Starting phenix.real_space_refine
on Sat Sep 12 15:00:44 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9lqq_63301/09_2026/9lqq_63301.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9lqq_63301/09_2026/9lqq_63301.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/9lqq_63301/09_2026/9lqq_63301.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9lqq_63301/09_2026/9lqq_63301.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9lqq_63301/09_2026/9lqq_63301.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9lqq_63301/09_2026/9lqq_63301.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=   0.081
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: 7
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     P     104      5.49       5
     Mg      1      5.21       5
     S     104      5.16       5
     C    9904      2.51       5
     N    2806      2.21       5
     O    3223      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 16144
  Number of models: 1
  Model: ""
    Number of chains: 12
    Chain: "I"
      Number of atoms: 506
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 506
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "J"
      Number of atoms: 519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 519
          Classifications: {'DNA': 25}
          Link IDs: {'rna3p': 24}
    Chain: "A"
      Number of atoms: 4365
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 543, 4365
          Classifications: {'peptide': 543}
          Link IDs: {'PTRANS': 25, 'TRANS': 517}
    Chain: "B"
      Number of atoms: 2642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 337, 2642
          Classifications: {'peptide': 337}
          Link IDs: {'PTRANS': 19, 'TRANS': 317}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 4373
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 544, 4373
          Classifications: {'peptide': 544}
          Link IDs: {'PTRANS': 25, 'TRANS': 518}
    Chain: "D"
      Number of atoms: 2629
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 335, 2629
          Classifications: {'peptide': 335}
          Link IDs: {'PTRANS': 18, 'TRANS': 316}
          Chain breaks: 2
    Chain: "L"
      Number of atoms: 249
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 249
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "y"
      Number of atoms: 243
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 243
          Classifications: {'DNA': 12}
          Link IDs: {'rna3p': 11}
    Chain: "M"
      Number of atoms: 314
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 314
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "x"
      Number of atoms: 301
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 15, 301
          Classifications: {'DNA': 15}
          Link IDs: {'rna3p': 14}
    Chain: "A"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}
    Chain: "C"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 1, ' ZN': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   3099  SG  CYS A 727      76.118  95.558  45.827  1.00 62.97           S
  ATOM   3120  SG  CYS A 730      78.832  97.606  43.907  1.00 65.16           S
  ATOM  10106  SG  CYS C 727      26.921  49.927  42.607  1.00 62.77           S
  ATOM  10127  SG  CYS C 730      24.244  48.395  40.515  1.00 67.56           S

  Time building chain proxies: 3.06, per 1000 atoms: 0.19
  Number of scatterers: 16144
  At special positions: 0
  Unit cell: (104.5, 151.8, 108.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      2     29.99
     S     104     16.00
     P     104     15.00
     Mg      1     11.99
     O    3223      8.00
     N    2806      7.00
     C    9904      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: 1.07
  Conformation dependent library (CDL) restraints added in 600.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1101 "
        pdb="ZN    ZN A1101 " - pdb=" NE2 HIS A 937 "
        pdb="ZN    ZN A1101 " - pdb=" NE2 HIS A 942 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 730 "
        pdb="ZN    ZN A1101 " - pdb=" SG  CYS A 727 "
      pdb="  ZN C1101 "
        pdb="ZN    ZN C1101 " - pdb=" NE2 HIS C 937 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 727 "
        pdb="ZN    ZN C1101 " - pdb=" NE2 HIS C 942 "
        pdb="ZN    ZN C1101 " - pdb=" SG  CYS C 730 "
      Number of angles added : 4


