Starting phenix.real_space_refine
on Thu Aug  6 16:48:14 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ne8_49301/08_2026/9ne8_49301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ne8_49301/08_2026/9ne8_49301.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ne8_49301/08_2026/9ne8_49301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ne8_49301/08_2026/9ne8_49301.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ne8_49301/08_2026/9ne8_49301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ne8_49301/08_2026/9ne8_49301.cif"
  }
  resolution = 3.6
  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=   0.001 sd=   0.021
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Fe      4      7.16       5
     P      46      5.49       5
     S     102      5.16       5
     C   10147      2.51       5
     N    2734      2.21       5
     O    3209      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16242
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 9265
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1138, 9265
          Classifications: {'peptide': 1138}
          Link IDs: {'PTRANS': 58, 'TRANS': 1079}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "C"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "D"
      Number of atoms: 2008
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 2008
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 7, 'TRANS': 253}
    Chain: "P"
      Number of atoms: 454
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 454
          Classifications: {'DNA': 22}
          Link IDs: {'rna3p': 21}
    Chain: "T"
      Number of atoms: 491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 24, 491
          Classifications: {'DNA': 24}
          Link IDs: {'rna3p': 23}
    Chain: "A"
      Number of atoms: 8
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 8
          Unusual residues: {'SF4': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   4815  SG  CYS A 651      41.621  76.963  96.718  1.00111.02           S
  ATOM   4831  SG  CYS A 654      39.353  76.239 101.663  1.00119.35           S
  ATOM   4897  SG  CYS A 663      44.486  81.065 100.175  1.00 87.53           S
  ATOM   5621  SG  CYS A 747      45.929  75.855 101.080  1.00 68.37           S

  Time building chain proxies: 3.89, per 1000 atoms: 0.24
  Number of scatterers: 16242
  At special positions: 0
  Unit cell: (104.328, 103.5, 143.244, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Fe      4     26.01
     S     102     16.00
     P      46     15.00
     O    3209      8.00
     N    2734      7.00
     C   10147      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: 1.21
  Conformation dependent library (CDL) restraints added in 710.2 milliseconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 A1301 "
        pdb="FE4  SF4 A1301 " - pdb=" SG  CYS A 747 "
        pdb="FE3  SF4 A1301 " - pdb=" SG  CYS A 663 "
        pdb="FE2  SF4 A1301 " - pdb=" SG  CYS A 654 "
        pdb="FE1  SF4 A1301 " - pdb=" SG  CYS A 651 "
      Number of angles added : 12


