 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   VAL F  65 " --> pdb=" O   PHE F  61 " (cutoff:3.500A)
      removed outlier: 4.205A  pdb=" N   ARG F  67 " --> pdb=" O   GLU F  63 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   THR F  71 " --> pdb=" O   ARG F  67 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 3.745A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   GLN F  93 " --> pdb=" O   ALA F  89 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 16 through 22
    Processing helix  chain 'C' and resid 26 through 37
      removed outlier: 3.575A  pdb=" N   ILE C  30 " --> pdb=" O   PRO C  26 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG C  35 " --> pdb=" O   HIS C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 73
      removed outlier: 4.101A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA C  60 " --> pdb=" O   GLU C  56 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU C  65 " --> pdb=" O   GLU C  61 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ASP C  72 " --> pdb=" O   ASN C  68 " (cutoff:3.500A)
      removed outlier: 3.844A  pdb=" N   ASN C  73 " --> pdb=" O   ALA C  69 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 79 through 90
      removed outlier: 3.505A  pdb=" N   ASN C  89 " --> pdb=" O   LEU C  85 " (cutoff:3.500A)
      removed outlier: 3.612A  pdb=" N   ASP C  90 " --> pdb=" O   ALA C  86 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 90 through 97
      removed outlier: 3.559A  pdb=" N   LYS C  95 " --> pdb=" O   GLU C  91 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   LEU C  96 " --> pdb=" O   GLU C  92 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'G' and resid 16 through 22
    Processing helix  chain 'G' and resid 26 through 37
      removed outlier: 3.627A  pdb=" N   ARG G  35 " --> pdb=" O   HIS G  31 " (cutoff:3.500A)
      removed outlier: 3.616A  pdb=" N   LYS G  36 " --> pdb=" O   ARG G  32 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 46 through 73
      removed outlier: 4.155A  pdb=" N   TYR G  50 " --> pdb=" O   GLY G  46 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU G  63 " --> pdb=" O   ALA G  59 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 79 through 90
      removed outlier: 3.717A  pdb=" N   ASN G  89 " --> pdb=" O   LEU G  85 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ASP G  90 " --> pdb=" O   ALA G  86 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 97
      removed outlier: 3.682A  pdb=" N   LEU G  96 " --> pdb=" O   GLU G  92 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 112 through 116
      removed outlier: 3.954A  pdb=" N   LEU G 116 " --> pdb=" O   ALA G 113 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 34 through 46
    Processing helix  chain 'D' and resid 52 through 81
      removed outlier: 3.536A  pdb=" N   ILE D  58 " --> pdb=" O   LYS D  54 " (cutoff:3.500A)
      removed outlier: 3.648A  pdb=" N   MET D  59 " --> pdb=" O   ALA D  55 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   ASN D  64 " --> pdb=" O   ASN D  60 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   ARG D  76 " --> pdb=" O   ALA D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 99
      removed outlier: 3.869A  pdb=" N   ILE D  91 " --> pdb=" O   THR D  87 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ARG D  96 " --> pdb=" O   GLN D  92 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU D  99 " --> pdb=" O   VAL D  95 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 121
      removed outlier: 3.891A  pdb=" N   SER D 109 " --> pdb=" O   LYS D 105 " (cutoff:3.500A)
      removed outlier: 4.028A  pdb=" N   ALA D 114 " --> pdb=" O   GLU D 110 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   THR D 116 " --> pdb=" O   THR D 112 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 34 through 44
    Processing helix  chain 'H' and resid 52 through 82
      removed outlier: 3.502A  pdb=" N   ASN H  64 " --> pdb=" O   ASN H  60 " (cutoff:3.500A)
      removed outlier: 3.907A  pdb=" N   GLU H  68 " --> pdb=" O   ASN H  64 " (cutoff:3.500A)
      removed outlier: 3.754A  pdb=" N   GLU H  73 " --> pdb=" O   ARG H  69 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 87 through 99
      removed outlier: 3.906A  pdb=" N   ILE H  91 " --> pdb=" O   THR H  87 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   LEU H  99 " --> pdb=" O   VAL H  95 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 100 through 120
      removed outlier: 3.805A  pdb=" N   THR H 112 " --> pdb=" O   VAL H 108 " (cutoff:3.500A)
      removed outlier: 3.603A  pdb=" N   LYS H 113 " --> pdb=" O   SER H 109 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   LYS H 117 " --> pdb=" O   LYS H 113 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   SER H 120 " --> pdb=" O   THR H 116 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 233 through 248
      removed outlier: 3.626A  pdb=" N   GLU K 239 " --> pdb=" O   ALA K 235 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   LEU K 242 " --> pdb=" O   LYS K 238 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ASN K 246 " --> pdb=" O   LEU K 242 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   ARG K 247 " --> pdb=" O   LYS K 243 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 249 through 258
      removed outlier: 3.706A  pdb=" N   MSE K 256 " --> pdb=" O   ASP K 252 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 260 through 271
      removed outlier: 3.736A  pdb=" N   LYS K 270 " --> pdb=" O   PHE K 266 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   ARG K 271 " --> pdb=" O   MSE K 267 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 275 through 281
    Processing helix  chain 'K' and resid 301 through 340
      removed outlier: 3.743A  pdb=" N   GLU K 312 " --> pdb=" O   GLY K 308 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   PHE K 318 " --> pdb=" O   MSE K 314 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLN K 326 " --> pdb=" O   ALA K 322 " (cutoff:3.500A)
      removed outlier: 3.767A  pdb=" N   LEU K 330 " --> pdb=" O   GLN K 326 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY K 332 " --> pdb=" O   GLU K 328 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   LYS K 333 " --> pdb=" O   GLN K 329 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 348 through 352
    Processing helix  chain 'K' and resid 359 through 366
      removed outlier: 3.514A  pdb=" N   PHE K 365 " --> pdb=" O   GLN K 361 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 388 through 404
      removed outlier: 3.673A  pdb=" N   ILE K 395 " --> pdb=" O   GLN K 391 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   ASN K 396 " --> pdb=" O   ILE K 392 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU K 404 " --> pdb=" O   LEU K 400 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 417 through 432
    Processing helix  chain 'K' and resid 443 through 446
    Processing helix  chain 'K' and resid 447 through 458
      removed outlier: 3.822A  pdb=" N   LEU K 451 " --> pdb=" O   MSE K 447 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ALA K 455 " --> pdb=" O   LEU K 451 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 469 through 482
    Processing helix  chain 'K' and resid 493 through 500
      removed outlier: 3.515A  pdb=" N   ALA K 497 " --> pdb=" O   THR K 493 " (cutoff:3.500A)
      removed outlier: 4.273A  pdb=" N   ALA K 498 " --> pdb=" O   TYR K 494 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   THR K 499 " --> pdb=" O   ARG K 495 " (cutoff:3.500A)
      removed outlier: 4.518A  pdb=" N   SER K 500 " --> pdb=" O   LEU K 496 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'K' and resid 493 through 500'
    Processing helix  chain 'K' and resid 500 through 509
    Processing helix  chain 'K' and resid 521 through 525
    Processing helix  chain 'K' and resid 528 through 537
      removed outlier: 3.768A  pdb=" N   ARG K 532 " --> pdb=" O   SER K 528 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ILE K 537 " --> pdb=" O   HIS K 533 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 553 through 565
      removed outlier: 3.836A  pdb=" N   SER K 559 " --> pdb=" O   LYS K 555 " (cutoff:3.500A)
      removed outlier: 4.030A  pdb=" N   PHE K 563 " --> pdb=" O   SER K 559 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 576 through 581
    Processing helix  chain 'K' and resid 593 through 607
      removed outlier: 3.866A  pdb=" N   MSE K 606 " --> pdb=" O   ARG K 602 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 636 through 644
      removed outlier: 3.961A  pdb=" N   ARG K 642 " --> pdb=" O   GLU K 638 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 645 through 648
    Processing helix  chain 'K' and resid 670 through 675
    Processing helix  chain 'K' and resid 678 through 689
      removed outlier: 4.317A  pdb=" N   LEU K 682 " --> pdb=" O   ALA K 678 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 691 through 695
      removed outlier: 3.548A  pdb=" N   PHE K 695 " --> pdb=" O   PRO K 692 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 702 through 710
      removed outlier: 3.646A  pdb=" N   GLN K 706 " --> pdb=" O   ASP K 702 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 724 through 729
    Processing helix  chain 'K' and resid 733 through 740
    Processing helix  chain 'K' and resid 760 through 765
      removed outlier: 3.571A  pdb=" N   LYS K 765 " --> pdb=" O   THR K 761 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 765 through 771
    Processing helix  chain 'K' and resid 786 through 794
    Processing helix  chain 'K' and resid 864 through 868
      removed outlier: 4.000A  pdb=" N   ASP K 868 " --> pdb=" O   GLN K 865 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 889 through 894
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 6.707A  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: 3.623A  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 'E' and resid 83 through 84
      removed outlier: 6.955A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119
      removed outlier: 3.759A  pdb=" N   ILE E 119 " --> pdb=" O   ARG F  45 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'F' and resid 96 through 97
      removed outlier: 6.741A  pdb=" N   THR F  96 " --> pdb=" O   THR C 101 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA7, first strand: chain 'G' and resid 77 through 78
    Processing sheet with id=AA8, first strand: chain 'K' and resid 407 through 410
      removed outlier: 6.719A  pdb=" N   ASN K 513 " --> pdb=" O   ALA K 539 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   GLU K 464 " --> pdb=" O   LEU K 491 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'K' and resid 627 through 628
      removed outlier: 6.595A  pdb=" N   THR K 627 " --> pdb=" O   VAL K 881 " (cutoff:3.500A)
      removed outlier: 8.410A  pdb=" N   LYS K 883 " --> pdb=" O   THR K 627 " (cutoff:3.500A)
      removed outlier: 6.136A  pdb=" N   VAL K 851 " --> pdb=" O   TYR K 882 " (cutoff:3.500A)
      removed outlier: 6.164A  pdb=" N   VAL K 781 " --> pdb=" O   ILE K 852 " (cutoff:3.500A)
      removed outlier: 4.123A  pdb=" N   PHE K 832 " --> pdb=" O   VAL K 780 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU K 782 " --> pdb=" O   PHE K 832 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9

