Starting phenix.real_space_refine
on Sun Aug 24 08:55:09 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hjw_34840/08_2025/8hjw_34840.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hjw_34840/08_2025/8hjw_34840.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hjw_34840/08_2025/8hjw_34840.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hjw_34840/08_2025/8hjw_34840.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hjw_34840/08_2025/8hjw_34840.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hjw_34840/08_2025/8hjw_34840.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   1.000
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      70      5.16       5
     C   11570      2.51       5
     N    3408      2.21       5
     O    3468      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 30 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 18516
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1215, 9258
          Classifications: {'peptide': 1215}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 59, 'TRANS': 1151}
    Chain: "B"
      Number of atoms: 9258
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1215, 9258
          Classifications: {'peptide': 1215}
          Modifications used: {'COO': 1}
          Link IDs: {'CIS': 2, 'PCIS': 2, 'PTRANS': 59, 'TRANS': 1151}
  Time building chain proxies: 4.77, per 1000 atoms: 0.26
  Number of scatterers: 18516
  At special positions: 0
  Unit cell: (95.45, 114.54, 170.15, 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      70     16.00
     O    3468      8.00
     N    3408      7.00
     C   11570      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.75
  Conformation dependent library (CDL) restraints added in 854.1 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  4464

  Finding SS restraints...
    Secondary structure from input PDB file:
      100 helices and 11 sheets defined
      54.6% alpha, 8.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.81
  Creating SS restraints...
    Processing helix  chain 'A' and resid 19 through 32
    Processing helix  chain 'A' and resid 42 through 57
    Processing helix  chain 'A' and resid 60 through 62
      No H-bonds generated for 'chain 'A' and resid 60 through 62'
    Processing helix  chain 'A' and resid 73 through 89
    Processing helix  chain 'A' and resid 106 through 110
      removed outlier: 3.501A  pdb=" N   ILE A 110 " --> pdb=" O   LEU A 107 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 113 through 117
    Processing helix  chain 'A' and resid 124 through 133
    Processing helix  chain 'A' and resid 133 through 144
    Processing helix  chain 'A' and resid 145 through 147
      No H-bonds generated for 'chain 'A' and resid 145 through 147'
    Processing helix  chain 'A' and resid 158 through 163
      removed outlier: 3.557A  pdb=" N   ALA A 163 " --> pdb=" O   PHE A 160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 193
      Proline residue:  A 174  - end of helix
      removed outlier: 4.177A  pdb=" N   ALA A 191 " --> pdb=" O   ARG A 187 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ARG A 192 " --> pdb=" O   GLU A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 206 through 221
      removed outlier: 3.539A  pdb=" N   ARG A 210 " --> pdb=" O   SER A 206 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 225 through 234
    Processing helix  chain 'A' and resid 252 through 265
      removed outlier: 3.738A  pdb=" N   VAL A 256 " --> pdb=" O   SER A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 269
    Processing helix  chain 'A' and resid 316 through 329
      removed outlier: 3.802A  pdb=" N   CYS A 329 " --> pdb=" O   MET A 325 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 358
    Processing helix  chain 'A' and resid 373 through 388
      removed outlier: 3.682A  pdb=" N   ILE A 377 " --> pdb=" O   ASP A 373 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 412 through 422
    Processing helix  chain 'A' and resid 424 through 440
    Processing helix  chain 'A' and resid 467 through 498
    Processing helix  chain 'A' and resid 519 through 534
    Processing helix  chain 'A' and resid 583 through 594
    Processing helix  chain 'A' and resid 605 through 623
    Processing helix  chain 'A' and resid 627 through 630
    Processing helix  chain 'A' and resid 642 through 658
    Processing helix  chain 'A' and resid 675 through 679
    Processing helix  chain 'A' and resid 680 through 692
    Processing helix  chain 'A' and resid 692 through 710
      removed outlier: 3.712A  pdb=" N   TYR A 696 " --> pdb=" O   LEU A 692 " (cutoff:3.500A)
      Proline residue:  A 704  - end of helix
    Processing helix  chain 'A' and resid 719 through 721
      No H-bonds generated for 'chain 'A' and resid 719 through 721'
    Processing helix  chain 'A' and resid 734 through 756
      removed outlier: 4.654A  pdb=" N   ARG A 753 " --> pdb=" O   GLU A 749 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   PHE A 754 " --> pdb=" O   VAL A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 783 through 811
      removed outlier: 3.507A  pdb=" N   ARG A 787 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
      removed outlier: 3.808A  pdb=" N   THR A 810 " --> pdb=" O   ALA A 806 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 821
    Processing helix  chain 'A' and resid 826 through 832
    Processing helix  chain 'A' and resid 837 through 851
    Processing helix  chain 'A' and resid 855 through 859
    Processing helix  chain 'A' and resid 863 through 877
    Processing helix  chain 'A' and resid 898 through 916
      removed outlier: 3.607A  pdb=" N   ILE A 902 " --> pdb=" O   THR A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 924 through 937
    Processing helix  chain 'A' and resid 968 through 975
      removed outlier: 3.727A  pdb=" N   LEU A 975 " --> pdb=" O   ARG A 971 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 987 through 1003
      removed outlier: 3.532A  pdb=" N   TYR A1002 " --> pdb=" O   TYR A 998 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1024
    Processing helix  chain 'A' and resid 1024 through 1030
    Processing helix  chain 'A' and resid 1041 through 1054
    Processing helix  chain 'A' and resid 1085 through 1097
    Processing helix  chain 'A' and resid 1097 through 1110
    Processing helix  chain 'A' and resid 1127 through 1155
      removed outlier: 3.917A  pdb=" N   ALA A1143 " --> pdb=" O   THR A1139 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   PHE A1144 " --> pdb=" O   THR A1140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1170 through 1174
    Processing helix  chain 'A' and resid 1177 through 1197
    Processing helix  chain 'A' and resid 1205 through 1212
    Processing helix  chain 'B' and resid 19 through 32
    Processing helix  chain 'B' and resid 42 through 58
    Processing helix  chain 'B' and resid 60 through 62
      No H-bonds generated for 'chain 'B' and resid 60 through 62'
    Processing helix  chain 'B' and resid 73 through 89
    Processing helix  chain 'B' and resid 106 through 110
    Processing helix  chain 'B' and resid 113 through 117
    Processing helix  chain 'B' and resid 124 through 133
    Processing helix  chain 'B' and resid 133 through 144
    Processing helix  chain 'B' and resid 145 through 147
      No H-bonds generated for 'chain 'B' and resid 145 through 147'
    Processing helix  chain 'B' and resid 158 through 163
      removed outlier: 3.605A  pdb=" N   ALA B 163 " --> pdb=" O   PHE B 160 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 168 through 190
      Proline residue:  B 174  - end of helix
    Processing helix  chain 'B' and resid 206 through 221
    Processing helix  chain 'B' and resid 225 through 234
    Processing helix  chain 'B' and resid 252 through 265
      removed outlier: 3.820A  pdb=" N   VAL B 256 " --> pdb=" O   SER B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 266 through 269
    Processing helix  chain 'B' and resid 316 through 329
      removed outlier: 3.740A  pdb=" N   CYS B 329 " --> pdb=" O   MET B 325 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 339 through 358
    Processing helix  chain 'B' and resid 373 through 388
      removed outlier: 3.779A  pdb=" N   ILE B 377 " --> pdb=" O   ASP B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 412 through 424
      removed outlier: 3.714A  pdb=" N   ILE B 424 " --> pdb=" O   LEU B 420 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 424 through 441
      removed outlier: 3.595A  pdb=" N   GLN B 441 " --> pdb=" O   TYR B 437 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 466 through 497
      removed outlier: 3.981A  pdb=" N   ARG B 470 " --> pdb=" O   ASN B 466 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 519 through 534
    Processing helix  chain 'B' and resid 583 through 595
    Processing helix  chain 'B' and resid 605 through 623
      removed outlier: 3.536A  pdb=" N   LEU B 609 " --> pdb=" O   ASP B 605 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 627 through 630
    Processing helix  chain 'B' and resid 642 through 658
    Processing helix  chain 'B' and resid 675 through 679
    Processing helix  chain 'B' and resid 680 through 692
    Processing helix  chain 'B' and resid 692 through 710
      removed outlier: 3.684A  pdb=" N   TYR B 696 " --> pdb=" O   LEU B 692 " (cutoff:3.500A)
      Proline residue:  B 704  - end of helix
    Processing helix  chain 'B' and resid 719 through 723
    Processing helix  chain 'B' and resid 734 through 756
      removed outlier: 5.030A  pdb=" N   ARG B 753 " --> pdb=" O   GLU B 749 " (cutoff:3.500A)
      removed outlier: 4.503A  pdb=" N   PHE B 754 " --> pdb=" O   VAL B 750 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 783 through 811
      removed outlier: 3.822A  pdb=" N   THR B 810 " --> pdb=" O   ALA B 806 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 814 through 821