  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3656

  Finding SS restraints...
    Secondary structure from input PDB file:
      60 helices and 17 sheets defined
      34.8% alpha, 22.9% beta
      21 base pairs and 39 stacking pairs defined.
    Time for finding SS restraints: 2.00
  Creating SS restraints...
    Processing helix  chain 'A' and resid 30 through 48
    Processing helix  chain 'A' and resid 113 through 121
    Processing helix  chain 'A' and resid 159 through 181
      Proline residue:  A 172  - end of helix
      removed outlier: 3.780A  pdb=" N   ASN A 177 " --> pdb=" O   ALA A 173 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 213 through 216
      removed outlier: 3.949A  pdb=" N   ASP A 216 " --> pdb=" O   ASP A 213 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 213 through 216'
    Processing helix  chain 'A' and resid 227 through 236
    Processing helix  chain 'A' and resid 309 through 313
      removed outlier: 3.627A  pdb=" N   ILE A 312 " --> pdb=" O   ASN A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 339 through 355
    Processing helix  chain 'A' and resid 367 through 379
      removed outlier: 3.786A  pdb=" N   VAL A 378 " --> pdb=" O   ALA A 374 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   HIS A 379 " --> pdb=" O   ARG A 375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 387
    Processing helix  chain 'A' and resid 407 through 414
      removed outlier: 3.716A  pdb=" N   VAL A 411 " --> pdb=" O   CYS A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 418 through 422
      removed outlier: 4.218A  pdb=" N   HIS A 422 " --> pdb=" O   VAL A 419 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 423 through 432
      removed outlier: 3.683A  pdb=" N   LYS A 431 " --> pdb=" O   ALA A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 443 through 451
    Processing helix  chain 'A' and resid 452 through 473
    Processing helix  chain 'A' and resid 473 through 482
    Processing helix  chain 'A' and resid 488 through 493
      removed outlier: 3.659A  pdb=" N   VAL A 492 " --> pdb=" O   GLU A 488 " (cutoff:3.500A)
      removed outlier: 3.611A  pdb=" N   LEU A 493 " --> pdb=" O   PRO A 489 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 488 through 493'
    Processing helix  chain 'A' and resid 496 through 512
      removed outlier: 3.539A  pdb=" N   LEU A 500 " --> pdb=" O   GLY A 496 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 563 through 572
      removed outlier: 3.559A  pdb=" N   PHE A 567 " --> pdb=" O   ASN A 563 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   GLN A 572 " --> pdb=" O   ASP A 568 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 573 through 584
      removed outlier: 4.048A  pdb=" N   LEU A 582 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 589 through 593
      removed outlier: 3.566A  pdb=" N   GLN A 592 " --> pdb=" O   PRO A 589 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 595 through 612
      removed outlier: 4.887A  pdb=" N   LYS A 604 " --> pdb=" O   CYS A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 629 through 638
    Processing helix  chain 'A' and resid 647 through 654
      removed outlier: 3.613A  pdb=" N   CYS A 651 " --> pdb=" O   ASP A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 679 through 690
      removed outlier: 4.149A  pdb=" N   ILE A 686 " --> pdb=" O   GLU A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 706 through 710
      removed outlier: 3.894A  pdb=" N   GLU A 709 " --> pdb=" O   ALA A 706 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 711 through 727
      removed outlier: 3.636A  pdb=" N   ASP A 725 " --> pdb=" O   ARG A 721 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   CYS A 727 " --> pdb=" O   LEU A 723 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 786
    Processing helix  chain 'A' and resid 787 through 814
      removed outlier: 3.661A  pdb=" N   SER A 814 " --> pdb=" O   CYS A 810 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 820
      removed outlier: 3.970A  pdb=" N   VAL A 819 " --> pdb=" O   PHE A 815 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   MET A 820 " --> pdb=" O   TYR A 816 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 828 through 854
      removed outlier: 4.013A  pdb=" N   ALA A 832 " --> pdb=" O   SER A 828 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A 843 " --> pdb=" O   GLY A 839 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 892 through 905
    Processing helix  chain 'A' and resid 971 through 975
      removed outlier: 4.051A  pdb=" N   LYS A 974 " --> pdb=" O   PHE A 971 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ARG A 975 " --> pdb=" O   GLU A 972 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 971 through 975'
    Processing helix  chain 'A' and resid 980 through 992
      removed outlier: 3.794A  pdb=" N   ILE A 984 " --> pdb=" O   GLN A 980 " (cutoff:3.500A)
      removed outlier: 3.704A  pdb=" N   PHE A 985 " --> pdb=" O   LEU A 981 " (cutoff:3.500A)
      removed outlier: 4.242A  pdb=" N   GLN A 986 " --> pdb=" O   ILE A 982 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   GLU A 991 " --> pdb=" O   SER A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 998 through 1011
      removed outlier: 3.641A  pdb=" N   TYR A1003 " --> pdb=" O   LEU A 999 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   VAL A1009 " --> pdb=" O   SER A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1011 through 1019
      removed outlier: 4.378A  pdb=" N   LEU A1017 " --> pdb=" O   TRP A1013 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1025 through 1028
      removed outlier: 3.607A  pdb=" N   GLU A1028 " --> pdb=" O   PRO A1025 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1025 through 1028'
    Processing helix  chain 'A' and resid 1029 through 1034
      removed outlier: 3.654A  pdb=" N   ILE A1033 " --> pdb=" O   LEU A1029 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   SER A1034 " --> pdb=" O   PHE A1030 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1029 through 1034'
    Processing helix  chain 'A' and resid 1042 through 1047
    Processing helix  chain 'A' and resid 1051 through 1062
    Processing helix  chain 'A' and resid 1065 through 1069
    Processing helix  chain 'A' and resid 1096 through 1101
      removed outlier: 3.503A  pdb=" N   GLN A1100 " --> pdb=" O   ALA A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1102 through 1115
    Processing helix  chain 'A' and resid 1123 through 1128
      removed outlier: 3.570A  pdb=" N   LEU A1128 " --> pdb=" O   ILE A1124 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1129 through 1145
      removed outlier: 3.989A  pdb=" N   TYR A1133 " --> pdb=" O   ASP A1129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1145 through 1152
    Processing helix  chain 'A' and resid 1164 through 1175
      removed outlier: 3.582A  pdb=" N   LYS A1170 " --> pdb=" O   TRP A1166 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 9 through 18
      removed outlier: 4.362A  pdb=" N   VAL B  15 " --> pdb=" O   ILE B  11 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 71 through 77
      removed outlier: 4.569A  pdb=" N   MET B  75 " --> pdb=" O   ASN B  71 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   SER B  76 " --> pdb=" O   LEU B  72 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   LYS B  77 " --> pdb=" O   THR B  73 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 71 through 77'
    Processing helix  chain 'B' and resid 140 through 152
    Processing helix  chain 'B' and resid 209 through 216
    Processing helix  chain 'C' and resid 9 through 18
      removed outlier: 5.034A  pdb=" N   VAL C  15 " --> pdb=" O   ILE C  11 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 71 through 81
      removed outlier: 3.768A  pdb=" N   MET C  75 " --> pdb=" O   ASN C  71 " (cutoff:3.500A)
      removed outlier: 3.791A  pdb=" N   CYS C  81 " --> pdb=" O   LYS C  77 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 141 through 152
    Processing helix  chain 'C' and resid 209 through 216
    Processing helix  chain 'D' and resid 9 through 23
      removed outlier: 3.521A  pdb=" N   LEU D  16 " --> pdb=" O   LEU D  12 " (cutoff:3.500A)
      removed outlier: 4.198A  pdb=" N   ASP D  21 " --> pdb=" O   GLU D  17 " (cutoff:3.500A)
      removed outlier: 4.422A  pdb=" N   LEU D  22 " --> pdb=" O   ALA D  18 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   ILE D  23 " --> pdb=" O   LEU D  19 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 57
      No H-bonds generated for 'chain 'D' and resid 55 through 57'
    Processing helix  chain 'D' and resid 72 through 80
    Processing helix  chain 'D' and resid 141 through 152
      removed outlier: 3.612A  pdb=" N   SER D 152 " --> pdb=" O   CYS D 148 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 209 through 216
    Processing helix  chain 'D' and resid 217 through 222
      Proline residue:  D 220  - end of helix
      No H-bonds generated for 'chain 'D' and resid 217 through 222'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 52
      removed outlier: 6.279A  pdb=" N   GLU A  51 " --> pdb=" O   LYS A  95 " (cutoff:3.500A)
      removed outlier: 8.150A  pdb=" N   ALA A  97 " --> pdb=" O   GLU A  51 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ASN A  65 " --> pdb=" O   TYR A  85 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   ILE A  87 " --> pdb=" O   LEU A  63 " (cutoff:3.500A)
      removed outlier: 5.614A  pdb=" N   LEU A  63 " --> pdb=" O   ILE A  87 " (cutoff:3.500A)
      removed outlier: 4.183A  pdb=" N   TRP A 243 " --> pdb=" O   ARG A 260 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 128 through 136
      removed outlier: 3.504A  pdb=" N   VAL A 134 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TYR A 152 " --> pdb=" O   VAL A 134 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   LYS A 136 " --> pdb=" O   ARG A 150 " (cutoff:3.500A)
      removed outlier: 7.151A  pdb=" N   ASN A 151 " --> pdb=" O   THR A 108 " (cutoff:3.500A)
      removed outlier: 5.362A  pdb=" N   THR A 108 " --> pdb=" O   ASN A 151 " (cutoff:3.500A)
      removed outlier: 7.365A  pdb=" N   TYR A 105 " --> pdb=" O   MET A 221 " (cutoff:3.500A)
      removed outlier: 5.275A  pdb=" N   MET A 221 " --> pdb=" O   TYR A 105 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   ALA A 107 " --> pdb=" O   VAL A 219 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 320 through 321
      removed outlier: 3.513A  pdb=" N   MET A 295 " --> pdb=" O   ALA A 277 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 534 through 539
      removed outlier: 3.658A  pdb=" N   PHE A 675 " --> pdb=" O   ILE A 736 " (cutoff:3.500A)
      removed outlier: 4.162A  pdb=" N   THR A 745 " --> pdb=" O   VAL A 646 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 544 through 546
      removed outlier: 6.502A  pdb=" N   TRP A 865 " --> pdb=" O   LEU A 857 " (cutoff:3.500A)
      removed outlier: 4.854A  pdb=" N   LEU A 859 " --> pdb=" O   GLY A 863 " (cutoff:3.500A)
      removed outlier: 7.121A  pdb=" N   GLY A 863 " --> pdb=" O   LEU A 859 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 550 through 553
      removed outlier: 4.181A  pdb=" N   ALA A 939 " --> pdb=" O   PHE A 959 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 558 through 561
      removed outlier: 3.611A  pdb=" N   GLU A 618 " --> pdb=" O   CYS A 558 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 875 through 879
    Processing sheet with id=AA9, first strand: chain 'A' and resid 910 through 915
      removed outlier: 3.844A  pdb=" N   TYR A 910 " --> pdb=" O   ARG A 924 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   THR A 920 " --> pdb=" O   ALA A 914 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1037 through 1038
      removed outlier: 3.535A  pdb=" N   ARG A1037 " --> pdb=" O   CYS A1076 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1079 through 1080
    Processing sheet with id=AB3, first strand: chain 'B' and resid 59 through 62
      removed outlier: 3.789A  pdb=" N   ARG B  61 " --> pdb=" O   GLU B   3 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLU B   3 " --> pdb=" O   ARG B  61 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   PHE B 103 " --> pdb=" O   SER B 112 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   SER B 112 " --> pdb=" O   PHE B 103 " (cutoff:3.500A)
      removed outlier: 4.357A  pdb=" N   ASN C 177 " --> pdb=" O   GLU B 115 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU C 182 " --> pdb=" O   VAL C 167 " (cutoff:3.500A)
      removed outlier: 4.538A  pdb=" N   VAL C 167 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   SER C 172 " --> pdb=" O   ALA C 157 " (cutoff:3.500A)
      removed outlier: 4.376A  pdb=" N   ALA C 157 " --> pdb=" O   SER C 172 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 66 through 70
      removed outlier: 3.651A  pdb=" N   LEU B  66 " --> pdb=" O   ILE B  30 " (cutoff:3.500A)
      removed outlier: 5.452A  pdb=" N   CYS B  27 " --> pdb=" O   GLN B  38 " (cutoff:3.500A)
      removed outlier: 4.402A  pdb=" N   GLN B  38 " --> pdb=" O   CYS B  27 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   THR B  51 " --> pdb=" O   HIS B 246 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   HIS B 246 " --> pdb=" O   THR B  51 " (cutoff:3.500A)
      removed outlier: 5.510A  pdb=" N   SER B 230 " --> pdb=" O   PRO B 234 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 203 through 208
      removed outlier: 4.795A  pdb=" N   ALA B 157 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   SER B 172 " --> pdb=" O   ALA B 157 " (cutoff:3.500A)
      removed outlier: 4.049A  pdb=" N   ASN B 179 " --> pdb=" O   ASP D 113 " (cutoff:3.500A)
      removed outlier: 3.564A  pdb=" N   ASP D 113 " --> pdb=" O   ASN B 179 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   VAL D 111 " --> pdb=" O   LYS B 181 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 59 through 62
      removed outlier: 4.471A  pdb=" N   VAL C 111 " --> pdb=" O   LYS D 181 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   LYS D 181 " --> pdb=" O   VAL C 111 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   SER D 172 " --> pdb=" O   ALA D 157 " (cutoff:3.500A)
      removed outlier: 4.865A  pdb=" N   ALA D 157 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   LEU D 205 " --> pdb=" O   ILE D 160 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'C' and resid 66 through 68
      removed outlier: 4.076A  pdb=" N   LEU C  66 " --> pdb=" O   ILE C  30 " (cutoff:3.500A)
      removed outlier: 3.622A  pdb=" N   VAL C 136 " --> pdb=" O   GLU C 198 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   THR C 196 " --> pdb=" O   LYS C 138 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 66 through 68
      removed outlier: 4.346A  pdb=" N   LYS D 240 " --> pdb=" O   THR D 224 " (cutoff:3.500A)
      removed outlier: 6.114A  pdb=" N   THR D 224 " --> pdb=" O   LYS D 240 " (cutoff:3.500A)

    723 hydrogen bonds defined for protein.
    2019 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      48 hydrogen bonds
      96 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      39 stacking parallelities
  Total time for adding SS restraints: 4.05

