Starting phenix.real_space_refine
on Sat Apr  4 22:43:33 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9non_49601/04_2026/9non_49601.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9non_49601/04_2026/9non_49601.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9non_49601/04_2026/9non_49601.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9non_49601/04_2026/9non_49601.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9non_49601/04_2026/9non_49601.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9non_49601/04_2026/9non_49601.map"
  }
  resolution = 2.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.005
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    3205      2.51       5
     N     930      2.21       5
     O     930      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5105
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "B"
      Number of atoms: 1021
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 133, 1021
          Classifications: {'peptide': 133}
          Link IDs: {'PTRANS': 9, 'TRANS': 123}
  Restraints were copied for chains:
    C, A, D, E
  Time building chain proxies: 0.67, per 1000 atoms: 0.13
  Number of scatterers: 5105
  At special positions: 0
  Unit cell: (86.814, 90.63, 47.7, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O     930      8.00
     N     930      7.00
     C    3205      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=15, symmetry=0
    Simple disulfide: pdb=" SG  CYS B   7 " - pdb=" SG  CYS B  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  18 " - pdb=" SG  CYS B  23 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  81 " - pdb=" SG  CYS B 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C   7 " - pdb=" SG  CYS C  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A   7 " - pdb=" SG  CYS A  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D   7 " - pdb=" SG  CYS D  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E   7 " - pdb=" SG  CYS E  42 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  18 " - pdb=" SG  CYS C  23 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  18 " - pdb=" SG  CYS A  23 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  18 " - pdb=" SG  CYS D  23 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  18 " - pdb=" SG  CYS E  23 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  81 " - pdb=" SG  CYS C 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  81 " - pdb=" SG  CYS A 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D  81 " - pdb=" SG  CYS D 124 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E  81 " - pdb=" SG  CYS E 124 " distance=2.03

  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: 0.31
  Conformation dependent library (CDL) restraints added in 317.5 milliseconds
  