      removed outlier: 3.580A  pdb=" N   LEU B 821 " --> pdb=" O   GLU B 817 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 826 through 832
    Processing helix  chain 'B' and resid 837 through 851
    Processing helix  chain 'B' and resid 855 through 859
    Processing helix  chain 'B' and resid 863 through 877
    Processing helix  chain 'B' and resid 898 through 916
    Processing helix  chain 'B' and resid 924 through 937
      removed outlier: 3.765A  pdb=" N   ALA B 937 " --> pdb=" O   VAL B 933 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 968 through 975
      removed outlier: 3.672A  pdb=" N   LEU B 975 " --> pdb=" O   ARG B 971 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 987 through 1003
      removed outlier: 3.569A  pdb=" N   TYR B1002 " --> pdb=" O   TYR B 998 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   GLY B1003 " --> pdb=" O   LEU B 999 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1013 through 1024
    Processing helix  chain 'B' and resid 1024 through 1030
    Processing helix  chain 'B' and resid 1041 through 1054
    Processing helix  chain 'B' and resid 1085 through 1097
    Processing helix  chain 'B' and resid 1097 through 1109
    Processing helix  chain 'B' and resid 1127 through 1155
      removed outlier: 3.944A  pdb=" N   ALA B1143 " --> pdb=" O   THR B1139 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   PHE B1144 " --> pdb=" O   THR B1140 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1170 through 1174
    Processing helix  chain 'B' and resid 1177 through 1197
    Processing helix  chain 'B' and resid 1205 through 1212
    Processing sheet with id=AA1, first strand: chain 'A' and resid 64 through 68
      removed outlier: 6.493A  pdb=" N   VAL A  36 " --> pdb=" O   ASP A  65 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   GLU A  67 " --> pdb=" O   VAL A  36 " (cutoff:3.500A)
      removed outlier: 6.266A  pdb=" N   ILE A  38 " --> pdb=" O   GLU A  67 " (cutoff:3.500A)
      removed outlier: 3.590A  pdb=" N   ILE A  14 " --> pdb=" O   ILE A  37 " (cutoff:3.500A)
      removed outlier: 5.930A  pdb=" N   LEU A  94 " --> pdb=" O   ILE A 154 " (cutoff:3.500A)
      removed outlier: 7.108A  pdb=" N   VAL A 156 " --> pdb=" O   LEU A  94 " (cutoff:3.500A)
      removed outlier: 6.891A  pdb=" N   ASN A  96 " --> pdb=" O   VAL A 156 " (cutoff:3.500A)
      removed outlier: 6.248A  pdb=" N   VAL A 153 " --> pdb=" O   ASN A 197 " (cutoff:3.500A)
      removed outlier: 7.756A  pdb=" N   ILE A 199 " --> pdb=" O   VAL A 153 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   ASN A 155 " --> pdb=" O   ILE A 199 " (cutoff:3.500A)
      removed outlier: 9.287A  pdb=" N   ILE A 276 " --> pdb=" O   VAL A 196 " (cutoff:3.500A)
      removed outlier: 6.915A  pdb=" N   THR A 198 " --> pdb=" O   ILE A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 239 through 240
    Processing sheet with id=AA3, first strand: chain 'A' and resid 289 through 291
      removed outlier: 6.678A  pdb=" N   THR A 290 " --> pdb=" O   ASN A 544 " (cutoff:3.500A)
      removed outlier: 5.842A  pdb=" N   THR A 308 " --> pdb=" O   ILE A 334 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   GLY A 336 " --> pdb=" O   THR A 308 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ILE A 310 " --> pdb=" O   GLY A 336 " (cutoff:3.500A)
      removed outlier: 7.750A  pdb=" N   VAL A 333 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
      removed outlier: 8.558A  pdb=" N   LEU A 367 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   ILE A 335 " --> pdb=" O   LEU A 367 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 635
      removed outlier: 3.564A  pdb=" N   ILE A 577 " --> pdb=" O   MET A 600 " (cutoff:3.500A)
      removed outlier: 6.626A  pdb=" N   VAL A 574 " --> pdb=" O   TYR A 662 " (cutoff:3.500A)
      removed outlier: 7.811A  pdb=" N   ILE A 664 " --> pdb=" O   VAL A 574 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   LEU A 576 " --> pdb=" O   ILE A 664 " (cutoff:3.500A)
      removed outlier: 6.489A  pdb=" N   LEU A 663 " --> pdb=" O   LEU A 715 " (cutoff:3.500A)
      removed outlier: 7.457A  pdb=" N   VAL A 717 " --> pdb=" O   LEU A 663 " (cutoff:3.500A)
      removed outlier: 7.688A  pdb=" N   ASN A 665 " --> pdb=" O   VAL A 717 " (cutoff:3.500A)
      removed outlier: 6.476A  pdb=" N   GLY A 712 " --> pdb=" O   GLN A 760 " (cutoff:3.500A)
      removed outlier: 8.299A  pdb=" N   ASN A 762 " --> pdb=" O   GLY A 712 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   ILE A 714 " --> pdb=" O   ASN A 762 " (cutoff:3.500A)
      removed outlier: 7.668A  pdb=" N   ILE A 764 " --> pdb=" O   ILE A 714 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASN A 716 " --> pdb=" O   ILE A 764 " (cutoff:3.500A)
      removed outlier: 8.649A  pdb=" N   PHE A 946 " --> pdb=" O   ILE A 761 " (cutoff:3.500A)
      removed outlier: 6.616A  pdb=" N   ALA A 763 " --> pdb=" O   PHE A 946 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 723 through 724
    Processing sheet with id=AA6, first strand: chain 'A' and resid 1033 through 1037
      removed outlier: 3.530A  pdb=" N   VAL A 980 " --> pdb=" O   GLN A1006 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   THR A 979 " --> pdb=" O   PRO A1058 " (cutoff:3.500A)
      removed outlier: 8.486A  pdb=" N   VAL A1060 " --> pdb=" O   THR A 979 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   TYR A 981 " --> pdb=" O   VAL A1060 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   LEU A1115 " --> pdb=" O   ASN A1162 " (cutoff:3.500A)
      removed outlier: 7.375A  pdb=" N   VAL A1164 " --> pdb=" O   LEU A1115 " (cutoff:3.500A)
      removed outlier: 6.024A  pdb=" N   LEU A1117 " --> pdb=" O   VAL A1164 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 64 through 68
      removed outlier: 3.515A  pdb=" N   SER B  39 " --> pdb=" O   ILE B  14 " (cutoff:3.500A)
      removed outlier: 5.995A  pdb=" N   LEU B  94 " --> pdb=" O   ILE B 154 " (cutoff:3.500A)
      removed outlier: 7.309A  pdb=" N   VAL B 156 " --> pdb=" O   LEU B  94 " (cutoff:3.500A)
      removed outlier: 6.992A  pdb=" N   ASN B  96 " --> pdb=" O   VAL B 156 " (cutoff:3.500A)
      removed outlier: 9.075A  pdb=" N   ILE B 276 " --> pdb=" O   VAL B 196 " (cutoff:3.500A)
      removed outlier: 6.591A  pdb=" N   THR B 198 " --> pdb=" O   ILE B 276 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 239 through 240
    Processing sheet with id=AA9, first strand: chain 'B' and resid 289 through 291
      removed outlier: 6.522A  pdb=" N   THR B 290 " --> pdb=" O   ASN B 544 " (cutoff:3.500A)
      removed outlier: 9.069A  pdb=" N   LEU B 543 " --> pdb=" O   ALA B 507 " (cutoff:3.500A)
      removed outlier: 6.786A  pdb=" N   GLN B 509 " --> pdb=" O   LEU B 543 " (cutoff:3.500A)
      removed outlier: 6.318A  pdb=" N   VAL B 454 " --> pdb=" O   ASN B 508 " (cutoff:3.500A)
      removed outlier: 7.657A  pdb=" N   ILE B 510 " --> pdb=" O   VAL B 454 " (cutoff:3.500A)
      removed outlier: 6.505A  pdb=" N   PHE B 456 " --> pdb=" O   ILE B 510 " (cutoff:3.500A)
      removed outlier: 6.190A  pdb=" N   THR B 307 " --> pdb=" O   ALA B 393 " (cutoff:3.500A)
      removed outlier: 7.641A  pdb=" N   VAL B 395 " --> pdb=" O   THR B 307 " (cutoff:3.500A)
      removed outlier: 5.917A  pdb=" N   LEU B 309 " --> pdb=" O   VAL B 395 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   THR B 308 " --> pdb=" O   ILE B 334 " (cutoff:3.500A)
      removed outlier: 7.543A  pdb=" N   GLY B 336 " --> pdb=" O   THR B 308 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   ILE B 310 " --> pdb=" O   GLY B 336 " (cutoff:3.500A)
      removed outlier: 8.457A  pdb=" N   LEU B 367 " --> pdb=" O   VAL B 333 " (cutoff:3.500A)
      removed outlier: 6.006A  pdb=" N   ILE B 335 " --> pdb=" O   LEU B 367 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 632 through 634
      removed outlier: 6.579A  pdb=" N   VAL B 574 " --> pdb=" O   TYR B 662 " (cutoff:3.500A)
      removed outlier: 7.731A  pdb=" N   ILE B 664 " --> pdb=" O   VAL B 574 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   LEU B 576 " --> pdb=" O   ILE B 664 " (cutoff:3.500A)
      removed outlier: 6.263A  pdb=" N   LEU B 663 " --> pdb=" O   LEU B 715 " (cutoff:3.500A)
      removed outlier: 7.339A  pdb=" N   VAL B 717 " --> pdb=" O   LEU B 663 " (cutoff:3.500A)
      removed outlier: 7.676A  pdb=" N   ASN B 665 " --> pdb=" O   VAL B 717 " (cutoff:3.500A)
      removed outlier: 8.628A  pdb=" N   PHE B 946 " --> pdb=" O   ILE B 761 " (cutoff:3.500A)
      removed outlier: 6.360A  pdb=" N   ALA B 763 " --> pdb=" O   PHE B 946 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 1033 through 1037
      removed outlier: 6.311A  pdb=" N   VAL B1007 " --> pdb=" O   MET B1034 " (cutoff:3.500A)
      removed outlier: 7.739A  pdb=" N   ILE B1036 " --> pdb=" O   VAL B1007 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   MET B1009 " --> pdb=" O   ILE B1036 " (cutoff:3.500A)
      removed outlier: 3.782A  pdb=" N   VAL B 980 " --> pdb=" O   GLN B1006 " (cutoff:3.500A)
      removed outlier: 6.343A  pdb=" N   THR B 979 " --> pdb=" O   PRO B1058 " (cutoff:3.500A)
      removed outlier: 8.278A  pdb=" N   VAL B1060 " --> pdb=" O   THR B 979 " (cutoff:3.500A)
      removed outlier: 6.368A  pdb=" N   TYR B 981 " --> pdb=" O   VAL B1060 " (cutoff:3.500A)
      removed outlier: 5.933A  pdb=" N   LEU B1115 " --> pdb=" O   ASN B1162 " (cutoff:3.500A)
      removed outlier: 6.941A  pdb=" N   VAL B1164 " --> pdb=" O   LEU B1115 " (cutoff:3.500A)
      removed outlier: 5.829A  pdb=" N   LEU B1117 " --> pdb=" O   VAL B1164 " (cutoff:3.500A)
      removed outlier: 9.256A  pdb=" N   ILE B1217 " --> pdb=" O   ILE B1161 " (cutoff:3.500A)
      removed outlier: 6.625A  pdb=" N   GLN B1163 " --> pdb=" O   ILE B1217 " (cutoff:3.500A)