  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3292

  Finding SS restraints...
    Secondary structure from input PDB file:
      50 helices and 23 sheets defined
      35.6% alpha, 19.2% beta
      44 base pairs and 74 stacking pairs defined.
    Time for finding SS restraints: 1.86
  Creating SS restraints...
    Processing helix  chain 'A' and resid 468 through 473
    Processing helix  chain 'A' and resid 477 through 493
    Processing helix  chain 'A' and resid 499 through 511
      removed outlier: 4.425A  pdb=" N   VAL A 509 " --> pdb=" O   ASN A 505 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LEU A 510 " --> pdb=" O   ALA A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 558 through 570
      removed outlier: 3.849A  pdb=" N   VAL A 564 " --> pdb=" O   ASP A 560 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   SER A 565 " --> pdb=" O   SER A 561 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 570 through 581
    Processing helix  chain 'A' and resid 664 through 683
      removed outlier: 3.531A  pdb=" N   THR A 669 " --> pdb=" O   HIS A 665 " (cutoff:3.500A)
      removed outlier: 4.547A  pdb=" N   ALA A 670 " --> pdb=" O   GLU A 666 " (cutoff:3.500A)
      Proline residue:  A 674  - end of helix
    Processing helix  chain 'A' and resid 708 through 716
    Processing helix  chain 'A' and resid 733 through 739
    Processing helix  chain 'A' and resid 749 through 762
    Processing helix  chain 'A' and resid 768 through 776
    Processing helix  chain 'A' and resid 792 through 814
    Processing helix  chain 'A' and resid 822 through 842
    Processing helix  chain 'A' and resid 850 through 858
    Processing helix  chain 'A' and resid 859 through 868
    Processing helix  chain 'A' and resid 872 through 895
      Proline residue:  A 891  - end of helix
    Processing helix  chain 'A' and resid 897 through 902
    Processing helix  chain 'A' and resid 902 through 923
      removed outlier: 5.074A  pdb=" N   SER A 910 " --> pdb=" O   LEU A 906 " (cutoff:3.500A)
      removed outlier: 5.310A  pdb=" N   PHE A 911 " --> pdb=" O   CYS A 907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 933 through 942
    Processing helix  chain 'A' and resid 942 through 951
    Processing helix  chain 'A' and resid 953 through 957
    Processing helix  chain 'A' and resid 958 through 975
      removed outlier: 3.878A  pdb=" N   LYS A 966 " --> pdb=" O   ASN A 962 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   LEU A 967 " --> pdb=" O   SER A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 996
    Processing helix  chain 'A' and resid 996 through 1003
      removed outlier: 3.841A  pdb=" N   GLN A1000 " --> pdb=" O   SER A 996 " (cutoff:3.500A)
      removed outlier: 3.879A  pdb=" N   PHE A1002 " --> pdb=" O   TYR A 998 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   MET A1003 " --> pdb=" O   LEU A 999 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 463 through 474
      removed outlier: 3.535A  pdb=" N   THR C 474 " --> pdb=" O   ILE C 470 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 477 through 492
      removed outlier: 3.516A  pdb=" N   HIS C 482 " --> pdb=" O   CYS C 478 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 499 through 511
    Processing helix  chain 'C' and resid 558 through 570
    Processing helix  chain 'C' and resid 570 through 581
      removed outlier: 3.781A  pdb=" N   MET C 578 " --> pdb=" O   ILE C 574 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 666 through 685
      Proline residue:  C 674  - end of helix
      removed outlier: 3.603A  pdb=" N   SER C 684 " --> pdb=" O   GLU C 680 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 708 through 716
    Processing helix  chain 'C' and resid 733 through 740
    Processing helix  chain 'C' and resid 749 through 763
    Processing helix  chain 'C' and resid 768 through 777
    Processing helix  chain 'C' and resid 793 through 813
      removed outlier: 3.753A  pdb=" N   GLY C 813 " --> pdb=" O   GLN C 809 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 822 through 840
      removed outlier: 3.963A  pdb=" N   GLN C 830 " --> pdb=" O   ARG C 826 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ALA C 831 " --> pdb=" O   LYS C 827 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 850 through 858
    Processing helix  chain 'C' and resid 859 through 868
    Processing helix  chain 'C' and resid 873 through 895
      Proline residue:  C 891  - end of helix
    Processing helix  chain 'C' and resid 897 through 902
    Processing helix  chain 'C' and resid 902 through 924