    519 hydrogen bonds defined for protein.
    1512 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      318 hydrogen bonds
      580 hydrogen bond angles
      0 basepair planarities
      132 basepair parallelities
      248 stacking parallelities
  Total time for adding SS restraints: 9.40

  Time building geometry restraints manager: 4.88 seconds

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

  Histogram of bond lengths:
        1.21 -     1.36: 5496
        1.36 -     1.52: 8388
        1.52 -     1.67: 4257
        1.67 -     1.83: 37
        1.83 -     1.98: 48
  Bond restraints: 18226
  Sorted by residual:
  bond pdb=" N   LYS K 583 "
       pdb=" CA  LYS K 583 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.032 1.22e-02 6.72e+03 6.79e+00
  bond pdb=" N   LYS K 574 "
       pdb=" CA  LYS K 574 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.034 1.31e-02 5.83e+03 6.57e+00
  bond pdb=" N   LYS K 753 "
       pdb=" CA  LYS K 753 "
    ideal  model  delta    sigma   weight residual
    1.457  1.489 -0.032 1.29e-02 6.01e+03 6.03e+00
  bond pdb=" N   GLU K 755 "
       pdb=" CA  GLU K 755 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.033 1.41e-02 5.03e+03 5.37e+00
  bond pdb=" N   ASP K 754 "
       pdb=" CA  ASP K 754 "
    ideal  model  delta    sigma   weight residual
    1.458  1.486 -0.028 1.35e-02 5.49e+03 4.30e+00
  ... (remaining 18221 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.30: 25040
        2.30 -     4.61: 725
        4.61 -     6.91: 64
        6.91 -     9.21: 9
        9.21 -    11.52: 5
  Bond angle restraints: 25843
  Sorted by residual:
  angle pdb=" N   PHE K 861 "
        pdb=" CA  PHE K 861 "
        pdb=" C   PHE K 861 "
      ideal   model   delta    sigma   weight residual
     114.04  108.01    6.03 1.24e+00 6.50e-01 2.36e+01
  angle pdb=" N   ASP K 754 "
        pdb=" CA  ASP K 754 "
        pdb=" C   ASP K 754 "
      ideal   model   delta    sigma   weight residual
     113.23  107.64    5.59 1.22e+00 6.72e-01 2.10e+01
  angle pdb=" N   LYS K 887 "
        pdb=" CA  LYS K 887 "
        pdb=" C   LYS K 887 "
      ideal   model   delta    sigma   weight residual
     110.97  115.90   -4.93 1.09e+00 8.42e-01 2.05e+01
  angle pdb=" C   VAL K 886 "
        pdb=" N   LYS K 887 "
        pdb=" CA  LYS K 887 "
      ideal   model   delta    sigma   weight residual
     120.65  126.52   -5.87 1.32e+00 5.74e-01 1.98e+01
  angle pdb=" N   ASP K 826 "
        pdb=" CA  ASP K 826 "
        pdb=" C   ASP K 826 "
      ideal   model   delta    sigma   weight residual
     110.97  115.79   -4.82 1.09e+00 8.42e-01 1.96e+01
  ... (remaining 25838 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    30.06: 8252
       30.06 -    60.12: 1934
       60.12 -    90.18: 109
       90.18 -   120.24: 0
      120.24 -   150.31: 3
  Dihedral angle restraints: 10298
    sinusoidal: 6153
      harmonic: 4145
  Sorted by residual:
  dihedral pdb=" CA  PRO H 100 "
           pdb=" C   PRO H 100 "
           pdb=" N   GLY H 101 "
           pdb=" CA  GLY H 101 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.00  -26.00     0      5.00e+00 4.00e-02 2.70e+01
  dihedral pdb=" CA  ALA K 710 "
           pdb=" C   ALA K 710 "
           pdb=" N   ILE K 711 "
           pdb=" CA  ILE K 711 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.24   23.76     0      5.00e+00 4.00e-02 2.26e+01
  dihedral pdb=" CA  LEU K 737 "
           pdb=" C   LEU K 737 "
           pdb=" N   HIS K 738 "
           pdb=" CA  HIS K 738 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.13   22.87     0      5.00e+00 4.00e-02 2.09e+01
  ... (remaining 10295 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 2154
       0.053 -    0.105: 655
       0.105 -    0.158: 97
       0.158 -    0.210: 17
       0.210 -    0.263: 3
  Chirality restraints: 2926
  Sorted by residual:
  chirality pdb=" CB  ILE K 747 "
            pdb=" CA  ILE K 747 "
            pdb=" CG1 ILE K 747 "
            pdb=" CG2 ILE K 747 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.38    0.26 2.00e-01 2.50e+01 1.73e+00
  chirality pdb=" CB  THR K 667 "
            pdb=" CA  THR K 667 "
            pdb=" OG1 THR K 667 "
            pdb=" CG2 THR K 667 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.32    0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CB  ILE K 309 "
            pdb=" CA  ILE K 309 "
            pdb=" CG1 ILE K 309 "
            pdb=" CG2 ILE K 309 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.42    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 2923 not shown)

  Planarity restraints: 2271
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE G  79 "   -0.063 5.00e-02 4.00e+02   9.53e-02 1.45e+01
        pdb=" N   PRO G  80 "    0.165 5.00e-02 4.00e+02
        pdb=" CA  PRO G  80 "   -0.050 5.00e-02 4.00e+02
        pdb=" CD  PRO G  80 "   -0.052 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU K 714 "    0.049 5.00e-02 4.00e+02   7.39e-02 8.74e+00
        pdb=" N   PRO K 715 "   -0.128 5.00e-02 4.00e+02
        pdb=" CA  PRO K 715 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO K 715 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS F  31 "    0.045 5.00e-02 4.00e+02   6.69e-02 7.16e+00
        pdb=" N   PRO F  32 "   -0.116 5.00e-02 4.00e+02
        pdb=" CA  PRO F  32 "    0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO F  32 "    0.038 5.00e-02 4.00e+02
  ... (remaining 2268 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 3010
        2.75 -     3.29: 16314
        3.29 -     3.83: 35172
        3.83 -     4.36: 40263
        4.36 -     4.90: 57843
  Nonbonded interactions: 152602
  Sorted by model distance:
  nonbonded pdb=" O   LEU E  61 "
            pdb=" NH2 ARG F  36 "
     model   vdw
     2.217 3.120
  nonbonded pdb=" OG1 THR H  87 "
            pdb=" OE1 GLU H  90 "
     model   vdw
     2.258 3.040
  nonbonded pdb=" OH  TYR K 466 "
            pdb=" OD1 ASP K 503 "
     model   vdw
     2.262 3.040
  nonbonded pdb=" O2   DC J  46 "
            pdb=" N1   DG I 101 "
     model   vdw
     2.264 2.496
  nonbonded pdb=" OG1 THR A  58 "
            pdb=" O   GLN G 104 "
     model   vdw
     2.274 3.040
  ... (remaining 152597 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'
  selection = (chain 'F' and resid 22 through 102)
}
ncs_group {
  reference = (chain 'C' and resid 14 through 118)
  selection = chain 'G'
}
ncs_group {
  reference = (chain 'D' and resid 29 through 121)
  selection = chain 'H'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.46 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:             0.720
  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:          0.700
  Check model and map are aligned:         0.130
  Set scattering table:                    0.170
  Process input model:                     48.160
  Find NCS groups from input model:        0.360
  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:2.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   53.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7948
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      :  0.008   0.070  18226  Z= 0.387
  Angle     :  0.930  11.516  25843  Z= 0.543
  Chirality :  0.050   0.263   2926
  Planarity :  0.007   0.095   2271
  Dihedral  : 27.107 150.305   7610
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 13.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.88 %
    Favored  : 95.12 %
  Rotamer:
    Outliers :  2.14 %
    Allowed  : 10.95 %
    Favored  : 86.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -4.98 (0.16), residues: 1394
  helix: -3.82 (0.10), residues: 783
  sheet: -1.65 (0.83), residues: 42
  loop : -2.38 (0.21), residues: 569