    983 hydrogen bonds defined for protein.
    2844 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: 4.17

  Time building geometry restraints manager: 2.29 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 6257
        1.34 -     1.46: 2343
        1.46 -     1.58: 10128
        1.58 -     1.70: 0
        1.70 -     1.82: 122
  Bond restraints: 18850
  Sorted by residual:
  bond pdb=" N   ILE B 549 "
       pdb=" CA  ILE B 549 "
    ideal  model  delta    sigma   weight residual
    1.459  1.495 -0.036 1.25e-02 6.40e+03 8.16e+00
  bond pdb=" N   THR A1196 "
       pdb=" CA  THR A1196 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.037 1.31e-02 5.83e+03 7.95e+00
  bond pdb=" N   ILE A 549 "
       pdb=" CA  ILE A 549 "
    ideal  model  delta    sigma   weight residual
    1.459  1.494 -0.035 1.25e-02 6.40e+03 7.62e+00
  bond pdb=" N   SER A 458 "
       pdb=" CA  SER A 458 "
    ideal  model  delta    sigma   weight residual
    1.457  1.490 -0.032 1.23e-02 6.61e+03 6.98e+00
  bond pdb=" N   VAL A1192 "
       pdb=" CA  VAL A1192 "
    ideal  model  delta    sigma   weight residual
    1.461  1.491 -0.030 1.19e-02 7.06e+03 6.51e+00
  ... (remaining 18845 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.90: 24877
        1.90 -     3.79: 627
        3.79 -     5.69: 74
        5.69 -     7.58: 16
        7.58 -     9.48: 4
  Bond angle restraints: 25598
  Sorted by residual:
  angle pdb=" N   GLU A 564 "
        pdb=" CA  GLU A 564 "
        pdb=" C   GLU A 564 "
      ideal   model   delta    sigma   weight residual
     114.75  108.40    6.35 1.26e+00 6.30e-01 2.54e+01
  angle pdb=" C   ARG B 556 "
        pdb=" CA  ARG B 556 "
        pdb=" CB  ARG B 556 "
      ideal   model   delta    sigma   weight residual
     116.54  111.42    5.12 1.15e+00 7.56e-01 1.98e+01
  angle pdb=" C   ARG A 556 "
        pdb=" CA  ARG A 556 "
        pdb=" CB  ARG A 556 "
      ideal   model   delta    sigma   weight residual
     116.54  111.46    5.08 1.15e+00 7.56e-01 1.95e+01
  angle pdb=" N   GLY B 460 "
        pdb=" CA  GLY B 460 "
        pdb=" C   GLY B 460 "
      ideal   model   delta    sigma   weight residual
     114.16  108.92    5.24 1.21e+00 6.83e-01 1.87e+01
  angle pdb=" N   GLY A 460 "
        pdb=" CA  GLY A 460 "
        pdb=" C   GLY A 460 "
      ideal   model   delta    sigma   weight residual
     113.99  108.71    5.28 1.28e+00 6.10e-01 1.70e+01
  ... (remaining 25593 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.07: 10507
       18.07 -    36.14: 769
       36.14 -    54.21: 123
       54.21 -    72.28: 28
       72.28 -    90.35: 23
  Dihedral angle restraints: 11450
    sinusoidal: 4512
      harmonic: 6938
  Sorted by residual:
  dihedral pdb=" CA  ALA A 563 "
           pdb=" C   ALA A 563 "
           pdb=" N   GLU A 564 "
           pdb=" CA  GLU A 564 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.49   23.51     0      5.00e+00 4.00e-02 2.21e+01
  dihedral pdb=" CA  ARG A 780 "
           pdb=" C   ARG A 780 "
           pdb=" N   PRO A 781 "
           pdb=" CA  PRO A 781 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.60   21.40     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" CA  TYR A 720 "
           pdb=" C   TYR A 720 "
           pdb=" N   PHE A 721 "
           pdb=" CA  PHE A 721 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -159.45  -20.55     0      5.00e+00 4.00e-02 1.69e+01
  ... (remaining 11447 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 1915
       0.034 -    0.068: 707
       0.068 -    0.103: 208
       0.103 -    0.137: 88
       0.137 -    0.171: 12
  Chirality restraints: 2930
  Sorted by residual:
  chirality pdb=" CB  THR A 552 "
            pdb=" CA  THR A 552 "
            pdb=" OG1 THR A 552 "
            pdb=" CG2 THR A 552 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 7.33e-01
  chirality pdb=" CB  THR B 553 "
            pdb=" CA  THR B 553 "
            pdb=" OG1 THR B 553 "
            pdb=" CG2 THR B 553 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 7.00e-01
  chirality pdb=" CB  THR B 552 "
            pdb=" CA  THR B 552 "
            pdb=" OG1 THR B 552 "
            pdb=" CG2 THR B 552 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.72   -0.17 2.00e-01 2.50e+01 6.98e-01
  ... (remaining 2927 not shown)