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1180

  Finding SS restraints...
    Secondary structure from input PDB file:
      0 helices and 13 sheets defined
      0.0% alpha, 39.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing sheet with id=AA1, first strand: chain 'A' and resid 15 through 19
      removed outlier: 6.470A  pdb=" N   ILE B  15 " --> pdb=" O   ARG A  16 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   CYS A  18 " --> pdb=" O   ILE B  15 " (cutoff:3.500A)
      removed outlier: 8.370A  pdb=" N   THR B  17 " --> pdb=" O   CYS A  18 " (cutoff:3.500A)
      removed outlier: 6.956A  pdb=" N   ASP C  19 " --> pdb=" O   CYS B  18 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   ASP D  19 " --> pdb=" O   CYS C  18 " (cutoff:3.500A)
      removed outlier: 6.960A  pdb=" N   ASP E  19 " --> pdb=" O   CYS D  18 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 29
      removed outlier: 6.472A  pdb=" N   ALA B  28 " --> pdb=" O   GLN A  29 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 35 through 41
      removed outlier: 3.513A  pdb=" N   ASP A  39 " --> pdb=" O   VAL B  38 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   VAL B  40 " --> pdb=" O   ASP A  39 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   LEU A  41 " --> pdb=" O   VAL B  40 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   HIS B  35 " --> pdb=" O   GLN C  36 " (cutoff:3.500A)
      removed outlier: 7.271A  pdb=" N   VAL C  38 " --> pdb=" O   HIS B  35 " (cutoff:3.500A)
      removed outlier: 5.697A  pdb=" N   GLY B  37 " --> pdb=" O   VAL C  38 " (cutoff:3.500A)
      removed outlier: 7.653A  pdb=" N   VAL C  40 " --> pdb=" O   GLY B  37 " (cutoff:3.500A)
      removed outlier: 7.630A  pdb=" N   ASP B  39 " --> pdb=" O   VAL C  40 " (cutoff:3.500A)
      removed outlier: 7.322A  pdb=" N   HIS C  35 " --> pdb=" O   GLN D  36 " (cutoff:3.500A)
      removed outlier: 7.291A  pdb=" N   VAL D  38 " --> pdb=" O   HIS C  35 " (cutoff:3.500A)
      removed outlier: 5.711A  pdb=" N   GLY C  37 " --> pdb=" O   VAL D  38 " (cutoff:3.500A)
      removed outlier: 7.663A  pdb=" N   VAL D  40 " --> pdb=" O   GLY C  37 " (cutoff:3.500A)
      removed outlier: 7.644A  pdb=" N   ASP C  39 " --> pdb=" O   VAL D  40 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   HIS D  35 " --> pdb=" O   GLN E  36 " (cutoff:3.500A)
      removed outlier: 7.266A  pdb=" N   VAL E  38 " --> pdb=" O   HIS D  35 " (cutoff:3.500A)
      removed outlier: 5.692A  pdb=" N   GLY D  37 " --> pdb=" O   VAL E  38 " (cutoff:3.500A)
      removed outlier: 7.646A  pdb=" N   VAL E  40 " --> pdb=" O   GLY D  37 " (cutoff:3.500A)
      removed outlier: 7.633A  pdb=" N   ASP D  39 " --> pdb=" O   VAL E  40 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 47 through 49
      removed outlier: 6.652A  pdb=" N   VAL B  48 " --> pdb=" O   TYR C  49 " (cutoff:3.500A)
      removed outlier: 6.639A  pdb=" N   VAL C  48 " --> pdb=" O   TYR D  49 " (cutoff:3.500A)
      removed outlier: 6.667A  pdb=" N   VAL D  48 " --> pdb=" O   TYR E  49 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 60
      removed outlier: 9.409A  pdb=" N   PHE B  52 " --> pdb=" O   THR A  53 " (cutoff:3.500A)
      removed outlier: 10.948A  pdb=" N   MET A  55 " --> pdb=" O   PHE B  52 " (cutoff:3.500A)
      removed outlier: 9.147A  pdb=" N   GLY B  54 " --> pdb=" O   MET A  55 " (cutoff:3.500A)
      removed outlier: 9.947A  pdb=" N   VAL A  57 " --> pdb=" O   GLY B  54 " (cutoff:3.500A)
      removed outlier: 6.014A  pdb=" N   ILE B  56 " --> pdb=" O   VAL A  57 " (cutoff:3.500A)
      removed outlier: 7.411A  pdb=" N   GLN A  59 " --> pdb=" O   ILE B  56 " (cutoff:3.500A)
      removed outlier: 7.321A  pdb=" N   GLY B  58 " --> pdb=" O   GLN A  59 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   THR B  53 " --> pdb=" O   PHE C  52 " (cutoff:3.500A)
      removed outlier: 6.965A  pdb=" N   GLY C  54 " --> pdb=" O   THR B  53 " (cutoff:3.500A)
      removed outlier: 6.987A  pdb=" N   MET B  55 " --> pdb=" O   GLY C  54 " (cutoff:3.500A)
      removed outlier: 6.983A  pdb=" N   ILE C  56 " --> pdb=" O   MET B  55 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   GLN B  59 " --> pdb=" O   GLY C  58 " (cutoff:3.500A)
      removed outlier: 7.129A  pdb=" N   GLU C  60 " --> pdb=" O   GLN B  59 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   THR C  53 " --> pdb=" O   PHE D  52 " (cutoff:3.500A)
      removed outlier: 6.972A  pdb=" N   GLY D  54 " --> pdb=" O   THR C  53 " (cutoff:3.500A)
      removed outlier: 7.000A  pdb=" N   MET C  55 " --> pdb=" O   GLY D  54 " (cutoff:3.500A)
      removed outlier: 6.991A  pdb=" N   ILE D  56 " --> pdb=" O   MET C  55 " (cutoff:3.500A)
      removed outlier: 7.017A  pdb=" N   GLN C  59 " --> pdb=" O   GLY D  58 " (cutoff:3.500A)
      removed outlier: 7.139A  pdb=" N   GLU D  60 " --> pdb=" O   GLN C  59 " (cutoff:3.500A)
      removed outlier: 7.002A  pdb=" N   THR D  53 " --> pdb=" O   PHE E  52 " (cutoff:3.500A)
      removed outlier: 6.980A  pdb=" N   GLY E  54 " --> pdb=" O   THR D  53 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   MET D  55 " --> pdb=" O   GLY E  54 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   ILE E  56 " --> pdb=" O   MET D  55 " (cutoff:3.500A)
      removed outlier: 7.008A  pdb=" N   GLN D  59 " --> pdb=" O   GLY E  58 " (cutoff:3.500A)
      removed outlier: 7.136A  pdb=" N   GLU E  60 " --> pdb=" O   GLN D  59 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 66 through 75
      removed outlier: 6.560A  pdb=" N   ASN B  67 " --> pdb=" O   ALA A  68 " (cutoff:3.500A)
      removed outlier: 8.085A  pdb=" N   ASN A  70 " --> pdb=" O   ASN B  67 " (cutoff:3.500A)
      removed outlier: 6.410A  pdb=" N   ILE B  69 " --> pdb=" O   ASN A  70 " (cutoff:3.500A)
      removed outlier: 7.705A  pdb=" N   GLY A  72 " --> pdb=" O   ILE B  69 " (cutoff:3.500A)
      removed outlier: 8.449A  pdb=" N   ASN B  71 " --> pdb=" O   GLY A  72 " (cutoff:3.500A)
      removed outlier: 8.310A  pdb=" N   ARG A  74 " --> pdb=" O   ASN B  71 " (cutoff:3.500A)
      removed outlier: 6.225A  pdb=" N   VAL B  73 " --> pdb=" O   ARG A  74 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL C  73 " --> pdb=" O   GLY B  72 " (cutoff:3.500A)