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.003   TRP K 757 
 HIS   0.015   0.002   HIS F  75 
 PHE   0.028   0.003   PHE K 832 
 TYR   0.014   0.002   TYR K 731 
 ARG   0.012   0.001   ARG K 495 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31582 (  837)
  hydrogen bonds       : angle      10.02553 ( 2092)
  covalent geometry    : bond        0.00832 (18226)
  covalent geometry    : angle       0.93023 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  368 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 342
  time to evaluate  : 1.507 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.8615 (ttm110) cc_final: 0.8190 (mmm-85)
REVERT: A   53 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8331 (tpt-90)
REVERT: A   61 LEU cc_start: 0.8936 (OUTLIER) cc_final: 0.8685 (tp)
REVERT: A   87 SER cc_start: 0.9039 (OUTLIER) cc_final: 0.8665 (p)
REVERT: A  129 ARG cc_start: 0.8533 (ttt90) cc_final: 0.8279 (tpp80)
REVERT: E   48 LEU cc_start: 0.9139 (tp) cc_final: 0.8635 (tp)
REVERT: E   53 ARG cc_start: 0.8514 (ttt180) cc_final: 0.8234 (ttm170)
REVERT: E   93 GLN cc_start: 0.8800 (tt0) cc_final: 0.8562 (tt0)
REVERT: E  126 LEU cc_start: 0.9480 (tp) cc_final: 0.9073 (tt)
REVERT: B   53 GLU cc_start: 0.8302 (tp30) cc_final: 0.7979 (tp30)
REVERT: B   79 LYS cc_start: 0.8629 (mttp) cc_final: 0.8200 (mmtm)
REVERT: F   62 LEU cc_start: 0.9277 (mp) cc_final: 0.9010 (mp)
REVERT: F   88 TYR cc_start: 0.8465 (m-10) cc_final: 0.7982 (m-80)
REVERT: C   75 LYS cc_start: 0.8511 (mmtm) cc_final: 0.8271 (mmtm)
REVERT: G   36 LYS cc_start: 0.9215 (mttt) cc_final: 0.8929 (mtpp)
REVERT: G   38 ASN cc_start: 0.9019 (m110) cc_final: 0.8801 (m110)
REVERT: G   79 ILE cc_start: 0.9490 (tp) cc_final: 0.9131 (tp)
REVERT: G   91 GLU cc_start: 0.7534 (tm-30) cc_final: 0.7292 (tm-30)
REVERT: G   92 GLU cc_start: 0.7617 (tt0) cc_final: 0.7260 (tt0)
REVERT: D   43 LYS cc_start: 0.9334 (mmtt) cc_final: 0.8584 (mtpt)
REVERT: D   92 GLN cc_start: 0.8734 (tt0) cc_final: 0.8226 (tm-30)
REVERT: D   96 ARG cc_start: 0.8423 (mtt180) cc_final: 0.8185 (ttm110)
REVERT: H   56 MET cc_start: 0.8449 (tpp) cc_final: 0.8173 (tpp)
REVERT: H  102 GLU cc_start: 0.8279 (tp30) cc_final: 0.7872 (tp30)
REVERT: K  256 MSE cc_start: 0.4645 (mtt) cc_final: 0.3918 (mtt)
REVERT: K  430 MSE cc_start: 0.5807 (ttm) cc_final: 0.5513 (mtp)
REVERT: K  535 MSE cc_start: 0.6099 (mmp) cc_final: 0.5601 (mmm)
REVERT: K  544 LEU cc_start: 0.6494 (tp) cc_final: 0.6240 (tp)
REVERT: K  712 MSE cc_start: -0.1428 (OUTLIER) cc_final: -0.1691 (mmt)
REVERT: K  724 TYR cc_start: 0.7215 (m-80) cc_final: 0.6979 (m-10)
REVERT: K  731 TYR cc_start: 0.5015 (m-80) cc_final: 0.4743 (m-80)
REVERT: K  732 MSE cc_start: -0.0859 (OUTLIER) cc_final: -0.2049 (mmt)
REVERT: K  786 PHE cc_start: 0.6131 (t80) cc_final: 0.5885 (t80)
REVERT: K  791 ASP cc_start: 0.6706 (m-30) cc_final: 0.6368 (t70)
REVERT: K  797 MSE cc_start: 0.2954 (mmm) cc_final: 0.2420 (mmt)
REVERT: K  806 ARG cc_start: 0.5690 (ttt180) cc_final: 0.4664 (ttp-110)
REVERT: K  851 VAL cc_start: -0.1058 (OUTLIER) cc_final: -0.1947 (p)
REVERT: K  872 ARG cc_start: 0.0772 (mmt180) cc_final: -0.0341 (mpt90)
  outliers start: 26
  outliers final: 7
  residues processed: 352
  average time/residue: 0.4007
  time to fit residues: 191.1155
Evaluate side-chains
  243 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 231
  time to evaluate  : 1.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:   20.0000
   chunk 125 optimal weight:    9.9990
   chunk 69 optimal weight:    0.8980
   chunk 42 optimal weight:    0.9990
   chunk 84 optimal weight:    6.9990
   chunk 66 optimal weight:    0.9990
   chunk 129 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 78 optimal weight:    5.9990
   chunk 96 optimal weight:    4.9990
   chunk 149 optimal weight:    5.9990
   overall best weight:    1.5788

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
E 125 GLN
** F  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  31 HIS
G  31 HIS
** G  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN
H  79 HIS
K 335 GLN
** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 510 GLN
K 706 GLN
K 772 ASN
K 812 GLN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4017 r_free = 0.4017 target = 0.102269 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.073196 restraints weight = 75527.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.072630 restraints weight = 50856.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.073023 restraints weight = 38755.150|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3377
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.070         |
| occupancies: max = 1.00  min = 0.46   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3377 r_free = 0.3377    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3377
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2778

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  18226  Z= 0.193
  Angle     :  0.688   7.968  25843  Z= 0.396
  Chirality :  0.041   0.164   2926
  Planarity :  0.006   0.072   2271
  Dihedral  : 30.593 139.332   4754
  Min Nonbonded Distance : 2.043

Molprobity Statistics.
  All-atom Clashscore : 14.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.59 %
    Favored  : 96.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.02 %
    Favored  : 94.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -2.90 (0.19), residues: 1394
  helix: -1.76 (0.15), residues: 817
  sheet: -1.63 (0.79), residues: 40
  loop : -1.98 (0.24), residues: 537

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.002   TRP K 397 
 HIS   0.006   0.001   HIS E 113 
 PHE   0.021   0.002   PHE K 832 
 TYR   0.037   0.002   TYR H  37 
 ARG   0.009   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08631 (  837)
  hydrogen bonds       : angle       4.63696 ( 2092)
  covalent geometry    : bond        0.00417 (18226)
  covalent geometry    : angle       0.68778 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  297 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 297
  time to evaluate  : 1.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ARG cc_start: 0.8506 (ttm110) cc_final: 0.8208 (mmm-85)
REVERT: A   53 ARG cc_start: 0.8412 (ttt180) cc_final: 0.8127 (tpt-90)
REVERT: A  120 MET cc_start: 0.8635 (mtp) cc_final: 0.8358 (mtp)
REVERT: A  126 LEU cc_start: 0.9274 (tp) cc_final: 0.9045 (tp)
REVERT: A  129 ARG cc_start: 0.8479 (ttt90) cc_final: 0.8269 (tpp80)
REVERT: E   48 LEU cc_start: 0.9254 (tp) cc_final: 0.8776 (tp)
REVERT: E   53 ARG cc_start: 0.8460 (ttt180) cc_final: 0.8173 (ttm170)
REVERT: E   61 LEU cc_start: 0.9045 (mt) cc_final: 0.8811 (mt)
REVERT: E  110 CYS cc_start: 0.8861 (m) cc_final: 0.8279 (m)
REVERT: E  126 LEU cc_start: 0.9405 (tp) cc_final: 0.9033 (tt)
REVERT: B   54 THR cc_start: 0.8860 (p) cc_final: 0.8614 (m)
REVERT: B   84 MET cc_start: 0.7757 (tpp) cc_final: 0.7443 (tpp)
REVERT: F   53 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7749 (tm-30)
REVERT: F   63 GLU cc_start: 0.8218 (mm-30) cc_final: 0.7817 (mm-30)
REVERT: F   88 TYR cc_start: 0.8329 (m-10) cc_final: 0.7699 (m-80)
REVERT: G   36 LYS cc_start: 0.8987 (mttt) cc_final: 0.8743 (mtpp)
REVERT: G   92 GLU cc_start: 0.7807 (tt0) cc_final: 0.7243 (tt0)
REVERT: G  102 ILE cc_start: 0.9723 (mm) cc_final: 0.9494 (mm)
REVERT: D   36 ILE cc_start: 0.8578 (pt) cc_final: 0.8073 (mp)
REVERT: D   43 LYS cc_start: 0.9311 (mmtt) cc_final: 0.8634 (mtpt)
REVERT: D   83 ARG cc_start: 0.7921 (mtp85) cc_final: 0.7395 (mtp85)
REVERT: D   92 GLN cc_start: 0.8572 (tt0) cc_final: 0.8071 (tm-30)
REVERT: D   93 THR cc_start: 0.9170 (m) cc_final: 0.8944 (p)
REVERT: H   64 ASN cc_start: 0.8878 (m-40) cc_final: 0.8036 (t0)
REVERT: H  102 GLU cc_start: 0.7754 (tp30) cc_final: 0.7177 (tp30)
REVERT: K  245 MSE cc_start: 0.0734 (tpt) cc_final: 0.0229 (tpt)
REVERT: K  311 MSE cc_start: 0.5319 (mtp) cc_final: 0.3095 (tmm)
REVERT: K  535 MSE cc_start: 0.6184 (mmp) cc_final: 0.5650 (mmm)
REVERT: K  582 MSE cc_start: 0.4460 (mtm) cc_final: -0.3914 (ttp)
REVERT: K  602 ARG cc_start: 0.7614 (tpt170) cc_final: 0.7177 (mmt-90)
REVERT: K  717 TYR cc_start: 0.7992 (t80) cc_final: 0.7716 (t80)
REVERT: K  724 TYR cc_start: 0.7199 (m-10) cc_final: 0.6864 (m-10)
  outliers start: 0
  outliers final: 0
  residues processed: 297
  average time/residue: 0.3777
  time to fit residues: 160.2712
Evaluate side-chains
  233 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 233
  time to evaluate  : 1.459 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 95 optimal weight:    8.9990
   chunk 68 optimal weight:    8.9990
   chunk 148 optimal weight:   20.0000
   chunk 107 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 113 optimal weight:    7.9990
   chunk 118 optimal weight:    5.9990
   chunk 42 optimal weight:    0.0980
   chunk 7 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F  27 GLN
F  75 HIS
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
D 106 HIS
H  44 GLN
H  81 ASN
** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4028 r_free = 0.4028 target = 0.102923 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.073975 restraints weight = 75122.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.074214 restraints weight = 48926.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.074165 restraints weight = 34912.285|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3406
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3406 r_free = 0.3406    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3406
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7975
moved from start:          0.3662