  Planarity restraints: 3402
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 457 "    0.014 2.00e-02 2.50e+03   2.76e-02 7.61e+00
        pdb=" C   LEU B 457 "   -0.048 2.00e-02 2.50e+03
        pdb=" O   LEU B 457 "    0.018 2.00e-02 2.50e+03
        pdb=" N   SER B 458 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B1080 "   -0.014 2.00e-02 2.50e+03   1.63e-02 6.64e+00
        pdb=" CG  TRP B1080 "    0.044 2.00e-02 2.50e+03
        pdb=" CD1 TRP B1080 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP B1080 "   -0.006 2.00e-02 2.50e+03
        pdb=" NE1 TRP B1080 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B1080 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP B1080 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B1080 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B1080 "   -0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP B1080 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 731 "   -0.020 2.00e-02 2.50e+03   1.58e-02 4.98e+00
        pdb=" CG  TYR B 731 "    0.039 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 731 "   -0.008 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 731 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 731 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 731 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 731 "   -0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR B 731 "   -0.003 2.00e-02 2.50e+03
  ... (remaining 3399 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.69: 345
        2.69 -     3.24: 18558
        3.24 -     3.79: 29933
        3.79 -     4.35: 38508
        4.35 -     4.90: 63212
  Nonbonded interactions: 150556
  Sorted by model distance:
  nonbonded pdb=" O   SER B 559 "
            pdb=" CG2 VAL B 560 "
     model   vdw
     2.134 3.460
  nonbonded pdb=" O   SER A 559 "
            pdb=" CG2 VAL A 560 "
     model   vdw
     2.140 3.460
  nonbonded pdb=" O   THR B 552 "
            pdb=" OG1 THR B 553 "
     model   vdw
     2.166 3.040
  nonbonded pdb=" O   THR A 552 "
            pdb=" OG1 THR A 553 "
     model   vdw
     2.177 3.040
  nonbonded pdb=" OG  SER B1085 "
            pdb=" OE1 GLU B1088 "
     model   vdw
     2.197 3.040
  ... (remaining 150551 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: 0.04
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             3.000
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.020
  Extract box with map and model:          0.320
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     19.630
  Find NCS groups from input model:        0.240
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.870
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6975
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057  18850  Z= 0.174
  Angle     :  0.701   9.479  25598  Z= 0.401
  Chirality :  0.042   0.171   2930
  Planarity :  0.005   0.059   3402
  Dihedral  : 13.474  90.353   6986
  Min Nonbonded Distance : 2.134

Molprobity Statistics.
  All-atom Clashscore : 13.02
  Ramachandran Plot:
    Outliers :  0.29 %
    Allowed  :  2.18 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.47 %
    Allowed  :  0.47 %
    Favored  : 99.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.71 (0.17), residues: 2426
  helix:  1.51 (0.15), residues: 1162
  sheet: -0.22 (0.29), residues: 348
  loop : -0.52 (0.20), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 306 
 TYR   0.039   0.002   TYR B 731 
 PHE   0.020   0.001   PHE A 897 
 TRP   0.044   0.002   TRP B1080 
 HIS   0.005   0.001   HIS A 990 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (18850)
  covalent geometry    : angle       0.70068 (25598)
  hydrogen bonds       : bond        0.13788 (  983)
  hydrogen bonds       : angle       5.82278 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  405 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 396
  time to evaluate  : 0.719 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A    7 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8270 (mt)
REVERT: A   13 LEU cc_start: 0.8900 (tp) cc_final: 0.8580 (mp)
REVERT: A  279 THR cc_start: 0.8165 (p) cc_final: 0.7723 (p)
REVERT: A  609 LEU cc_start: 0.9210 (mm) cc_final: 0.8559 (tp)
REVERT: A  628 VAL cc_start: 0.8626 (m) cc_final: 0.8033 (m)
REVERT: A  833 ASN cc_start: 0.7718 (t0) cc_final: 0.7299 (t0)
REVERT: A  843 LEU cc_start: 0.8508 (tp) cc_final: 0.8114 (tp)
REVERT: B   77 VAL cc_start: 0.8952 (t) cc_final: 0.8646 (m)
REVERT: B  279 THR cc_start: 0.7763 (p) cc_final: 0.7334 (p)
REVERT: B  600 MET cc_start: 0.8194 (tpp) cc_final: 0.7186 (ttt)
REVERT: B  609 LEU cc_start: 0.8996 (mt) cc_final: 0.8565 (tp)
REVERT: B  777 THR cc_start: 0.6301 (p) cc_final: 0.5945 (p)
REVERT: B  833 ASN cc_start: 0.8467 (t0) cc_final: 0.8236 (t0)
REVERT: B  914 MET cc_start: 0.7546 (mmm) cc_final: 0.7294 (mmm)
REVERT: B  930 MET cc_start: 0.8181 (tpt) cc_final: 0.7879 (tpp)
REVERT: B 1009 MET cc_start: 0.8090 (mmm) cc_final: 0.7014 (mmp)
  outliers start: 9
  outliers final: 1
  residues processed: 404
  average time/residue: 0.1599
  time to fit residues: 95.4179
Evaluate side-chains
  195 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 193
  time to evaluate  : 0.673 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 216 optimal weight:    2.9990
   chunk 98 optimal weight:    8.9990
   chunk 194 optimal weight:    5.9990
   chunk 227 optimal weight:    5.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    8.9990
   chunk 66 optimal weight:   10.0000
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    6.9990
   chunk 103 optimal weight:    7.9990
   chunk 235 optimal weight:    2.9990
   overall best weight:    3.9990

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 214 GLN
A 459 ASN
A 500 HIS
A 530 GLN
A 607 HIS
A 613 GLN
** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 794 ASN
A1048 GLN
** A1142 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1157 GLN
B  96 ASN
** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 GLN
B 459 ASN
B 500 HIS
** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 ASN
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 716 ASN
** B1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1048 GLN

Total number of N/Q/H flips: 18

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.117530 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.092502 restraints weight = 61340.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.091657 restraints weight = 53232.867|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.092821 restraints weight = 48145.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.093335 restraints weight = 37265.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.093467 restraints weight = 36877.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3695
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7556
moved from start:          0.3114

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.068  18850  Z= 0.246
  Angle     :  0.723   9.141  25598  Z= 0.379
  Chirality :  0.046   0.211   2930
  Planarity :  0.006   0.064   3402
  Dihedral  :  4.811  28.963   2690
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 13.07
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.01 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.63 %
    Allowed  :  6.00 %
    Favored  : 93.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.34 (0.17), residues: 2426
  helix:  1.09 (0.15), residues: 1216
  sheet: -0.52 (0.28), residues: 350
  loop : -0.56 (0.22), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.020   0.001   ARG A 306 
 TYR   0.018   0.002   TYR B 981 
 PHE   0.028   0.003   PHE B  29 
 TRP   0.029   0.004   TRP B 383 
 HIS   0.010   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00557 (18850)
  covalent geometry    : angle       0.72302 (25598)
  hydrogen bonds       : bond        0.04930 (  983)
  hydrogen bonds       : angle       4.82327 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 234
  time to evaluate  : 0.720 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8145 (tpt) cc_final: 0.7430 (tpp)
REVERT: A   59 VAL cc_start: 0.6832 (t) cc_final: 0.6403 (t)
REVERT: A  609 LEU cc_start: 0.9193 (mm) cc_final: 0.8528 (tp)
REVERT: A  930 MET cc_start: 0.8065 (tpp) cc_final: 0.7787 (tpp)
REVERT: A  935 TYR cc_start: 0.8461 (t80) cc_final: 0.8155 (t80)
REVERT: A  991 LEU cc_start: 0.9094 (mt) cc_final: 0.8820 (tp)
REVERT: A 1020 MET cc_start: 0.8623 (mmp) cc_final: 0.8376 (mmp)
REVERT: A 1165 ASP cc_start: 0.8310 (m-30) cc_final: 0.8058 (m-30)
REVERT: B  147 MET cc_start: 0.7178 (mmt) cc_final: 0.6593 (mmm)
REVERT: B  311 CYS cc_start: 0.8411 (t) cc_final: 0.8149 (m)
REVERT: B  609 LEU cc_start: 0.9044 (mt) cc_final: 0.8761 (tp)
REVERT: B  914 MET cc_start: 0.7861 (mmm) cc_final: 0.7481 (mmm)
REVERT: B  930 MET cc_start: 0.8256 (tpt) cc_final: 0.8003 (tpp)
REVERT: B 1009 MET cc_start: 0.7810 (mmm) cc_final: 0.7470 (mmp)
  outliers start: 12
  outliers final: 2
  residues processed: 245
  average time/residue: 0.1168
  time to fit residues: 46.1613
Evaluate side-chains
  155 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 153
  time to evaluate  : 0.610 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 33 optimal weight:    0.9990
   chunk 45 optimal weight:    5.9990
   chunk 227 optimal weight:    7.9990
   chunk 150 optimal weight:    3.9990
   chunk 192 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 209 optimal weight:    0.0020
   chunk 173 optimal weight:    0.9990
   chunk 68 optimal weight:    6.9990
   chunk 185 optimal weight:    1.9990
   overall best weight:    0.9996