      removed outlier: 4.926A  pdb=" N   SER C 910 " --> pdb=" O   LEU C 906 " (cutoff:3.500A)
      removed outlier: 5.223A  pdb=" N   PHE C 911 " --> pdb=" O   CYS C 907 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE C 924 " --> pdb=" O   LEU C 920 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 933 through 942
    Processing helix  chain 'C' and resid 942 through 950
    Processing helix  chain 'C' and resid 952 through 957
      removed outlier: 4.155A  pdb=" N   TRP C 956 " --> pdb=" O   SER C 952 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA C 957 " --> pdb=" O   ILE C 953 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 952 through 957'
    Processing helix  chain 'C' and resid 960 through 975
      removed outlier: 4.042A  pdb=" N   LYS C 966 " --> pdb=" O   ASN C 962 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LEU C 967 " --> pdb=" O   SER C 963 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 979 through 996
      removed outlier: 4.713A  pdb=" N   MET C 984 " --> pdb=" O   LYS C 980 " (cutoff:3.500A)
      removed outlier: 5.253A  pdb=" N   GLU C 985 " --> pdb=" O   CYS C 981 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP C 986 " --> pdb=" O   TYR C 982 " (cutoff:3.500A)
      removed outlier: 3.581A  pdb=" N   VAL C 987 " --> pdb=" O   GLU C 983 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 999 through 1004
      removed outlier: 3.955A  pdb=" N   MET C1003 " --> pdb=" O   LEU C 999 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 11 through 15
      removed outlier: 3.847A  pdb=" N   LEU D  14 " --> pdb=" O   ASN D  11 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   ILE D  15 " --> pdb=" O   ILE D  12 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 11 through 15'
    Processing helix  chain 'D' and resid 163 through 167
      removed outlier: 3.903A  pdb=" N   ARG D 167 " --> pdb=" O   SER D 164 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 168 through 172
      removed outlier: 3.816A  pdb=" N   TRP D 172 " --> pdb=" O   THR D 169 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 308 through 313
    Processing sheet with id=AA1, first strand: chain 'A' and resid 535 through 536
      removed outlier: 6.699A  pdb=" N   PHE A 622 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   LEU A 657 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   VAL A 620 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   VAL A 594 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 4.309A  pdb=" N   ILE A 629 " --> pdb=" O   THR A 592 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   THR A 592 " --> pdb=" O   ILE A 629 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 535 through 536
      removed outlier: 6.699A  pdb=" N   PHE A 622 " --> pdb=" O   LEU A 655 " (cutoff:3.500A)
      removed outlier: 5.061A  pdb=" N   LEU A 657 " --> pdb=" O   VAL A 620 " (cutoff:3.500A)
      removed outlier: 7.307A  pdb=" N   VAL A 620 " --> pdb=" O   LEU A 657 " (cutoff:3.500A)
      removed outlier: 7.883A  pdb=" N   MET A 627 " --> pdb=" O   GLU A 642 " (cutoff:3.500A)
      removed outlier: 4.985A  pdb=" N   GLU A 642 " --> pdb=" O   MET A 627 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   ILE A 629 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 687 through 691
    Processing sheet with id=AA4, first strand: chain 'B' and resid 2 through 6
      removed outlier: 3.559A  pdb=" N   ARG B 343 " --> pdb=" O   SER B   2 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   THR B 341 " --> pdb=" O   GLN B   4 " (cutoff:3.500A)
      removed outlier: 4.554A  pdb=" N   PHE B 339 " --> pdb=" O   VAL B   6 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 22 through 24
    Processing sheet with id=AA6, first strand: chain 'B' and resid 46 through 51
    Processing sheet with id=AA7, first strand: chain 'B' and resid 76 through 80
      removed outlier: 6.760A  pdb=" N   THR B 121 " --> pdb=" O   ALA B 113 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 76 through 80
      removed outlier: 4.024A  pdb=" N   ILE B 107 " --> pdb=" O   LYS B 127 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 141 through 146
      removed outlier: 3.632A  pdb=" N   VAL B 145 " --> pdb=" O   MET B 152 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   CYS B 191 " --> pdb=" O   ASP B 186 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 159 through 161
    Processing sheet with id=AB2, first strand: chain 'B' and resid 208 through 212