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  18226  Z= 0.173
  Angle     :  0.647  10.719  25843  Z= 0.370
  Chirality :  0.038   0.168   2926
  Planarity :  0.005   0.066   2271
  Dihedral  : 30.058 142.097   4754
  Min Nonbonded Distance : 2.029

Molprobity Statistics.
  All-atom Clashscore : 14.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.03 %
    Favored  : 95.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.42 (0.21), residues: 1394
  helix: -0.38 (0.17), residues: 807
  sheet: -1.40 (0.84), residues: 40
  loop : -1.65 (0.25), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP K 397 
 HIS   0.004   0.001   HIS E 113 
 PHE   0.018   0.001   PHE A  78 
 TYR   0.039   0.002   TYR H  37 
 ARG   0.008   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.07347 (  837)
  hydrogen bonds       : angle       4.03774 ( 2092)
  covalent geometry    : bond        0.00377 (18226)
  covalent geometry    : angle       0.64716 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  285 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 285
  time to evaluate  : 1.544 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.9059 (tp) cc_final: 0.8829 (tp)
REVERT: A  120 MET cc_start: 0.8596 (mtp) cc_final: 0.8118 (mtp)
REVERT: A  126 LEU cc_start: 0.9328 (tp) cc_final: 0.9072 (tp)
REVERT: E   48 LEU cc_start: 0.9237 (tp) cc_final: 0.8708 (tp)
REVERT: E   50 GLU cc_start: 0.7985 (mm-30) cc_final: 0.7238 (tp30)
REVERT: E   93 GLN cc_start: 0.8371 (tm-30) cc_final: 0.8010 (tm-30)
REVERT: E  110 CYS cc_start: 0.8775 (m) cc_final: 0.8234 (m)
REVERT: E  120 MET cc_start: 0.8871 (mmm) cc_final: 0.8662 (mmm)
REVERT: E  126 LEU cc_start: 0.9366 (tp) cc_final: 0.9097 (tt)
REVERT: B   68 ASP cc_start: 0.8592 (m-30) cc_final: 0.7004 (m-30)
REVERT: B   92 ARG cc_start: 0.8027 (ptm-80) cc_final: 0.7477 (ttp-170)
REVERT: B  100 PHE cc_start: 0.8914 (m-80) cc_final: 0.8697 (m-80)
REVERT: F   27 GLN cc_start: 0.8888 (mm110) cc_final: 0.8425 (mp10)
REVERT: F   46 ILE cc_start: 0.9263 (mt) cc_final: 0.9001 (mt)
REVERT: F   88 TYR cc_start: 0.8326 (m-10) cc_final: 0.7634 (m-80)
REVERT: C   85 LEU cc_start: 0.9296 (mt) cc_final: 0.9029 (tt)
REVERT: G   19 ASN cc_start: 0.8609 (m-40) cc_final: 0.8275 (t0)
REVERT: G   36 LYS cc_start: 0.9153 (mttt) cc_final: 0.8767 (mtpp)
REVERT: G   38 ASN cc_start: 0.8821 (m110) cc_final: 0.8376 (m110)
REVERT: G   92 GLU cc_start: 0.7606 (tt0) cc_final: 0.7320 (tt0)
REVERT: D   43 LYS cc_start: 0.9303 (mmtt) cc_final: 0.8498 (mtpp)
REVERT: D   58 ILE cc_start: 0.9447 (mm) cc_final: 0.9176 (mm)
REVERT: D   83 ARG cc_start: 0.7732 (mtp85) cc_final: 0.7418 (mtp85)
REVERT: D   97 LEU cc_start: 0.9194 (tp) cc_final: 0.8800 (tp)
REVERT: H   56 MET cc_start: 0.8540 (tpp) cc_final: 0.8256 (tpp)
REVERT: H   64 ASN cc_start: 0.8979 (m-40) cc_final: 0.8226 (t0)
REVERT: H   68 GLU cc_start: 0.8559 (tt0) cc_final: 0.8213 (tt0)
REVERT: K  311 MSE cc_start: 0.5710 (mtp) cc_final: 0.5068 (mmm)
REVERT: K  535 MSE cc_start: 0.6272 (mmp) cc_final: 0.5695 (mmm)
REVERT: K  554 LEU cc_start: 0.3625 (pp) cc_final: 0.3195 (tp)
REVERT: K  712 MSE cc_start: 0.7047 (tpp) cc_final: 0.6286 (tpp)
  outliers start: 0
  outliers final: 0
  residues processed: 285
  average time/residue: 0.3437
  time to fit residues: 139.2344
Evaluate side-chains
  221 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.425 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 141 optimal weight:   50.0000
   chunk 155 optimal weight:    5.9990
   chunk 89 optimal weight:    8.9990
   chunk 102 optimal weight:   20.0000
   chunk 85 optimal weight:   10.0000
   chunk 0 optimal weight:   10.0000
   chunk 127 optimal weight:   10.0000
   chunk 74 optimal weight:    8.9990
   chunk 44 optimal weight:    0.8980
   chunk 128 optimal weight:    9.9990
   chunk 52 optimal weight:    6.9990
   overall best weight:    6.3788

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
A 125 GLN
E  68 GLN
E 125 GLN
** B  25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  19 ASN
** C  24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** G  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  44 GLN
H  79 HIS
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 533 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 716 GLN
** K 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 895 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.098481 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.070346 restraints weight = 75733.164|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.068720 restraints weight = 57239.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3339 r_free = 0.3339 target = 0.069195 restraints weight = 50275.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.3291
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3291
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3291 r_free = 0.3291    target_work(ls_wunit_k1) = 0.066         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3291
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8111
moved from start:          0.4062

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.104  18226  Z= 0.357
  Angle     :  0.789  10.193  25843  Z= 0.442
  Chirality :  0.044   0.203   2926
  Planarity :  0.006   0.075   2271
  Dihedral  : 30.183 145.441   4754
  Min Nonbonded Distance : 1.944