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

Flipped N/Q/H residues before XYZ refinement:
A 155 ASN
A 179 ASN
A 530 GLN
A 537 HIS
A 607 HIS
** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
** A 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 709 GLN
A 876 ASN
** B 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 280 HIS
** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1048 GLN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.119592 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3777 r_free = 0.3777 target = 0.095083 restraints weight = 61392.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3756 r_free = 0.3756 target = 0.095700 restraints weight = 51565.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.096923 restraints weight = 43843.115|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.097547 restraints weight = 33750.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.097743 restraints weight = 32318.758|
|-----------------------------------------------------------------------------|
r_work (final): 0.3786
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.3436

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  18850  Z= 0.124
  Angle     :  0.593   8.698  25598  Z= 0.304
  Chirality :  0.041   0.191   2930
  Planarity :  0.005   0.047   3402
  Dihedral  :  4.400  35.517   2690
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 11.10
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.94 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.84 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.73 (0.17), residues: 2426
  helix:  1.39 (0.15), residues: 1200
  sheet: -0.18 (0.30), residues: 332
  loop : -0.38 (0.21), residues: 894

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 306 
 TYR   0.031   0.002   TYR A 731 
 PHE   0.028   0.001   PHE A  29 
 TRP   0.030   0.002   TRP A1080 
 HIS   0.003   0.001   HIS B  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (18850)
  covalent geometry    : angle       0.59267 (25598)
  hydrogen bonds       : bond        0.04118 (  983)
  hydrogen bonds       : angle       4.51073 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 223
  time to evaluate  : 0.771 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.9237 (tt) cc_final: 0.8813 (mp)
REVERT: A   53 MET cc_start: 0.8067 (tpt) cc_final: 0.7290 (tpp)
REVERT: A   59 VAL cc_start: 0.6795 (t) cc_final: 0.6330 (t)
REVERT: A  552 THR cc_start: 0.7677 (p) cc_final: 0.7442 (p)
REVERT: A  609 LEU cc_start: 0.9189 (mm) cc_final: 0.8597 (tp)
REVERT: A  699 MET cc_start: 0.8677 (tpt) cc_final: 0.8369 (tpt)
REVERT: A  914 MET cc_start: 0.7387 (mmp) cc_final: 0.7146 (mmp)
REVERT: A  930 MET cc_start: 0.8017 (tpp) cc_final: 0.7697 (tpp)
REVERT: A  935 TYR cc_start: 0.8355 (t80) cc_final: 0.8002 (t80)
REVERT: A  991 LEU cc_start: 0.9121 (mt) cc_final: 0.8824 (tp)
REVERT: A 1020 MET cc_start: 0.8383 (mmp) cc_final: 0.8136 (mmp)
REVERT: A 1165 ASP cc_start: 0.8156 (m-30) cc_final: 0.7911 (m-30)
REVERT: B  147 MET cc_start: 0.7137 (mmt) cc_final: 0.6510 (mmm)
REVERT: B  165 TYR cc_start: 0.5981 (t80) cc_final: 0.5625 (t80)
REVERT: B  777 THR cc_start: 0.6641 (p) cc_final: 0.6310 (p)
REVERT: B  833 ASN cc_start: 0.8683 (t0) cc_final: 0.8472 (t0)
REVERT: B  914 MET cc_start: 0.7533 (mmm) cc_final: 0.7155 (mmm)
REVERT: B  930 MET cc_start: 0.7818 (tpt) cc_final: 0.7600 (tpp)
REVERT: B 1009 MET cc_start: 0.7886 (mmm) cc_final: 0.7580 (mmm)
  outliers start: 4
  outliers final: 1
  residues processed: 226
  average time/residue: 0.1442
  time to fit residues: 51.0580
Evaluate side-chains
  152 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.838 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 178 optimal weight:    0.6980
   chunk 42 optimal weight:    0.8980
   chunk 165 optimal weight:    8.9990
   chunk 80 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 95 optimal weight:    0.6980
   chunk 106 optimal weight:    0.3980
   chunk 16 optimal weight:    0.0270
   chunk 44 optimal weight:    8.9990
   chunk 133 optimal weight:    7.9990
   chunk 57 optimal weight:    4.9990
   overall best weight:    0.5438

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 155 ASN
A 179 ASN
A 387 ASN
A 530 GLN
A 537 HIS
A 607 HIS
A 665 ASN
A 666 ASN
A 695 ASN
A 794 ASN
A 876 ASN
A1048 GLN
B 472 GLN
B 665 ASN
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 695 ASN
B1048 GLN

Total number of N/Q/H flips: 16

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.120477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.096078 restraints weight = 61331.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3784 r_free = 0.3784 target = 0.097120 restraints weight = 50556.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.098122 restraints weight = 41918.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.098567 restraints weight = 32931.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.098770 restraints weight = 31695.503|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7366
moved from start:          0.3770