  Time building geometry restraints manager: 1.66 seconds

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

  Histogram of bond lengths:
        1.22 -     1.43: 6984
        1.43 -     1.64: 9500
        1.64 -     1.85: 158
        1.85 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 16654
  Sorted by residual:
  bond pdb=" C1'  DT T  14 "
       pdb=" N1   DT T  14 "
    ideal  model  delta    sigma   weight residual
    1.468  1.529 -0.061 1.40e-02 5.10e+03 1.89e+01
  bond pdb=" C3'  DT T  21 "
       pdb=" C2'  DT T  21 "
    ideal  model  delta    sigma   weight residual
    1.516  1.543 -0.027 8.00e-03 1.56e+04 1.13e+01
  bond pdb=" C3'  DA T  17 "
       pdb=" C2'  DA T  17 "
    ideal  model  delta    sigma   weight residual
    1.516  1.541 -0.025 8.00e-03 1.56e+04 1.01e+01
  bond pdb=" CA  THR D 216 "
       pdb=" C   THR D 216 "
    ideal  model  delta    sigma   weight residual
    1.524  1.595 -0.072 2.25e-02 1.98e+03 1.01e+01
  bond pdb=" N   ASP A1176 "
       pdb=" CA  ASP A1176 "
    ideal  model  delta    sigma   weight residual
    1.454  1.492 -0.038 1.19e-02 7.06e+03 1.01e+01
  ... (remaining 16649 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.98: 21800
        1.98 -     3.96: 761
        3.96 -     5.94: 104
        5.94 -     7.92: 32
        7.92 -     9.90: 4
  Bond angle restraints: 22701
  Sorted by residual:
  angle pdb=" N3   DT T  21 "
        pdb=" C4   DT T  21 "
        pdb=" O4   DT T  21 "
      ideal   model   delta    sigma   weight residual
     119.90  122.72   -2.82 6.00e-01 2.78e+00 2.20e+01
  angle pdb=" CA  ILE C 241 "
        pdb=" C   ILE C 241 "
        pdb=" O   ILE C 241 "
      ideal   model   delta    sigma   weight residual
     121.68  117.99    3.69 7.90e-01 1.60e+00 2.18e+01
  angle pdb=" N3   DT T  30 "
        pdb=" C4   DT T  30 "
        pdb=" O4   DT T  30 "
      ideal   model   delta    sigma   weight residual
     119.90  122.57   -2.67 6.00e-01 2.78e+00 1.99e+01
  angle pdb=" N3   DT P  22 "
        pdb=" C4   DT P  22 "
        pdb=" O4   DT P  22 "
      ideal   model   delta    sigma   weight residual
     119.90  122.55   -2.65 6.00e-01 2.78e+00 1.95e+01
  angle pdb=" N3   DT P  23 "
        pdb=" C4   DT P  23 "
        pdb=" O4   DT P  23 "
      ideal   model   delta    sigma   weight residual
     119.90  122.48   -2.58 6.00e-01 2.78e+00 1.84e+01
  ... (remaining 22696 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 8756
       17.93 -    35.87: 924
       35.87 -    53.80: 295
       53.80 -    71.74: 76
       71.74 -    89.67: 22
  Dihedral angle restraints: 10073
    sinusoidal: 4432
      harmonic: 5641
  Sorted by residual:
  dihedral pdb=" CA  CYS A 600 "
           pdb=" C   CYS A 600 "
           pdb=" N   ASP A 601 "
           pdb=" CA  ASP A 601 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.31   26.69     0      5.00e+00 4.00e-02 2.85e+01
  dihedral pdb=" CA  PHE D 215 "
           pdb=" C   PHE D 215 "
           pdb=" N   THR D 216 "
           pdb=" CA  THR D 216 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -157.26  -22.74     0      5.00e+00 4.00e-02 2.07e+01
  dihedral pdb=" CA  ILE A 276 "
           pdb=" C   ILE A 276 "
           pdb=" N   ALA A 277 "
           pdb=" CA  ALA A 277 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.56   22.44     0      5.00e+00 4.00e-02 2.01e+01
  ... (remaining 10070 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 2436
       0.113 -    0.227: 87
       0.227 -    0.340: 3
       0.340 -    0.453: 1
       0.453 -    0.567: 4
  Chirality restraints: 2531
  Sorted by residual:
  chirality pdb=" P    DT P  32 "
            pdb=" OP1  DT P  32 "
            pdb=" OP2  DT P  32 "
            pdb=" O5'  DT P  32 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.90   -0.57 2.00e-01 2.50e+01 8.03e+00
  chirality pdb=" P    DG P  26 "
            pdb=" OP1  DG P  26 "
            pdb=" OP2  DG P  26 "
            pdb=" O5'  DG P  26 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.90   -0.56 2.00e-01 2.50e+01 7.92e+00
  chirality pdb=" P    DT T  23 "
            pdb=" OP1  DT T  23 "
            pdb=" OP2  DT T  23 "
            pdb=" O5'  DT T  23 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.89   -0.55 2.00e-01 2.50e+01 7.59e+00
  ... (remaining 2528 not shown)

  Planarity restraints: 2767
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 639 "    0.222 9.50e-02 1.11e+02   9.97e-02 6.17e+00
        pdb=" NE  ARG A 639 "   -0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 639 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 639 "   -0.004 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 639 "    0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 669 "    0.018 2.00e-02 2.50e+03   1.52e-02 5.75e+00
        pdb=" CG  TRP A 669 "   -0.041 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 669 "    0.016 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 669 "    0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 669 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 669 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 669 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 669 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 669 "    0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 669 "    0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS A 619 "    0.038 5.00e-02 4.00e+02   5.81e-02 5.41e+00
        pdb=" N   PRO A 620 "   -0.101 5.00e-02 4.00e+02
        pdb=" CA  PRO A 620 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 620 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2764 not shown)

  Histogram of nonbonded interaction distances:
        2.48 -     2.97: 7052
        2.97 -     3.45: 16774
        3.45 -     3.93: 27066
        3.93 -     4.42: 29868
        4.42 -     4.90: 48286
  Nonbonded interactions: 129046
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 639 "
            pdb=" O   GLU A 750 "
     model   vdw
     2.484 3.120
  nonbonded pdb=" O   PHE A 753 "
            pdb=" OG1 THR A 757 "
     model   vdw
     2.534 3.040
  nonbonded pdb=" O4'  DT T  21 "
            pdb=" C6   DT T  21 "
     model   vdw
     2.578 2.672
  nonbonded pdb=" NE2 GLN A 641 "
            pdb=" O   ASN A 751 "
     model   vdw
     2.596 3.120
  nonbonded pdb=" CA  PRO A  56 "
            pdb=" O   TYR A 248 "
     model   vdw
     2.599 2.776
  ... (remaining 129041 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = chain 'C'
  selection = chain 'D'
}

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:             3.350
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     20.000
  Find NCS groups from input model:        0.160
  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:1.090
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.950
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6410
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      :  0.005   0.072  16658  Z= 0.295
  Angle     :  0.940  29.298  22713  Z= 0.509
  Chirality :  0.058   0.567   2531
  Planarity :  0.006   0.100   2767
  Dihedral  : 17.122  89.671   6417
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 8.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  0.47 %
    Favored  : 99.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.96 (0.17), residues: 1911
  helix: -1.29 (0.19), residues: 563
  sheet: -0.46 (0.22), residues: 521
  loop : -1.77 (0.19), residues: 827

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 705 
 TYR   0.018   0.002   TYR C  60 
 PHE   0.025   0.002   PHE A 389 
 TRP   0.041   0.002   TRP A 669 
 HIS   0.011   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00479 /  0.29 (16654)
  covalent geometry    : angle       0.85766 /  0.51 (22701)
  hydrogen bonds       : bond        0.14657 /  9.67 (  771)
  hydrogen bonds       : angle       7.25720 /  5.23 ( 2115)
  metal coordination   : bond        0.00521 /  0.26 (    4)
  metal coordination   : angle      16.76252 /  9.84 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  335 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 332
  time to evaluate  : 0.493 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  161 GLU cc_start: 0.8241 (tp30) cc_final: 0.7745 (tt0)
REVERT: A  169 GLU cc_start: 0.7845 (tm-30) cc_final: 0.7446 (tm-30)
REVERT: A  561 ARG cc_start: 0.7873 (ppt170) cc_final: 0.7507 (ppt170)
REVERT: A  674 GLU cc_start: 0.6116 (mp0) cc_final: 0.5701 (mp0)
REVERT: A  720 LYS cc_start: 0.6905 (tmtt) cc_final: 0.6441 (tppt)
REVERT: A  820 MET cc_start: 0.7220 (pmm) cc_final: 0.6777 (pmm)
REVERT: A  907 ASN cc_start: 0.6402 (t0) cc_final: 0.6158 (p0)
REVERT: A  928 SER cc_start: 0.7939 (m) cc_final: 0.7343 (t)
REVERT: A 1024 MET cc_start: 0.4050 (tmm) cc_final: 0.2069 (tmm)
REVERT: A 1039 MET cc_start: 0.7925 (mmm) cc_final: 0.7608 (mmm)
REVERT: A 1048 GLU cc_start: 0.5680 (pm20) cc_final: 0.5310 (mp0)
REVERT: A 1197 MET cc_start: 0.4427 (mmp) cc_final: 0.3535 (tmm)
REVERT: B   11 ILE cc_start: 0.6495 (OUTLIER) cc_final: 0.6040 (pt)
REVERT: B  189 ASP cc_start: 0.8036 (t70) cc_final: 0.7526 (p0)
REVERT: C   27 CYS cc_start: 0.7958 (m) cc_final: 0.7262 (t)
REVERT: C   80 LYS cc_start: 0.7660 (tttm) cc_final: 0.7295 (ttpt)
REVERT: D   79 LEU cc_start: 0.7073 (tp) cc_final: 0.6470 (mm)
REVERT: D  125 GLN cc_start: 0.7352 (tp-100) cc_final: 0.7124 (tp40)
  outliers start: 3
  outliers final: 0
  residues processed: 334
  average time/residue: 0.1145
  time to fit residues: 57.3759
Evaluate side-chains
  227 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 226
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue   11 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 194 optimal weight:   20.0000
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.1980
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    9.9990
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    0.9990
   chunk 77 optimal weight:    0.5980
   chunk 122 optimal weight:    7.9990
   chunk 91 optimal weight:    0.0770
   overall best weight:    0.5740

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 404 HIS
** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 751 ASN
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1108 HIS
C  49 GLN
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 213 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4579 r_free = 0.4579 target = 0.186498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.153180 restraints weight = 30417.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.158071 restraints weight = 16364.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.161292 restraints weight = 10890.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4309 r_free = 0.4309 target = 0.163257 restraints weight = 8372.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.164566 restraints weight = 7095.349|
|-----------------------------------------------------------------------------|
r_work (final): 0.4322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6505
moved from start:          0.1155

