Starting phenix.real_space_refine
on Tue Jan 21 21:33:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9g8b_51127/01_2025/9g8b_51127.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9g8b_51127/01_2025/9g8b_51127.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9g8b_51127/01_2025/9g8b_51127.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9g8b_51127/01_2025/9g8b_51127.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9g8b_51127/01_2025/9g8b_51127.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9g8b_51127/01_2025/9g8b_51127.cif"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.141
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      91      5.16       5
     C   10703      2.51       5
     N    2849      2.21       5
     O    3703      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib"
  Total number of atoms: 17346
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 2478
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 345, 2478
          Classifications: {'peptide': 345}
          Link IDs: {'PTRANS': 23, 'TRANS': 321}
  Restraints were copied for chains:
    C, B, E, D, G, F
  Time building chain proxies: 6.14, per 1000 atoms: 0.35
  Number of scatterers: 17346
  At special positions: 0
  Unit cell: (101.175, 102.24, 185.31, 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      91     16.00
     O    3703      8.00
     N    2849      7.00
     C   10703      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A2906 " - pdb=" SG  CYS A3058 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A2988 " - pdb=" SG  CYS A3140 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A3001 " - pdb=" SG  CYS A3051 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A3085 " - pdb=" SG  CYS A3222 " distance=2.04

  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: 4.17
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4382