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028  18850  Z= 0.109
  Angle     :  0.555   9.093  25598  Z= 0.283
  Chirality :  0.040   0.161   2930
  Planarity :  0.004   0.053   3402
  Dihedral  :  4.167  35.929   2690
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.98 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.74 %
    Favored  : 97.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.92 (0.17), residues: 2426
  helix:  1.53 (0.15), residues: 1196
  sheet: -0.06 (0.30), residues: 334
  loop : -0.29 (0.22), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 354 
 TYR   0.030   0.001   TYR A 998 
 PHE   0.028   0.001   PHE A  29 
 TRP   0.034   0.002   TRP B1080 
 HIS   0.006   0.001   HIS B 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00237 (18850)
  covalent geometry    : angle       0.55475 (25598)
  hydrogen bonds       : bond        0.03660 (  983)
  hydrogen bonds       : angle       4.27232 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 214
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.9250 (tt) cc_final: 0.8849 (mp)
REVERT: A   53 MET cc_start: 0.8027 (tpt) cc_final: 0.7095 (tpp)
REVERT: A   59 VAL cc_start: 0.6617 (t) cc_final: 0.6270 (m)
REVERT: A  552 THR cc_start: 0.7603 (p) cc_final: 0.7318 (p)
REVERT: A  609 LEU cc_start: 0.9147 (mm) cc_final: 0.8509 (tp)
REVERT: A  764 ILE cc_start: 0.8864 (pt) cc_final: 0.8412 (mm)
REVERT: A  914 MET cc_start: 0.7393 (mmp) cc_final: 0.7075 (mmp)
REVERT: A  930 MET cc_start: 0.7976 (tpp) cc_final: 0.7761 (tpp)
REVERT: A  935 TYR cc_start: 0.8172 (t80) cc_final: 0.7863 (t80)
REVERT: A  991 LEU cc_start: 0.9221 (mt) cc_final: 0.8847 (tp)
REVERT: A 1020 MET cc_start: 0.8394 (mmp) cc_final: 0.8153 (mmp)
REVERT: B  147 MET cc_start: 0.6996 (mmt) cc_final: 0.6395 (mmm)
REVERT: B  165 TYR cc_start: 0.5912 (t80) cc_final: 0.5448 (t80)
REVERT: B  325 MET cc_start: 0.8169 (tpt) cc_final: 0.7819 (mmm)
REVERT: B  458 SER cc_start: 0.8225 (m) cc_final: 0.7869 (t)
REVERT: B  833 ASN cc_start: 0.8703 (t0) cc_final: 0.8462 (t0)
REVERT: B  914 MET cc_start: 0.7409 (mmm) cc_final: 0.7099 (mmm)
REVERT: B 1020 MET cc_start: 0.8942 (mmp) cc_final: 0.8489 (mmp)
  outliers start: 4
  outliers final: 0
  residues processed: 217
  average time/residue: 0.1461
  time to fit residues: 50.1970
Evaluate side-chains
  150 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 86 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0670
   chunk 40 optimal weight:    9.9990
   chunk 121 optimal weight:   20.0000
   chunk 223 optimal weight:    7.9990
   chunk 72 optimal weight:    0.3980
   chunk 132 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 173 optimal weight:    7.9990
   chunk 65 optimal weight:    2.9990
   chunk 119 optimal weight:    0.0970
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 607 HIS
A 665 ASN
A 666 ASN
A 733 ASN
A 876 ASN
A1048 GLN
** B 666 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1048 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4234 r_free = 0.4234 target = 0.120302 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3800 r_free = 0.3800 target = 0.096407 restraints weight = 61472.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.096007 restraints weight = 51576.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.097342 restraints weight = 45225.243|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.097909 restraints weight = 36206.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.098080 restraints weight = 33149.887|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7387
moved from start:          0.3979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033  18850  Z= 0.105
  Angle     :  0.555   9.061  25598  Z= 0.279
  Chirality :  0.040   0.205   2930
  Planarity :  0.004   0.040   3402
  Dihedral  :  4.053  35.948   2690
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  1.73 %
    Favored  : 98.10 %
  Rotamer:
    Outliers :  0.21 %
    Allowed  :  2.37 %
    Favored  : 97.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.17), residues: 2426
  helix:  1.55 (0.15), residues: 1192
  sheet: -0.08 (0.30), residues: 338
  loop : -0.25 (0.22), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 354 
 TYR   0.019   0.001   TYR B 731 
 PHE   0.025   0.001   PHE A  29 
 TRP   0.012   0.001   TRP A1080 
 HIS   0.003   0.000   HIS A 485 

Details of bonding type rmsd
  covalent geometry    : bond        0.00234 (18850)
  covalent geometry    : angle       0.55470 (25598)
  hydrogen bonds       : bond        0.03529 (  983)
  hydrogen bonds       : angle       4.19508 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  203 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 199
  time to evaluate  : 0.734 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.9258 (tt) cc_final: 0.8869 (mp)
REVERT: A   53 MET cc_start: 0.8094 (tpt) cc_final: 0.7171 (tpp)
REVERT: A   59 VAL cc_start: 0.6666 (t) cc_final: 0.6345 (m)
REVERT: A  279 THR cc_start: 0.8772 (p) cc_final: 0.8166 (p)
REVERT: A  552 THR cc_start: 0.7672 (p) cc_final: 0.7391 (p)
REVERT: A  914 MET cc_start: 0.7405 (mmp) cc_final: 0.7060 (mmp)
REVERT: A  930 MET cc_start: 0.8011 (tpp) cc_final: 0.7681 (tpp)
REVERT: A  935 TYR cc_start: 0.8128 (t80) cc_final: 0.7782 (t80)
REVERT: A  991 LEU cc_start: 0.9201 (mt) cc_final: 0.8851 (tp)
REVERT: A 1020 MET cc_start: 0.8404 (mmp) cc_final: 0.8140 (mmp)
REVERT: B  147 MET cc_start: 0.6934 (mmt) cc_final: 0.6355 (mmm)
REVERT: B  325 MET cc_start: 0.8052 (tpt) cc_final: 0.7734 (mmm)
REVERT: B  458 SER cc_start: 0.8230 (m) cc_final: 0.7901 (t)
REVERT: B  612 MET cc_start: 0.8534 (tpt) cc_final: 0.8330 (tpp)
REVERT: B  815 MET cc_start: 0.5497 (ptp) cc_final: 0.4858 (ptp)
REVERT: B  833 ASN cc_start: 0.8692 (t0) cc_final: 0.8452 (t0)
REVERT: B  914 MET cc_start: 0.7441 (mmm) cc_final: 0.7086 (mmm)
REVERT: B 1020 MET cc_start: 0.8942 (mmp) cc_final: 0.8513 (mmp)
  outliers start: 4
  outliers final: 0
  residues processed: 203
  average time/residue: 0.1428
  time to fit residues: 45.7585
Evaluate side-chains
  150 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.725 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 183 optimal weight:    0.2980
   chunk 147 optimal weight:    4.9990
   chunk 23 optimal weight:    7.9990
   chunk 65 optimal weight:    9.9990
   chunk 16 optimal weight:    5.9990
   chunk 91 optimal weight:    9.9990
   chunk 195 optimal weight:    1.9990
   chunk 221 optimal weight:    7.9990
   chunk 26 optimal weight:   10.0000
   chunk 199 optimal weight:    8.9990
   chunk 55 optimal weight:   10.0000
   overall best weight:    4.2588

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 155 ASN
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 466 ASN
A 530 GLN
** A 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
A 716 ASN
A 762 ASN
A 794 ASN
A 798 ASN
A 876 ASN
A1048 GLN
B 218 GLN
** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 ASN
** B1027 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1048 GLN
B1099 HIS
B1142 HIS

Total number of N/Q/H flips: 15

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.113755 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.089323 restraints weight = 62516.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.088402 restraints weight = 57729.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.089493 restraints weight = 51631.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.090102 restraints weight = 38261.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.090283 restraints weight = 36677.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7641
moved from start:          0.4892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069  18850  Z= 0.242
  Angle     :  0.685   8.610  25598  Z= 0.355
  Chirality :  0.044   0.206   2930
  Planarity :  0.006   0.094   3402
  Dihedral  :  4.730  45.860   2690
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 13.23
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  3.13 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  0.16 %
    Allowed  :  3.05 %
    Favored  : 96.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.54 (0.17), residues: 2426
  helix:  1.20 (0.15), residues: 1206
  sheet: -0.29 (0.30), residues: 304
  loop : -0.45 (0.21), residues: 916

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 306 
 TYR   0.017   0.002   TYR A 934 
 PHE   0.020   0.002   PHE B  29 
 TRP   0.014   0.002   TRP B 438 
 HIS   0.010   0.002   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00552 (18850)
  covalent geometry    : angle       0.68502 (25598)
  hydrogen bonds       : bond        0.04600 (  983)
  hydrogen bonds       : angle       4.57965 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  180 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 177
  time to evaluate  : 0.928 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.9327 (tt) cc_final: 0.8877 (mp)
REVERT: A   53 MET cc_start: 0.8140 (tpt) cc_final: 0.7383 (tpp)
REVERT: A   59 VAL cc_start: 0.6911 (t) cc_final: 0.6377 (t)
REVERT: A  216 MET cc_start: 0.0702 (mmm) cc_final: 0.0440 (mmm)
REVERT: A  552 THR cc_start: 0.7987 (p) cc_final: 0.7711 (p)
REVERT: A  914 MET cc_start: 0.7520 (mmp) cc_final: 0.7104 (mmp)
REVERT: A  935 TYR cc_start: 0.8794 (t80) cc_final: 0.8577 (t80)
REVERT: A  991 LEU cc_start: 0.9313 (mt) cc_final: 0.9005 (tp)
REVERT: A 1020 MET cc_start: 0.8576 (mmp) cc_final: 0.8375 (mmp)
REVERT: B  147 MET cc_start: 0.7190 (mmt) cc_final: 0.6981 (mmt)
REVERT: B  165 TYR cc_start: 0.6427 (t80) cc_final: 0.6223 (t80)
REVERT: B  815 MET cc_start: 0.5949 (ptp) cc_final: 0.4855 (ptp)
REVERT: B  833 ASN cc_start: 0.8756 (t0) cc_final: 0.8528 (t0)
REVERT: B  914 MET cc_start: 0.7606 (mmm) cc_final: 0.7248 (mmm)
REVERT: B 1020 MET cc_start: 0.8913 (mmp) cc_final: 0.8634 (mmp)
  outliers start: 3
  outliers final: 1
  residues processed: 179
  average time/residue: 0.1522
  time to fit residues: 42.1708
Evaluate side-chains
  125 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 124
  time to evaluate  : 0.667 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 66 optimal weight:    0.7980
   chunk 56 optimal weight:    3.9990
   chunk 193 optimal weight:    7.9990
   chunk 131 optimal weight:    3.9990
   chunk 127 optimal weight:    5.9990
   chunk 168 optimal weight:    0.9980
   chunk 51 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 223 optimal weight:    9.9990
   chunk 164 optimal weight:    0.5980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 607 HIS
A 666 ASN
A 876 ASN
A 986 HIS
A1048 GLN
** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 ASN
B 686 HIS
B 733 ASN
B1048 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.116163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3699 r_free = 0.3699 target = 0.091038 restraints weight = 62351.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.090405 restraints weight = 54145.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3680 r_free = 0.3680 target = 0.091552 restraints weight = 48657.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.092075 restraints weight = 38353.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.092293 restraints weight = 36708.978|
|-----------------------------------------------------------------------------|
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7575
moved from start:          0.5036