      removed outlier: 7.081A  pdb=" N   ARG B  74 " --> pdb=" O   VAL C  73 " (cutoff:3.500A)
      removed outlier: 7.009A  pdb=" N   VAL D  73 " --> pdb=" O   GLY C  72 " (cutoff:3.500A)
      removed outlier: 7.101A  pdb=" N   ARG C  74 " --> pdb=" O   VAL D  73 " (cutoff:3.500A)
      removed outlier: 7.015A  pdb=" N   VAL E  73 " --> pdb=" O   GLY D  72 " (cutoff:3.500A)
      removed outlier: 7.100A  pdb=" N   ARG D  74 " --> pdb=" O   VAL E  73 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 78 through 79
      removed outlier: 6.106A  pdb=" N   ARG B  78 " --> pdb=" O   GLY C  79 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   ARG C  78 " --> pdb=" O   GLY D  79 " (cutoff:3.500A)
      removed outlier: 6.119A  pdb=" N   ARG D  78 " --> pdb=" O   GLY E  79 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 85 through 87
      removed outlier: 6.584A  pdb=" N   TYR B  86 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   TYR C  86 " --> pdb=" O   PHE B  85 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   TYR D  86 " --> pdb=" O   PHE C  85 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   TYR E  86 " --> pdb=" O   PHE D  85 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 96 through 98
      removed outlier: 6.312A  pdb=" N   ILE B  96 " --> pdb=" O   LYS C  97 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   ILE C  96 " --> pdb=" O   LYS D  97 " (cutoff:3.500A)
      removed outlier: 6.332A  pdb=" N   ILE D  96 " --> pdb=" O   LYS E  97 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 101 through 105
      removed outlier: 6.940A  pdb=" N   GLY A 103 " --> pdb=" O   LEU B 102 " (cutoff:3.500A)
      removed outlier: 7.113A  pdb=" N   THR B 104 " --> pdb=" O   GLY A 103 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   LEU A 105 " --> pdb=" O   THR B 104 " (cutoff:3.500A)
      removed outlier: 8.584A  pdb=" N   LYS B 101 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
      removed outlier: 8.076A  pdb=" N   THR C 104 " --> pdb=" O   LYS B 101 " (cutoff:3.500A)
      removed outlier: 9.244A  pdb=" N   GLY B 103 " --> pdb=" O   THR C 104 " (cutoff:3.500A)
      removed outlier: 8.578A  pdb=" N   LYS C 101 " --> pdb=" O   LEU D 102 " (cutoff:3.500A)
      removed outlier: 8.068A  pdb=" N   THR D 104 " --> pdb=" O   LYS C 101 " (cutoff:3.500A)
      removed outlier: 9.242A  pdb=" N   GLY C 103 " --> pdb=" O   THR D 104 " (cutoff:3.500A)
      removed outlier: 8.615A  pdb=" N   LYS D 101 " --> pdb=" O   LEU E 102 " (cutoff:3.500A)
      removed outlier: 8.096A  pdb=" N   THR E 104 " --> pdb=" O   LYS D 101 " (cutoff:3.500A)
      removed outlier: 9.270A  pdb=" N   GLY D 103 " --> pdb=" O   THR E 104 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 108 through 111
      removed outlier: 7.013A  pdb=" N   VAL B 111 " --> pdb=" O   LYS A 110 " (cutoff:3.500A)
      removed outlier: 5.975A  pdb=" N   LEU B 108 " --> pdb=" O   GLN C 109 " (cutoff:3.500A)
      removed outlier: 5.686A  pdb=" N   VAL C 111 " --> pdb=" O   LEU B 108 " (cutoff:3.500A)
      removed outlier: 7.801A  pdb=" N   LYS B 110 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 5.973A  pdb=" N   LEU C 108 " --> pdb=" O   GLN D 109 " (cutoff:3.500A)
      removed outlier: 5.680A  pdb=" N   VAL D 111 " --> pdb=" O   LEU C 108 " (cutoff:3.500A)
      removed outlier: 7.803A  pdb=" N   LYS C 110 " --> pdb=" O   VAL D 111 " (cutoff:3.500A)
      removed outlier: 5.985A  pdb=" N   LEU D 108 " --> pdb=" O   GLN E 109 " (cutoff:3.500A)
      removed outlier: 5.702A  pdb=" N   VAL E 111 " --> pdb=" O   LEU D 108 " (cutoff:3.500A)
      removed outlier: 7.825A  pdb=" N   LYS D 110 " --> pdb=" O   VAL E 111 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 114 through 123
      removed outlier: 7.058A  pdb=" N   GLN B 116 " --> pdb=" O   ILE A 115 " (cutoff:3.500A)
      removed outlier: 7.032A  pdb=" N   SER A 117 " --> pdb=" O   GLN B 116 " (cutoff:3.500A)
      removed outlier: 7.993A  pdb=" N   ILE B 115 " --> pdb=" O   GLN C 116 " (cutoff:3.500A)
      removed outlier: 9.437A  pdb=" N   HIS C 118 " --> pdb=" O   ILE B 115 " (cutoff:3.500A)
      removed outlier: 7.057A  pdb=" N   SER B 117 " --> pdb=" O   HIS C 118 " (cutoff:3.500A)
      removed outlier: 8.122A  pdb=" N   HIS C 120 " --> pdb=" O   SER B 117 " (cutoff:3.500A)
      removed outlier: 6.825A  pdb=" N   VAL B 119 " --> pdb=" O   HIS C 120 " (cutoff:3.500A)
      removed outlier: 8.551A  pdb=" N   GLU C 122 " --> pdb=" O   VAL B 119 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   ILE B 121 " --> pdb=" O   GLU C 122 " (cutoff:3.500A)
      removed outlier: 7.994A  pdb=" N   ILE C 115 " --> pdb=" O   GLN D 116 " (cutoff:3.500A)
      removed outlier: 9.442A  pdb=" N   HIS D 118 " --> pdb=" O   ILE C 115 " (cutoff:3.500A)
      removed outlier: 7.067A  pdb=" N   SER C 117 " --> pdb=" O   HIS D 118 " (cutoff:3.500A)
      removed outlier: 8.129A  pdb=" N   HIS D 120 " --> pdb=" O   SER C 117 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL C 119 " --> pdb=" O   HIS D 120 " (cutoff:3.500A)
      removed outlier: 8.557A  pdb=" N   GLU D 122 " --> pdb=" O   VAL C 119 " (cutoff:3.500A)
      removed outlier: 6.546A  pdb=" N   ILE C 121 " --> pdb=" O   GLU D 122 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   ILE D 115 " --> pdb=" O   GLN E 116 " (cutoff:3.500A)
      removed outlier: 9.446A  pdb=" N   HIS E 118 " --> pdb=" O   ILE D 115 " (cutoff:3.500A)
      removed outlier: 7.061A  pdb=" N   SER D 117 " --> pdb=" O   HIS E 118 " (cutoff:3.500A)
      removed outlier: 8.125A  pdb=" N   HIS E 120 " --> pdb=" O   SER D 117 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   VAL D 119 " --> pdb=" O   HIS E 120 " (cutoff:3.500A)
      removed outlier: 8.552A  pdb=" N   GLU E 122 " --> pdb=" O   VAL D 119 " (cutoff:3.500A)
      removed outlier: 6.542A  pdb=" N   ILE D 121 " --> pdb=" O   GLU E 122 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 130 through 132
      removed outlier: 6.342A  pdb=" N   THR B 130 " --> pdb=" O   ALA C 131 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   THR C 130 " --> pdb=" O   ALA D 131 " (cutoff:3.500A)
      removed outlier: 6.356A  pdb=" N   THR D 130 " --> pdb=" O   ALA E 131 " (cutoff:3.500A)