Molprobity Statistics.
  All-atom Clashscore : 22.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    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: -1.25 (0.22), residues: 1394
  helix: -0.28 (0.17), residues: 806
  sheet: -1.42 (0.88), residues: 40
  loop : -1.49 (0.26), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP K 397 
 HIS   0.009   0.002   HIS G  31 
 PHE   0.037   0.003   PHE A  78 
 TYR   0.042   0.003   TYR H  37 
 ARG   0.018   0.001   ARG E  40 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.08109 (  837)
  hydrogen bonds       : angle       4.63779 ( 2092)
  covalent geometry    : bond        0.00785 (18226)
  covalent geometry    : angle       0.78945 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  237 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 237
  time to evaluate  : 1.557 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   65 LEU cc_start: 0.9105 (tp) cc_final: 0.8889 (tp)
REVERT: A   94 GLU cc_start: 0.8280 (tt0) cc_final: 0.8038 (tt0)
REVERT: A  106 ASP cc_start: 0.7714 (t70) cc_final: 0.7274 (t70)
REVERT: A  120 MET cc_start: 0.8788 (mtp) cc_final: 0.8489 (mtp)
REVERT: A  125 GLN cc_start: 0.8924 (tp-100) cc_final: 0.8691 (tp40)
REVERT: A  126 LEU cc_start: 0.9384 (tp) cc_final: 0.9179 (tt)
REVERT: E   50 GLU cc_start: 0.7837 (mm-30) cc_final: 0.6024 (tp30)
REVERT: E   53 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8025 (ttm170)
REVERT: E   54 TYR cc_start: 0.9098 (m-10) cc_final: 0.8702 (m-10)
REVERT: E   79 LYS cc_start: 0.9066 (tmtt) cc_final: 0.8713 (tttp)
REVERT: E   80 THR cc_start: 0.8402 (t) cc_final: 0.7562 (t)
REVERT: E   81 ASP cc_start: 0.8455 (m-30) cc_final: 0.8212 (m-30)
REVERT: E   93 GLN cc_start: 0.8527 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: B   35 ARG cc_start: 0.7990 (ttm-80) cc_final: 0.7682 (ttm-80)
REVERT: G   24 GLN cc_start: 0.8657 (mp10) cc_final: 0.8447 (mp10)
REVERT: G   36 LYS cc_start: 0.9241 (mttt) cc_final: 0.8909 (mmmt)
REVERT: G   38 ASN cc_start: 0.8917 (m110) cc_final: 0.8626 (m110)
REVERT: G   92 GLU cc_start: 0.7977 (tt0) cc_final: 0.7551 (tt0)
REVERT: D   43 LYS cc_start: 0.9355 (mmtt) cc_final: 0.8635 (mtpt)
REVERT: D   92 GLN cc_start: 0.8780 (tt0) cc_final: 0.8022 (tm-30)
REVERT: D   93 THR cc_start: 0.9471 (p) cc_final: 0.9041 (p)
REVERT: H   56 MET cc_start: 0.8410 (tpp) cc_final: 0.8079 (tpp)
REVERT: H   64 ASN cc_start: 0.9045 (m-40) cc_final: 0.8236 (t0)
REVERT: K  256 MSE cc_start: 0.5387 (mtp) cc_final: 0.4835 (mtt)
REVERT: K  311 MSE cc_start: 0.5542 (mtp) cc_final: 0.4921 (mmm)
REVERT: K  535 MSE cc_start: 0.6438 (mmp) cc_final: 0.6014 (mmm)
REVERT: K  554 LEU cc_start: 0.3630 (pp) cc_final: 0.3000 (tp)
REVERT: K  712 MSE cc_start: 0.6666 (tpp) cc_final: 0.6285 (tpp)
REVERT: K  724 TYR cc_start: 0.7118 (m-10) cc_final: 0.6730 (m-10)
REVERT: K  815 PHE cc_start: 0.6289 (p90) cc_final: 0.5984 (p90)
REVERT: K  850 MSE cc_start: -0.0071 (tpt) cc_final: -0.0464 (tpt)
  outliers start: 0
  outliers final: 0
  residues processed: 237
  average time/residue: 0.3317
  time to fit residues: 113.2919
Evaluate side-chains
  199 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 1.379 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 126 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9980
   chunk 117 optimal weight:   20.0000
   chunk 40 optimal weight:    5.9990
   chunk 145 optimal weight:    4.9990
   chunk 122 optimal weight:    9.9990
   chunk 89 optimal weight:    7.9990
   chunk 29 optimal weight:    0.9990
   chunk 27 optimal weight:    2.9990
   chunk 5 optimal weight:    0.8980
   chunk 72 optimal weight:   10.0000
   overall best weight:    2.1786

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
B  75 HIS
C  24 GLN
G  73 ASN
G 110 ASN
D  44 GLN
H  44 GLN
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
K 668 ASN
** K 739 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 812 GLN
** K 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.101581 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.073624 restraints weight = 75603.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.072785 restraints weight = 55560.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.072445 restraints weight = 42855.768|
|-----------------------------------------------------------------------------|
r_work (final): 0.3362
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.4435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18226  Z= 0.182
  Angle     :  0.650   9.613  25843  Z= 0.370
  Chirality :  0.039   0.189   2926
  Planarity :  0.005   0.063   2271
  Dihedral  : 30.010 137.754   4754
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 16.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.95 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.13 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.65 (0.22), residues: 1394
  helix:  0.23 (0.18), residues: 804
  sheet: -1.61 (0.82), residues: 45
  loop : -1.23 (0.26), residues: 545

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K 397 
 HIS   0.006   0.001   HIS G  82 
 PHE   0.026   0.002   PHE A  78 
 TYR   0.017   0.002   TYR C  57 
 ARG   0.008   0.001   ARG G  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06958 (  837)
  hydrogen bonds       : angle       3.95717 ( 2092)
  covalent geometry    : bond        0.00402 (18226)
  covalent geometry    : angle       0.64983 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  257 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 256
  time to evaluate  : 1.360 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8734 (mtp) cc_final: 0.8288 (mtp)
REVERT: A  125 GLN cc_start: 0.8890 (tp-100) cc_final: 0.8682 (tp40)
REVERT: A  126 LEU cc_start: 0.9395 (tp) cc_final: 0.9150 (tp)
REVERT: E   50 GLU cc_start: 0.7905 (mm-30) cc_final: 0.7318 (tp30)
REVERT: E   54 TYR cc_start: 0.9003 (m-10) cc_final: 0.8753 (m-10)
REVERT: E   79 LYS cc_start: 0.9023 (tmtt) cc_final: 0.8714 (tttp)
REVERT: E   80 THR cc_start: 0.8342 (t) cc_final: 0.7609 (t)
REVERT: E   81 ASP cc_start: 0.8434 (m-30) cc_final: 0.8191 (m-30)
REVERT: E   93 GLN cc_start: 0.8431 (tm-30) cc_final: 0.8063 (tm-30)
REVERT: E  110 CYS cc_start: 0.8641 (m) cc_final: 0.8025 (m)
REVERT: E  113 HIS cc_start: 0.8476 (t70) cc_final: 0.8263 (t70)
REVERT: B   35 ARG cc_start: 0.7876 (ttm-80) cc_final: 0.7543 (ttm-80)
REVERT: F   26 ILE cc_start: 0.9361 (tp) cc_final: 0.9059 (tp)
REVERT: F   27 GLN cc_start: 0.8963 (mm110) cc_final: 0.8716 (mp10)
REVERT: F   93 GLN cc_start: 0.8308 (mp10) cc_final: 0.8082 (mp10)
REVERT: C   55 MET cc_start: 0.7924 (mtp) cc_final: 0.7701 (mtm)
REVERT: G   36 LYS cc_start: 0.9173 (mttt) cc_final: 0.8820 (mmmt)
REVERT: G   38 ASN cc_start: 0.8904 (m110) cc_final: 0.8533 (m110)
REVERT: G   92 GLU cc_start: 0.7923 (tt0) cc_final: 0.7385 (tt0)
REVERT: D   38 ILE cc_start: 0.9609 (pt) cc_final: 0.9031 (tt)
REVERT: D   43 LYS cc_start: 0.9331 (mmtt) cc_final: 0.8633 (mtpt)
REVERT: D   54 LYS cc_start: 0.8510 (mmtt) cc_final: 0.8282 (tppt)
REVERT: D   92 GLN cc_start: 0.8858 (tt0) cc_final: 0.7947 (tm-30)
REVERT: D   93 THR cc_start: 0.9422 (p) cc_final: 0.9022 (p)
REVERT: H   64 ASN cc_start: 0.9012 (m-40) cc_final: 0.8224 (t0)
REVERT: K  256 MSE cc_start: 0.5636 (mtp) cc_final: 0.4932 (mtt)
REVERT: K  267 MSE cc_start: 0.3180 (tmm) cc_final: 0.2675 (tmm)
REVERT: K  311 MSE cc_start: 0.5424 (mtp) cc_final: 0.4759 (mmm)
REVERT: K  535 MSE cc_start: 0.6257 (mmp) cc_final: 0.6045 (mmm)
REVERT: K  554 LEU cc_start: 0.3013 (pp) cc_final: 0.2567 (tp)
REVERT: K  712 MSE cc_start: 0.6604 (tpp) cc_final: 0.6349 (tpp)
REVERT: K  815 PHE cc_start: 0.6327 (p90) cc_final: 0.6062 (p90)
  outliers start: 1
  outliers final: 0
  residues processed: 257
  average time/residue: 0.3193
  time to fit residues: 119.7440
Evaluate side-chains
  202 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 202
  time to evaluate  : 1.597 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 116 optimal weight:    2.9990
   chunk 3 optimal weight:    2.9990
   chunk 145 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 29 optimal weight:    1.9990
   chunk 90 optimal weight:    8.9990
   chunk 36 optimal weight:    8.9990
   chunk 59 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 89 optimal weight:    8.9990
   chunk 71 optimal weight:    7.9990
   overall best weight:    1.9788

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
G 110 ASN
H  44 GLN
H  79 HIS
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.101895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.072328 restraints weight = 75147.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.071470 restraints weight = 49572.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.072509 restraints weight = 38020.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3361
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3361
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3361 r_free = 0.3361    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3361
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  18226  Z= 0.176
  Angle     :  0.642  11.075  25843  Z= 0.364
  Chirality :  0.039   0.213   2926
  Planarity :  0.005   0.091   2271
  Dihedral  : 29.798 137.485   4754
  Min Nonbonded Distance : 2.005