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061  16658  Z= 0.135
  Angle     :  0.738  30.143  22713  Z= 0.342
  Chirality :  0.045   0.221   2531
  Planarity :  0.005   0.050   2767
  Dihedral  : 15.824  79.528   2595
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 12.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.56 %
    Favored  : 96.44 %
  Rotamer:
    Outliers :  1.00 %
    Allowed  :  7.91 %
    Favored  : 91.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.49 (0.18), residues: 1911
  helix: -0.62 (0.21), residues: 574
  sheet: -0.40 (0.22), residues: 531
  loop : -1.57 (0.20), residues: 806

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 231 
 TYR   0.022   0.002   TYR A 434 
 PHE   0.023   0.002   PHE A1187 
 TRP   0.016   0.001   TRP A 669 
 HIS   0.007   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00292 /  0.13 (16654)
  covalent geometry    : angle       0.63795 /  0.34 (22701)
  hydrogen bonds       : bond        0.04660 /  3.01 (  771)
  hydrogen bonds       : angle       6.04205 /  4.34 ( 2115)
  metal coordination   : bond        0.00472 /  0.22 (    4)
  metal coordination   : angle      16.13955 /  9.50 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  265 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 248
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 TYR cc_start: 0.5676 (OUTLIER) cc_final: 0.3113 (m-80)
REVERT: A  161 GLU cc_start: 0.8143 (tp30) cc_final: 0.7670 (tt0)
REVERT: A  235 ASP cc_start: 0.7842 (m-30) cc_final: 0.7641 (m-30)
REVERT: A  412 LYS cc_start: 0.7815 (tppt) cc_final: 0.7562 (ttmm)
REVERT: A  487 MET cc_start: 0.8033 (mmt) cc_final: 0.7455 (mtm)
REVERT: A  561 ARG cc_start: 0.7647 (ppt170) cc_final: 0.7397 (ppt170)
REVERT: A  674 GLU cc_start: 0.6212 (mp0) cc_final: 0.6005 (mp0)
REVERT: A  720 LYS cc_start: 0.7204 (tmtt) cc_final: 0.6660 (tppt)
REVERT: A  831 MET cc_start: 0.7368 (tmm) cc_final: 0.7047 (tmm)
REVERT: A  928 SER cc_start: 0.7863 (m) cc_final: 0.7089 (t)
REVERT: A  930 PHE cc_start: 0.6437 (m-80) cc_final: 0.5851 (m-10)
REVERT: A 1024 MET cc_start: 0.3938 (tmm) cc_final: 0.1823 (tmm)
REVERT: A 1197 MET cc_start: 0.3984 (mmp) cc_final: 0.3330 (tmm)
REVERT: B    1 MET cc_start: 0.7665 (mmt) cc_final: 0.7140 (mmp)
REVERT: B    5 ARG cc_start: 0.5821 (ptm-80) cc_final: 0.5593 (ptm160)
REVERT: B  189 ASP cc_start: 0.8048 (t70) cc_final: 0.7524 (p0)
REVERT: C   27 CYS cc_start: 0.7736 (m) cc_final: 0.7013 (t)
REVERT: C   80 LYS cc_start: 0.8055 (tttm) cc_final: 0.7679 (mtpt)
REVERT: C  199 MET cc_start: 0.4710 (mpp) cc_final: 0.4184 (mpp)
REVERT: C  248 LYS cc_start: 0.6266 (OUTLIER) cc_final: 0.5938 (mmtm)
REVERT: D   75 MET cc_start: 0.5138 (mmt) cc_final: 0.4763 (tpp)
REVERT: D   79 LEU cc_start: 0.7159 (tp) cc_final: 0.6492 (mm)
  outliers start: 17
  outliers final: 11
  residues processed: 258
  average time/residue: 0.1174
  time to fit residues: 45.1927
Evaluate side-chains
  229 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 216
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 TYR
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  647 ASP
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue 1108 HIS
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue  248 LYS
Chi-restraints excluded: chain D residue   37 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 180 optimal weight:   10.0000
   chunk 138 optimal weight:    4.9990
   chunk 134 optimal weight:    5.9990
   chunk 68 optimal weight:    6.9990
   chunk 7 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9980
   chunk 58 optimal weight:    4.9990
   chunk 175 optimal weight:    7.9990
   chunk 21 optimal weight:    1.9990
   chunk 161 optimal weight:    2.9990
   chunk 136 optimal weight:    1.9990
   overall best weight:    2.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 242 HIS
A 404 HIS
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1108 HIS
D 153 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4514 r_free = 0.4514 target = 0.180575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4101 r_free = 0.4101 target = 0.146400 restraints weight = 30750.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.151022 restraints weight = 16832.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.154086 restraints weight = 11339.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.156036 restraints weight = 8777.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.157313 restraints weight = 7463.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.4241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6668
moved from start:          0.1639

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  16658  Z= 0.192
  Angle     :  0.768  34.792  22713  Z= 0.352
  Chirality :  0.045   0.231   2531
  Planarity :  0.005   0.049   2767
  Dihedral  : 15.837  78.783   2593
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 10.51 %
    Favored  : 87.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.18), residues: 1911
  helix: -0.44 (0.21), residues: 575
  sheet: -0.44 (0.22), residues: 532
  loop : -1.51 (0.20), residues: 804

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 231 
 TYR   0.021   0.002   TYR A 244 
 PHE   0.025   0.002   PHE A 516 
 TRP   0.013   0.001   TRP A 669 
 HIS   0.019   0.002   HIS A1108 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00434 /  0.19 (16654)
  covalent geometry    : angle       0.65877 /  0.35 (22701)
  hydrogen bonds       : bond        0.04381 /  2.83 (  771)
  hydrogen bonds       : angle       5.86424 /  4.19 ( 2115)
  metal coordination   : bond        0.00740 /  0.37 (    4)
  metal coordination   : angle      17.18226 / 10.20 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  269 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 237
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 TYR cc_start: 0.5705 (OUTLIER) cc_final: 0.2877 (m-80)
REVERT: A  161 GLU cc_start: 0.8189 (tp30) cc_final: 0.7724 (tt0)
REVERT: A  169 GLU cc_start: 0.7760 (tm-30) cc_final: 0.7494 (tm-30)
REVERT: A  235 ASP cc_start: 0.8000 (m-30) cc_final: 0.7628 (m-30)
REVERT: A  289 GLU cc_start: 0.6906 (pm20) cc_final: 0.6460 (mp0)
REVERT: A  299 MET cc_start: 0.4726 (tpp) cc_final: 0.3993 (mpp)
REVERT: A  349 GLU cc_start: 0.8357 (pp20) cc_final: 0.7367 (mm-30)
REVERT: A  412 LYS cc_start: 0.7897 (tppt) cc_final: 0.7605 (ttmm)
REVERT: A  487 MET cc_start: 0.8089 (mmt) cc_final: 0.7638 (mtm)
REVERT: A  561 ARG cc_start: 0.7690 (ppt170) cc_final: 0.7417 (ppt170)
REVERT: A  720 LYS cc_start: 0.7210 (tmtt) cc_final: 0.6675 (tppt)
REVERT: A  752 SER cc_start: 0.7775 (OUTLIER) cc_final: 0.7561 (t)
REVERT: A  928 SER cc_start: 0.8112 (m) cc_final: 0.7542 (t)
REVERT: A  930 PHE cc_start: 0.6646 (m-80) cc_final: 0.6166 (m-10)
REVERT: A 1197 MET cc_start: 0.4198 (mmp) cc_final: 0.3357 (ptm)
REVERT: B    1 MET cc_start: 0.7564 (mmt) cc_final: 0.6662 (mmp)
REVERT: B   59 THR cc_start: 0.6140 (p) cc_final: 0.5851 (p)
REVERT: B  189 ASP cc_start: 0.8095 (t70) cc_final: 0.7545 (p0)
REVERT: C   27 CYS cc_start: 0.7782 (m) cc_final: 0.6999 (t)
REVERT: C   80 LYS cc_start: 0.8271 (tttm) cc_final: 0.7930 (mtpt)
REVERT: C  116 MET cc_start: 0.6842 (tpt) cc_final: 0.6337 (ttp)
REVERT: C  199 MET cc_start: 0.4596 (mpp) cc_final: 0.3911 (mpp)
REVERT: D   79 LEU cc_start: 0.7212 (tp) cc_final: 0.7001 (tp)
REVERT: D  125 GLN cc_start: 0.7636 (tp40) cc_final: 0.7223 (tp-100)
  outliers start: 32
  outliers final: 22
  residues processed: 256
  average time/residue: 0.1006
  time to fit residues: 39.9859
Evaluate side-chains
  238 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 214
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 TYR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  752 SER
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1154 VAL
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1177 VAL
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain B residue   21 ASP
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue  223 SER
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   37 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 100 optimal weight:    0.9990
   chunk 77 optimal weight:    0.9980
   chunk 136 optimal weight:    0.0870
   chunk 157 optimal weight:    5.9990
   chunk 82 optimal weight:    0.2980
   chunk 89 optimal weight:    0.9980
   chunk 181 optimal weight:    0.4980
   chunk 32 optimal weight:    8.9990
   chunk 85 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 193 optimal weight:    9.9990
   overall best weight:    0.5358