      removed outlier: 3.923A  pdb=" N   TYR B 217 " --> pdb=" O   ILE B 210 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   THR B 215 " --> pdb=" O   ARG B 212 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   TYR B 234 " --> pdb=" O   ILE B 218 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   LEU B 233 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 262 through 264
      removed outlier: 3.589A  pdb=" N   ILE B 262 " --> pdb=" O   VAL B 274 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   GLU B 298 " --> pdb=" O   SER B 291 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'C' and resid 518 through 519
      removed outlier: 4.079A  pdb=" N   ILE C 694 " --> pdb=" O   MET C 691 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'C' and resid 535 through 536
      removed outlier: 7.254A  pdb=" N   CYS C 652 " --> pdb=" O   VAL C 626 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   VAL C 626 " --> pdb=" O   CYS C 652 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   PHE C 624 " --> pdb=" O   PRO C 654 " (cutoff:3.500A)
      removed outlier: 6.302A  pdb=" N   ILE C 629 " --> pdb=" O   VAL C 640 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'C' and resid 535 through 536
      removed outlier: 7.254A  pdb=" N   CYS C 652 " --> pdb=" O   VAL C 626 " (cutoff:3.500A)
      removed outlier: 8.037A  pdb=" N   VAL C 626 " --> pdb=" O   CYS C 652 " (cutoff:3.500A)
      removed outlier: 5.600A  pdb=" N   PHE C 624 " --> pdb=" O   PRO C 654 " (cutoff:3.500A)
      removed outlier: 3.882A  pdb=" N   ARG C 621 " --> pdb=" O   ASP C 600 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   ASP C 600 " --> pdb=" O   ARG C 621 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   VAL C 594 " --> pdb=" O   MET C 627 " (cutoff:3.500A)
      removed outlier: 4.624A  pdb=" N   ILE C 629 " --> pdb=" O   THR C 592 " (cutoff:3.500A)
      removed outlier: 6.243A  pdb=" N   THR C 592 " --> pdb=" O   ILE C 629 " (cutoff:3.500A)
      removed outlier: 8.024A  pdb=" N   ILE C 701 " --> pdb=" O   PHE C 591 " (cutoff:3.500A)
      removed outlier: 6.557A  pdb=" N   VAL C 593 " --> pdb=" O   ILE C 701 " (cutoff:3.500A)
      removed outlier: 7.887A  pdb=" N   ARG C 703 " --> pdb=" O   VAL C 593 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   VAL C 595 " --> pdb=" O   ARG C 703 " (cutoff:3.500A)
      removed outlier: 7.058A  pdb=" N   THR C 705 " --> pdb=" O   VAL C 595 " (cutoff:3.500A)
      removed outlier: 7.486A  pdb=" N   GLU C 597 " --> pdb=" O   THR C 705 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 30
      removed outlier: 3.603A  pdb=" N   LYS D  58 " --> pdb=" O   HIS D  47 " (cutoff:3.500A)
      removed outlier: 3.513A  pdb=" N   LYS D  51 " --> pdb=" O   HIS D  54 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   HIS D  54 " --> pdb=" O   LYS D  51 " (cutoff:3.500A)
      removed outlier: 7.804A  pdb=" N   LEU D  55 " --> pdb=" O   MET D   5 " (cutoff:3.500A)
      removed outlier: 6.477A  pdb=" N   THR D   7 " --> pdb=" O   LEU D  55 " (cutoff:3.500A)
      removed outlier: 8.419A  pdb=" N   LEU D  57 " --> pdb=" O   THR D   7 " (cutoff:3.500A)
      removed outlier: 4.414A  pdb=" N   PHE D 339 " --> pdb=" O   VAL D   6 " (cutoff:3.500A)
      removed outlier: 6.831A  pdb=" N   VAL D   8 " --> pdb=" O   PHE D 337 " (cutoff:3.500A)
      removed outlier: 9.494A  pdb=" N   PHE D 337 " --> pdb=" O   VAL D   8 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'D' and resid 77 through 80
    Processing sheet with id=AB9, first strand: chain 'D' and resid 112 through 116
      removed outlier: 7.058A  pdb=" N   THR D 121 " --> pdb=" O   ALA D 113 " (cutoff:3.500A)
      removed outlier: 4.533A  pdb=" N   LYS D 115 " --> pdb=" O   LYS D 119 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   LYS D 119 " --> pdb=" O   LYS D 115 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'D' and resid 130 through 131
      removed outlier: 6.697A  pdb=" N   VAL D 130 " --> pdb=" O   ALA D 192 " (cutoff:3.500A)
      removed outlier: 8.238A  pdb=" N   SER D 194 " --> pdb=" O   VAL D 130 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   THR D 193 " --> pdb=" O   LEU D 184 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'D' and resid 160 through 161
    Processing sheet with id=AC3, first strand: chain 'D' and resid 208 through 210
      removed outlier: 3.689A  pdb=" N   ASN D 248 " --> pdb=" O   ARG D 237 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'D' and resid 208 through 210
      removed outlier: 4.020A  pdb=" N   LEU D 233 " --> pdb=" O   LEU D 252 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'D' and resid 263 through 265