    62 hydrogen bonds defined for protein.
    186 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.65

  Time building geometry restraints manager: 0.42 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1685
        1.34 -     1.46: 1055
        1.46 -     1.58: 2435
        1.58 -     1.70: 0
        1.70 -     1.81: 50
  Bond restraints: 5225
  Sorted by residual:
  bond pdb=" CG  PRO E  62 "
       pdb=" CD  PRO E  62 "
    ideal  model  delta    sigma   weight residual
    1.503  1.482  0.021 3.40e-02 8.65e+02 3.66e-01
  bond pdb=" CG  PRO C  62 "
       pdb=" CD  PRO C  62 "
    ideal  model  delta    sigma   weight residual
    1.503  1.483  0.020 3.40e-02 8.65e+02 3.56e-01
  bond pdb=" CA  PRO E  34 "
       pdb=" CB  PRO E  34 "
    ideal  model  delta    sigma   weight residual
    1.536  1.529  0.007 1.13e-02 7.83e+03 3.53e-01
  bond pdb=" CG  PRO A  62 "
       pdb=" CD  PRO A  62 "
    ideal  model  delta    sigma   weight residual
    1.503  1.483  0.020 3.40e-02 8.65e+02 3.50e-01
  bond pdb=" CG  PRO B  62 "
       pdb=" CD  PRO B  62 "
    ideal  model  delta    sigma   weight residual
    1.503  1.483  0.020 3.40e-02 8.65e+02 3.43e-01
  ... (remaining 5220 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.79: 6834
        1.79 -     3.59: 182
        3.59 -     5.38: 24
        5.38 -     7.17: 5
        7.17 -     8.97: 5
  Bond angle restraints: 7050
  Sorted by residual:
  angle pdb=" CA  LEU D 133 "
        pdb=" CB  LEU D 133 "
        pdb=" CG  LEU D 133 "
      ideal   model   delta    sigma   weight residual
     116.30  125.27   -8.97 3.50e+00 8.16e-02 6.56e+00
  angle pdb=" CA  LEU A 133 "
        pdb=" CB  LEU A 133 "
        pdb=" CG  LEU A 133 "
      ideal   model   delta    sigma   weight residual
     116.30  125.25   -8.95 3.50e+00 8.16e-02 6.54e+00
  angle pdb=" CA  LEU B 133 "
        pdb=" CB  LEU B 133 "
        pdb=" CG  LEU B 133 "
      ideal   model   delta    sigma   weight residual
     116.30  125.25   -8.95 3.50e+00 8.16e-02 6.54e+00
  angle pdb=" CA  LEU E 133 "
        pdb=" CB  LEU E 133 "
        pdb=" CG  LEU E 133 "
      ideal   model   delta    sigma   weight residual
     116.30  125.24   -8.94 3.50e+00 8.16e-02 6.52e+00
  angle pdb=" CA  LEU C 133 "
        pdb=" CB  LEU C 133 "
        pdb=" CG  LEU C 133 "
      ideal   model   delta    sigma   weight residual
     116.30  125.23   -8.93 3.50e+00 8.16e-02 6.51e+00
  ... (remaining 7045 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.94: 2705
       15.94 -    31.89: 365
       31.89 -    47.83: 100
       47.83 -    63.77: 10
       63.77 -    79.71: 20
  Dihedral angle restraints: 3200
    sinusoidal: 1325
      harmonic: 1875
  Sorted by residual:
  dihedral pdb=" CA  SER B  46 "
           pdb=" C   SER B  46 "
           pdb=" N   THR B  47 "
           pdb=" CA  THR B  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.80  -18.20     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  SER C  46 "
           pdb=" C   SER C  46 "
           pdb=" N   THR C  47 "
           pdb=" CA  THR C  47 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -161.80  -18.20     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  SER E  46 "
           pdb=" C   SER E  46 "
           pdb=" N   THR E  47 "
           pdb=" CA  THR E  47 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.81  -18.19     0      5.00e+00 4.00e-02 1.32e+01
  ... (remaining 3197 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 363
       0.028 -    0.057: 231
       0.057 -    0.085: 51
       0.085 -    0.114: 40
       0.114 -    0.142: 50
  Chirality restraints: 735
  Sorted by residual:
  chirality pdb=" CA  ILE E 121 "
            pdb=" N   ILE E 121 "
            pdb=" C   ILE E 121 "
            pdb=" CB  ILE E 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.05e-01
  chirality pdb=" CA  ILE C 121 "
            pdb=" N   ILE C 121 "
            pdb=" C   ILE C 121 "
            pdb=" CB  ILE C 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.96e-01
  chirality pdb=" CA  ILE D 121 "
            pdb=" N   ILE D 121 "
            pdb=" C   ILE D 121 "
            pdb=" CB  ILE D 121 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 732 not shown)

  Planarity restraints: 925
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C  85 "    0.009 2.00e-02 2.50e+03   1.12e-02 2.21e+00
        pdb=" CG  PHE C  85 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE C  85 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE C  85 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE C  85 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE C  85 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE C  85 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A  85 "    0.009 2.00e-02 2.50e+03   1.12e-02 2.18e+00
        pdb=" CG  PHE A  85 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE A  85 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE A  85 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE A  85 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE A  85 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE A  85 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE E  85 "    0.009 2.00e-02 2.50e+03   1.12e-02 2.18e+00
        pdb=" CG  PHE E  85 "   -0.025 2.00e-02 2.50e+03
        pdb=" CD1 PHE E  85 "    0.011 2.00e-02 2.50e+03
        pdb=" CD2 PHE E  85 "    0.004 2.00e-02 2.50e+03
        pdb=" CE1 PHE E  85 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE E  85 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ  PHE E  85 "   -0.001 2.00e-02 2.50e+03
  ... (remaining 922 not shown)

  Histogram of nonbonded interaction distances:
        2.51 -     2.99: 2360
        2.99 -     3.46: 4853
        3.46 -     3.94: 8145
        3.94 -     4.42: 9394
        4.42 -     4.90: 14913
  Nonbonded interactions: 39665
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS C  97 "
            pdb=" OE1 GLU C 100 "
     model   vdw
     2.508 3.120
  nonbonded pdb=" NZ  LYS B  97 "
            pdb=" OE1 GLU B 100 "
     model   vdw
     2.509 3.120
  nonbonded pdb=" NZ  LYS A  97 "
            pdb=" OE1 GLU A 100 "
     model   vdw
     2.509 3.120
  nonbonded pdb=" NZ  LYS D  97 "
            pdb=" OE1 GLU D 100 "
     model   vdw
     2.509 3.120
  nonbonded pdb=" NZ  LYS E  97 "
            pdb=" OE1 GLU E 100 "
     model   vdw
     2.509 3.120
  ... (remaining 39660 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'A'
  selection = chain 'D'
  selection = chain 'E'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.650
  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:             0.000
  Extract box with map and model:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.380
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  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:6.160
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
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      :  0.003   0.027   5240  Z= 0.126
  Angle     :  0.717   8.966   7080  Z= 0.363
  Chirality :  0.051   0.142    735
  Planarity :  0.003   0.022    925
  Dihedral  : 16.606  79.715   1975
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  0.90 %
    Allowed  : 18.92 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.95 (0.25), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -3.01 (0.19), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  74 
 TYR   0.010   0.001   TYR E 132 
 PHE   0.025   0.003   PHE C  85 
 TRP   0.009   0.002   TRP D   3 
 HIS   0.006   0.002   HIS D 120 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5225)
  covalent geometry    : angle       0.71526 ( 7050)
  SS BOND              : bond        0.00297 (   15)
  SS BOND              : angle       1.08718 (   30)
  hydrogen bonds       : bond        0.27912 (   62)
  hydrogen bonds       : angle       8.34260 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 104
  time to evaluate  : 0.194 
Fit side-chains
REVERT: A   60 GLU cc_start: 0.8673 (tt0) cc_final: 0.8443 (tt0)
REVERT: A   84 MET cc_start: 0.8341 (ttp) cc_final: 0.8000 (ttt)
REVERT: A   91 LYS cc_start: 0.8299 (mttt) cc_final: 0.7833 (mmmt)
REVERT: A   93 LYS cc_start: 0.8223 (mtpp) cc_final: 0.7898 (mttp)
REVERT: A  100 GLU cc_start: 0.8172 (tt0) cc_final: 0.7916 (tt0)
REVERT: D   16 ARG cc_start: 0.8392 (mtt180) cc_final: 0.8081 (mtt180)
REVERT: D   78 ARG cc_start: 0.7819 (mtm180) cc_final: 0.7455 (mtp85)
REVERT: E   78 ARG cc_start: 0.7476 (mtm180) cc_final: 0.6928 (ttt-90)
REVERT: E  122 GLU cc_start: 0.8654 (tt0) cc_final: 0.8426 (tt0)
REVERT: E  125 ASP cc_start: 0.8411 (t0) cc_final: 0.8120 (t0)
  outliers start: 5
  outliers final: 0
  residues processed: 109
  average time/residue: 0.6000
  time to fit residues: 67.6090
Evaluate side-chains
  97 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    5.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0370
   chunk 27 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   overall best weight:    2.6064