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 144 HIS
A 242 HIS
A 404 HIS
** A 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 204 GLN
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 213 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4549 r_free = 0.4549 target = 0.183904 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.150355 restraints weight = 30650.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4210 r_free = 0.4210 target = 0.155124 restraints weight = 16576.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.158230 restraints weight = 11054.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4273 r_free = 0.4273 target = 0.160259 restraints weight = 8538.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4289 r_free = 0.4289 target = 0.161577 restraints weight = 7221.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.4288
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6573
moved from start:          0.1755

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  16658  Z= 0.121
  Angle     :  0.714  33.759  22713  Z= 0.323
  Chirality :  0.043   0.209   2531
  Planarity :  0.004   0.049   2767
  Dihedral  : 15.749  79.119   2593
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 12.40 %
    Favored  : 85.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.23 (0.18), residues: 1911
  helix: -0.21 (0.21), residues: 576
  sheet: -0.42 (0.22), residues: 532
  loop : -1.44 (0.20), residues: 803

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 231 
 TYR   0.022   0.002   TYR A 434 
 PHE   0.019   0.002   PHE A 552 
 TRP   0.010   0.001   TRP A 669 
 HIS   0.008   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00263 /  0.12 (16654)
  covalent geometry    : angle       0.60731 /  0.32 (22701)
  hydrogen bonds       : bond        0.03872 /  2.51 (  771)
  hydrogen bonds       : angle       5.64500 /  4.02 ( 2115)
  metal coordination   : bond        0.00532 /  0.25 (    4)
  metal coordination   : angle      16.37694 /  9.75 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  266 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 236
  time to evaluate  : 0.403 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  169 GLU cc_start: 0.7746 (tm-30) cc_final: 0.7480 (tm-30)
REVERT: A  235 ASP cc_start: 0.7873 (m-30) cc_final: 0.7527 (m-30)
REVERT: A  289 GLU cc_start: 0.6716 (pm20) cc_final: 0.6429 (mp0)
REVERT: A  299 MET cc_start: 0.4797 (tpp) cc_final: 0.4279 (mpp)
REVERT: A  349 GLU cc_start: 0.8294 (pp20) cc_final: 0.7245 (mm-30)
REVERT: A  412 LYS cc_start: 0.7842 (tppt) cc_final: 0.7568 (ttmm)
REVERT: A  487 MET cc_start: 0.8143 (mmt) cc_final: 0.7674 (mtm)
REVERT: A  561 ARG cc_start: 0.7644 (ppt170) cc_final: 0.7399 (ppt170)
REVERT: A  720 LYS cc_start: 0.7192 (tmtt) cc_final: 0.6652 (tppt)
REVERT: A  928 SER cc_start: 0.7922 (m) cc_final: 0.7222 (t)
REVERT: A  930 PHE cc_start: 0.6550 (m-80) cc_final: 0.6108 (m-10)
REVERT: A 1068 MET cc_start: 0.5887 (tpp) cc_final: 0.5534 (tpp)
REVERT: A 1197 MET cc_start: 0.4195 (mmp) cc_final: 0.3463 (ttt)
REVERT: B    1 MET cc_start: 0.7709 (mmt) cc_final: 0.7093 (mmp)
REVERT: B   40 MET cc_start: 0.8084 (tmm) cc_final: 0.7836 (tmm)
REVERT: B  189 ASP cc_start: 0.8083 (t70) cc_final: 0.7524 (p0)
REVERT: C   27 CYS cc_start: 0.7727 (m) cc_final: 0.6908 (t)
REVERT: C   80 LYS cc_start: 0.8173 (tttm) cc_final: 0.7803 (mtpt)
REVERT: C  199 MET cc_start: 0.4705 (mpp) cc_final: 0.4011 (mpp)
REVERT: D   79 LEU cc_start: 0.7281 (tp) cc_final: 0.7076 (tp)
REVERT: D  214 PHE cc_start: 0.8207 (m-80) cc_final: 0.7979 (m-80)
  outliers start: 30
  outliers final: 19
  residues processed: 256
  average time/residue: 0.0984
  time to fit residues: 39.5219
Evaluate side-chains
  236 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 217
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  312 ILE
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   37 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 141 optimal weight:    1.9990
   chunk 151 optimal weight:    7.9990
   chunk 34 optimal weight:    0.8980
   chunk 154 optimal weight:   10.0000
   chunk 57 optimal weight:    0.6980
   chunk 149 optimal weight:    7.9990
   chunk 144 optimal weight:    9.9990
   chunk 172 optimal weight:    3.9990
   chunk 72 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 185 optimal weight:    0.0570
   overall best weight:    0.9300

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 242 HIS
A 404 HIS
A 453 GLN
A 532 HIS
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  49 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4541 r_free = 0.4541 target = 0.183196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.149726 restraints weight = 30441.613|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4204 r_free = 0.4204 target = 0.154423 restraints weight = 16517.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.157503 restraints weight = 11069.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.4267 r_free = 0.4267 target = 0.159534 restraints weight = 8532.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.160848 restraints weight = 7212.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6590
moved from start:          0.1908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  16658  Z= 0.127
  Angle     :  0.704  33.816  22713  Z= 0.317
  Chirality :  0.044   0.207   2531
  Planarity :  0.004   0.048   2767
  Dihedral  : 15.723  78.309   2593
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  2.07 %
    Allowed  : 13.47 %
    Favored  : 84.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.18 (0.18), residues: 1911
  helix: -0.11 (0.21), residues: 577
  sheet: -0.42 (0.22), residues: 536
  loop : -1.44 (0.20), residues: 798

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 231 
 TYR   0.019   0.001   TYR A 434 
 PHE   0.026   0.001   PHE C 207 
 TRP   0.008   0.001   TRP A1166 
 HIS   0.010   0.001   HIS D 246 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.13 (16654)
  covalent geometry    : angle       0.59516 /  0.31 (22701)
  hydrogen bonds       : bond        0.03790 /  2.47 (  771)
  hydrogen bonds       : angle       5.50951 /  3.93 ( 2115)
  metal coordination   : bond        0.00613 /  0.28 (    4)
  metal coordination   : angle      16.33313 /  9.73 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  263 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 228
  time to evaluate  : 0.569 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 TYR cc_start: 0.5636 (OUTLIER) cc_final: 0.2802 (m-80)
REVERT: A  169 GLU cc_start: 0.7743 (tm-30) cc_final: 0.7491 (tm-30)
REVERT: A  235 ASP cc_start: 0.7853 (m-30) cc_final: 0.7511 (m-30)
REVERT: A  289 GLU cc_start: 0.6738 (pm20) cc_final: 0.6402 (mp0)
REVERT: A  299 MET cc_start: 0.4850 (tpp) cc_final: 0.4335 (mpp)
REVERT: A  349 GLU cc_start: 0.8332 (pp20) cc_final: 0.7321 (mm-30)
REVERT: A  412 LYS cc_start: 0.7878 (tppt) cc_final: 0.7541 (ttmt)
REVERT: A  487 MET cc_start: 0.8137 (mmt) cc_final: 0.7928 (mtt)
REVERT: A  561 ARG cc_start: 0.7624 (ppt170) cc_final: 0.7378 (ppt170)
REVERT: A  720 LYS cc_start: 0.7258 (tmtt) cc_final: 0.6690 (tppt)
REVERT: A  928 SER cc_start: 0.8029 (m) cc_final: 0.7500 (t)
REVERT: A 1068 MET cc_start: 0.5985 (tpp) cc_final: 0.5665 (tpp)
REVERT: A 1180 GLN cc_start: 0.5603 (OUTLIER) cc_final: 0.5358 (tp-100)
REVERT: A 1197 MET cc_start: 0.4191 (mmp) cc_final: 0.3455 (ttt)
REVERT: B    1 MET cc_start: 0.7724 (mmt) cc_final: 0.7051 (mmp)
REVERT: B  189 ASP cc_start: 0.8095 (t70) cc_final: 0.7560 (p0)
REVERT: C    5 ARG cc_start: 0.8493 (tpp80) cc_final: 0.8201 (tpp80)
REVERT: C   27 CYS cc_start: 0.7769 (m) cc_final: 0.6941 (t)
REVERT: C   80 LYS cc_start: 0.8236 (tttm) cc_final: 0.7906 (mtpt)
REVERT: C  199 MET cc_start: 0.4843 (mpp) cc_final: 0.4193 (mpp)
REVERT: D   49 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7358 (tp40)
REVERT: D   79 LEU cc_start: 0.7281 (tp) cc_final: 0.7066 (tp)
REVERT: D  214 PHE cc_start: 0.8229 (m-80) cc_final: 0.8007 (m-80)
  outliers start: 35
  outliers final: 26
  residues processed: 255
  average time/residue: 0.0998
  time to fit residues: 39.9623
Evaluate side-chains
  244 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 215
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  105 TYR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  242 HIS
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  867 VAL
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1180 GLN
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain C residue   39 SER
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   49 GLN
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  241 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 69 optimal weight:    0.7980
   chunk 124 optimal weight:    4.9990
   chunk 59 optimal weight:    3.9990
   chunk 162 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 91 optimal weight:    5.9990
   chunk 21 optimal weight:    0.9990
   chunk 172 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    1.3586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 404 HIS
A 911 GLN
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4525 r_free = 0.4525 target = 0.181797 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.147882 restraints weight = 30684.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4181 r_free = 0.4181 target = 0.152578 restraints weight = 16775.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4219 r_free = 0.4219 target = 0.155672 restraints weight = 11283.460|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.157665 restraints weight = 8720.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.158955 restraints weight = 7393.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.4257
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6628
moved from start:          0.2039