    582 hydrogen bonds defined for protein.
    1608 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      107 hydrogen bonds
      214 hydrogen bond angles
      0 basepair planarities
      44 basepair parallelities
      74 stacking parallelities
  Total time for adding SS restraints: 2.90

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.22 -     1.33: 4481
        1.33 -     1.45: 3434
        1.45 -     1.57: 8444
        1.57 -     1.69: 202
        1.69 -     1.81: 160
  Bond restraints: 16721
  Sorted by residual:
  bond pdb=" C1'  DT I  34 "
       pdb=" N1   DT I  34 "
    ideal  model  delta    sigma   weight residual
    1.468  1.528 -0.060 1.40e-02 5.10e+03 1.84e+01
  bond pdb=" C1'  DC I  30 "
       pdb=" N1   DC I  30 "
    ideal  model  delta    sigma   weight residual
    1.468  1.525 -0.057 1.40e-02 5.10e+03 1.65e+01
  bond pdb=" C3'  DT I  33 "
       pdb=" C2'  DT I  33 "
    ideal  model  delta    sigma   weight residual
    1.516  1.546 -0.030 8.00e-03 1.56e+04 1.44e+01
  bond pdb=" CA  SER B   2 "
       pdb=" CB  SER B   2 "
    ideal  model  delta    sigma   weight residual
    1.533  1.462  0.072 1.89e-02 2.80e+03 1.44e+01
  bond pdb=" C3'  DG M  14 "
       pdb=" C2'  DG M  14 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.07e+01
  ... (remaining 16716 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.64: 22061
        1.64 -     3.28: 861
        3.28 -     4.92: 89
        4.92 -     6.56: 23
        6.56 -     8.20: 2
  Bond angle restraints: 23036
  Sorted by residual:
  angle pdb=" O4'  DG J  29 "
        pdb=" C4'  DG J  29 "
        pdb=" C3'  DG J  29 "
      ideal   model   delta    sigma   weight residual
     106.00  103.16    2.84 6.00e-01 2.78e+00 2.24e+01
  angle pdb=" O4'  DA M   2 "
        pdb=" C4'  DA M   2 "
        pdb=" C3'  DA M   2 "
      ideal   model   delta    sigma   weight residual
     106.00  103.17    2.83 6.00e-01 2.78e+00 2.22e+01
  angle pdb=" N3   DT I  34 "
        pdb=" C4   DT I  34 "
        pdb=" O4   DT I  34 "
      ideal   model   delta    sigma   weight residual
     119.90  122.63   -2.73 6.00e-01 2.78e+00 2.07e+01
  angle pdb=" N3   DT x  42 "
        pdb=" C4   DT x  42 "
        pdb=" O4   DT x  42 "
      ideal   model   delta    sigma   weight residual
     119.90  122.54   -2.64 6.00e-01 2.78e+00 1.93e+01
  angle pdb=" N3   DT L   9 "
        pdb=" C4   DT L   9 "
        pdb=" O4   DT L   9 "
      ideal   model   delta    sigma   weight residual
     119.90  122.52   -2.62 6.00e-01 2.78e+00 1.91e+01
  ... (remaining 23031 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.63: 9286
       35.63 -    71.26: 487
       71.26 -   106.89: 14
      106.89 -   142.52: 4
      142.52 -   178.15: 3
  Dihedral angle restraints: 9794
    sinusoidal: 4682
      harmonic: 5112
  Sorted by residual:
  dihedral pdb=" CA  SER C 648 "
           pdb=" C   SER C 648 "
           pdb=" N   GLU C 649 "
           pdb=" CA  GLU C 649 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.63   22.37     0      5.00e+00 4.00e-02 2.00e+01
  dihedral pdb=" CA  ALA A 941 "
           pdb=" C   ALA A 941 "
           pdb=" N   HIS A 942 "
           pdb=" CA  HIS A 942 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -157.86  -22.14     0      5.00e+00 4.00e-02 1.96e+01
  dihedral pdb=" CA  ARG D 137 "
           pdb=" C   ARG D 137 "
           pdb=" N   TYR D 138 "
           pdb=" CA  TYR D 138 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -158.64  -21.36     0      5.00e+00 4.00e-02 1.82e+01
  ... (remaining 9791 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.122: 2492
       0.122 -    0.244: 22
       0.244 -    0.367: 1
       0.367 -    0.489: 1
       0.489 -    0.611: 1
  Chirality restraints: 2517
  Sorted by residual:
  chirality pdb=" P    DC L   1 "
            pdb=" OP1  DC L   1 "
            pdb=" OP2  DC L   1 "
            pdb=" O5'  DC L   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34    2.95   -0.61 2.00e-01 2.50e+01 9.33e+00
  chirality pdb=" P    DA L   2 "
            pdb=" OP1  DA L   2 "
            pdb=" OP2  DA L   2 "
            pdb=" O5'  DA L   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.34   -2.76   -0.42 2.00e-01 2.50e+01 4.47e+00
  chirality pdb=" CA  GLN B   4 "
            pdb=" N   GLN B   4 "
            pdb=" C   GLN B   4 "
            pdb=" CB  GLN B   4 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.06e+00
  ... (remaining 2514 not shown)