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 70 sheets defined
      6.1% alpha, 37.7% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 3.35
  Creating SS restraints...
    Processing helix  chain 'A' and resid 2927 through 2929
      No H-bonds generated for 'chain 'A' and resid 2927 through 2929'
    Processing helix  chain 'A' and resid 2944 through 2948
    Processing helix  chain 'A' and resid 3107 through 3111
      removed outlier: 4.290A  pdb=" N   THR A3111 " --> pdb=" O   SER A3108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 3188 through 3190
      No H-bonds generated for 'chain 'A' and resid 3188 through 3190'
    Processing helix  chain 'A' and resid 3205 through 3209
    Processing helix  chain 'B' and resid 2927 through 2929
      No H-bonds generated for 'chain 'B' and resid 2927 through 2929'
    Processing helix  chain 'B' and resid 2944 through 2948
    Processing helix  chain 'B' and resid 3107 through 3111
      removed outlier: 4.290A  pdb=" N   THR B3111 " --> pdb=" O   SER B3108 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 3188 through 3190
      No H-bonds generated for 'chain 'B' and resid 3188 through 3190'
    Processing helix  chain 'B' and resid 3205 through 3209
    Processing helix  chain 'C' and resid 2927 through 2929
      No H-bonds generated for 'chain 'C' and resid 2927 through 2929'
    Processing helix  chain 'C' and resid 2944 through 2948
    Processing helix  chain 'C' and resid 3107 through 3111
      removed outlier: 4.291A  pdb=" N   THR C3111 " --> pdb=" O   SER C3108 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 3188 through 3190
      No H-bonds generated for 'chain 'C' and resid 3188 through 3190'
    Processing helix  chain 'C' and resid 3205 through 3209
    Processing helix  chain 'D' and resid 2927 through 2929
      No H-bonds generated for 'chain 'D' and resid 2927 through 2929'
    Processing helix  chain 'D' and resid 2944 through 2948
    Processing helix  chain 'D' and resid 3107 through 3111
      removed outlier: 4.290A  pdb=" N   THR D3111 " --> pdb=" O   SER D3108 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 3188 through 3190
      No H-bonds generated for 'chain 'D' and resid 3188 through 3190'
    Processing helix  chain 'D' and resid 3205 through 3209
    Processing helix  chain 'E' and resid 2927 through 2929
      No H-bonds generated for 'chain 'E' and resid 2927 through 2929'
    Processing helix  chain 'E' and resid 2944 through 2948
    Processing helix  chain 'E' and resid 3107 through 3111
      removed outlier: 4.290A  pdb=" N   THR E3111 " --> pdb=" O   SER E3108 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 3188 through 3190
      No H-bonds generated for 'chain 'E' and resid 3188 through 3190'
    Processing helix  chain 'E' and resid 3205 through 3209
    Processing helix  chain 'F' and resid 2927 through 2929
      No H-bonds generated for 'chain 'F' and resid 2927 through 2929'
    Processing helix  chain 'F' and resid 2944 through 2948
    Processing helix  chain 'F' and resid 3107 through 3111
      removed outlier: 4.290A  pdb=" N   THR F3111 " --> pdb=" O   SER F3108 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 3188 through 3190
      No H-bonds generated for 'chain 'F' and resid 3188 through 3190'
    Processing helix  chain 'F' and resid 3205 through 3209
    Processing helix  chain 'G' and resid 2927 through 2929
      No H-bonds generated for 'chain 'G' and resid 2927 through 2929'
    Processing helix  chain 'G' and resid 2944 through 2948
    Processing helix  chain 'G' and resid 3107 through 3111
      removed outlier: 4.290A  pdb=" N   THR G3111 " --> pdb=" O   SER G3108 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 3188 through 3190
      No H-bonds generated for 'chain 'G' and resid 3188 through 3190'
    Processing helix  chain 'G' and resid 3205 through 3209
    Processing sheet with id=AA1, first strand: chain 'A' and resid 2903 through 2906
      removed outlier: 6.549A  pdb=" N   PHE A2903 " --> pdb=" O   GLY A2971 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   ASN A2973 " --> pdb=" O   PHE A2903 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL A2905 " --> pdb=" O   ASN A2973 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 2981 through 2982
    Processing sheet with id=AA3, first strand: chain 'A' and resid 2987 through 2988
      removed outlier: 7.051A  pdb=" N   ILE A2987 " --> pdb=" O   ASN A3070 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 3027 through 3028
    Processing sheet with id=AA5, first strand: chain 'A' and resid 3027 through 3028
    Processing sheet with id=AA6, first strand: chain 'A' and resid 3078 through 3080
      removed outlier: 5.901A  pdb=" N   GLY A3088 " --> pdb=" O   ASN A3124 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN A3124 " --> pdb=" O   GLY A3088 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 3084 through 3085
      removed outlier: 6.548A  pdb=" N   VAL A3084 " --> pdb=" O   HIS A3152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA7
    Processing sheet with id=AA8, first strand: chain 'A' and resid 3113 through 3115
    Processing sheet with id=AA9, first strand: chain 'A' and resid 3113 through 3115
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3164 through 3167
      removed outlier: 6.865A  pdb=" N   PHE A3164 " --> pdb=" O   THR A3232 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   ASP A3234 " --> pdb=" O   PHE A3164 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL A3166 " --> pdb=" O   ASP A3234 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER A3182 " --> pdb=" O   ILE A3217 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 2903 through 2906
      removed outlier: 6.549A  pdb=" N   PHE B2903 " --> pdb=" O   GLY B2971 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   ASN B2973 " --> pdb=" O   PHE B2903 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   VAL B2905 " --> pdb=" O   ASN B2973 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 2981 through 2982
    Processing sheet with id=AB4, first strand: chain 'B' and resid 2987 through 2988
      removed outlier: 7.051A  pdb=" N   ILE B2987 " --> pdb=" O   ASN B3070 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4
    Processing sheet with id=AB5, first strand: chain 'B' and resid 3027 through 3028
    Processing sheet with id=AB6, first strand: chain 'B' and resid 3027 through 3028
    Processing sheet with id=AB7, first strand: chain 'B' and resid 3078 through 3080
      removed outlier: 5.901A  pdb=" N   GLY B3088 " --> pdb=" O   ASN B3124 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASN B3124 " --> pdb=" O   GLY B3088 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 3084 through 3085
      removed outlier: 6.548A  pdb=" N   VAL B3084 " --> pdb=" O   HIS B3152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB8
    Processing sheet with id=AB9, first strand: chain 'B' and resid 3113 through 3115
    Processing sheet with id=AC1, first strand: chain 'B' and resid 3113 through 3115
    Processing sheet with id=AC2, first strand: chain 'B' and resid 3164 through 3167
      removed outlier: 6.865A  pdb=" N   PHE B3164 " --> pdb=" O   THR B3232 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   ASP B3234 " --> pdb=" O   PHE B3164 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL B3166 " --> pdb=" O   ASP B3234 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER B3182 " --> pdb=" O   ILE B3217 " (cutoff:3.500A)
    Processing sheet with id=AC3, first strand: chain 'C' and resid 2903 through 2906
      removed outlier: 6.549A  pdb=" N   PHE C2903 " --> pdb=" O   GLY C2971 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   ASN C2973 " --> pdb=" O   PHE C2903 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL C2905 " --> pdb=" O   ASN C2973 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 2981 through 2982
    Processing sheet with id=AC5, first strand: chain 'C' and resid 2987 through 2988
      removed outlier: 7.050A  pdb=" N   ILE C2987 " --> pdb=" O   ASN C3070 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC5
    Processing sheet with id=AC6, first strand: chain 'C' and resid 3027 through 3028
    Processing sheet with id=AC7, first strand: chain 'C' and resid 3027 through 3028
    Processing sheet with id=AC8, first strand: chain 'C' and resid 3078 through 3080
      removed outlier: 5.902A  pdb=" N   GLY C3088 " --> pdb=" O   ASN C3124 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN C3124 " --> pdb=" O   GLY C3088 " (cutoff:3.500A)
    Processing sheet with id=AC9, first strand: chain 'C' and resid 3084 through 3085
      removed outlier: 6.548A  pdb=" N   VAL C3084 " --> pdb=" O   HIS C3152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC9
    Processing sheet with id=AD1, first strand: chain 'C' and resid 3113 through 3115
    Processing sheet with id=AD2, first strand: chain 'C' and resid 3113 through 3115
    Processing sheet with id=AD3, first strand: chain 'C' and resid 3164 through 3167
      removed outlier: 6.865A  pdb=" N   PHE C3164 " --> pdb=" O   THR C3232 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ASP C3234 " --> pdb=" O   PHE C3164 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL C3166 " --> pdb=" O   ASP C3234 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER C3182 " --> pdb=" O   ILE C3217 " (cutoff:3.500A)
    Processing sheet with id=AD4, first strand: chain 'D' and resid 2903 through 2906
      removed outlier: 6.549A  pdb=" N   PHE D2903 " --> pdb=" O   GLY D2971 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   ASN D2973 " --> pdb=" O   PHE D2903 " (cutoff:3.500A)
      removed outlier: 6.945A  pdb=" N   VAL D2905 " --> pdb=" O   ASN D2973 " (cutoff:3.500A)
    Processing sheet with id=AD5, first strand: chain 'D' and resid 2981 through 2982
    Processing sheet with id=AD6, first strand: chain 'D' and resid 2987 through 2988
      removed outlier: 7.051A  pdb=" N   ILE D2987 " --> pdb=" O   ASN D3070 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AD6
    Processing sheet with id=AD7, first strand: chain 'D' and resid 3027 through 3028
    Processing sheet with id=AD8, first strand: chain 'D' and resid 3027 through 3028
    Processing sheet with id=AD9, first strand: chain 'D' and resid 3078 through 3080
      removed outlier: 5.901A  pdb=" N   GLY D3088 " --> pdb=" O   ASN D3124 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN D3124 " --> pdb=" O   GLY D3088 " (cutoff:3.500A)
    Processing sheet with id=AE1, first strand: chain 'D' and resid 3084 through 3085
      removed outlier: 6.549A  pdb=" N   VAL D3084 " --> pdb=" O   HIS D3152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE1
    Processing sheet with id=AE2, first strand: chain 'D' and resid 3113 through 3115
    Processing sheet with id=AE3, first strand: chain 'D' and resid 3113 through 3115
    Processing sheet with id=AE4, first strand: chain 'D' and resid 3164 through 3167
      removed outlier: 6.866A  pdb=" N   PHE D3164 " --> pdb=" O   THR D3232 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ASP D3234 " --> pdb=" O   PHE D3164 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   VAL D3166 " --> pdb=" O   ASP D3234 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   SER D3182 " --> pdb=" O   ILE D3217 " (cutoff:3.500A)
    Processing sheet with id=AE5, first strand: chain 'E' and resid 2903 through 2906
      removed outlier: 6.549A  pdb=" N   PHE E2903 " --> pdb=" O   GLY E2971 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   ASN E2973 " --> pdb=" O   PHE E2903 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL E2905 " --> pdb=" O   ASN E2973 " (cutoff:3.500A)
    Processing sheet with id=AE6, first strand: chain 'E' and resid 2981 through 2982
    Processing sheet with id=AE7, first strand: chain 'E' and resid 2987 through 2988
      removed outlier: 7.051A  pdb=" N   ILE E2987 " --> pdb=" O   ASN E3070 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AE7
    Processing sheet with id=AE8, first strand: chain 'E' and resid 3027 through 3028
    Processing sheet with id=AE9, first strand: chain 'E' and resid 3027 through 3028
    Processing sheet with id=AF1, first strand: chain 'E' and resid 3078 through 3080
      removed outlier: 5.901A  pdb=" N   GLY E3088 " --> pdb=" O   ASN E3124 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN E3124 " --> pdb=" O   GLY E3088 " (cutoff:3.500A)
    Processing sheet with id=AF2, first strand: chain 'E' and resid 3084 through 3085
      removed outlier: 6.548A  pdb=" N   VAL E3084 " --> pdb=" O   HIS E3152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF2
    Processing sheet with id=AF3, first strand: chain 'E' and resid 3113 through 3115
    Processing sheet with id=AF4, first strand: chain 'E' and resid 3113 through 3115
    Processing sheet with id=AF5, first strand: chain 'E' and resid 3164 through 3167
      removed outlier: 6.866A  pdb=" N   PHE E3164 " --> pdb=" O   THR E3232 " (cutoff:3.500A)
      removed outlier: 8.043A  pdb=" N   ASP E3234 " --> pdb=" O   PHE E3164 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL E3166 " --> pdb=" O   ASP E3234 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER E3182 " --> pdb=" O   ILE E3217 " (cutoff:3.500A)
    Processing sheet with id=AF6, first strand: chain 'F' and resid 2903 through 2906
      removed outlier: 6.548A  pdb=" N   PHE F2903 " --> pdb=" O   GLY F2971 " (cutoff:3.500A)
      removed outlier: 8.029A  pdb=" N   ASN F2973 " --> pdb=" O   PHE F2903 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL F2905 " --> pdb=" O   ASN F2973 " (cutoff:3.500A)
    Processing sheet with id=AF7, first strand: chain 'F' and resid 2981 through 2982
    Processing sheet with id=AF8, first strand: chain 'F' and resid 2987 through 2988
      removed outlier: 7.050A  pdb=" N   ILE F2987 " --> pdb=" O   ASN F3070 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AF8
    Processing sheet with id=AF9, first strand: chain 'F' and resid 3027 through 3028
    Processing sheet with id=AG1, first strand: chain 'F' and resid 3027 through 3028
    Processing sheet with id=AG2, first strand: chain 'F' and resid 3078 through 3080
      removed outlier: 5.900A  pdb=" N   GLY F3088 " --> pdb=" O   ASN F3124 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   ASN F3124 " --> pdb=" O   GLY F3088 " (cutoff:3.500A)
    Processing sheet with id=AG3, first strand: chain 'F' and resid 3084 through 3085
      removed outlier: 6.548A  pdb=" N   VAL F3084 " --> pdb=" O   HIS F3152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG3
    Processing sheet with id=AG4, first strand: chain 'F' and resid 3113 through 3115
    Processing sheet with id=AG5, first strand: chain 'F' and resid 3113 through 3115
    Processing sheet with id=AG6, first strand: chain 'F' and resid 3164 through 3167
      removed outlier: 6.866A  pdb=" N   PHE F3164 " --> pdb=" O   THR F3232 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   ASP F3234 " --> pdb=" O   PHE F3164 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   VAL F3166 " --> pdb=" O   ASP F3234 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER F3182 " --> pdb=" O   ILE F3217 " (cutoff:3.500A)
    Processing sheet with id=AG7, first strand: chain 'G' and resid 2903 through 2906
      removed outlier: 6.549A  pdb=" N   PHE G2903 " --> pdb=" O   GLY G2971 " (cutoff:3.500A)
      removed outlier: 8.030A  pdb=" N   ASN G2973 " --> pdb=" O   PHE G2903 " (cutoff:3.500A)
      removed outlier: 6.946A  pdb=" N   VAL G2905 " --> pdb=" O   ASN G2973 " (cutoff:3.500A)
    Processing sheet with id=AG8, first strand: chain 'G' and resid 2981 through 2982
    Processing sheet with id=AG9, first strand: chain 'G' and resid 2987 through 2988
      removed outlier: 7.051A  pdb=" N   ILE G2987 " --> pdb=" O   ASN G3070 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AG9
    Processing sheet with id=AH1, first strand: chain 'G' and resid 3027 through 3028
    Processing sheet with id=AH2, first strand: chain 'G' and resid 3027 through 3028
    Processing sheet with id=AH3, first strand: chain 'G' and resid 3078 through 3080
      removed outlier: 5.901A  pdb=" N   GLY G3088 " --> pdb=" O   ASN G3124 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN G3124 " --> pdb=" O   GLY G3088 " (cutoff:3.500A)
    Processing sheet with id=AH4, first strand: chain 'G' and resid 3084 through 3085
      removed outlier: 6.548A  pdb=" N   VAL G3084 " --> pdb=" O   HIS G3152 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AH4
    Processing sheet with id=AH5, first strand: chain 'G' and resid 3113 through 3115
    Processing sheet with id=AH6, first strand: chain 'G' and resid 3113 through 3115
    Processing sheet with id=AH7, first strand: chain 'G' and resid 3164 through 3167
      removed outlier: 6.865A  pdb=" N   PHE G3164 " --> pdb=" O   THR G3232 " (cutoff:3.500A)
      removed outlier: 8.044A  pdb=" N   ASP G3234 " --> pdb=" O   PHE G3164 " (cutoff:3.500A)
      removed outlier: 7.029A  pdb=" N   VAL G3166 " --> pdb=" O   ASP G3234 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   SER G3182 " --> pdb=" O   ILE G3217 " (cutoff:3.500A)