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16658  Z= 0.142
  Angle     :  0.713  34.784  22713  Z= 0.321
  Chirality :  0.044   0.208   2531
  Planarity :  0.004   0.048   2767
  Dihedral  : 15.713  78.037   2593
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 14.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.24 %
    Allowed  : 15.00 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.13 (0.18), residues: 1911
  helix: -0.06 (0.21), residues: 576
  sheet: -0.42 (0.22), residues: 536
  loop : -1.40 (0.20), residues: 799

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 231 
 TYR   0.023   0.002   TYR A 726 
 PHE   0.036   0.002   PHE A 516 
 TRP   0.008   0.001   TRP A1166 
 HIS   0.007   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.14 (16654)
  covalent geometry    : angle       0.60186 /  0.32 (22701)
  hydrogen bonds       : bond        0.03822 /  2.48 (  771)
  hydrogen bonds       : angle       5.47656 /  3.90 ( 2115)
  metal coordination   : bond        0.00593 /  0.28 (    4)
  metal coordination   : angle      16.61525 /  9.91 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 226
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  105 TYR cc_start: 0.5638 (OUTLIER) cc_final: 0.2797 (m-80)
REVERT: A  169 GLU cc_start: 0.7789 (tm-30) cc_final: 0.7526 (tm-30)
REVERT: A  235 ASP cc_start: 0.7861 (m-30) cc_final: 0.7625 (m-30)
REVERT: A  289 GLU cc_start: 0.6806 (pm20) cc_final: 0.6436 (mp0)
REVERT: A  299 MET cc_start: 0.4959 (tpp) cc_final: 0.4486 (mpp)
REVERT: A  349 GLU cc_start: 0.8323 (pp20) cc_final: 0.7393 (mm-30)
REVERT: A  412 LYS cc_start: 0.7880 (tppt) cc_final: 0.7491 (ttmm)
REVERT: A  561 ARG cc_start: 0.7618 (ppt170) cc_final: 0.7334 (ppt170)
REVERT: A  720 LYS cc_start: 0.7238 (tmtt) cc_final: 0.6696 (tppt)
REVERT: A  928 SER cc_start: 0.8078 (m) cc_final: 0.7595 (t)
REVERT: A 1039 MET cc_start: 0.7977 (mmm) cc_final: 0.7707 (mmm)
REVERT: A 1068 MET cc_start: 0.6054 (tpp) cc_final: 0.5749 (tpp)
REVERT: A 1180 GLN cc_start: 0.5785 (OUTLIER) cc_final: 0.5533 (tp-100)
REVERT: A 1197 MET cc_start: 0.4292 (mmp) cc_final: 0.3484 (ttt)
REVERT: B    1 MET cc_start: 0.7776 (mmt) cc_final: 0.7067 (mmp)
REVERT: B   40 MET cc_start: 0.8043 (tmm) cc_final: 0.7829 (tmm)
REVERT: B  189 ASP cc_start: 0.8152 (t70) cc_final: 0.7580 (p0)
REVERT: C   27 CYS cc_start: 0.7770 (m) cc_final: 0.6952 (t)
REVERT: C   80 LYS cc_start: 0.8256 (tttm) cc_final: 0.7897 (mtpt)
REVERT: C  199 MET cc_start: 0.4744 (mpp) cc_final: 0.4124 (mpp)
REVERT: D  214 PHE cc_start: 0.8244 (m-80) cc_final: 0.8016 (m-80)
  outliers start: 38
  outliers final: 31
  residues processed: 251
  average time/residue: 0.0975
  time to fit residues: 38.3137
Evaluate side-chains
  248 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 215
  time to evaluate  : 0.473 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  105 TYR
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  866 CYS
Chi-restraints excluded: chain A residue  867 VAL
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1108 HIS
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1180 GLN
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  244 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 174 optimal weight:    5.9990
   chunk 185 optimal weight:    1.9990
   chunk 152 optimal weight:    9.9990
   chunk 89 optimal weight:    0.7980
   chunk 184 optimal weight:    0.8980
   chunk 123 optimal weight:    6.9990
   chunk 190 optimal weight:    0.8980
   chunk 150 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 76 optimal weight:    0.6980
   chunk 138 optimal weight:    4.9990
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 404 HIS
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  49 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4526 r_free = 0.4526 target = 0.182015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.148477 restraints weight = 30242.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4186 r_free = 0.4186 target = 0.153184 restraints weight = 16428.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4224 r_free = 0.4224 target = 0.156228 restraints weight = 10983.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4248 r_free = 0.4248 target = 0.158229 restraints weight = 8501.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.159577 restraints weight = 7184.543|
|-----------------------------------------------------------------------------|
r_work (final): 0.4264
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6616
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  16658  Z= 0.129
  Angle     :  0.711  34.973  22713  Z= 0.318
  Chirality :  0.043   0.202   2531
  Planarity :  0.004   0.048   2767
  Dihedral  : 15.682  77.653   2593
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 15.59 %
    Favored  : 81.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.07 (0.18), residues: 1911
  helix: -0.03 (0.21), residues: 578
  sheet: -0.39 (0.22), residues: 536
  loop : -1.36 (0.21), residues: 797

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 231 
 TYR   0.027   0.002   TYR A 244 
 PHE   0.031   0.002   PHE A 516 
 TRP   0.008   0.001   TRP A1166 
 HIS   0.007   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00289 /  0.13 (16654)
  covalent geometry    : angle       0.60045 /  0.32 (22701)
  hydrogen bonds       : bond        0.03728 /  2.43 (  771)
  hydrogen bonds       : angle       5.38195 /  3.83 ( 2115)
  metal coordination   : bond        0.00561 /  0.26 (    4)
  metal coordination   : angle      16.56103 /  9.88 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 223
  time to evaluate  : 0.600 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.5010 (mt) cc_final: 0.4792 (mp)
REVERT: A  169 GLU cc_start: 0.7762 (tm-30) cc_final: 0.7484 (tm-30)
REVERT: A  235 ASP cc_start: 0.7904 (m-30) cc_final: 0.7574 (m-30)
REVERT: A  289 GLU cc_start: 0.6726 (pm20) cc_final: 0.6407 (mp0)
REVERT: A  299 MET cc_start: 0.4913 (tpp) cc_final: 0.4510 (mpp)
REVERT: A  349 GLU cc_start: 0.8301 (pp20) cc_final: 0.7377 (mm-30)
REVERT: A  412 LYS cc_start: 0.7871 (tppt) cc_final: 0.7493 (ttmm)
REVERT: A  561 ARG cc_start: 0.7582 (ppt170) cc_final: 0.7326 (ppt170)
REVERT: A  594 THR cc_start: 0.7814 (m) cc_final: 0.7563 (t)
REVERT: A  720 LYS cc_start: 0.7282 (tmtt) cc_final: 0.6714 (tppt)
REVERT: A  928 SER cc_start: 0.8011 (m) cc_final: 0.7553 (t)
REVERT: A 1024 MET cc_start: 0.4230 (ppp) cc_final: 0.2603 (ppp)
REVERT: A 1039 MET cc_start: 0.7974 (mmm) cc_final: 0.7736 (mmm)
REVERT: A 1180 GLN cc_start: 0.5872 (OUTLIER) cc_final: 0.5624 (tp-100)
REVERT: A 1197 MET cc_start: 0.4261 (mmp) cc_final: 0.3476 (ttt)
REVERT: B    1 MET cc_start: 0.7791 (mmt) cc_final: 0.7067 (mmp)
REVERT: B  189 ASP cc_start: 0.8147 (t70) cc_final: 0.7582 (p0)
REVERT: C    5 ARG cc_start: 0.8488 (tpp80) cc_final: 0.8224 (tpp80)
REVERT: C   27 CYS cc_start: 0.7611 (m) cc_final: 0.6846 (t)
REVERT: C   80 LYS cc_start: 0.8227 (tttm) cc_final: 0.7865 (mtpt)
REVERT: C  199 MET cc_start: 0.4751 (mpp) cc_final: 0.4110 (mpp)
REVERT: D   79 LEU cc_start: 0.6812 (tp) cc_final: 0.6611 (mm)
REVERT: D  214 PHE cc_start: 0.8235 (m-80) cc_final: 0.8006 (m-80)
  outliers start: 41
  outliers final: 34
  residues processed: 249
  average time/residue: 0.0902
  time to fit residues: 35.3737
Evaluate side-chains
  253 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 218
  time to evaluate  : 0.542 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  866 CYS
Chi-restraints excluded: chain A residue  867 VAL
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1048 GLU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1108 HIS
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1180 GLN
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  244 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 99 optimal weight:    4.9990
   chunk 42 optimal weight:    1.9990
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    6.9990
   chunk 106 optimal weight:    1.9990
   chunk 163 optimal weight:    0.1980
   chunk 30 optimal weight:    0.8980
   chunk 22 optimal weight:    1.9990
   chunk 108 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 88 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  88 GLN
A 404 HIS
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.182290 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4127 r_free = 0.4127 target = 0.148496 restraints weight = 30810.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.153222 restraints weight = 16784.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.156396 restraints weight = 11256.321|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4250 r_free = 0.4250 target = 0.158366 restraints weight = 8655.514|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4265 r_free = 0.4265 target = 0.159657 restraints weight = 7344.397|
|-----------------------------------------------------------------------------|
r_work (final): 0.4263
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6618
moved from start:          0.2232