  Planarity restraints: 2602
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  98 "    0.029 5.00e-02 4.00e+02   4.35e-02 3.02e+00
        pdb=" N   PRO D  99 "   -0.075 5.00e-02 4.00e+02
        pdb=" CA  PRO D  99 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO D  99 "    0.024 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP C 774 "   -0.008 2.00e-02 2.50e+03   1.71e-02 2.93e+00
        pdb=" C   ASP C 774 "    0.030 2.00e-02 2.50e+03
        pdb=" O   ASP C 774 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   ARG C 775 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  98 "   -0.028 5.00e-02 4.00e+02   4.16e-02 2.77e+00
        pdb=" N   PRO B  99 "    0.072 5.00e-02 4.00e+02
        pdb=" CA  PRO B  99 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO B  99 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 2599 not shown)

  Histogram of nonbonded interaction distances:
        1.83 -     2.44: 6
        2.44 -     3.06: 9989
        3.06 -     3.67: 24283
        3.67 -     4.29: 35256
        4.29 -     4.90: 58310
  Nonbonded interactions: 127844
  Sorted by model distance:
  nonbonded pdb=" O3'  DG x  45 "
            pdb="MG    MG C1102 "
     model   vdw
     1.826 2.170
  nonbonded pdb=" OD2 ASP C 600 "
            pdb="MG    MG C1102 "
     model   vdw
     2.068 2.170
  nonbonded pdb=" O   TYR D 138 "
            pdb=" O   GLY D 158 "
     model   vdw
     2.390 3.040
  nonbonded pdb=" NZ  LYS C 489 "
            pdb=" OP1  DC y  24 "
     model   vdw
     2.391 3.120
  nonbonded pdb=" O4'  DC I  30 "
            pdb=" O2   DC I  30 "
     model   vdw
     2.415 3.040
  ... (remaining 127839 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and resid 461 through 1003)
  selection = (chain 'C' and resid 461 through 1003)
}
ncs_group {
  reference = (chain 'B' and (resid 1 through 240 or resid 244 through 344))
  selection = (chain 'D' and resid 1 through 344)
}