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  13 ASN
C  35 HIS
A  13 ASN
D  13 ASN
D  35 HIS
E  13 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.101678 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.091924 restraints weight = 6178.878|
|-----------------------------------------------------------------------------|
r_work (start): 0.3344 rms_B_bonded: 1.26
r_work: 0.3259 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3172 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8561
moved from start:          0.1414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   5240  Z= 0.234
  Angle     :  0.905   9.044   7080  Z= 0.482
  Chirality :  0.059   0.171    735
  Planarity :  0.005   0.037    925
  Dihedral  :  5.494  21.257    725
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 2.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.53 %
    Favored  : 89.47 %
  Rotamer:
    Outliers :  2.52 %
    Allowed  : 17.12 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.81 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E  33 
 TYR   0.020   0.003   TYR D 132 
 PHE   0.030   0.003   PHE C  85 
 TRP   0.015   0.003   TRP E   3 
 HIS   0.012   0.003   HIS A  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00547 ( 5225)
  covalent geometry    : angle       0.90211 ( 7050)
  SS BOND              : bond        0.00409 (   15)
  SS BOND              : angle       1.35820 (   30)
  hydrogen bonds       : bond        0.08753 (   62)
  hydrogen bonds       : angle       6.91397 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 106
  time to evaluate  : 0.191 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7729 (mmtt) cc_final: 0.7432 (mptp)
REVERT: A   84 MET cc_start: 0.8439 (OUTLIER) cc_final: 0.8129 (ttm)
REVERT: A   91 LYS cc_start: 0.8472 (mttt) cc_final: 0.8121 (mmmt)
REVERT: A   93 LYS cc_start: 0.8381 (mtpp) cc_final: 0.8017 (mptt)
REVERT: D   16 ARG cc_start: 0.8589 (mtt180) cc_final: 0.8388 (mtm-85)
REVERT: E   78 ARG cc_start: 0.7808 (mtm180) cc_final: 0.6756 (ppt90)
  outliers start: 14
  outliers final: 7
  residues processed: 113
  average time/residue: 0.6589
  time to fit residues: 76.8321
Evaluate side-chains
  108 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 100
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain E residue   57 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 11 optimal weight:    5.9990
   chunk 19 optimal weight:    5.9990
   chunk 47 optimal weight:    6.9990
   chunk 0 optimal weight:   10.0000
   chunk 42 optimal weight:    0.7980
   chunk 39 optimal weight:    7.9990
   chunk 28 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 1 optimal weight:    3.9990
   chunk 52 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    1.9184

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  13 ASN
C  35 HIS
D  35 HIS
E  13 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.103245 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.093412 restraints weight = 6096.816|
|-----------------------------------------------------------------------------|
r_work (start): 0.3368 rms_B_bonded: 1.27
r_work: 0.3284 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3198 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.3198
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8536
moved from start:          0.1534

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   5240  Z= 0.188
  Angle     :  0.816   8.119   7080  Z= 0.437
  Chirality :  0.056   0.175    735
  Planarity :  0.004   0.031    925
  Dihedral  :  5.436  20.194    725
  Min Nonbonded Distance : 2.657

Molprobity Statistics.
  All-atom Clashscore : 2.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.22 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.83 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C  33 
 TYR   0.017   0.002   TYR D 132 
 PHE   0.024   0.003   PHE B  85 
 TRP   0.013   0.002   TRP A   3 
 HIS   0.010   0.003   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00431 ( 5225)
  covalent geometry    : angle       0.81384 ( 7050)
  SS BOND              : bond        0.00413 (   15)
  SS BOND              : angle       1.28149 (   30)
  hydrogen bonds       : bond        0.07620 (   62)
  hydrogen bonds       : angle       6.80608 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.146 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7678 (mmtt) cc_final: 0.7411 (mptp)
REVERT: A   84 MET cc_start: 0.8396 (ttp) cc_final: 0.8095 (ttm)
REVERT: A   91 LYS cc_start: 0.8433 (mttt) cc_final: 0.7930 (mmtt)
REVERT: A   93 LYS cc_start: 0.8384 (mtpp) cc_final: 0.8075 (mttp)
REVERT: A  100 GLU cc_start: 0.8515 (tt0) cc_final: 0.8230 (tt0)
REVERT: E   78 ARG cc_start: 0.7877 (mtm180) cc_final: 0.6680 (ppt90)
  outliers start: 13
  outliers final: 7
  residues processed: 113
  average time/residue: 0.6471
  time to fit residues: 75.4748
Evaluate side-chains
  106 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 99
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain E residue  128 ASP
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 37 optimal weight:    0.0170
   chunk 57 optimal weight:    0.2980
   chunk 61 optimal weight:    3.9990
   chunk 49 optimal weight:    1.9990
   chunk 42 optimal weight:    6.9990
   chunk 44 optimal weight:    0.8980
   chunk 16 optimal weight:    1.9990
   chunk 39 optimal weight:    5.9990
   chunk 58 optimal weight:    1.9990
   chunk 18 optimal weight:    2.9990
   chunk 26 optimal weight:    7.9990
   overall best weight:    1.0422