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  16658  Z= 0.127
  Angle     :  0.713  34.956  22713  Z= 0.319
  Chirality :  0.043   0.204   2531
  Planarity :  0.004   0.049   2767
  Dihedral  : 15.660  77.189   2593
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 13.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.48 %
    Favored  : 81.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.06 (0.18), residues: 1911
  helix: -0.02 (0.21), residues: 579
  sheet: -0.35 (0.22), residues: 536
  loop : -1.36 (0.21), residues: 796

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 231 
 TYR   0.019   0.002   TYR A 244 
 PHE   0.030   0.001   PHE A 516 
 TRP   0.008   0.001   TRP A 669 
 HIS   0.007   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00283 /  0.13 (16654)
  covalent geometry    : angle       0.60492 /  0.32 (22701)
  hydrogen bonds       : bond        0.03657 /  2.39 (  771)
  hydrogen bonds       : angle       5.33843 /  3.80 ( 2115)
  metal coordination   : bond        0.00556 /  0.26 (    4)
  metal coordination   : angle      16.46954 /  9.83 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 228
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  145 LEU cc_start: 0.5044 (mt) cc_final: 0.4799 (mp)
REVERT: A  169 GLU cc_start: 0.7816 (tm-30) cc_final: 0.7518 (tm-30)
REVERT: A  235 ASP cc_start: 0.7935 (m-30) cc_final: 0.7582 (m-30)
REVERT: A  289 GLU cc_start: 0.6758 (pm20) cc_final: 0.6428 (mp0)
REVERT: A  299 MET cc_start: 0.4929 (tpp) cc_final: 0.4492 (mpp)
REVERT: A  349 GLU cc_start: 0.8331 (pp20) cc_final: 0.7356 (mm-30)
REVERT: A  412 LYS cc_start: 0.7854 (tppt) cc_final: 0.7477 (ttmm)
REVERT: A  561 ARG cc_start: 0.7598 (ppt170) cc_final: 0.7323 (ppt170)
REVERT: A  594 THR cc_start: 0.7900 (m) cc_final: 0.7666 (t)
REVERT: A  720 LYS cc_start: 0.7220 (tmtt) cc_final: 0.6660 (tppt)
REVERT: A  820 MET cc_start: 0.7505 (pmm) cc_final: 0.7097 (pmm)
REVERT: A  928 SER cc_start: 0.8062 (m) cc_final: 0.7523 (t)
REVERT: A  930 PHE cc_start: 0.6595 (m-80) cc_final: 0.5909 (m-10)
REVERT: A 1024 MET cc_start: 0.4243 (ppp) cc_final: 0.2672 (ppp)
REVERT: A 1039 MET cc_start: 0.7940 (mmm) cc_final: 0.7732 (mmm)
REVERT: A 1068 MET cc_start: 0.5886 (tpp) cc_final: 0.5479 (tpp)
REVERT: A 1180 GLN cc_start: 0.5916 (OUTLIER) cc_final: 0.5658 (tp-100)
REVERT: A 1197 MET cc_start: 0.4304 (mmp) cc_final: 0.3428 (ttt)
REVERT: B    1 MET cc_start: 0.7875 (mmt) cc_final: 0.7111 (mmp)
REVERT: B  189 ASP cc_start: 0.8155 (t70) cc_final: 0.7586 (p0)
REVERT: C    5 ARG cc_start: 0.8470 (tpp80) cc_final: 0.8173 (tpp80)
REVERT: C   27 CYS cc_start: 0.7652 (m) cc_final: 0.6851 (t)
REVERT: C   80 LYS cc_start: 0.8055 (tttm) cc_final: 0.7685 (mtpt)
REVERT: C  199 MET cc_start: 0.4739 (mpp) cc_final: 0.4189 (mpp)
REVERT: D  214 PHE cc_start: 0.8242 (m-80) cc_final: 0.8016 (m-80)
  outliers start: 36
  outliers final: 34
  residues processed: 250
  average time/residue: 0.0995
  time to fit residues: 38.8383
Evaluate side-chains
  254 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 219
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  223 GLU
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  866 CYS
Chi-restraints excluded: chain A residue  867 VAL
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1048 GLU
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1180 GLN
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain B residue  229 MET
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  244 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 172 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 132 optimal weight:    6.9990
   chunk 65 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 93 optimal weight:    0.9990
   chunk 158 optimal weight:    7.9990
   chunk 39 optimal weight:    9.9990
   chunk 0 optimal weight:   20.0000
   chunk 52 optimal weight:    1.9990
   chunk 125 optimal weight:    8.9990
   overall best weight:    2.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 242 HIS
A 404 HIS
** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4486 r_free = 0.4486 target = 0.178073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4074 r_free = 0.4074 target = 0.143939 restraints weight = 30675.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.148415 restraints weight = 17039.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.151392 restraints weight = 11612.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.153330 restraints weight = 9055.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4207 r_free = 0.4207 target = 0.154576 restraints weight = 7711.368|
|-----------------------------------------------------------------------------|
r_work (final): 0.4202
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6738
moved from start:          0.2505

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  16658  Z= 0.192
  Angle     :  0.792  39.981  22713  Z= 0.354
  Chirality :  0.046   0.216   2531
  Planarity :  0.005   0.051   2767
  Dihedral  : 15.736  76.728   2593
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 16.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.30 %
    Allowed  : 16.54 %
    Favored  : 81.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.15 (0.18), residues: 1911
  helix: -0.16 (0.21), residues: 574
  sheet: -0.39 (0.22), residues: 532
  loop : -1.38 (0.21), residues: 805

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 231 
 TYR   0.022   0.002   TYR C 249 
 PHE   0.033   0.002   PHE A 516 
 TRP   0.012   0.001   TRP A1166 
 HIS   0.008   0.001   HIS A 422 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00440 /  0.19 (16654)
  covalent geometry    : angle       0.67193 /  0.35 (22701)
  hydrogen bonds       : bond        0.04071 /  2.66 (  771)
  hydrogen bonds       : angle       5.48163 /  3.90 ( 2115)
  metal coordination   : bond        0.00596 /  0.30 (    4)
  metal coordination   : angle      18.23124 / 10.84 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  261 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 222
  time to evaluate  : 0.406 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASP cc_start: 0.7971 (m-30) cc_final: 0.7681 (m-30)
REVERT: A  289 GLU cc_start: 0.6879 (pm20) cc_final: 0.6437 (mp0)
REVERT: A  299 MET cc_start: 0.5073 (tpp) cc_final: 0.4405 (mpp)
REVERT: A  349 GLU cc_start: 0.8363 (pp20) cc_final: 0.7446 (mm-30)
REVERT: A  412 LYS cc_start: 0.7850 (tppt) cc_final: 0.7479 (ttmm)
REVERT: A  561 ARG cc_start: 0.7596 (ppt170) cc_final: 0.7289 (ppt170)
REVERT: A  594 THR cc_start: 0.7930 (m) cc_final: 0.7692 (t)
REVERT: A  720 LYS cc_start: 0.7163 (tmtt) cc_final: 0.6649 (tppt)
REVERT: A  821 ARG cc_start: 0.7202 (mmp80) cc_final: 0.5712 (mtp-110)
REVERT: A  928 SER cc_start: 0.8227 (m) cc_final: 0.7796 (t)
REVERT: A  930 PHE cc_start: 0.6754 (m-80) cc_final: 0.6051 (m-10)
REVERT: A 1024 MET cc_start: 0.4310 (ppp) cc_final: 0.3098 (ppp)
REVERT: A 1068 MET cc_start: 0.5915 (tpp) cc_final: 0.5510 (tpp)
REVERT: A 1197 MET cc_start: 0.4567 (mmp) cc_final: 0.3579 (ttt)
REVERT: B    1 MET cc_start: 0.7946 (mmt) cc_final: 0.7395 (mmp)
REVERT: B   15 VAL cc_start: 0.7673 (OUTLIER) cc_final: 0.7430 (t)
REVERT: B  139 MET cc_start: 0.7473 (tmm) cc_final: 0.7199 (tmm)
REVERT: B  189 ASP cc_start: 0.8144 (t70) cc_final: 0.7544 (p0)
REVERT: C    5 ARG cc_start: 0.8495 (tpp80) cc_final: 0.8178 (tpp80)
REVERT: C   27 CYS cc_start: 0.7538 (m) cc_final: 0.6870 (t)
REVERT: C   80 LYS cc_start: 0.8248 (tttm) cc_final: 0.7877 (mtpt)
REVERT: C  199 MET cc_start: 0.4753 (mpp) cc_final: 0.4386 (mpp)
  outliers start: 39
  outliers final: 34
  residues processed: 250
  average time/residue: 0.1057
  time to fit residues: 40.5498
Evaluate side-chains
  249 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 214
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  236 LEU
Chi-restraints excluded: chain A residue  242 HIS
Chi-restraints excluded: chain A residue  294 MET
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  866 CYS
Chi-restraints excluded: chain A residue  867 VAL
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1154 VAL
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  244 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 170 optimal weight:    0.8980
   chunk 67 optimal weight:    0.9990
   chunk 181 optimal weight:   10.0000
   chunk 140 optimal weight:    1.9990
   chunk 76 optimal weight:    0.8980
   chunk 127 optimal weight:    0.9980
   chunk 166 optimal weight:    1.9990
   chunk 52 optimal weight:    5.9990
   chunk 194 optimal weight:   20.0000
   chunk 133 optimal weight:    0.7980
   chunk 193 optimal weight:   10.0000
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 242 HIS
A 404 HIS
** A 592 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 980 GLN
A1180 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4507 r_free = 0.4507 target = 0.180184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4099 r_free = 0.4099 target = 0.146219 restraints weight = 30634.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.150856 restraints weight = 16713.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4198 r_free = 0.4198 target = 0.153990 restraints weight = 11278.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.155939 restraints weight = 8706.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.157283 restraints weight = 7387.837|
|-----------------------------------------------------------------------------|
r_work (final): 0.4237
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6666
moved from start:          0.2496