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:                         0.010
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.580
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.050
  Process input model:                     17.150
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.610
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
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   0.295  16729  Z= 0.326
  Angle     :  0.698   8.200  23040  Z= 0.484
  Chirality :  0.047   0.611   2517
  Planarity :  0.004   0.045   2602
  Dihedral  : 18.492 178.153   6502
  Min Nonbonded Distance : 1.826

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.02 %
    Favored  : 91.92 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  0.58 %
    Favored  : 99.23 %
  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 (0.21), residues: 1745
  helix:  0.80 (0.23), residues: 538
  sheet: -0.97 (0.32), residues: 323
  loop : -1.70 (0.21), residues: 884

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG D 343 
 TYR   0.025   0.001   TYR A 757 
 PHE   0.027   0.001   PHE A 936 
 TRP   0.016   0.001   TRP D 317 
 HIS   0.005   0.001   HIS D  10 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.31 (16721)
  covalent geometry    : angle       0.69726 /  0.48 (23036)
  hydrogen bonds       : bond        0.15903 / 17.63 (  656)
  hydrogen bonds       : angle       7.20710 /  9.23 ( 1822)
  metal coordination   : bond        0.14974 / 17.82 (    8)
  metal coordination   : angle       2.37609 /  4.23 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 134
  time to evaluate  : 0.504 
Fit side-chains
   revert: symmetry clash
REVERT: A  757 TYR cc_start: 0.7831 (t80) cc_final: 0.7450 (t80)
REVERT: A  761 ARG cc_start: 0.7468 (ttp80) cc_final: 0.6968 (ttm-80)
REVERT: C  568 MET cc_start: 0.8288 (mmm) cc_final: 0.8076 (mmm)
REVERT: C  726 ILE cc_start: 0.7744 (pt) cc_final: 0.7428 (pt)
REVERT: C  746 ILE cc_start: 0.7852 (mm) cc_final: 0.7577 (mm)
REVERT: D  110 MET cc_start: 0.7680 (mmt) cc_final: 0.7252 (mmt)
  outliers start: 3
  outliers final: 0
  residues processed: 136
  average time/residue: 0.1228
  time to fit residues: 26.1027
Evaluate side-chains
  99 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 99
  time to evaluate  : 0.583 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 98 optimal weight:    0.9990
   chunk 107 optimal weight:    1.9990
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    0.9980
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    1.5786

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 473 ASN
A 495 GLN
A 609 HIS
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  10 HIS
D  33 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.107356 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3285 r_free = 0.3285 target = 0.087938 restraints weight = 34445.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.089979 restraints weight = 22257.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.091391 restraints weight = 16751.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.092333 restraints weight = 13838.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.092878 restraints weight = 12194.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3368
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8103
moved from start:          0.0854

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  16729  Z= 0.190
  Angle     :  0.653   7.941  23040  Z= 0.359
  Chirality :  0.046   0.364   2517
  Planarity :  0.005   0.048   2602
  Dihedral  : 21.986 174.702   3050
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.25 %
    Favored  : 91.69 %
  Rotamer:
    Outliers :  0.96 %
    Allowed  :  6.68 %
    Favored  : 92.35 %
  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: -1.05 (0.21), residues: 1745
  helix:  0.87 (0.23), residues: 543
  sheet: -0.78 (0.31), residues: 336
  loop : -1.72 (0.21), residues: 866