    616 hydrogen bonds defined for protein.
    1449 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: 7.09

  Time building geometry restraints manager: 4.86 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 3828
        1.32 -     1.45: 4699
        1.45 -     1.58: 9057
        1.58 -     1.71: 21
        1.71 -     1.84: 112
  Bond restraints: 17717
  Sorted by residual:
  bond pdb=" CA  GLU D3061 "
       pdb=" C   GLU D3061 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.081 1.33e-02 5.65e+03 3.73e+01
  bond pdb=" CA  GLU E3061 "
       pdb=" C   GLU E3061 "
    ideal  model  delta    sigma   weight residual
    1.524  1.442  0.081 1.33e-02 5.65e+03 3.72e+01
  bond pdb=" CA  GLU B3061 "
       pdb=" C   GLU B3061 "
    ideal  model  delta    sigma   weight residual
    1.524  1.443  0.081 1.33e-02 5.65e+03 3.67e+01
  bond pdb=" CA  GLU C3061 "
       pdb=" C   GLU C3061 "
    ideal  model  delta    sigma   weight residual
    1.524  1.443  0.080 1.33e-02 5.65e+03 3.66e+01
  bond pdb=" CA  GLU A3061 "
       pdb=" C   GLU A3061 "
    ideal  model  delta    sigma   weight residual
    1.524  1.443  0.080 1.33e-02 5.65e+03 3.65e+01
  ... (remaining 17712 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.39: 22164
        2.39 -     4.79: 2026
        4.79 -     7.18: 247
        7.18 -     9.57: 28
        9.57 -    11.97: 21
  Bond angle restraints: 24486
  Sorted by residual:
  angle pdb=" CA  TYR E3048 "
        pdb=" CB  TYR E3048 "
        pdb=" CG  TYR E3048 "
      ideal   model   delta    sigma   weight residual
     113.90  125.69  -11.79 1.80e+00 3.09e-01 4.29e+01
  angle pdb=" CA  TYR F3048 "
        pdb=" CB  TYR F3048 "
        pdb=" CG  TYR F3048 "
      ideal   model   delta    sigma   weight residual
     113.90  125.66  -11.76 1.80e+00 3.09e-01 4.27e+01
  angle pdb=" CA  TYR D3048 "
        pdb=" CB  TYR D3048 "
        pdb=" CG  TYR D3048 "
      ideal   model   delta    sigma   weight residual
     113.90  125.66  -11.76 1.80e+00 3.09e-01 4.27e+01
  angle pdb=" CA  TYR A3048 "
        pdb=" CB  TYR A3048 "
        pdb=" CG  TYR A3048 "
      ideal   model   delta    sigma   weight residual
     113.90  125.65  -11.75 1.80e+00 3.09e-01 4.26e+01
  angle pdb=" CA  TYR C3048 "
        pdb=" CB  TYR C3048 "
        pdb=" CG  TYR C3048 "
      ideal   model   delta    sigma   weight residual
     113.90  125.64  -11.74 1.80e+00 3.09e-01 4.25e+01
  ... (remaining 24481 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    14.00: 9914
       14.00 -    28.00: 362
       28.00 -    42.00: 52
       42.00 -    56.00: 8
       56.00 -    70.00: 8
  Dihedral angle restraints: 10344
    sinusoidal: 3484
      harmonic: 6860
  Sorted by residual:
  dihedral pdb=" CB  CYS A2906 "
           pdb=" SG  CYS A2906 "
           pdb=" SG  CYS A3058 "
           pdb=" CB  CYS A3058 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  126.94  -33.94     1      1.00e+01 1.00e-02 1.64e+01
  dihedral pdb=" C   HIS E3152 "
           pdb=" N   HIS E3152 "
           pdb=" CA  HIS E3152 "
           pdb=" CB  HIS E3152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.79   -9.81     0      2.50e+00 1.60e-01 1.54e+01
  dihedral pdb=" C   HIS G3152 "
           pdb=" N   HIS G3152 "
           pdb=" CA  HIS G3152 "
           pdb=" CB  HIS G3152 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.80   -9.80     0      2.50e+00 1.60e-01 1.54e+01
  ... (remaining 10341 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.083: 2221
       0.083 -    0.167: 704
       0.167 -    0.250: 71
       0.250 -    0.334: 14
       0.334 -    0.417: 7
  Chirality restraints: 3017
  Sorted by residual:
  chirality pdb=" CA  ASN C3012 "
            pdb=" N   ASN C3012 "
            pdb=" C   ASN C3012 "
            pdb=" CB  ASN C3012 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.36e+00
  chirality pdb=" CA  ASN D3012 "
            pdb=" N   ASN D3012 "
            pdb=" C   ASN D3012 "
            pdb=" CB  ASN D3012 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.35e+00
  chirality pdb=" CA  ASN F3012 "
            pdb=" N   ASN F3012 "
            pdb=" C   ASN F3012 "
            pdb=" CB  ASN F3012 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.33e+00
  ... (remaining 3014 not shown)

  Planarity restraints: 3213
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER B3062 "   -0.025 2.00e-02 2.50e+03   5.07e-02 2.57e+01
        pdb=" C   SER B3062 "    0.088 2.00e-02 2.50e+03
        pdb=" O   SER B3062 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   ASN B3063 "   -0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER E3062 "    0.025 2.00e-02 2.50e+03   5.07e-02 2.57e+01
        pdb=" C   SER E3062 "   -0.088 2.00e-02 2.50e+03
        pdb=" O   SER E3062 "    0.034 2.00e-02 2.50e+03
        pdb=" N   ASN E3063 "    0.029 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER G3062 "   -0.025 2.00e-02 2.50e+03   5.06e-02 2.56e+01
        pdb=" C   SER G3062 "    0.088 2.00e-02 2.50e+03
        pdb=" O   SER G3062 "   -0.034 2.00e-02 2.50e+03
        pdb=" N   ASN G3063 "   -0.029 2.00e-02 2.50e+03
  ... (remaining 3210 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.60: 213
        2.60 -     3.18: 15424
        3.18 -     3.75: 25794
        3.75 -     4.33: 36105
        4.33 -     4.90: 59186
  Nonbonded interactions: 136722
  Sorted by model distance:
  nonbonded pdb=" SG  CYS E3001 "
            pdb=" SG  CYS E3051 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS D3001 "
            pdb=" SG  CYS D3051 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS G3001 "
            pdb=" SG  CYS G3051 "
     model   vdw
     2.028 3.760
  nonbonded pdb=" SG  CYS C3001 "
            pdb=" SG  CYS C3051 "
     model   vdw
     2.029 3.760
  nonbonded pdb=" SG  CYS B3001 "
            pdb=" SG  CYS B3051 "
     model   vdw
     2.029 3.760
  ... (remaining 136717 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: 0.15
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'C'
  selection = chain 'B'
  selection = chain 'E'
  selection = chain 'D'
  selection = chain 'G'
  selection = chain 'F'
}

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 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:             2.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.730
  Check model and map are aligned:         0.120
  Set scattering table:                    0.170
  Process input model:                     37.460
  Find NCS groups from input model:        0.370
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.770
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   44.100
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7957
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      :  0.018   0.135  17717  Z= 1.195
  Angle     :  1.485  11.966  24486  Z= 0.970
  Chirality :  0.080   0.417   3017
  Planarity :  0.008   0.051   3213
  Dihedral  :  8.253  69.997   5950
  Min Nonbonded Distance : 2.028

Molprobity Statistics.
  All-atom Clashscore : 3.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  0.29 %
    Favored  : 99.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.00 %
    Favored  : 100.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.59 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  1.03 (0.16), residues: 868
  loop :  1.26 (0.16), residues: 1533

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.006   TRP F3185 
 HIS   0.009   0.006   HIS B3152 
 PHE   0.055   0.008   PHE B3164 
 TYR   0.049   0.007   TYR B3048 
 ARG   0.001   0.000   ARG F2969 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  396 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 396
  time to evaluate  : 1.948 
Fit side-chains
REVERT: A 3156 VAL cc_start: 0.8355 (t) cc_final: 0.7996 (m)
REVERT: B 3213 THR cc_start: 0.9127 (m) cc_final: 0.8838 (p)
REVERT: C 3005 GLN cc_start: 0.8205 (tt0) cc_final: 0.7917 (tt0)
REVERT: C 3156 VAL cc_start: 0.8226 (t) cc_final: 0.7939 (m)
REVERT: C 3205 THR cc_start: 0.8601 (p) cc_final: 0.8334 (m)
REVERT: C 3213 THR cc_start: 0.9192 (m) cc_final: 0.8911 (p)
REVERT: D 3205 THR cc_start: 0.8507 (p) cc_final: 0.8289 (m)
REVERT: E 3156 VAL cc_start: 0.8199 (t) cc_final: 0.7931 (m)
REVERT: E 3205 THR cc_start: 0.8618 (p) cc_final: 0.8394 (m)
REVERT: E 3213 THR cc_start: 0.9105 (m) cc_final: 0.8847 (p)
REVERT: F 3205 THR cc_start: 0.8500 (p) cc_final: 0.8238 (m)
REVERT: F 3213 THR cc_start: 0.9161 (m) cc_final: 0.8911 (p)
REVERT: G 3205 THR cc_start: 0.8468 (p) cc_final: 0.8232 (m)
REVERT: G 3213 THR cc_start: 0.9173 (m) cc_final: 0.8898 (p)
  outliers start: 0
  outliers final: 0
  residues processed: 396
  average time/residue: 0.1889
  time to fit residues: 131.7194
Evaluate side-chains
  151 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 151
  time to evaluate  : 2.004 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 200 optimal weight:    1.9990
   chunk 180 optimal weight:    3.9990
   chunk 100 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9990
   chunk 121 optimal weight:    0.9990
   chunk 96 optimal weight:    2.9990
   chunk 186 optimal weight:    0.7980
   chunk 72 optimal weight:    2.9990
   chunk 113 optimal weight:    0.9990
   chunk 138 optimal weight:    0.9980
   chunk 216 optimal weight:    0.9980
   overall best weight:    0.9382