Molprobity Statistics.
  All-atom Clashscore : 15.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.73 %
    Favored  : 95.27 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  2.39 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.22), residues: 1394
  helix:  0.45 (0.18), residues: 801
  sheet: -1.91 (0.76), residues: 45
  loop : -1.06 (0.27), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP K 397 
 HIS   0.006   0.001   HIS G  82 
 PHE   0.029   0.002   PHE K 832 
 TYR   0.013   0.001   TYR C  57 
 ARG   0.006   0.001   ARG G  71 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06875 (  837)
  hydrogen bonds       : angle       3.84459 ( 2092)
  covalent geometry    : bond        0.00388 (18226)
  covalent geometry    : angle       0.64198 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  250 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 249
  time to evaluate  : 1.474 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8745 (mtp) cc_final: 0.8242 (mtp)
REVERT: E   50 GLU cc_start: 0.7851 (mm-30) cc_final: 0.6892 (tp30)
REVERT: E   93 GLN cc_start: 0.8515 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: E  110 CYS cc_start: 0.8625 (m) cc_final: 0.8020 (m)
REVERT: E  113 HIS cc_start: 0.8426 (t70) cc_final: 0.8149 (t70)
REVERT: B   35 ARG cc_start: 0.7970 (ttm-80) cc_final: 0.7547 (ttm-80)
REVERT: B   79 LYS cc_start: 0.8015 (tppt) cc_final: 0.7683 (tppt)
REVERT: B   88 TYR cc_start: 0.8365 (m-10) cc_final: 0.8133 (m-10)
REVERT: F   26 ILE cc_start: 0.9395 (tp) cc_final: 0.9075 (tp)
REVERT: F   27 GLN cc_start: 0.8973 (mm110) cc_final: 0.8712 (mp10)
REVERT: F   46 ILE cc_start: 0.9326 (mt) cc_final: 0.9105 (mt)
REVERT: G   36 LYS cc_start: 0.9142 (mttt) cc_final: 0.8808 (mmmt)
REVERT: G   38 ASN cc_start: 0.8808 (m110) cc_final: 0.8408 (m110)
REVERT: G   92 GLU cc_start: 0.7759 (tt0) cc_final: 0.7100 (tt0)
REVERT: D   38 ILE cc_start: 0.9659 (pt) cc_final: 0.9186 (tt)
REVERT: D   43 LYS cc_start: 0.9291 (mmtt) cc_final: 0.8649 (mtpt)
REVERT: D   92 GLN cc_start: 0.8679 (tt0) cc_final: 0.7786 (tm-30)
REVERT: D   93 THR cc_start: 0.9371 (p) cc_final: 0.8916 (p)
REVERT: D   96 ARG cc_start: 0.8378 (ptp-110) cc_final: 0.7511 (ptp-110)
REVERT: H   64 ASN cc_start: 0.9119 (m-40) cc_final: 0.8342 (t0)
REVERT: K  245 MSE cc_start: -0.0411 (tpt) cc_final: -0.0834 (mmm)
REVERT: K  256 MSE cc_start: 0.5815 (mtp) cc_final: 0.5368 (mtt)
REVERT: K  267 MSE cc_start: 0.3373 (tmm) cc_final: 0.2560 (tmm)
REVERT: K  311 MSE cc_start: 0.5438 (mtp) cc_final: 0.4753 (mmm)
REVERT: K  466 TYR cc_start: 0.6259 (t80) cc_final: 0.5826 (t80)
REVERT: K  554 LEU cc_start: 0.3198 (pp) cc_final: 0.2705 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 249
  average time/residue: 0.3302
  time to fit residues: 121.1729
Evaluate side-chains
  210 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 1.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 28 optimal weight:    7.9990
   chunk 118 optimal weight:    5.9990
   chunk 16 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   chunk 113 optimal weight:    8.9990
   chunk 117 optimal weight:   20.0000
   chunk 44 optimal weight:    0.9990
   chunk 145 optimal weight:    8.9990
   chunk 26 optimal weight:    3.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    3.3990

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

Flipped N/Q/H residues before XYZ refinement:
A 125 GLN
G  73 ASN
G 110 ASN
H  44 GLN
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.100498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.072652 restraints weight = 76104.000|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.071592 restraints weight = 60457.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.071750 restraints weight = 47320.591|
|-----------------------------------------------------------------------------|
r_work (final): 0.3350
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3349
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3349 r_free = 0.3349    target_work(ls_wunit_k1) = 0.069         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3349
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.4883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.069  18226  Z= 0.227
  Angle     :  0.675  12.581  25843  Z= 0.380
  Chirality :  0.040   0.172   2926
  Planarity :  0.006   0.120   2271
  Dihedral  : 29.740 139.245   4754
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 16.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.32 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.34 (0.22), residues: 1394
  helix:  0.47 (0.18), residues: 810
  sheet: -1.96 (0.75), residues: 45
  loop : -1.03 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP K 397 
 HIS   0.007   0.002   HIS F  75 
 PHE   0.034   0.002   PHE A  78 
 TYR   0.020   0.002   TYR K 487 
 ARG   0.009   0.001   ARG K 705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06970 (  837)
  hydrogen bonds       : angle       4.04003 ( 2092)
  covalent geometry    : bond        0.00499 (18226)
  covalent geometry    : angle       0.67492 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 234
  time to evaluate  : 1.409 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8782 (mtp) cc_final: 0.8327 (mtp)
REVERT: A  125 GLN cc_start: 0.9062 (tp-100) cc_final: 0.8726 (tp40)
REVERT: E   79 LYS cc_start: 0.9109 (tmtt) cc_final: 0.8776 (tttp)
REVERT: E   93 GLN cc_start: 0.8489 (tm-30) cc_final: 0.8143 (tm-30)
REVERT: E  120 MET cc_start: 0.8819 (mmm) cc_final: 0.8618 (mmm)
REVERT: B   35 ARG cc_start: 0.8019 (ttm-80) cc_final: 0.7558 (ttm-80)
REVERT: F   26 ILE cc_start: 0.9394 (tp) cc_final: 0.9097 (tp)
REVERT: F   27 GLN cc_start: 0.8966 (mm110) cc_final: 0.8746 (mp10)
REVERT: C   56 GLU cc_start: 0.8380 (mt-10) cc_final: 0.7866 (tm-30)
REVERT: G   36 LYS cc_start: 0.9169 (mttt) cc_final: 0.8836 (mmmt)
REVERT: G   38 ASN cc_start: 0.8877 (m110) cc_final: 0.8521 (m110)
REVERT: G   92 GLU cc_start: 0.7969 (tt0) cc_final: 0.7401 (tt0)
REVERT: D   38 ILE cc_start: 0.9673 (pt) cc_final: 0.9202 (tt)
REVERT: D   43 LYS cc_start: 0.9358 (mmtt) cc_final: 0.8589 (mtpp)
REVERT: D   92 GLN cc_start: 0.8772 (tt0) cc_final: 0.7954 (tm-30)
REVERT: D   93 THR cc_start: 0.9392 (p) cc_final: 0.8949 (p)
REVERT: D   96 ARG cc_start: 0.8308 (ptp-110) cc_final: 0.7864 (ptp-110)
REVERT: H   64 ASN cc_start: 0.9198 (m-40) cc_final: 0.8308 (t0)
REVERT: K  245 MSE cc_start: -0.0412 (tpt) cc_final: -0.1163 (mmm)
REVERT: K  256 MSE cc_start: 0.5362 (mtp) cc_final: 0.5025 (mtt)
REVERT: K  267 MSE cc_start: 0.3613 (tmm) cc_final: 0.3062 (tmm)
REVERT: K  283 LYS cc_start: 0.2860 (pttm) cc_final: 0.1957 (mttm)
REVERT: K  311 MSE cc_start: 0.5620 (mtp) cc_final: 0.5012 (mmm)
REVERT: K  517 TYR cc_start: 0.5279 (m-80) cc_final: 0.4905 (m-80)
REVERT: K  535 MSE cc_start: 0.6574 (mmm) cc_final: 0.6028 (mmm)
REVERT: K  712 MSE cc_start: 0.6563 (tpp) cc_final: 0.5760 (tpp)
REVERT: K  717 TYR cc_start: 0.8012 (t80) cc_final: 0.7808 (t80)
REVERT: K  872 ARG cc_start: -0.0027 (mmt180) cc_final: -0.1244 (mmt-90)
  outliers start: 0
  outliers final: 0
  residues processed: 234
  average time/residue: 0.3124
  time to fit residues: 108.3957
Evaluate side-chains
  196 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 1.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 162 optimal weight:   20.0000
   chunk 69 optimal weight:    4.9990
   chunk 72 optimal weight:   10.0000
   chunk 50 optimal weight:    6.9990
   chunk 88 optimal weight:    8.9990
   chunk 59 optimal weight:    0.3980
   chunk 57 optimal weight:    0.7980
   chunk 90 optimal weight:   10.0000
   chunk 157 optimal weight:    9.9990
   chunk 123 optimal weight:    9.9990
   chunk 122 optimal weight:    0.9980
   overall best weight:    2.8384