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  35 HIS
D  35 HIS
E  13 ASN
E  64 GLN
E  65 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.105459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.095676 restraints weight = 6110.183|
|-----------------------------------------------------------------------------|
r_work (start): 0.3404 rms_B_bonded: 1.28
r_work: 0.3319 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3233 rms_B_bonded: 2.56 restraints_weight: 0.2500
r_work (final): 0.3233
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8509
moved from start:          0.1578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5240  Z= 0.136
  Angle     :  0.712   7.513   7080  Z= 0.379
  Chirality :  0.053   0.164    735
  Planarity :  0.003   0.025    925
  Dihedral  :  5.191  18.526    725
  Min Nonbonded Distance : 2.658

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.15 %
    Favored  : 88.85 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.66 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.83 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.91 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B  74 
 TYR   0.013   0.002   TYR E  63 
 PHE   0.020   0.002   PHE B  85 
 TRP   0.011   0.002   TRP C   3 
 HIS   0.010   0.003   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 5225)
  covalent geometry    : angle       0.70986 ( 7050)
  SS BOND              : bond        0.00350 (   15)
  SS BOND              : angle       1.15197 (   30)
  hydrogen bonds       : bond        0.05867 (   62)
  hydrogen bonds       : angle       6.43615 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 99
  time to evaluate  : 0.177 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7627 (mmtt) cc_final: 0.7418 (mptp)
REVERT: A   84 MET cc_start: 0.8323 (OUTLIER) cc_final: 0.8042 (ttm)
REVERT: A   91 LYS cc_start: 0.8406 (mttt) cc_final: 0.7924 (mmtt)
REVERT: A   93 LYS cc_start: 0.8347 (mtpp) cc_final: 0.8046 (mttp)
REVERT: A  100 GLU cc_start: 0.8494 (tt0) cc_final: 0.8211 (tt0)
REVERT: E   78 ARG cc_start: 0.7858 (mtm180) cc_final: 0.7507 (ttt-90)
REVERT: E   84 MET cc_start: 0.8322 (ttm) cc_final: 0.8108 (ttm)
  outliers start: 12
  outliers final: 5
  residues processed: 106
  average time/residue: 0.6722
  time to fit residues: 73.4098
Evaluate side-chains
  104 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 98
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain E residue   57 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 6 optimal weight:    6.9990
   chunk 1 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 52 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 26 optimal weight:   10.0000
   chunk 39 optimal weight:    5.9990
   chunk 2 optimal weight:    0.9990
   chunk 28 optimal weight:    4.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.5988

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  35 HIS
D  35 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.104209 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.094326 restraints weight = 6173.611|
|-----------------------------------------------------------------------------|
r_work (start): 0.3389 rms_B_bonded: 1.28
r_work: 0.3303 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.3217 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8526
moved from start:          0.1604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   5240  Z= 0.166
  Angle     :  0.766   7.431   7080  Z= 0.411
  Chirality :  0.055   0.169    735
  Planarity :  0.004   0.027    925
  Dihedral  :  5.283  19.384    725
  Min Nonbonded Distance : 2.653

Molprobity Statistics.
  All-atom Clashscore : 3.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 16.04 %
    Favored  : 80.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.84 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.92 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  74 
 TYR   0.017   0.002   TYR D 132 
 PHE   0.029   0.003   PHE C  85 
 TRP   0.010   0.002   TRP A   3 
 HIS   0.010   0.003   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00374 ( 5225)
  covalent geometry    : angle       0.76354 ( 7050)
  SS BOND              : bond        0.00361 (   15)
  SS BOND              : angle       1.21549 (   30)
  hydrogen bonds       : bond        0.06705 (   62)
  hydrogen bonds       : angle       6.57551 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 101
  time to evaluate  : 0.201 
Fit side-chains
REVERT: A   10 LYS cc_start: 0.7573 (mmtt) cc_final: 0.7359 (mptp)
REVERT: A   84 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.8082 (ttt)
REVERT: A   91 LYS cc_start: 0.8384 (mttt) cc_final: 0.7920 (mmtt)
REVERT: A   93 LYS cc_start: 0.8358 (mtpp) cc_final: 0.8056 (mttp)
REVERT: A  100 GLU cc_start: 0.8525 (tt0) cc_final: 0.8238 (tt0)
REVERT: E   78 ARG cc_start: 0.7852 (mtm180) cc_final: 0.7508 (ttt-90)
REVERT: E   84 MET cc_start: 0.8309 (ttm) cc_final: 0.8078 (ttm)
  outliers start: 21
  outliers final: 12
  residues processed: 113
  average time/residue: 0.6308
  time to fit residues: 73.7781
Evaluate side-chains
  109 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 96
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   47 THR
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue   76 SER
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain E residue   57 VAL
Chi-restraints excluded: chain E residue  128 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 34 optimal weight:    0.6980
   chunk 40 optimal weight:    9.9990
   chunk 24 optimal weight:    1.9990
   chunk 63 optimal weight:    0.0970
   chunk 38 optimal weight:    4.9990
   chunk 51 optimal weight:    6.9990
   chunk 48 optimal weight:    0.9990
   chunk 57 optimal weight:    0.7980
   chunk 11 optimal weight:    0.7980
   chunk 6 optimal weight:    4.9990
   chunk 33 optimal weight:    7.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  35 HIS
D  35 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.107373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.097683 restraints weight = 6167.768|
|-----------------------------------------------------------------------------|
r_work (start): 0.3439 rms_B_bonded: 1.28
r_work: 0.3354 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3268 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3268
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8484
moved from start:          0.1591

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5240  Z= 0.115
  Angle     :  0.652   5.257   7080  Z= 0.348
  Chirality :  0.051   0.155    735
  Planarity :  0.003   0.028    925
  Dihedral  :  4.986  17.576    725
  Min Nonbonded Distance : 2.645