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

Flipped N/Q/H residues before XYZ refinement:
A3063 ASN
B3063 ASN
C2942 ASN
D3063 ASN
E3063 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.109419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.093709 restraints weight = 22573.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 52)----------------|
| r_work = 0.2861 r_free = 0.2861 target = 0.092979 restraints weight = 30754.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.093752 restraints weight = 27649.966|
|-----------------------------------------------------------------------------|
r_work (final): 0.2906
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8193
moved from start:          0.2193

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  17717  Z= 0.244
  Angle     :  0.589   7.097  24486  Z= 0.325
  Chirality :  0.050   0.146   3017
  Planarity :  0.005   0.032   3213
  Dihedral  :  4.749  17.563   2499
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 3.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.46 %
    Favored  : 98.54 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  :  7.27 %
    Favored  : 89.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.46 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  1.07 (0.16), residues: 854
  loop :  1.08 (0.17), residues: 1547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP E3047 
 HIS   0.002   0.001   HIS F3152 
 PHE   0.007   0.001   PHE C2903 
 TYR   0.015   0.001   TYR F3048 
 ARG   0.003   0.001   ARG D2969 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  306 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 62
    poor density    : 244
  time to evaluate  : 2.117 
Fit side-chains
   revert: symmetry clash
REVERT: A 3156 VAL cc_start: 0.8680 (t) cc_final: 0.8431 (m)
REVERT: B 3007 ILE cc_start: 0.9062 (mm) cc_final: 0.8824 (mt)
REVERT: B 3213 THR cc_start: 0.9073 (m) cc_final: 0.8803 (p)
REVERT: C 3213 THR cc_start: 0.9252 (m) cc_final: 0.8906 (p)
REVERT: D 3007 ILE cc_start: 0.8977 (mm) cc_final: 0.8754 (mt)
REVERT: D 3093 SER cc_start: 0.8923 (p) cc_final: 0.8708 (p)
REVERT: E 3213 THR cc_start: 0.9130 (m) cc_final: 0.8812 (p)
REVERT: F 3093 SER cc_start: 0.8874 (p) cc_final: 0.8635 (m)
REVERT: F 3213 THR cc_start: 0.9152 (m) cc_final: 0.8755 (p)
REVERT: G 3213 THR cc_start: 0.9212 (m) cc_final: 0.8880 (p)
  outliers start: 62
  outliers final: 38
  residues processed: 279
  average time/residue: 0.1950
  time to fit residues: 95.6310
Evaluate side-chains
  199 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 161
  time to evaluate  : 1.899 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2941 THR
Chi-restraints excluded: chain A residue 2967 THR
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3063 ASN
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain B residue 2967 THR
Chi-restraints excluded: chain B residue 3063 ASN
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3157 THR
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain C residue 2967 THR
Chi-restraints excluded: chain C residue 3023 SER
Chi-restraints excluded: chain C residue 3037 MET
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3216 ILE
Chi-restraints excluded: chain D residue 2967 THR
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3063 ASN
Chi-restraints excluded: chain D residue 3074 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3157 THR
Chi-restraints excluded: chain E residue 2967 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3023 SER
Chi-restraints excluded: chain E residue 3063 ASN
Chi-restraints excluded: chain F residue 2941 THR
Chi-restraints excluded: chain F residue 2967 THR
Chi-restraints excluded: chain F residue 2982 VAL
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3074 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3157 THR
Chi-restraints excluded: chain G residue 2967 THR
Chi-restraints excluded: chain G residue 2982 VAL
Chi-restraints excluded: chain G residue 3074 ASP
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3157 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 138 optimal weight:    0.3980
   chunk 88 optimal weight:    0.8980
   chunk 152 optimal weight:    2.9990
   chunk 215 optimal weight:    1.9990
   chunk 167 optimal weight:    4.9990
   chunk 126 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 79 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 148 optimal weight:    4.9990
   chunk 221 optimal weight:    0.0870
   overall best weight:    0.6158

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

Flipped N/Q/H residues before XYZ refinement:
A3063 ASN
B2942 ASN
B3041 ASN
B3063 ASN
** C3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2942 ASN
D3041 ASN
D3063 ASN
E3041 ASN
E3063 ASN
G2942 ASN
G3063 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3073 r_free = 0.3073 target = 0.109112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2858 r_free = 0.2858 target = 0.093067 restraints weight = 22396.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2853 r_free = 0.2853 target = 0.092632 restraints weight = 28999.811|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2856 r_free = 0.2856 target = 0.092855 restraints weight = 28962.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.2898
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8215
moved from start:          0.2580

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  17717  Z= 0.173
  Angle     :  0.510   5.885  24486  Z= 0.279
  Chirality :  0.047   0.140   3017
  Planarity :  0.004   0.031   3213
  Dihedral  :  4.303  17.848   2499
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 3.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.42 %
    Favored  : 98.58 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 10.75 %
    Favored  : 86.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.47 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  1.01 (0.16), residues: 854
  loop :  1.13 (0.17), residues: 1547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP G3185 
 HIS   0.002   0.001   HIS C3152 
 PHE   0.006   0.001   PHE E3164 
 TYR   0.013   0.001   TYR F3048 
 ARG   0.005   0.000   ARG C3059 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 65
    poor density    : 166
  time to evaluate  : 1.951 
Fit side-chains
REVERT: A 3007 ILE cc_start: 0.8812 (mm) cc_final: 0.8561 (mt)
REVERT: A 3063 ASN cc_start: 0.8697 (OUTLIER) cc_final: 0.8399 (p0)
REVERT: A 3156 VAL cc_start: 0.8735 (t) cc_final: 0.8505 (m)
REVERT: B 3063 ASN cc_start: 0.8646 (OUTLIER) cc_final: 0.8433 (p0)
REVERT: B 3213 THR cc_start: 0.9028 (m) cc_final: 0.8758 (p)
REVERT: C 3093 SER cc_start: 0.8910 (p) cc_final: 0.8684 (p)
REVERT: C 3110 LEU cc_start: 0.8638 (mp) cc_final: 0.8408 (mt)
REVERT: C 3213 THR cc_start: 0.9228 (m) cc_final: 0.8905 (p)
REVERT: E 2987 ILE cc_start: 0.8698 (OUTLIER) cc_final: 0.8478 (tp)
REVERT: E 3213 THR cc_start: 0.9116 (m) cc_final: 0.8874 (p)
REVERT: F 3007 ILE cc_start: 0.8895 (mm) cc_final: 0.8683 (mt)
REVERT: F 3093 SER cc_start: 0.8796 (p) cc_final: 0.8591 (m)
REVERT: F 3213 THR cc_start: 0.9166 (m) cc_final: 0.8812 (p)
REVERT: G 2987 ILE cc_start: 0.8568 (OUTLIER) cc_final: 0.8334 (tp)
REVERT: G 3213 THR cc_start: 0.9190 (m) cc_final: 0.8886 (p)
  outliers start: 65
  outliers final: 44
  residues processed: 213
  average time/residue: 0.2010
  time to fit residues: 75.9727
Evaluate side-chains
  189 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 141
  time to evaluate  : 1.887 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2967 THR
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3063 ASN
Chi-restraints excluded: chain A residue 3110 LEU
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain B residue 2934 LEU
Chi-restraints excluded: chain B residue 2967 THR
Chi-restraints excluded: chain B residue 3063 ASN
Chi-restraints excluded: chain B residue 3121 MET
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain B residue 3216 ILE
Chi-restraints excluded: chain C residue 2967 THR
Chi-restraints excluded: chain C residue 3023 SER
Chi-restraints excluded: chain C residue 3074 ASP
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3157 THR
Chi-restraints excluded: chain C residue 3205 THR
Chi-restraints excluded: chain D residue 2967 THR
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3074 ASP
Chi-restraints excluded: chain D residue 3114 VAL
Chi-restraints excluded: chain D residue 3121 MET
Chi-restraints excluded: chain D residue 3123 VAL
Chi-restraints excluded: chain D residue 3128 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3205 THR
Chi-restraints excluded: chain E residue 2967 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 2987 ILE
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3123 VAL
Chi-restraints excluded: chain E residue 3157 THR
Chi-restraints excluded: chain E residue 3205 THR
Chi-restraints excluded: chain E residue 3216 ILE
Chi-restraints excluded: chain F residue 2967 THR
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3074 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3205 THR
Chi-restraints excluded: chain F residue 3216 ILE
Chi-restraints excluded: chain G residue 2946 ILE
Chi-restraints excluded: chain G residue 2967 THR
Chi-restraints excluded: chain G residue 2987 ILE
Chi-restraints excluded: chain G residue 3074 ASP
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3195 VAL
Chi-restraints excluded: chain G residue 3205 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 164 optimal weight:    5.9990
   chunk 53 optimal weight:    0.0370
   chunk 77 optimal weight:    0.9980
   chunk 210 optimal weight:    5.9990
   chunk 92 optimal weight:    2.9990
   chunk 86 optimal weight:    1.9990
   chunk 211 optimal weight:    3.9990
   chunk 175 optimal weight:    7.9990
   chunk 204 optimal weight:    0.6980
   chunk 109 optimal weight:    7.9990
   chunk 18 optimal weight:    4.9990
   overall best weight:    1.3462