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18850  Z= 0.121
  Angle     :  0.581   9.277  25598  Z= 0.295
  Chirality :  0.041   0.203   2930
  Planarity :  0.004   0.064   3402
  Dihedral  :  4.337  45.927   2690
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 10.19
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.27 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.26 %
    Favored  : 98.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.75 (0.17), residues: 2426
  helix:  1.45 (0.15), residues: 1206
  sheet: -0.44 (0.29), residues: 328
  loop : -0.34 (0.21), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 590 
 TYR   0.036   0.002   TYR B 731 
 PHE   0.025   0.001   PHE B  29 
 TRP   0.026   0.002   TRP B 562 
 HIS   0.010   0.001   HIS B 686 

Details of bonding type rmsd
  covalent geometry    : bond        0.00272 (18850)
  covalent geometry    : angle       0.58085 (25598)
  hydrogen bonds       : bond        0.03774 (  983)
  hydrogen bonds       : angle       4.30401 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  174 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 173
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.9282 (tt) cc_final: 0.8853 (mp)
REVERT: A   53 MET cc_start: 0.8152 (tpt) cc_final: 0.7517 (tpp)
REVERT: A  325 MET cc_start: 0.8327 (tpt) cc_final: 0.7907 (mmm)
REVERT: A  552 THR cc_start: 0.8071 (p) cc_final: 0.7655 (p)
REVERT: A  731 TYR cc_start: 0.2523 (t80) cc_final: 0.2315 (t80)
REVERT: A  914 MET cc_start: 0.7427 (mmp) cc_final: 0.7005 (mmp)
REVERT: A  930 MET cc_start: 0.8041 (tpp) cc_final: 0.7795 (tpp)
REVERT: A  935 TYR cc_start: 0.8605 (t80) cc_final: 0.8400 (t80)
REVERT: A 1020 MET cc_start: 0.8673 (mmp) cc_final: 0.8423 (mmp)
REVERT: B  165 TYR cc_start: 0.6568 (t80) cc_final: 0.6206 (t80)
REVERT: B  815 MET cc_start: 0.6188 (ptp) cc_final: 0.5185 (ptp)
REVERT: B  833 ASN cc_start: 0.8738 (t0) cc_final: 0.8514 (t0)
REVERT: B  914 MET cc_start: 0.7443 (mmm) cc_final: 0.6989 (mmm)
REVERT: B  983 ILE cc_start: 0.9037 (mt) cc_final: 0.8653 (mm)
REVERT: B 1020 MET cc_start: 0.8917 (mmp) cc_final: 0.8686 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 174
  average time/residue: 0.1382
  time to fit residues: 38.5164
Evaluate side-chains
  128 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 213 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 147 optimal weight:    3.9990
   chunk 128 optimal weight:   10.0000
   chunk 133 optimal weight:    0.9990
   chunk 106 optimal weight:    2.9990
   chunk 38 optimal weight:    0.0070
   chunk 118 optimal weight:   10.0000
   chunk 223 optimal weight:   10.0000
   chunk 227 optimal weight:    2.9990
   chunk 89 optimal weight:   20.0000
   overall best weight:    1.2002

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 607 HIS
A 666 ASN
A 686 HIS
A 876 ASN
A1048 GLN
** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 ASN
B1048 GLN
B1142 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.116185 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3697 r_free = 0.3697 target = 0.090895 restraints weight = 61907.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.090175 restraints weight = 55284.633|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.091342 restraints weight = 46480.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3681 r_free = 0.3681 target = 0.091629 restraints weight = 38367.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.092287 restraints weight = 36190.791|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7567
moved from start:          0.5249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029  18850  Z= 0.115
  Angle     :  0.566   8.857  25598  Z= 0.287
  Chirality :  0.040   0.194   2930
  Planarity :  0.004   0.074   3402
  Dihedral  :  4.209  44.954   2690
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 10.11
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.39 %
    Favored  : 97.53 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  1.05 %
    Favored  : 98.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.84 (0.17), residues: 2426
  helix:  1.52 (0.15), residues: 1198
  sheet: -0.30 (0.29), residues: 328
  loop : -0.32 (0.22), residues: 900

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 306 
 TYR   0.044   0.002   TYR B 731 
 PHE   0.022   0.001   PHE A  29 
 TRP   0.031   0.002   TRP B 562 
 HIS   0.009   0.001   HIS A 686 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (18850)
  covalent geometry    : angle       0.56610 (25598)
  hydrogen bonds       : bond        0.03606 (  983)
  hydrogen bonds       : angle       4.28820 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 172
  time to evaluate  : 0.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   53 MET cc_start: 0.8103 (tpt) cc_final: 0.7822 (tpp)
REVERT: A  552 THR cc_start: 0.8007 (p) cc_final: 0.7583 (p)
REVERT: A  914 MET cc_start: 0.7474 (mmp) cc_final: 0.7000 (mmp)
REVERT: A  930 MET cc_start: 0.7946 (tpp) cc_final: 0.7711 (tpp)
REVERT: A  935 TYR cc_start: 0.8562 (t80) cc_final: 0.8322 (t80)
REVERT: A 1020 MET cc_start: 0.8709 (mmp) cc_final: 0.8439 (mmp)
REVERT: A 1034 MET cc_start: 0.6408 (ptp) cc_final: 0.6194 (ptp)
REVERT: B  165 TYR cc_start: 0.6414 (t80) cc_final: 0.6089 (t80)
REVERT: B  458 SER cc_start: 0.8494 (m) cc_final: 0.8228 (t)
REVERT: B  625 TYR cc_start: 0.7617 (m-80) cc_final: 0.7381 (m-80)
REVERT: B  815 MET cc_start: 0.6358 (ptp) cc_final: 0.5403 (ptp)
REVERT: B  833 ASN cc_start: 0.8745 (t0) cc_final: 0.8522 (t0)
REVERT: B  914 MET cc_start: 0.7425 (mmm) cc_final: 0.6964 (mmm)
REVERT: B 1020 MET cc_start: 0.8972 (mmp) cc_final: 0.8657 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 173
  average time/residue: 0.1321
  time to fit residues: 37.3814
Evaluate side-chains
  128 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.741 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 196 optimal weight:    0.9980
   chunk 87 optimal weight:    8.9990
   chunk 215 optimal weight:    4.9990
   chunk 79 optimal weight:    0.9990
   chunk 69 optimal weight:    0.9990
   chunk 182 optimal weight:    8.9990
   chunk 241 optimal weight:   40.0000
   chunk 183 optimal weight:    3.9990
   chunk 160 optimal weight:    0.9980
   chunk 16 optimal weight:    1.9990
   chunk 114 optimal weight:    5.9990
   overall best weight:    1.1986

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 607 HIS
A 666 ASN
A 876 ASN
** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 ASN
B1048 GLN
B1142 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.116440 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3718 r_free = 0.3718 target = 0.091765 restraints weight = 62151.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.091283 restraints weight = 53451.316|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.092474 restraints weight = 47033.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3716 r_free = 0.3716 target = 0.093213 restraints weight = 35826.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.093491 restraints weight = 33703.051|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7526
moved from start:          0.5383