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

Flipped N/Q/H residues before XYZ refinement:
E 125 GLN
G 110 ASN
H  44 GLN
H  79 HIS
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 510 GLN
** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3983 r_free = 0.3983 target = 0.100993 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.072811 restraints weight = 76270.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.070909 restraints weight = 57369.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.071812 restraints weight = 46964.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3346
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3346 r_free = 0.3346    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3347 r_free = 0.3347    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3347
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.5079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  18226  Z= 0.200
  Angle     :  0.655   8.153  25843  Z= 0.371
  Chirality :  0.039   0.165   2926
  Planarity :  0.005   0.063   2271
  Dihedral  : 29.677 137.049   4754
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 16.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.40 %
    Favored  : 98.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.21 (0.22), residues: 1394
  helix:  0.56 (0.18), residues: 807
  sheet: -1.84 (0.78), residues: 45
  loop : -0.95 (0.28), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP K 397 
 HIS   0.007   0.001   HIS F  75 
 PHE   0.030   0.002   PHE A  78 
 TYR   0.014   0.002   TYR G  57 
 ARG   0.006   0.001   ARG K 779 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06827 (  837)
  hydrogen bonds       : angle       3.94774 ( 2092)
  covalent geometry    : bond        0.00441 (18226)
  covalent geometry    : angle       0.65524 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 229
  time to evaluate  : 1.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8914 (mtp) cc_final: 0.8450 (mtp)
REVERT: A  125 GLN cc_start: 0.8963 (tp-100) cc_final: 0.8645 (tp40)
REVERT: E   50 GLU cc_start: 0.8148 (mm-30) cc_final: 0.7673 (mm-30)
REVERT: E   79 LYS cc_start: 0.8810 (tmtt) cc_final: 0.8533 (tttp)
REVERT: E   93 GLN cc_start: 0.8563 (tm-30) cc_final: 0.8159 (tm-30)
REVERT: E  110 CYS cc_start: 0.8481 (m) cc_final: 0.7971 (m)
REVERT: E  113 HIS cc_start: 0.8412 (t70) cc_final: 0.7525 (t-90)
REVERT: E  120 MET cc_start: 0.8771 (mmm) cc_final: 0.8567 (mmm)
REVERT: B   35 ARG cc_start: 0.8041 (ttm-80) cc_final: 0.7552 (ttm-80)
REVERT: B   79 LYS cc_start: 0.8009 (tppt) cc_final: 0.7626 (tppt)
REVERT: F   26 ILE cc_start: 0.9374 (tp) cc_final: 0.9049 (tp)
REVERT: F   27 GLN cc_start: 0.8990 (mm110) cc_final: 0.8763 (mp10)
REVERT: C   56 GLU cc_start: 0.8553 (mt-10) cc_final: 0.7862 (tm-30)
REVERT: G   36 LYS cc_start: 0.9122 (mttt) cc_final: 0.8876 (mmmt)
REVERT: G   38 ASN cc_start: 0.8800 (m110) cc_final: 0.8414 (m110)
REVERT: G   92 GLU cc_start: 0.7822 (tt0) cc_final: 0.7418 (mm-30)
REVERT: D   38 ILE cc_start: 0.9651 (pt) cc_final: 0.9136 (tt)
REVERT: D   43 LYS cc_start: 0.9290 (mmtt) cc_final: 0.8668 (mtpt)
REVERT: D   92 GLN cc_start: 0.8699 (tt0) cc_final: 0.7938 (tm-30)
REVERT: D   93 THR cc_start: 0.9326 (p) cc_final: 0.8860 (p)
REVERT: D   96 ARG cc_start: 0.8327 (ptp-110) cc_final: 0.7915 (ptp-110)
REVERT: H   64 ASN cc_start: 0.8849 (m-40) cc_final: 0.8342 (t0)
REVERT: H  102 GLU cc_start: 0.8020 (tp30) cc_final: 0.7449 (tp30)
REVERT: K  256 MSE cc_start: 0.5758 (mtp) cc_final: 0.5156 (mtt)
REVERT: K  267 MSE cc_start: 0.3582 (tmm) cc_final: 0.3116 (tmm)
REVERT: K  283 LYS cc_start: 0.3378 (pttm) cc_final: 0.2708 (tptt)
REVERT: K  311 MSE cc_start: 0.5358 (mtp) cc_final: 0.4659 (mmm)
REVERT: K  535 MSE cc_start: 0.6291 (mmm) cc_final: 0.5781 (mmm)
REVERT: K  712 MSE cc_start: 0.6523 (tpp) cc_final: 0.5927 (tpp)
REVERT: K  872 ARG cc_start: -0.0178 (mmt180) cc_final: -0.1415 (mmt-90)
  outliers start: 1
  outliers final: 0
  residues processed: 229
  average time/residue: 0.3765
  time to fit residues: 131.0579
Evaluate side-chains
  200 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 1.528 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 144 optimal weight:   20.0000
   chunk 158 optimal weight:   30.0000
   chunk 0 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 97 optimal weight:    7.9990
   chunk 44 optimal weight:    2.9990
   chunk 83 optimal weight:   10.0000
   chunk 128 optimal weight:    0.6980
   chunk 110 optimal weight:    0.0970
   chunk 5 optimal weight:    1.9990
   chunk 70 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
G 110 ASN
H  92 GLN
** K 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 875 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.103377 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.074300 restraints weight = 76565.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.072951 restraints weight = 51577.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.074131 restraints weight = 41529.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3394
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3395
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3395 r_free = 0.3395    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.3395
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.5344

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18226  Z= 0.150
  Angle     :  0.615   7.568  25843  Z= 0.350
  Chirality :  0.038   0.178   2926
  Planarity :  0.005   0.065   2271
  Dihedral  : 29.443 135.702   4754
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 14.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.16 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.09 (0.23), residues: 1394
  helix:  0.80 (0.18), residues: 801
  sheet: -1.59 (0.80), residues: 45
  loop : -0.82 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP K 397 
 HIS   0.006   0.001   HIS F  75 
 PHE   0.022   0.001   PHE K 832 
 TYR   0.018   0.001   TYR A  54 
 ARG   0.007   0.001   ARG K 705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06796 (  837)
  hydrogen bonds       : angle       3.70485 ( 2092)
  covalent geometry    : bond        0.00325 (18226)
  covalent geometry    : angle       0.61503 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  245 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 245
  time to evaluate  : 1.589 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8867 (mtp) cc_final: 0.8204 (mtp)
REVERT: A  125 GLN cc_start: 0.8982 (tp-100) cc_final: 0.8632 (tp40)
REVERT: E   50 GLU cc_start: 0.8096 (mm-30) cc_final: 0.7351 (mm-30)
REVERT: E   82 LEU cc_start: 0.8561 (mt) cc_final: 0.8289 (mp)
REVERT: E   93 GLN cc_start: 0.8538 (tm-30) cc_final: 0.8132 (tm-30)
REVERT: E   94 GLU cc_start: 0.8126 (mt-10) cc_final: 0.7590 (tm-30)
REVERT: E  110 CYS cc_start: 0.8393 (m) cc_final: 0.8095 (m)
REVERT: E  113 HIS cc_start: 0.8147 (t70) cc_final: 0.7851 (t-170)
REVERT: E  120 MET cc_start: 0.8801 (mmm) cc_final: 0.8569 (mmm)
REVERT: B   35 ARG cc_start: 0.8005 (ttm-80) cc_final: 0.7492 (ttm-80)
REVERT: B   79 LYS cc_start: 0.7896 (tppt) cc_final: 0.7543 (tppt)
REVERT: B   88 TYR cc_start: 0.8345 (m-10) cc_final: 0.7961 (m-10)
REVERT: F   27 GLN cc_start: 0.8915 (mm110) cc_final: 0.8698 (mp10)
REVERT: F   93 GLN cc_start: 0.8027 (mp10) cc_final: 0.7809 (mp10)
REVERT: C   56 GLU cc_start: 0.8409 (mt-10) cc_final: 0.7733 (tm-30)
REVERT: G   36 LYS cc_start: 0.9134 (mttt) cc_final: 0.8848 (mmmt)
REVERT: G   38 ASN cc_start: 0.8600 (m110) cc_final: 0.8207 (m110)
REVERT: G   85 LEU cc_start: 0.8620 (mm) cc_final: 0.8411 (mt)
REVERT: G   92 GLU cc_start: 0.7599 (tt0) cc_final: 0.6913 (tt0)
REVERT: D   38 ILE cc_start: 0.9600 (pt) cc_final: 0.9052 (tt)
REVERT: D   43 LYS cc_start: 0.9027 (mmtt) cc_final: 0.8624 (mtpt)
REVERT: D   80 TYR cc_start: 0.8118 (m-10) cc_final: 0.5962 (m-10)
REVERT: D   92 GLN cc_start: 0.8607 (tt0) cc_final: 0.7915 (tm-30)
REVERT: D   93 THR cc_start: 0.9265 (p) cc_final: 0.8861 (p)
REVERT: H   42 LEU cc_start: 0.9479 (tt) cc_final: 0.9117 (tt)
REVERT: H   64 ASN cc_start: 0.9029 (m-40) cc_final: 0.8376 (t0)
REVERT: H   92 GLN cc_start: 0.8514 (tm130) cc_final: 0.8252 (tm-30)
REVERT: H  102 GLU cc_start: 0.7641 (tp30) cc_final: 0.6970 (tp30)
REVERT: K  247 ARG cc_start: 0.7182 (ttm-80) cc_final: 0.6707 (ptt-90)
REVERT: K  256 MSE cc_start: 0.5788 (mtp) cc_final: 0.5373 (mtp)
REVERT: K  267 MSE cc_start: 0.3597 (tmm) cc_final: 0.2946 (tmm)
REVERT: K  283 LYS cc_start: 0.3522 (pttm) cc_final: 0.2907 (mttm)
REVERT: K  311 MSE cc_start: 0.5495 (mtp) cc_final: 0.4738 (mmm)
REVERT: K  397 TRP cc_start: 0.6564 (t60) cc_final: 0.6262 (t60)
REVERT: K  535 MSE cc_start: 0.6546 (mmm) cc_final: 0.6292 (mmm)
REVERT: K  712 MSE cc_start: 0.6639 (tpp) cc_final: 0.5808 (tpp)
REVERT: K  717 TYR cc_start: 0.8061 (t80) cc_final: 0.7853 (t80)
REVERT: K  729 MSE cc_start: 0.2205 (tpp) cc_final: 0.1900 (tpp)
REVERT: K  850 MSE cc_start: -0.0428 (tpt) cc_final: -0.0693 (tpt)
REVERT: K  872 ARG cc_start: -0.0167 (mmt180) cc_final: -0.1583 (mmt90)
  outliers start: 0
  outliers final: 0
  residues processed: 245
  average time/residue: 0.3093
  time to fit residues: 112.8655
Evaluate side-chains
  211 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 1.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 96 optimal weight:    8.9990
   chunk 61 optimal weight:    5.9990
   chunk 119 optimal weight:    5.9990
   chunk 113 optimal weight:    0.9980
   chunk 120 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 55 optimal weight:    0.9980
   chunk 122 optimal weight:    0.9990
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    7.9990
   chunk 149 optimal weight:    0.9980
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A  39 HIS
E  76 GLN
H  79 HIS
** K 513 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
K 691 HIS
K 875 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4034 r_free = 0.4034 target = 0.103931 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.074822 restraints weight = 76327.465|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.073340 restraints weight = 52709.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.074488 restraints weight = 42213.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3403
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3401
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3401 r_free = 0.3401    target_work(ls_wunit_k1) = 0.071         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3401
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8020
moved from start:          0.5539