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

Flipped N/Q/H residues before XYZ refinement:
A3041 ASN
A3063 ASN
B3063 ASN
C3063 ASN
D2942 ASN
F3063 ASN
G3041 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.105776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.2804 r_free = 0.2804 target = 0.089158 restraints weight = 22690.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.2794 r_free = 0.2794 target = 0.088401 restraints weight = 32148.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.089056 restraints weight = 28548.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.2797
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8275
moved from start:          0.2910

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038  17717  Z= 0.272
  Angle     :  0.515   5.310  24486  Z= 0.283
  Chirality :  0.048   0.179   3017
  Planarity :  0.005   0.044   3213
  Dihedral  :  4.180  17.316   2499
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 2.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  4.32 %
    Allowed  : 10.51 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.25 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  0.81 (0.15), residues: 875
  loop :  1.01 (0.17), residues: 1526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP B2924 
 HIS   0.002   0.002   HIS F3152 
 PHE   0.008   0.001   PHE A3191 
 TYR   0.015   0.001   TYR F3048 
 ARG   0.003   0.000   ARG C3059 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 88
    poor density    : 163
  time to evaluate  : 2.042 
Fit side-chains
REVERT: A 3007 ILE cc_start: 0.8868 (mm) cc_final: 0.8612 (mt)
REVERT: B 3063 ASN cc_start: 0.8681 (OUTLIER) cc_final: 0.8435 (p0)
REVERT: C 3093 SER cc_start: 0.8898 (p) cc_final: 0.8676 (p)
REVERT: C 3213 THR cc_start: 0.9283 (m) cc_final: 0.8905 (p)
REVERT: D 3074 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6856 (m-30)
REVERT: D 3093 SER cc_start: 0.8821 (p) cc_final: 0.8544 (m)
REVERT: E 2987 ILE cc_start: 0.8763 (OUTLIER) cc_final: 0.8548 (tp)
REVERT: E 3213 THR cc_start: 0.9148 (m) cc_final: 0.8824 (p)
REVERT: F 3007 ILE cc_start: 0.8930 (mm) cc_final: 0.8691 (mt)
REVERT: F 3093 SER cc_start: 0.8836 (p) cc_final: 0.8599 (m)
REVERT: F 3213 THR cc_start: 0.9161 (m) cc_final: 0.8734 (p)
REVERT: G 2987 ILE cc_start: 0.8680 (OUTLIER) cc_final: 0.8478 (tp)
  outliers start: 88
  outliers final: 57
  residues processed: 227
  average time/residue: 0.2036
  time to fit residues: 81.5372
Evaluate side-chains
  214 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 153
  time to evaluate  : 2.047 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2967 THR
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3037 MET
Chi-restraints excluded: chain A residue 3110 LEU
Chi-restraints excluded: chain A residue 3157 THR
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain B residue 2967 THR
Chi-restraints excluded: chain B residue 3049 MET
Chi-restraints excluded: chain B residue 3063 ASN
Chi-restraints excluded: chain B residue 3121 MET
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3157 THR
Chi-restraints excluded: chain B residue 3195 VAL
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain B residue 3216 ILE
Chi-restraints excluded: chain C residue 2967 THR
Chi-restraints excluded: chain C residue 2982 VAL
Chi-restraints excluded: chain C residue 3007 ILE
Chi-restraints excluded: chain C residue 3049 MET
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3157 THR
Chi-restraints excluded: chain C residue 3205 THR
Chi-restraints excluded: chain C residue 3216 ILE
Chi-restraints excluded: chain D residue 2967 THR
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3074 ASP
Chi-restraints excluded: chain D residue 3114 VAL
Chi-restraints excluded: chain D residue 3121 MET
Chi-restraints excluded: chain D residue 3123 VAL
Chi-restraints excluded: chain D residue 3128 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3157 THR
Chi-restraints excluded: chain D residue 3205 THR
Chi-restraints excluded: chain E residue 2967 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 2987 ILE
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3037 MET
Chi-restraints excluded: chain E residue 3157 THR
Chi-restraints excluded: chain E residue 3195 VAL
Chi-restraints excluded: chain E residue 3205 THR
Chi-restraints excluded: chain E residue 3216 ILE
Chi-restraints excluded: chain F residue 2967 THR
Chi-restraints excluded: chain F residue 2982 VAL
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3049 MET
Chi-restraints excluded: chain F residue 3063 ASN
Chi-restraints excluded: chain F residue 3074 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3157 THR
Chi-restraints excluded: chain F residue 3205 THR
Chi-restraints excluded: chain F residue 3216 ILE
Chi-restraints excluded: chain G residue 2967 THR
Chi-restraints excluded: chain G residue 2982 VAL
Chi-restraints excluded: chain G residue 2987 ILE
Chi-restraints excluded: chain G residue 3049 MET
Chi-restraints excluded: chain G residue 3074 ASP
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3157 THR
Chi-restraints excluded: chain G residue 3195 VAL
Chi-restraints excluded: chain G residue 3205 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 4 optimal weight:    0.0050
   chunk 226 optimal weight:    0.7980
   chunk 34 optimal weight:    7.9990
   chunk 81 optimal weight:    2.9990
   chunk 15 optimal weight:    4.9990
   chunk 76 optimal weight:    6.9990
   chunk 55 optimal weight:    0.9990
   chunk 218 optimal weight:    1.9990
   chunk 130 optimal weight:    4.9990
   chunk 84 optimal weight:    0.9990
   chunk 142 optimal weight:    0.5980
   overall best weight:    0.6798

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

Flipped N/Q/H residues before XYZ refinement:
** A2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B3063 ASN
D2942 ASN
F2980 ASN
F3063 ASN
G2980 ASN
** G3063 ASN ** 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 = 0.3049 r_free = 0.3049 target = 0.107296 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2823 r_free = 0.2823 target = 0.090639 restraints weight = 22877.850|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.089834 restraints weight = 32042.615|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.2821 r_free = 0.2821 target = 0.090432 restraints weight = 30541.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.2817
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8252
moved from start:          0.3121

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026  17717  Z= 0.170
  Angle     :  0.474   6.280  24486  Z= 0.258
  Chirality :  0.047   0.143   3017
  Planarity :  0.004   0.049   3213
  Dihedral  :  3.994  17.219   2499
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.78 %
    Allowed  : 11.34 %
    Favored  : 84.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  0.82 (0.15), residues: 875
  loop :  1.03 (0.17), residues: 1526