Molprobity Statistics.
  All-atom Clashscore : 3.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.08 %
    Favored  : 89.92 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 17.30 %
    Favored  : 80.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.80 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  74 
 TYR   0.009   0.001   TYR D 132 
 PHE   0.024   0.002   PHE C  85 
 TRP   0.010   0.002   TRP C   3 
 HIS   0.010   0.002   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 ( 5225)
  covalent geometry    : angle       0.64943 ( 7050)
  SS BOND              : bond        0.00300 (   15)
  SS BOND              : angle       1.05057 (   30)
  hydrogen bonds       : bond        0.04933 (   62)
  hydrogen bonds       : angle       6.16073 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 96
  time to evaluate  : 0.208 
Fit side-chains
REVERT: A   75 ILE cc_start: 0.8919 (OUTLIER) cc_final: 0.8406 (mp)
REVERT: A   84 MET cc_start: 0.8188 (OUTLIER) cc_final: 0.7933 (ttt)
REVERT: A   91 LYS cc_start: 0.8374 (mttt) cc_final: 0.7931 (mmtt)
REVERT: A   93 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8042 (mttp)
REVERT: A  100 GLU cc_start: 0.8492 (tt0) cc_final: 0.8236 (tt0)
REVERT: E   78 ARG cc_start: 0.7721 (mtm180) cc_final: 0.7517 (ttt-90)
REVERT: E   84 MET cc_start: 0.8282 (ttm) cc_final: 0.8048 (ttm)
  outliers start: 12
  outliers final: 5
  residues processed: 102
  average time/residue: 0.6677
  time to fit residues: 70.2831
Evaluate side-chains
  102 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 95
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain D residue  128 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 51 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 34 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 31 optimal weight:    0.0870
   chunk 49 optimal weight:    0.0670
   chunk 27 optimal weight:    5.9990
   chunk 36 optimal weight:    0.7980
   chunk 29 optimal weight:    3.9990
   chunk 43 optimal weight:    0.6980
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.9298

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  35 HIS
D  35 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.106607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.096881 restraints weight = 6072.445|
|-----------------------------------------------------------------------------|
r_work (start): 0.3424 rms_B_bonded: 1.25
r_work: 0.3341 rms_B_bonded: 1.47 restraints_weight: 0.5000
r_work: 0.3256 rms_B_bonded: 2.54 restraints_weight: 0.2500
r_work (final): 0.3256
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5240  Z= 0.126
  Angle     :  0.669   5.217   7080  Z= 0.359
  Chirality :  0.052   0.156    735
  Planarity :  0.003   0.029    925
  Dihedral  :  4.968  18.392    725
  Min Nonbonded Distance : 2.643

Molprobity Statistics.
  All-atom Clashscore : 2.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.30 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 16.76 %
    Favored  : 80.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.78 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.87 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  74 
 TYR   0.013   0.002   TYR E  63 
 PHE   0.028   0.003   PHE C  85 
 TRP   0.009   0.002   TRP C   3 
 HIS   0.010   0.002   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5225)
  covalent geometry    : angle       0.66732 ( 7050)
  SS BOND              : bond        0.00298 (   15)
  SS BOND              : angle       1.05944 (   30)
  hydrogen bonds       : bond        0.05436 (   62)
  hydrogen bonds       : angle       6.21692 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.149 
Fit side-chains
REVERT: A   75 ILE cc_start: 0.8966 (OUTLIER) cc_final: 0.8420 (mp)
REVERT: A   84 MET cc_start: 0.8195 (OUTLIER) cc_final: 0.7921 (ttt)
REVERT: A   91 LYS cc_start: 0.8369 (mttt) cc_final: 0.7928 (mmtt)
REVERT: A   93 LYS cc_start: 0.8332 (mtpp) cc_final: 0.8036 (mttp)
REVERT: A  100 GLU cc_start: 0.8497 (tt0) cc_final: 0.8233 (tt0)
REVERT: E   84 MET cc_start: 0.8279 (ttm) cc_final: 0.8043 (ttm)
  outliers start: 16
  outliers final: 10
  residues processed: 105
  average time/residue: 0.6245
  time to fit residues: 67.6877
Evaluate side-chains
  107 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 95
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain B residue   53 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain E residue   11 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 57 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 28 optimal weight:    6.9990
   chunk 44 optimal weight:    0.7980
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 59 optimal weight:    5.9990
   chunk 35 optimal weight:    3.9990
   chunk 2 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  35 HIS
D  35 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.106942 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.097236 restraints weight = 6164.419|
|-----------------------------------------------------------------------------|
r_work (start): 0.3431 rms_B_bonded: 1.28
r_work: 0.3347 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3262 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3262
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8488
moved from start:          0.1640

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5240  Z= 0.123
  Angle     :  0.666   5.187   7080  Z= 0.357
  Chirality :  0.051   0.155    735
  Planarity :  0.003   0.029    925
  Dihedral  :  4.948  18.098    725
  Min Nonbonded Distance : 2.644

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.69 %
    Favored  : 89.31 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.48 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.79 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  74 
 TYR   0.011   0.002   TYR D 132 
 PHE   0.037   0.003   PHE C  85 
 TRP   0.009   0.002   TRP C   3 
 HIS   0.010   0.002   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 5225)
  covalent geometry    : angle       0.66400 ( 7050)
  SS BOND              : bond        0.00319 (   15)
  SS BOND              : angle       1.05010 (   30)
  hydrogen bonds       : bond        0.05344 (   62)
  hydrogen bonds       : angle       6.18473 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.228 
Fit side-chains
REVERT: A   75 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8424 (mp)
REVERT: A   84 MET cc_start: 0.8209 (OUTLIER) cc_final: 0.7944 (ttt)
REVERT: A   91 LYS cc_start: 0.8391 (mttt) cc_final: 0.7949 (mmtt)
REVERT: A   93 LYS cc_start: 0.8340 (mtpp) cc_final: 0.8046 (mttp)
REVERT: A  100 GLU cc_start: 0.8501 (tt0) cc_final: 0.8238 (tt0)
REVERT: E   84 MET cc_start: 0.8328 (ttm) cc_final: 0.8091 (ttm)
  outliers start: 15
  outliers final: 9
  residues processed: 101
  average time/residue: 0.6513
  time to fit residues: 67.8742
Evaluate side-chains
  105 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   55 MET
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain E residue   11 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 57 optimal weight:    1.9990
   chunk 4 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 48 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 28 optimal weight:    5.9990
   chunk 46 optimal weight:   10.0000
   chunk 62 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.5386

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  35 HIS
D  35 HIS
E  64 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.105019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.095234 restraints weight = 6177.311|
|-----------------------------------------------------------------------------|
r_work (start): 0.3402 rms_B_bonded: 1.27
r_work: 0.3315 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.3227 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8517
moved from start:          0.1697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   5240  Z= 0.161
  Angle     :  0.738   5.747   7080  Z= 0.399
  Chirality :  0.054   0.164    735
  Planarity :  0.004   0.026    925
  Dihedral  :  5.154  19.190    725
  Min Nonbonded Distance : 2.646