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16658  Z= 0.134
  Angle     :  0.764  39.127  22713  Z= 0.339
  Chirality :  0.044   0.213   2531
  Planarity :  0.004   0.059   2767
  Dihedral  : 15.700  76.833   2593
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.40 %
    Favored  : 96.60 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 17.42 %
    Favored  : 80.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.08 (0.19), residues: 1911
  helix: -0.06 (0.21), residues: 577
  sheet: -0.40 (0.22), residues: 527
  loop : -1.32 (0.21), residues: 807

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 579 
 TYR   0.023   0.002   TYR A 244 
 PHE   0.028   0.002   PHE A 516 
 TRP   0.010   0.001   TRP A 669 
 HIS   0.024   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.13 (16654)
  covalent geometry    : angle       0.64957 /  0.34 (22701)
  hydrogen bonds       : bond        0.03729 /  2.44 (  771)
  hydrogen bonds       : angle       5.40130 /  3.84 ( 2115)
  metal coordination   : bond        0.00477 /  0.22 (    4)
  metal coordination   : angle      17.51599 / 10.45 (   12)

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

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

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3822 Ramachandran restraints generated.
    1911 Oldfield, 0 Emsley, 1911 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 222
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
REVERT: A  235 ASP cc_start: 0.7949 (m-30) cc_final: 0.7541 (m-30)
REVERT: A  289 GLU cc_start: 0.6785 (pm20) cc_final: 0.6413 (mp0)
REVERT: A  299 MET cc_start: 0.5123 (tpp) cc_final: 0.4688 (mpp)
REVERT: A  349 GLU cc_start: 0.8324 (pp20) cc_final: 0.7383 (mm-30)
REVERT: A  412 LYS cc_start: 0.7813 (tppt) cc_final: 0.7451 (ttmm)
REVERT: A  561 ARG cc_start: 0.7592 (ppt170) cc_final: 0.7280 (ppt170)
REVERT: A  594 THR cc_start: 0.7911 (m) cc_final: 0.7666 (t)
REVERT: A  720 LYS cc_start: 0.7229 (tmtt) cc_final: 0.6690 (tppt)
REVERT: A  820 MET cc_start: 0.7629 (pmm) cc_final: 0.7186 (pmm)
REVERT: A  821 ARG cc_start: 0.7107 (mmp80) cc_final: 0.5835 (mtm180)
REVERT: A  928 SER cc_start: 0.8119 (m) cc_final: 0.7623 (t)
REVERT: A  930 PHE cc_start: 0.6643 (m-80) cc_final: 0.5950 (m-10)
REVERT: A 1024 MET cc_start: 0.4215 (ppp) cc_final: 0.2643 (ppp)
REVERT: A 1068 MET cc_start: 0.5867 (tpp) cc_final: 0.5475 (tpp)
REVERT: A 1197 MET cc_start: 0.4564 (mmp) cc_final: 0.3610 (ttt)
REVERT: B    1 MET cc_start: 0.7807 (mmt) cc_final: 0.7353 (mmp)
REVERT: B   15 VAL cc_start: 0.7664 (OUTLIER) cc_final: 0.7417 (t)
REVERT: B  139 MET cc_start: 0.7531 (tmm) cc_final: 0.7277 (tmm)
REVERT: B  189 ASP cc_start: 0.8158 (t70) cc_final: 0.7556 (p0)
REVERT: C    5 ARG cc_start: 0.8424 (tpp80) cc_final: 0.8197 (tpt-90)
REVERT: C   27 CYS cc_start: 0.7519 (m) cc_final: 0.6876 (t)
REVERT: C   80 LYS cc_start: 0.8104 (tttm) cc_final: 0.7724 (mtpt)
REVERT: C  199 MET cc_start: 0.4870 (mpp) cc_final: 0.4525 (mpp)
REVERT: D   79 LEU cc_start: 0.7229 (tp) cc_final: 0.6391 (mm)
  outliers start: 34
  outliers final: 31
  residues processed: 246
  average time/residue: 0.1035
  time to fit residues: 39.7250
Evaluate side-chains
  242 residues out of total 1693 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 210
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   98 LEU
Chi-restraints excluded: chain A residue  108 THR
Chi-restraints excluded: chain A residue  242 HIS
Chi-restraints excluded: chain A residue  440 ASP
Chi-restraints excluded: chain A residue  484 ILE
Chi-restraints excluded: chain A residue  538 THR
Chi-restraints excluded: chain A residue  559 ARG
Chi-restraints excluded: chain A residue  828 SER
Chi-restraints excluded: chain A residue  866 CYS
Chi-restraints excluded: chain A residue  867 VAL
Chi-restraints excluded: chain A residue  889 THR
Chi-restraints excluded: chain A residue  971 PHE
Chi-restraints excluded: chain A residue  973 VAL
Chi-restraints excluded: chain A residue 1033 ILE
Chi-restraints excluded: chain A residue 1052 THR
Chi-restraints excluded: chain A residue 1167 LEU
Chi-restraints excluded: chain A residue 1186 LEU
Chi-restraints excluded: chain B residue   15 VAL
Chi-restraints excluded: chain B residue   35 VAL
Chi-restraints excluded: chain B residue   89 THR
Chi-restraints excluded: chain B residue  137 VAL
Chi-restraints excluded: chain B residue  158 VAL
Chi-restraints excluded: chain B residue  219 THR
Chi-restraints excluded: chain C residue  182 LEU
Chi-restraints excluded: chain C residue  195 VAL
Chi-restraints excluded: chain C residue  225 VAL
Chi-restraints excluded: chain D residue   37 LEU
Chi-restraints excluded: chain D residue   50 LEU
Chi-restraints excluded: chain D residue  111 VAL
Chi-restraints excluded: chain D residue  196 THR
Chi-restraints excluded: chain D residue  241 ILE
Chi-restraints excluded: chain D residue  244 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 195
   random chunks:
   chunk 9 optimal weight:    0.0570
   chunk 182 optimal weight:    0.4980
   chunk 119 optimal weight:   20.0000
   chunk 158 optimal weight:   10.0000
   chunk 13 optimal weight:    0.0070
   chunk 168 optimal weight:   20.0000
   chunk 26 optimal weight:    7.9990
   chunk 136 optimal weight:    0.7980
   chunk 73 optimal weight:    5.9990
   chunk 11 optimal weight:    0.0050
   chunk 75 optimal weight:    0.6980
   overall best weight:    0.2530

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 404 HIS
A 592 GLN
** A 911 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 927 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4527 r_free = 0.4527 target = 0.182180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.149065 restraints weight = 30185.346|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.153834 restraints weight = 16132.087|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.156985 restraints weight = 10653.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.4259 r_free = 0.4259 target = 0.159079 restraints weight = 8115.242|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.160279 restraints weight = 6808.520|
|-----------------------------------------------------------------------------|
r_work (final): 0.4278
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6580
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  16658  Z= 0.121
  Angle     :  0.740  36.134  22713  Z= 0.334
  Chirality :  0.044   0.238   2531
  Planarity :  0.004   0.051   2767
  Dihedral  : 15.646  76.272   2593
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 17.66 %
    Favored  : 80.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.05 (0.19), residues: 1911
  helix:  0.00 (0.21), residues: 579
  sheet: -0.40 (0.22), residues: 532
  loop : -1.33 (0.21), residues: 800

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 260 
 TYR   0.023   0.002   TYR A 244 
 PHE   0.024   0.002   PHE A 516 
 TRP   0.014   0.001   TRP A 243 
 HIS   0.032   0.001   HIS A 242 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00260 /  0.12 (16654)
  covalent geometry    : angle       0.63749 /  0.33 (22701)
  hydrogen bonds       : bond        0.03561 /  2.33 (  771)
  hydrogen bonds       : angle       5.31735 /  3.78 ( 2115)
  metal coordination   : bond        0.00608 /  0.27 (    4)
  metal coordination   : angle      16.34078 /  9.78 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2522.16 seconds
wall clock time: 44 minutes 27.12 seconds (2667.12 seconds total)