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP E3185 
 HIS   0.002   0.001   HIS F3152 
 PHE   0.006   0.001   PHE A3191 
 TYR   0.014   0.001   TYR F3048 
 ARG   0.003   0.000   ARG B2969 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 77
    poor density    : 183
  time to evaluate  : 1.930 
Fit side-chains
REVERT: A 3007 ILE cc_start: 0.8823 (mm) cc_final: 0.8607 (mt)
REVERT: C 3093 SER cc_start: 0.8831 (p) cc_final: 0.8616 (m)
REVERT: C 3213 THR cc_start: 0.9260 (m) cc_final: 0.8868 (p)
REVERT: D 3074 ASP cc_start: 0.7110 (OUTLIER) cc_final: 0.6867 (m-30)
REVERT: D 3093 SER cc_start: 0.8788 (p) cc_final: 0.8565 (m)
REVERT: E 2987 ILE cc_start: 0.8733 (OUTLIER) cc_final: 0.8501 (tp)
REVERT: F 3007 ILE cc_start: 0.8915 (mm) cc_final: 0.8689 (mt)
REVERT: F 3213 THR cc_start: 0.9147 (m) cc_final: 0.8712 (p)
REVERT: G 2987 ILE cc_start: 0.8746 (OUTLIER) cc_final: 0.8511 (tp)
  outliers start: 77
  outliers final: 51
  residues processed: 242
  average time/residue: 0.2008
  time to fit residues: 87.6071
Evaluate side-chains
  213 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 159
  time to evaluate  : 1.909 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3037 MET
Chi-restraints excluded: chain A residue 3110 LEU
Chi-restraints excluded: chain A residue 3157 THR
Chi-restraints excluded: chain A residue 3195 VAL
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain B residue 2909 ASP
Chi-restraints excluded: chain B residue 3049 MET
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3157 THR
Chi-restraints excluded: chain B residue 3195 VAL
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain B residue 3216 ILE
Chi-restraints excluded: chain C residue 2982 VAL
Chi-restraints excluded: chain C residue 3049 MET
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3157 THR
Chi-restraints excluded: chain C residue 3205 THR
Chi-restraints excluded: chain C residue 3216 ILE
Chi-restraints excluded: chain D residue 2934 LEU
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3074 ASP
Chi-restraints excluded: chain D residue 3114 VAL
Chi-restraints excluded: chain D residue 3128 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3157 THR
Chi-restraints excluded: chain D residue 3195 VAL
Chi-restraints excluded: chain D residue 3205 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 2987 ILE
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3037 MET
Chi-restraints excluded: chain E residue 3157 THR
Chi-restraints excluded: chain E residue 3195 VAL
Chi-restraints excluded: chain E residue 3205 THR
Chi-restraints excluded: chain E residue 3216 ILE
Chi-restraints excluded: chain F residue 2982 VAL
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3037 MET
Chi-restraints excluded: chain F residue 3049 MET
Chi-restraints excluded: chain F residue 3128 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3157 THR
Chi-restraints excluded: chain F residue 3195 VAL
Chi-restraints excluded: chain F residue 3205 THR
Chi-restraints excluded: chain F residue 3216 ILE
Chi-restraints excluded: chain G residue 2946 ILE
Chi-restraints excluded: chain G residue 2987 ILE
Chi-restraints excluded: chain G residue 3049 MET
Chi-restraints excluded: chain G residue 3074 ASP
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3157 THR
Chi-restraints excluded: chain G residue 3195 VAL
Chi-restraints excluded: chain G residue 3205 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 88 optimal weight:    0.0970
   chunk 53 optimal weight:    4.9990
   chunk 49 optimal weight:    0.6980
   chunk 189 optimal weight:    4.9990
   chunk 97 optimal weight:    0.4980
   chunk 126 optimal weight:    2.9990
   chunk 212 optimal weight:    4.9990
   chunk 13 optimal weight:    5.9990
   chunk 87 optimal weight:    0.5980
   chunk 59 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A2980 ASN
B2980 ASN
B3063 ASN
C2980 ASN
D2980 ASN
E2980 ASN
F2980 ASN
G3063 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.107384 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2822 r_free = 0.2822 target = 0.090611 restraints weight = 22891.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2810 r_free = 0.2810 target = 0.089731 restraints weight = 33688.753|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.2818 r_free = 0.2818 target = 0.090301 restraints weight = 31114.390|
|-----------------------------------------------------------------------------|
r_work (final): 0.2815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8257
moved from start:          0.3302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023  17717  Z= 0.181
  Angle     :  0.465   5.493  24486  Z= 0.252
  Chirality :  0.047   0.195   3017
  Planarity :  0.005   0.049   3213
  Dihedral  :  3.923  20.742   2499
  Min Nonbonded Distance : 2.401

Molprobity Statistics.
  All-atom Clashscore : 3.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 12.13 %
    Favored  : 84.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  0.73 (0.15), residues: 917
  loop :  1.05 (0.17), residues: 1484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B2924 
 HIS   0.002   0.001   HIS F3152 
 PHE   0.006   0.001   PHE G3191 
 TYR   0.012   0.001   TYR F3048 
 ARG   0.004   0.000   ARG B2969 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  251 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 173
  time to evaluate  : 1.938 
Fit side-chains
REVERT: A 3007 ILE cc_start: 0.8845 (mm) cc_final: 0.8611 (mt)
REVERT: C 3213 THR cc_start: 0.9218 (m) cc_final: 0.8822 (p)
REVERT: D 3093 SER cc_start: 0.8716 (p) cc_final: 0.8501 (m)
REVERT: E 2987 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8523 (tp)
REVERT: E 3213 THR cc_start: 0.8949 (m) cc_final: 0.8640 (p)
REVERT: F 3007 ILE cc_start: 0.8886 (mm) cc_final: 0.8676 (mt)
REVERT: F 3213 THR cc_start: 0.9112 (m) cc_final: 0.8673 (p)
REVERT: G 2987 ILE cc_start: 0.8747 (OUTLIER) cc_final: 0.8518 (tp)
  outliers start: 78
  outliers final: 52
  residues processed: 227
  average time/residue: 0.2028
  time to fit residues: 81.5644
Evaluate side-chains
  210 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 156
  time to evaluate  : 1.884 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2967 THR
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3037 MET
Chi-restraints excluded: chain A residue 3110 LEU
Chi-restraints excluded: chain A residue 3157 THR
Chi-restraints excluded: chain A residue 3195 VAL
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain A residue 3216 ILE
Chi-restraints excluded: chain B residue 2909 ASP
Chi-restraints excluded: chain B residue 3037 MET
Chi-restraints excluded: chain B residue 3049 MET
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3157 THR
Chi-restraints excluded: chain B residue 3195 VAL
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain B residue 3213 THR
Chi-restraints excluded: chain B residue 3216 ILE
Chi-restraints excluded: chain C residue 2982 VAL
Chi-restraints excluded: chain C residue 3049 MET
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3195 VAL
Chi-restraints excluded: chain C residue 3205 THR
Chi-restraints excluded: chain C residue 3216 ILE
Chi-restraints excluded: chain D residue 2934 LEU
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3128 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3157 THR
Chi-restraints excluded: chain D residue 3195 VAL
Chi-restraints excluded: chain D residue 3205 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 2987 ILE
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3037 MET
Chi-restraints excluded: chain E residue 3157 THR
Chi-restraints excluded: chain E residue 3195 VAL
Chi-restraints excluded: chain E residue 3205 THR
Chi-restraints excluded: chain E residue 3216 ILE
Chi-restraints excluded: chain F residue 2982 VAL
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3037 MET
Chi-restraints excluded: chain F residue 3049 MET
Chi-restraints excluded: chain F residue 3128 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3157 THR
Chi-restraints excluded: chain F residue 3195 VAL
Chi-restraints excluded: chain F residue 3205 THR
Chi-restraints excluded: chain G residue 2946 ILE
Chi-restraints excluded: chain G residue 2987 ILE
Chi-restraints excluded: chain G residue 3049 MET
Chi-restraints excluded: chain G residue 3063 ASN
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3195 VAL
Chi-restraints excluded: chain G residue 3205 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 9 optimal weight:    0.9990
   chunk 96 optimal weight:    0.4980
   chunk 24 optimal weight:    0.6980
   chunk 223 optimal weight:    4.9990
   chunk 78 optimal weight:    4.9990
   chunk 100 optimal weight:    3.9990
   chunk 192 optimal weight:    0.6980
   chunk 55 optimal weight:    1.9990
   chunk 138 optimal weight:    6.9990
   chunk 164 optimal weight:    0.0670
   chunk 14 optimal weight:    0.7980
   overall best weight:    0.5518

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

Flipped N/Q/H residues before XYZ refinement:
A2980 ASN
B2980 ASN
C2980 ASN
D2980 ASN
E2980 ASN
F2980 ASN
F3063 ASN
G2980 ASN
G3063 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3063 r_free = 0.3063 target = 0.108491 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.091856 restraints weight = 22650.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.090787 restraints weight = 34310.259|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.2834 r_free = 0.2834 target = 0.091437 restraints weight = 31759.479|
|-----------------------------------------------------------------------------|
r_work (final): 0.2833
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8238
moved from start:          0.3422

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.020  17717  Z= 0.151
  Angle     :  0.459   6.290  24486  Z= 0.247
  Chirality :  0.047   0.159   3017
  Planarity :  0.004   0.047   3213
  Dihedral  :  3.818  22.993   2499
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.92 %
    Favored  : 98.08 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.35 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  0.93 (0.16), residues: 847
  loop :  0.91 (0.17), residues: 1554