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  18850  Z= 0.113
  Angle     :  0.568   9.020  25598  Z= 0.285
  Chirality :  0.040   0.182   2930
  Planarity :  0.004   0.067   3402
  Dihedral  :  4.177  44.718   2690
  Min Nonbonded Distance : 2.383

Molprobity Statistics.
  All-atom Clashscore : 10.24
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.14 %
    Favored  : 97.77 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.79 %
    Favored  : 99.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.87 (0.17), residues: 2426
  helix:  1.54 (0.15), residues: 1198
  sheet: -0.27 (0.29), residues: 332
  loop : -0.31 (0.22), residues: 896

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 306 
 TYR   0.038   0.002   TYR B 731 
 PHE   0.031   0.001   PHE A 847 
 TRP   0.033   0.002   TRP B 562 
 HIS   0.003   0.001   HIS A 990 

Details of bonding type rmsd
  covalent geometry    : bond        0.00258 (18850)
  covalent geometry    : angle       0.56767 (25598)
  hydrogen bonds       : bond        0.03523 (  983)
  hydrogen bonds       : angle       4.23777 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 166
  time to evaluate  : 0.780 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.9239 (tt) cc_final: 0.8869 (mp)
REVERT: A   53 MET cc_start: 0.8130 (tpt) cc_final: 0.7922 (tpp)
REVERT: A  552 THR cc_start: 0.7989 (p) cc_final: 0.7593 (p)
REVERT: A  699 MET cc_start: 0.8762 (tpt) cc_final: 0.8461 (tpt)
REVERT: A  914 MET cc_start: 0.7400 (mmp) cc_final: 0.6969 (mmp)
REVERT: A  930 MET cc_start: 0.8001 (tpp) cc_final: 0.7745 (tpp)
REVERT: A 1020 MET cc_start: 0.8578 (mmp) cc_final: 0.8293 (mmp)
REVERT: A 1034 MET cc_start: 0.6528 (ptp) cc_final: 0.6312 (ptp)
REVERT: B  165 TYR cc_start: 0.6367 (t80) cc_final: 0.6020 (t80)
REVERT: B  458 SER cc_start: 0.8480 (m) cc_final: 0.8212 (t)
REVERT: B  521 LEU cc_start: 0.8862 (tt) cc_final: 0.8629 (tp)
REVERT: B  815 MET cc_start: 0.6434 (ptp) cc_final: 0.5433 (ptp)
REVERT: B  833 ASN cc_start: 0.8793 (t0) cc_final: 0.8573 (t0)
REVERT: B  914 MET cc_start: 0.7412 (mmm) cc_final: 0.6957 (mmm)
REVERT: B 1020 MET cc_start: 0.8834 (mmp) cc_final: 0.8548 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1317
  time to fit residues: 35.9455
Evaluate side-chains
  121 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.868 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 44 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0470
   chunk 78 optimal weight:    3.9990
   chunk 41 optimal weight:    0.8980
   chunk 218 optimal weight:    6.9990
   chunk 194 optimal weight:    5.9990
   chunk 197 optimal weight:    0.0270
   chunk 29 optimal weight:    9.9990
   chunk 38 optimal weight:    1.9990
   chunk 51 optimal weight:    0.9990
   chunk 191 optimal weight:    0.9980
   overall best weight:    0.5938

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 218 GLN
A 666 ASN
A 876 ASN
** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 ASN
B1048 GLN
B1142 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.117271 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.092399 restraints weight = 62085.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.091934 restraints weight = 52991.447|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.093117 restraints weight = 47214.367|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.093408 restraints weight = 37563.069|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.093660 restraints weight = 36009.193|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7522
moved from start:          0.5523

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.036  18850  Z= 0.103
  Angle     :  0.573   9.065  25598  Z= 0.284
  Chirality :  0.040   0.151   2930
  Planarity :  0.004   0.062   3402
  Dihedral  :  4.111  42.160   2690
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 9.70
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  2.35 %
    Favored  : 97.61 %
  Rotamer:
    Outliers :  0.05 %
    Allowed  :  0.53 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.98 (0.18), residues: 2426
  helix:  1.60 (0.15), residues: 1202
  sheet: -0.10 (0.29), residues: 332
  loop : -0.26 (0.22), residues: 892

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 236 
 TYR   0.033   0.002   TYR B 731 
 PHE   0.027   0.001   PHE A 847 
 TRP   0.039   0.002   TRP B 562 
 HIS   0.004   0.001   HIS A 607 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 (18850)
  covalent geometry    : angle       0.57344 (25598)
  hydrogen bonds       : bond        0.03364 (  983)
  hydrogen bonds       : angle       4.18500 ( 2844)

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

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

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4852 Ramachandran restraints generated.
    2426 Oldfield, 0 Emsley, 2426 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  166 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 165
  time to evaluate  : 0.895 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   13 LEU cc_start: 0.9226 (tt) cc_final: 0.8877 (mp)
REVERT: A  552 THR cc_start: 0.8066 (p) cc_final: 0.7668 (p)
REVERT: A  914 MET cc_start: 0.7315 (mmp) cc_final: 0.7077 (mmm)
REVERT: A  930 MET cc_start: 0.7912 (tpp) cc_final: 0.7696 (tpp)
REVERT: A 1020 MET cc_start: 0.8661 (mmp) cc_final: 0.8359 (mmp)
REVERT: B  165 TYR cc_start: 0.6301 (t80) cc_final: 0.5929 (t80)
REVERT: B  279 THR cc_start: 0.8529 (p) cc_final: 0.8307 (p)
REVERT: B  458 SER cc_start: 0.8367 (m) cc_final: 0.8119 (t)
REVERT: B  815 MET cc_start: 0.6488 (ptp) cc_final: 0.5541 (ptp)
REVERT: B  833 ASN cc_start: 0.8786 (t0) cc_final: 0.8556 (t0)
REVERT: B  914 MET cc_start: 0.7412 (mmm) cc_final: 0.6964 (mmm)
REVERT: B 1020 MET cc_start: 0.8917 (mmp) cc_final: 0.8617 (mmp)
  outliers start: 1
  outliers final: 0
  residues processed: 166
  average time/residue: 0.1305
  time to fit residues: 35.7284
Evaluate side-chains
  122 residues out of total 1900 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 122
  time to evaluate  : 0.754 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 242
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 221 optimal weight:    5.9990
   chunk 155 optimal weight:   20.0000
   chunk 10 optimal weight:    7.9990
   chunk 54 optimal weight:    6.9990
   chunk 222 optimal weight:    5.9990
   chunk 83 optimal weight:    9.9990
   chunk 233 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 126 optimal weight:    0.0770
   chunk 124 optimal weight:    3.9990
   overall best weight:    3.0146

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

Flipped N/Q/H residues before XYZ refinement:
** A 138 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 218 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN
A 876 ASN
** B 665 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 666 ASN
B1048 GLN
B1142 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.113390 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3661 r_free = 0.3661 target = 0.088943 restraints weight = 62727.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3618 r_free = 0.3618 target = 0.088486 restraints weight = 58935.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.089954 restraints weight = 54369.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.089976 restraints weight = 38919.658|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.090724 restraints weight = 37274.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7616
moved from start:          0.5962

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  18850  Z= 0.186
  Angle     :  0.636   8.846  25598  Z= 0.325
  Chirality :  0.042   0.246   2930
  Planarity :  0.005   0.050   3402
  Dihedral  :  4.452  45.394   2690
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 12.21
  Ramachandran Plot:
    Outliers :  0.04 %
    Allowed  :  3.22 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.53 %
    Favored  : 99.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.28 %
    Cis-general     : 0.17 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.79 (0.17), residues: 2426
  helix:  1.45 (0.15), residues: 1208
  sheet: -0.23 (0.30), residues: 306
  loop : -0.37 (0.22), residues: 912

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 306 
 TYR   0.029   0.002   TYR B 731 
 PHE   0.019   0.002   PHE A 751 
 TRP   0.031   0.002   TRP B 562 
 HIS   0.005   0.001   HIS A 537 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 (18850)
  covalent geometry    : angle       0.63552 (25598)
  hydrogen bonds       : bond        0.03967 (  983)
  hydrogen bonds       : angle       4.37039 ( 2844)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2780.72 seconds
wall clock time: 49 minutes 17.06 seconds (2957.06 seconds total)