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  18226  Z= 0.147
  Angle     :  0.615   9.006  25843  Z= 0.348
  Chirality :  0.038   0.188   2926
  Planarity :  0.005   0.066   2271
  Dihedral  : 29.257 134.992   4754
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 13.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.81 %
    Favored  : 95.19 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  0.33 %
    Favored  : 99.51 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.23), residues: 1394
  helix:  0.86 (0.18), residues: 807
  sheet: -1.58 (0.79), residues: 45
  loop : -0.79 (0.28), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP K 397 
 HIS   0.008   0.001   HIS F  75 
 PHE   0.024   0.001   PHE K 266 
 TYR   0.028   0.001   TYR C  57 
 ARG   0.008   0.001   ARG K 705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06773 (  837)
  hydrogen bonds       : angle       3.62513 ( 2092)
  covalent geometry    : bond        0.00321 (18226)
  covalent geometry    : angle       0.61464 (25843)

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

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

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2788 Ramachandran restraints generated.
    1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 246
  time to evaluate  : 1.523 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  120 MET cc_start: 0.8917 (mtp) cc_final: 0.8160 (mtp)
REVERT: A  125 GLN cc_start: 0.8938 (tp-100) cc_final: 0.8729 (tp40)
REVERT: E   50 GLU cc_start: 0.8132 (mm-30) cc_final: 0.7450 (mm-30)
REVERT: E   93 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8324 (tm-30)
REVERT: E   94 GLU cc_start: 0.8267 (mt-10) cc_final: 0.7623 (tm-30)
REVERT: E  113 HIS cc_start: 0.8199 (t70) cc_final: 0.7923 (t-170)
REVERT: E  120 MET cc_start: 0.8880 (mmm) cc_final: 0.8617 (mmm)
REVERT: B   35 ARG cc_start: 0.8053 (ttm-80) cc_final: 0.7524 (ttm-80)
REVERT: B   79 LYS cc_start: 0.7960 (tppt) cc_final: 0.7715 (tppt)
REVERT: B   88 TYR cc_start: 0.8278 (m-10) cc_final: 0.8060 (m-10)
REVERT: F   27 GLN cc_start: 0.8964 (mm110) cc_final: 0.8702 (mp10)
REVERT: F   46 ILE cc_start: 0.9315 (mt) cc_final: 0.9058 (mt)
REVERT: F   53 GLU cc_start: 0.8386 (tm-30) cc_final: 0.8183 (tm-30)
REVERT: F   63 GLU cc_start: 0.8355 (mm-30) cc_final: 0.7948 (mm-30)
REVERT: F   93 GLN cc_start: 0.8163 (mp10) cc_final: 0.7320 (mp10)
REVERT: C   56 GLU cc_start: 0.8413 (mt-10) cc_final: 0.7781 (tm-30)
REVERT: G   36 LYS cc_start: 0.9193 (mttt) cc_final: 0.8825 (mmmt)
REVERT: G   38 ASN cc_start: 0.8581 (m110) cc_final: 0.8183 (m110)
REVERT: G   85 LEU cc_start: 0.8704 (mm) cc_final: 0.8446 (mt)
REVERT: D   31 LYS cc_start: 0.8044 (pttm) cc_final: 0.7549 (tmtt)
REVERT: D   43 LYS cc_start: 0.9060 (mmtt) cc_final: 0.8561 (mtpp)
REVERT: D   80 TYR cc_start: 0.8090 (m-10) cc_final: 0.5939 (m-10)
REVERT: H   34 TYR cc_start: 0.8586 (m-80) cc_final: 0.8364 (m-10)
REVERT: H   64 ASN cc_start: 0.8952 (m-40) cc_final: 0.8589 (t0)
REVERT: H  102 GLU cc_start: 0.7720 (tp30) cc_final: 0.7491 (tp30)
REVERT: K  245 MSE cc_start: -0.0475 (tpt) cc_final: -0.0909 (mmm)
REVERT: K  247 ARG cc_start: 0.7171 (ttm-80) cc_final: 0.6750 (ptt-90)
REVERT: K  256 MSE cc_start: 0.5861 (mtp) cc_final: 0.5460 (mtp)
REVERT: K  267 MSE cc_start: 0.3538 (tmm) cc_final: 0.2820 (tmm)
REVERT: K  283 LYS cc_start: 0.3496 (pttm) cc_final: 0.2915 (mttm)
REVERT: K  311 MSE cc_start: 0.5284 (mtp) cc_final: 0.4554 (mmm)
REVERT: K  397 TRP cc_start: 0.6565 (t60) cc_final: 0.6297 (t60)
REVERT: K  729 MSE cc_start: 0.1450 (tpp) cc_final: 0.1061 (tpp)
REVERT: K  850 MSE cc_start: -0.0306 (tpt) cc_final: -0.0914 (tpt)
REVERT: K  872 ARG cc_start: -0.0185 (mmt180) cc_final: -0.0911 (mmt-90)
REVERT: K  875 GLN cc_start: 0.2850 (OUTLIER) cc_final: 0.1698 (mt0)
  outliers start: 2
  outliers final: 0
  residues processed: 247
  average time/residue: 0.3250
  time to fit residues: 118.1343
Evaluate side-chains
  213 residues out of total 1216 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 212
  time to evaluate  : 1.555 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 151 optimal weight:    4.9990
   chunk 109 optimal weight:    5.9990
   chunk 6 optimal weight:    0.9980
   chunk 54 optimal weight:    4.9990
   chunk 141 optimal weight:   20.0000
   chunk 64 optimal weight:    3.9990
   chunk 75 optimal weight:    8.9990
   chunk 108 optimal weight:    3.9990
   chunk 101 optimal weight:   10.0000
   chunk 117 optimal weight:   20.0000
   chunk 10 optimal weight:    5.9990
   overall best weight:    3.7988

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

Flipped N/Q/H residues before XYZ refinement:
E  68 GLN
E  76 GLN
G 110 ASN
** H  92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** K 691 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.100720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.071485 restraints weight = 76581.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.070796 restraints weight = 51169.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.071711 restraints weight = 40857.864|
|-----------------------------------------------------------------------------|
r_work (final): 0.3341
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3341
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3341 r_free = 0.3341    target_work(ls_wunit_k1) = 0.068         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        2 |
|-----------------------------------------------------------------------------|
r_final: 0.3341
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.5543

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061  18226  Z= 0.242
  Angle     :  0.677   8.943  25843  Z= 0.382
  Chirality :  0.040   0.173   2926
  Planarity :  0.005   0.066   2271
  Dihedral  : 29.359 138.426   4754
  Min Nonbonded Distance : 1.956

Molprobity Statistics.
  All-atom Clashscore : 17.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.52 %
    Favored  : 95.48 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.41 %
    Favored  : 99.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.35 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.04 (0.23), residues: 1394
  helix:  0.70 (0.18), residues: 803
  sheet: -1.49 (0.82), residues: 43
  loop : -0.75 (0.28), residues: 548

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP K 397 
 HIS   0.009   0.002   HIS K 691 
 PHE   0.029   0.002   PHE A  78 
 TYR   0.025   0.002   TYR C  57 
 ARG   0.011   0.001   ARG K 705 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06968 (  837)
  hydrogen bonds       : angle       3.97202 ( 2092)
  covalent geometry    : bond        0.00536 (18226)
  covalent geometry    : angle       0.67738 (25843)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6059.04 seconds
wall clock time: 107 minutes 11.55 seconds (6431.55 seconds total)