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP F3185 
 HIS   0.002   0.001   HIS F3152 
 PHE   0.005   0.001   PHE A3191 
 TYR   0.012   0.001   TYR F3048 
 ARG   0.004   0.000   ARG B2969 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 174
  time to evaluate  : 1.867 
Fit side-chains
REVERT: A 3007 ILE cc_start: 0.8816 (mm) cc_final: 0.8613 (mt)
REVERT: B 2953 LEU cc_start: 0.8954 (tp) cc_final: 0.8707 (tp)
REVERT: C 3213 THR cc_start: 0.9219 (m) cc_final: 0.8795 (p)
REVERT: E 2987 ILE cc_start: 0.8729 (OUTLIER) cc_final: 0.8504 (tp)
REVERT: F 3007 ILE cc_start: 0.8879 (mm) cc_final: 0.8669 (mt)
REVERT: F 3213 THR cc_start: 0.9105 (m) cc_final: 0.8651 (p)
REVERT: G 2987 ILE cc_start: 0.8738 (OUTLIER) cc_final: 0.8505 (tp)
  outliers start: 74
  outliers final: 50
  residues processed: 226
  average time/residue: 0.2017
  time to fit residues: 80.3480
Evaluate side-chains
  216 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 164
  time to evaluate  : 1.844 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3037 MET
Chi-restraints excluded: chain A residue 3110 LEU
Chi-restraints excluded: chain A residue 3157 THR
Chi-restraints excluded: chain A residue 3195 VAL
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain A residue 3216 ILE
Chi-restraints excluded: chain B residue 2909 ASP
Chi-restraints excluded: chain B residue 3037 MET
Chi-restraints excluded: chain B residue 3049 MET
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3157 THR
Chi-restraints excluded: chain B residue 3195 VAL
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain B residue 3216 ILE
Chi-restraints excluded: chain C residue 2982 VAL
Chi-restraints excluded: chain C residue 3049 MET
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3195 VAL
Chi-restraints excluded: chain C residue 3205 THR
Chi-restraints excluded: chain C residue 3216 ILE
Chi-restraints excluded: chain D residue 2934 LEU
Chi-restraints excluded: chain D residue 2987 ILE
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3128 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3157 THR
Chi-restraints excluded: chain D residue 3195 VAL
Chi-restraints excluded: chain D residue 3205 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 2987 ILE
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3037 MET
Chi-restraints excluded: chain E residue 3195 VAL
Chi-restraints excluded: chain E residue 3205 THR
Chi-restraints excluded: chain E residue 3216 ILE
Chi-restraints excluded: chain F residue 2967 THR
Chi-restraints excluded: chain F residue 2982 VAL
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3037 MET
Chi-restraints excluded: chain F residue 3128 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3195 VAL
Chi-restraints excluded: chain F residue 3205 THR
Chi-restraints excluded: chain F residue 3216 ILE
Chi-restraints excluded: chain G residue 2946 ILE
Chi-restraints excluded: chain G residue 2987 ILE
Chi-restraints excluded: chain G residue 3049 MET
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3157 THR
Chi-restraints excluded: chain G residue 3195 VAL
Chi-restraints excluded: chain G residue 3205 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 131 optimal weight:    0.8980
   chunk 228 optimal weight:    1.9990
   chunk 163 optimal weight:    2.9990
   chunk 107 optimal weight:    6.9990
   chunk 206 optimal weight:    6.9990
   chunk 83 optimal weight:    3.9990
   chunk 25 optimal weight:    3.9990
   chunk 230 optimal weight:    0.0370
   chunk 161 optimal weight:    3.9990
   chunk 229 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    1.1862

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

Flipped N/Q/H residues before XYZ refinement:
A2980 ASN
B2980 ASN
C2980 ASN
C3089 ASN
D2980 ASN
E2980 ASN
F2980 ASN
F3063 ASN
** G2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.106214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2802 r_free = 0.2802 target = 0.089133 restraints weight = 22771.665|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.2788 r_free = 0.2788 target = 0.088119 restraints weight = 35762.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2796 r_free = 0.2796 target = 0.088720 restraints weight = 32764.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.2794
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8279
moved from start:          0.3510

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028  17717  Z= 0.235
  Angle     :  0.483   5.206  24486  Z= 0.261
  Chirality :  0.048   0.161   3017
  Planarity :  0.005   0.042   3213
  Dihedral  :  3.917  24.012   2499
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 3.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 13.89 %
    Favored  : 82.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.16 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  0.73 (0.15), residues: 903
  loop :  0.98 (0.17), residues: 1498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B2924 
 HIS   0.002   0.001   HIS G3152 
 PHE   0.008   0.001   PHE G3191 
 TYR   0.013   0.001   TYR A3048 
 ARG   0.004   0.000   ARG B2969 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 74
    poor density    : 164
  time to evaluate  : 1.830 
Fit side-chains
REVERT: E 2987 ILE cc_start: 0.8773 (OUTLIER) cc_final: 0.8548 (tp)
REVERT: F 3007 ILE cc_start: 0.8938 (mm) cc_final: 0.8726 (mt)
REVERT: F 3213 THR cc_start: 0.9128 (m) cc_final: 0.8661 (p)
REVERT: G 2987 ILE cc_start: 0.8749 (OUTLIER) cc_final: 0.8516 (tp)
  outliers start: 74
  outliers final: 51
  residues processed: 217
  average time/residue: 0.2065
  time to fit residues: 77.8223
Evaluate side-chains
  210 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 157
  time to evaluate  : 1.916 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3037 MET
Chi-restraints excluded: chain A residue 3110 LEU
Chi-restraints excluded: chain A residue 3157 THR
Chi-restraints excluded: chain A residue 3195 VAL
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain A residue 3216 ILE
Chi-restraints excluded: chain B residue 2909 ASP
Chi-restraints excluded: chain B residue 3037 MET
Chi-restraints excluded: chain B residue 3049 MET
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3157 THR
Chi-restraints excluded: chain B residue 3195 VAL
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain B residue 3213 THR
Chi-restraints excluded: chain B residue 3216 ILE
Chi-restraints excluded: chain C residue 2982 VAL
Chi-restraints excluded: chain C residue 3049 MET
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3089 ASN
Chi-restraints excluded: chain C residue 3195 VAL
Chi-restraints excluded: chain C residue 3205 THR
Chi-restraints excluded: chain C residue 3216 ILE
Chi-restraints excluded: chain D residue 2967 THR
Chi-restraints excluded: chain D residue 2987 ILE
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3123 VAL
Chi-restraints excluded: chain D residue 3128 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3195 VAL
Chi-restraints excluded: chain D residue 3205 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 2987 ILE
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3037 MET
Chi-restraints excluded: chain E residue 3195 VAL
Chi-restraints excluded: chain E residue 3205 THR
Chi-restraints excluded: chain E residue 3216 ILE
Chi-restraints excluded: chain F residue 2967 THR
Chi-restraints excluded: chain F residue 2982 VAL
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3037 MET
Chi-restraints excluded: chain F residue 3128 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3195 VAL
Chi-restraints excluded: chain F residue 3205 THR
Chi-restraints excluded: chain G residue 2946 ILE
Chi-restraints excluded: chain G residue 2987 ILE
Chi-restraints excluded: chain G residue 3049 MET
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3157 THR
Chi-restraints excluded: chain G residue 3195 VAL
Chi-restraints excluded: chain G residue 3205 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 1 optimal weight:    0.0050
   chunk 42 optimal weight:    0.0870
   chunk 171 optimal weight:    0.9980
   chunk 165 optimal weight:    0.9990
   chunk 213 optimal weight:    0.8980
   chunk 184 optimal weight:    0.5980
   chunk 65 optimal weight:    8.9990
   chunk 68 optimal weight:    7.9990
   chunk 118 optimal weight:    0.5980
   chunk 23 optimal weight:    0.9980
   chunk 74 optimal weight:    3.9990
   overall best weight:    0.4372