Molprobity Statistics.
  All-atom Clashscore : 2.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.99 %
    Favored  : 89.01 %
  Rotamer:
    Outliers :  2.70 %
    Allowed  : 17.48 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.80 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.89 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  33 
 TYR   0.015   0.002   TYR D 132 
 PHE   0.043   0.004   PHE C  85 
 TRP   0.009   0.002   TRP A   3 
 HIS   0.011   0.003   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00367 ( 5225)
  covalent geometry    : angle       0.73603 ( 7050)
  SS BOND              : bond        0.00354 (   15)
  SS BOND              : angle       1.17653 (   30)
  hydrogen bonds       : bond        0.06474 (   62)
  hydrogen bonds       : angle       6.43842 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   75 ILE cc_start: 0.8962 (OUTLIER) cc_final: 0.8410 (mp)
REVERT: A   84 MET cc_start: 0.8218 (OUTLIER) cc_final: 0.7941 (ttt)
REVERT: A   91 LYS cc_start: 0.8360 (mttt) cc_final: 0.7926 (mmtt)
REVERT: A   93 LYS cc_start: 0.8360 (mtpp) cc_final: 0.8063 (mttp)
REVERT: A  100 GLU cc_start: 0.8516 (tt0) cc_final: 0.8251 (tt0)
REVERT: E   84 MET cc_start: 0.8341 (ttm) cc_final: 0.8119 (ttm)
  outliers start: 15
  outliers final: 9
  residues processed: 105
  average time/residue: 0.6413
  time to fit residues: 69.4668
Evaluate side-chains
  105 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 94
  time to evaluate  : 0.188 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain A residue   84 MET
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain E residue   11 SER
Chi-restraints excluded: chain E residue  128 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 20 optimal weight:    0.9990
   chunk 25 optimal weight:    0.5980
   chunk 41 optimal weight:    7.9990
   chunk 39 optimal weight:    6.9990
   chunk 3 optimal weight:    6.9990
   chunk 53 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   chunk 47 optimal weight:    0.7980
   chunk 37 optimal weight:    0.9980
   chunk 6 optimal weight:    5.9990
   chunk 34 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:
B  13 ASN
C  35 HIS
D  35 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3565 r_free = 0.3565 target = 0.106934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.097130 restraints weight = 6192.456|
|-----------------------------------------------------------------------------|
r_work (start): 0.3430 rms_B_bonded: 1.29
r_work: 0.3344 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1698

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   5240  Z= 0.126
  Angle     :  0.677   5.391   7080  Z= 0.362
  Chirality :  0.052   0.157    735
  Planarity :  0.003   0.027    925
  Dihedral  :  5.033  18.189    725
  Min Nonbonded Distance : 2.647

Molprobity Statistics.
  All-atom Clashscore : 3.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.38 %
    Favored  : 89.62 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.20 %
    Favored  : 79.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.79 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E  30 
 TYR   0.015   0.002   TYR E  63 
 PHE   0.039   0.003   PHE C  85 
 TRP   0.010   0.002   TRP C   3 
 HIS   0.011   0.002   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 5225)
  covalent geometry    : angle       0.67508 ( 7050)
  SS BOND              : bond        0.00318 (   15)
  SS BOND              : angle       1.09440 (   30)
  hydrogen bonds       : bond        0.05460 (   62)
  hydrogen bonds       : angle       6.20624 (  186)

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

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

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1310 Ramachandran restraints generated.
    655 Oldfield, 0 Emsley, 655 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 95
  time to evaluate  : 0.196 
Fit side-chains
REVERT: A   75 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8415 (mp)
REVERT: A   84 MET cc_start: 0.8250 (ttp) cc_final: 0.7981 (ttm)
REVERT: A   91 LYS cc_start: 0.8358 (mttt) cc_final: 0.7922 (mmtt)
REVERT: A   93 LYS cc_start: 0.8341 (mtpp) cc_final: 0.8041 (mttp)
REVERT: A  100 GLU cc_start: 0.8509 (tt0) cc_final: 0.8246 (tt0)
REVERT: E   84 MET cc_start: 0.8293 (ttm) cc_final: 0.8072 (ttm)
  outliers start: 11
  outliers final: 8
  residues processed: 102
  average time/residue: 0.6466
  time to fit residues: 68.1287
Evaluate side-chains
  103 residues out of total 555 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 94
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 SER
Chi-restraints excluded: chain B residue   47 THR
Chi-restraints excluded: chain C residue   11 SER
Chi-restraints excluded: chain C residue   57 VAL
Chi-restraints excluded: chain C residue  106 LEU
Chi-restraints excluded: chain A residue   75 ILE
Chi-restraints excluded: chain D residue   57 VAL
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain E residue   11 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    5.9990
   chunk 15 optimal weight:   10.0000
   chunk 21 optimal weight:    0.7980
   chunk 57 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 24 optimal weight:    0.0970
   chunk 45 optimal weight:    2.9990
   chunk 17 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   overall best weight:    0.7178

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

Flipped N/Q/H residues before XYZ refinement:
B  13 ASN
C  35 HIS
D  35 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.107547 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.097828 restraints weight = 6188.377|
|-----------------------------------------------------------------------------|
r_work (start): 0.3440 rms_B_bonded: 1.28
r_work: 0.3357 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.3272 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.3272
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8480
moved from start:          0.1699

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5240  Z= 0.117
  Angle     :  0.655   5.297   7080  Z= 0.349
  Chirality :  0.051   0.155    735
  Planarity :  0.003   0.027    925
  Dihedral  :  4.934  17.899    725
  Min Nonbonded Distance : 2.642

Molprobity Statistics.
  All-atom Clashscore : 3.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.30 %
    Favored  : 88.70 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 18.38 %
    Favored  : 79.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.79 (0.26), residues: 655
  helix:  None (None), residues: 0
  sheet:  None (None), residues: 0
  loop : -2.88 (0.20), residues: 655

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  74 
 TYR   0.012   0.002   TYR C  63 
 PHE   0.040   0.003   PHE C  85 
 TRP   0.010   0.002   TRP C   3 
 HIS   0.010   0.002   HIS D  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 5225)
  covalent geometry    : angle       0.65255 ( 7050)
  SS BOND              : bond        0.00308 (   15)
  SS BOND              : angle       1.02799 (   30)
  hydrogen bonds       : bond        0.05135 (   62)
  hydrogen bonds       : angle       6.09255 (  186)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1989.18 seconds
wall clock time: 34 minutes 37.31 seconds (2077.31 seconds total)