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

Flipped N/Q/H residues before XYZ refinement:
A2980 ASN
B2980 ASN
** C2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D2980 ASN
E2980 ASN
F2980 ASN
F3063 ASN
F3171 ASN
G2980 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.108609 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2846 r_free = 0.2846 target = 0.092146 restraints weight = 22768.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.091133 restraints weight = 33697.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.2839 r_free = 0.2839 target = 0.091644 restraints weight = 31178.363|
|-----------------------------------------------------------------------------|
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8240
moved from start:          0.3614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034  17717  Z= 0.140
  Angle     :  0.456   7.409  24486  Z= 0.245
  Chirality :  0.047   0.156   3017
  Planarity :  0.004   0.042   3213
  Dihedral  :  3.787  27.571   2499
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 3.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.33 %
    Favored  : 97.67 %
  Rotamer:
    Outliers :  3.39 %
    Allowed  : 14.19 %
    Favored  : 82.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.18 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  0.95 (0.16), residues: 840
  loop :  0.84 (0.17), residues: 1561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP G3185 
 HIS   0.001   0.001   HIS E3152 
 PHE   0.005   0.001   PHE A3191 
 TYR   0.012   0.001   TYR F3048 
 ARG   0.004   0.000   ARG B2969 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  242 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 173
  time to evaluate  : 1.905 
Fit side-chains
REVERT: A 3007 ILE cc_start: 0.8799 (mm) cc_final: 0.8588 (mt)
REVERT: D 2987 ILE cc_start: 0.8519 (OUTLIER) cc_final: 0.8281 (tp)
REVERT: E 2987 ILE cc_start: 0.8723 (OUTLIER) cc_final: 0.8492 (tp)
REVERT: F 3007 ILE cc_start: 0.8837 (mm) cc_final: 0.8631 (mt)
REVERT: F 3213 THR cc_start: 0.9097 (m) cc_final: 0.8614 (p)
  outliers start: 69
  outliers final: 49
  residues processed: 219
  average time/residue: 0.2020
  time to fit residues: 76.5676
Evaluate side-chains
  209 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 158
  time to evaluate  : 1.717 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3037 MET
Chi-restraints excluded: chain A residue 3110 LEU
Chi-restraints excluded: chain A residue 3157 THR
Chi-restraints excluded: chain A residue 3195 VAL
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain A residue 3216 ILE
Chi-restraints excluded: chain B residue 2909 ASP
Chi-restraints excluded: chain B residue 3037 MET
Chi-restraints excluded: chain B residue 3049 MET
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3157 THR
Chi-restraints excluded: chain B residue 3195 VAL
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain B residue 3216 ILE
Chi-restraints excluded: chain C residue 2982 VAL
Chi-restraints excluded: chain C residue 3049 MET
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3089 ASN
Chi-restraints excluded: chain C residue 3205 THR
Chi-restraints excluded: chain C residue 3216 ILE
Chi-restraints excluded: chain D residue 2987 ILE
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3128 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3205 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 2987 ILE
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3037 MET
Chi-restraints excluded: chain E residue 3195 VAL
Chi-restraints excluded: chain E residue 3205 THR
Chi-restraints excluded: chain E residue 3216 ILE
Chi-restraints excluded: chain F residue 2967 THR
Chi-restraints excluded: chain F residue 2982 VAL
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3029 ILE
Chi-restraints excluded: chain F residue 3037 MET
Chi-restraints excluded: chain F residue 3128 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3195 VAL
Chi-restraints excluded: chain F residue 3205 THR
Chi-restraints excluded: chain G residue 2946 ILE
Chi-restraints excluded: chain G residue 2982 VAL
Chi-restraints excluded: chain G residue 2987 ILE
Chi-restraints excluded: chain G residue 3049 MET
Chi-restraints excluded: chain G residue 3110 LEU
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3157 THR
Chi-restraints excluded: chain G residue 3195 VAL
Chi-restraints excluded: chain G residue 3205 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 99 optimal weight:    7.9990
   chunk 24 optimal weight:    1.9990
   chunk 80 optimal weight:    3.9990
   chunk 62 optimal weight:    5.9990
   chunk 193 optimal weight:    0.9990
   chunk 195 optimal weight:    4.9990
   chunk 88 optimal weight:    2.9990
   chunk 97 optimal weight:    1.9990
   chunk 5 optimal weight:    7.9990
   chunk 156 optimal weight:    2.9990
   chunk 32 optimal weight:    5.9990
   overall best weight:    2.1990

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

Flipped N/Q/H residues before XYZ refinement:
A2980 ASN
B2980 ASN
** C2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C3089 ASN
D2980 ASN
E2980 ASN
E3171 ASN
F2980 ASN
F3063 ASN
G2980 ASN
G3063 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2995 r_free = 0.2995 target = 0.103033 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2775 r_free = 0.2775 target = 0.087149 restraints weight = 23146.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.2760 r_free = 0.2760 target = 0.086044 restraints weight = 28873.570|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.086251 restraints weight = 28305.927|
|-----------------------------------------------------------------------------|
r_work (final): 0.2758
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8318
moved from start:          0.3648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  17717  Z= 0.395
  Angle     :  0.559   6.138  24486  Z= 0.302
  Chirality :  0.050   0.204   3017
  Planarity :  0.005   0.050   3213
  Dihedral  :  4.280  29.875   2499
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 2.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 14.19 %
    Favored  : 82.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.72 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  0.57 (0.16), residues: 882
  loop :  0.55 (0.17), residues: 1519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP B2924 
 HIS   0.002   0.001   HIS F3152 
 PHE   0.011   0.002   PHE G3191 
 TYR   0.017   0.002   TYR A3048 
 ARG   0.003   0.000   ARG B2969 

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

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

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4802 Ramachandran restraints generated.
    2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  234 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 72
    poor density    : 162
  time to evaluate  : 1.826 
Fit side-chains
REVERT: C 3007 ILE cc_start: 0.8707 (OUTLIER) cc_final: 0.8447 (mt)
REVERT: E 2987 ILE cc_start: 0.8813 (OUTLIER) cc_final: 0.8586 (tp)
REVERT: F 3007 ILE cc_start: 0.8954 (mm) cc_final: 0.8752 (mt)
  outliers start: 72
  outliers final: 52
  residues processed: 213
  average time/residue: 0.2289
  time to fit residues: 82.6784
Evaluate side-chains
  202 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 148
  time to evaluate  : 2.079 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 2982 VAL
Chi-restraints excluded: chain A residue 3037 MET
Chi-restraints excluded: chain A residue 3157 THR
Chi-restraints excluded: chain A residue 3195 VAL
Chi-restraints excluded: chain A residue 3205 THR
Chi-restraints excluded: chain A residue 3220 ASN
Chi-restraints excluded: chain B residue 2909 ASP
Chi-restraints excluded: chain B residue 3037 MET
Chi-restraints excluded: chain B residue 3049 MET
Chi-restraints excluded: chain B residue 3121 MET
Chi-restraints excluded: chain B residue 3156 VAL
Chi-restraints excluded: chain B residue 3157 THR
Chi-restraints excluded: chain B residue 3195 VAL
Chi-restraints excluded: chain B residue 3205 THR
Chi-restraints excluded: chain B residue 3213 THR
Chi-restraints excluded: chain B residue 3216 ILE
Chi-restraints excluded: chain C residue 2982 VAL
Chi-restraints excluded: chain C residue 3007 ILE
Chi-restraints excluded: chain C residue 3049 MET
Chi-restraints excluded: chain C residue 3081 ASP
Chi-restraints excluded: chain C residue 3089 ASN
Chi-restraints excluded: chain C residue 3195 VAL
Chi-restraints excluded: chain C residue 3205 THR
Chi-restraints excluded: chain C residue 3216 ILE
Chi-restraints excluded: chain D residue 2967 THR
Chi-restraints excluded: chain D residue 2987 ILE
Chi-restraints excluded: chain D residue 3019 THR
Chi-restraints excluded: chain D residue 3128 ASP
Chi-restraints excluded: chain D residue 3156 VAL
Chi-restraints excluded: chain D residue 3205 THR
Chi-restraints excluded: chain E residue 2982 VAL
Chi-restraints excluded: chain E residue 2987 ILE
Chi-restraints excluded: chain E residue 3019 THR
Chi-restraints excluded: chain E residue 3037 MET
Chi-restraints excluded: chain E residue 3195 VAL
Chi-restraints excluded: chain E residue 3205 THR
Chi-restraints excluded: chain E residue 3216 ILE
Chi-restraints excluded: chain F residue 2982 VAL
Chi-restraints excluded: chain F residue 3019 THR
Chi-restraints excluded: chain F residue 3037 MET
Chi-restraints excluded: chain F residue 3063 ASN
Chi-restraints excluded: chain F residue 3128 ASP
Chi-restraints excluded: chain F residue 3156 VAL
Chi-restraints excluded: chain F residue 3195 VAL
Chi-restraints excluded: chain F residue 3205 THR
Chi-restraints excluded: chain G residue 2982 VAL
Chi-restraints excluded: chain G residue 2987 ILE
Chi-restraints excluded: chain G residue 3049 MET
Chi-restraints excluded: chain G residue 3063 ASN
Chi-restraints excluded: chain G residue 3110 LEU
Chi-restraints excluded: chain G residue 3156 VAL
Chi-restraints excluded: chain G residue 3157 THR
Chi-restraints excluded: chain G residue 3195 VAL
Chi-restraints excluded: chain G residue 3205 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 238
   random chunks:
   chunk 164 optimal weight:    2.9990
   chunk 146 optimal weight:    0.3980
   chunk 109 optimal weight:    7.9990
   chunk 96 optimal weight:    1.9990
   chunk 201 optimal weight:    7.9990
   chunk 194 optimal weight:    0.5980
   chunk 91 optimal weight:    0.8980
   chunk 158 optimal weight:    0.9990
   chunk 180 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 162 optimal weight:    3.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
A2980 ASN
B2980 ASN
C2980 ASN
D2980 ASN
E2980 ASN
** F2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
G2980 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.103334 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2777 r_free = 0.2777 target = 0.087300 restraints weight = 23018.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.2763 r_free = 0.2763 target = 0.086315 restraints weight = 37402.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.2768 r_free = 0.2768 target = 0.086598 restraints weight = 32992.601|
|-----------------------------------------------------------------------------|
r_work (final): 0.2763
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8307
moved from start:          0.3659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.144  17717  Z= 0.376
  Angle     :  0.902  59.198  24486  Z= 0.540
  Chirality :  0.053   0.641   3017
  Planarity :  0.006   0.182   3213
  Dihedral  :  4.347  29.789   2499
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 3.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.50 %
    Favored  : 96.50 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 15.02 %
    Favored  : 81.93 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.69 (0.17), residues: 2401
  helix:  None (None), residues: 0
  sheet:  0.54 (0.16), residues: 882
  loop :  0.54 (0.17), residues: 1519

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP B2924 
 HIS   0.002   0.001   HIS F3152 
 PHE   0.011   0.002   PHE G3191 
 TYR   0.017   0.001   TYR A3048 
 ARG   0.003   0.000   ARG B2969 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4328.73 seconds
wall clock time: 79 minutes 23.34 seconds (4763.34 seconds total)