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 343 
 TYR   0.021   0.002   TYR A 559 
 PHE   0.020   0.002   PHE D  48 
 TRP   0.010   0.001   TRP C 893 
 HIS   0.013   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00417 /  0.19 (16721)
  covalent geometry    : angle       0.65039 /  0.36 (23036)
  hydrogen bonds       : bond        0.04999 /  5.60 (  656)
  hydrogen bonds       : angle       5.62376 /  7.27 ( 1822)
  metal coordination   : bond        0.01395 /  1.51 (    8)
  metal coordination   : angle       4.83967 /  8.13 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 106
  time to evaluate  : 0.830 
Fit side-chains
   revert: symmetry clash
REVERT: A  604 ASP cc_start: 0.7888 (t0) cc_final: 0.7660 (t0)
REVERT: A  757 TYR cc_start: 0.7883 (t80) cc_final: 0.7404 (t80)
REVERT: A  761 ARG cc_start: 0.7508 (ttp80) cc_final: 0.7126 (ttm170)
REVERT: C  568 MET cc_start: 0.8147 (mmm) cc_final: 0.7914 (mmm)
REVERT: C  726 ILE cc_start: 0.7993 (pt) cc_final: 0.7711 (pt)
REVERT: C  746 ILE cc_start: 0.7885 (mm) cc_final: 0.7549 (mm)
REVERT: D    5 MET cc_start: 0.8041 (mmm) cc_final: 0.7537 (tpt)
  outliers start: 15
  outliers final: 11
  residues processed: 115
  average time/residue: 0.1027
  time to fit residues: 19.6820
Evaluate side-chains
  111 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 100
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain B residue    5 MET
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  578 MET
Chi-restraints excluded: chain C residue  788 VAL
Chi-restraints excluded: chain D residue    8 VAL
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain D residue  249 CYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 22 optimal weight:    3.9990
   chunk 172 optimal weight:    3.9990
   chunk 56 optimal weight:    0.7980
   chunk 164 optimal weight:    1.9990
   chunk 127 optimal weight:    2.9990
   chunk 1 optimal weight:   20.0000
   chunk 107 optimal weight:    1.9990
   chunk 155 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 58 optimal weight:    3.9990
   chunk 161 optimal weight:    3.9990
   overall best weight:    2.1588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 473 ASN
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 100 ASN
D  10 HIS
** D 248 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3597 r_free = 0.3597 target = 0.105830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.085044 restraints weight = 35954.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.087533 restraints weight = 20689.056|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.089217 restraints weight = 14580.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.090312 restraints weight = 11637.356|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.091036 restraints weight = 10065.603|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8145
moved from start:          0.1312

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.057  16729  Z= 0.224
  Angle     :  0.673   8.878  23040  Z= 0.367
  Chirality :  0.047   0.369   2517
  Planarity :  0.005   0.049   2602
  Dihedral  : 22.126 174.890   3050
  Min Nonbonded Distance : 1.966

Molprobity Statistics.
  All-atom Clashscore : 9.11
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.88 %
    Favored  : 91.06 %
  Rotamer:
    Outliers :  1.67 %
    Allowed  :  8.93 %
    Favored  : 89.40 %
  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 (0.21), residues: 1745
  helix:  0.82 (0.23), residues: 544
  sheet: -0.89 (0.30), residues: 342
  loop : -1.75 (0.21), residues: 859

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 628 
 TYR   0.030   0.002   TYR A 559 
 PHE   0.023   0.002   PHE A 936 
 TRP   0.010   0.002   TRP D 317 
 HIS   0.012   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00506 /  0.22 (16721)
  covalent geometry    : angle       0.66979 /  0.37 (23036)
  hydrogen bonds       : bond        0.05211 /  5.84 (  656)
  hydrogen bonds       : angle       5.35615 /  7.02 ( 1822)
  metal coordination   : bond        0.01620 /  1.83 (    8)
  metal coordination   : angle       4.96473 /  7.08 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.583 
Fit side-chains
REVERT: A  602 MET cc_start: 0.6523 (mtp) cc_final: 0.6103 (mtp)
REVERT: A  757 TYR cc_start: 0.8104 (t80) cc_final: 0.7899 (t80)
REVERT: A  761 ARG cc_start: 0.7703 (ttp80) cc_final: 0.7258 (tmm-80)
REVERT: A  882 LEU cc_start: 0.8537 (tp) cc_final: 0.8261 (tp)
REVERT: B  263 LEU cc_start: 0.8586 (tp) cc_final: 0.8364 (tp)
REVERT: D    5 MET cc_start: 0.7861 (mmm) cc_final: 0.7496 (tpt)
REVERT: D  138 TYR cc_start: 0.7138 (OUTLIER) cc_final: 0.6290 (t80)
  outliers start: 26
  outliers final: 15
  residues processed: 119
  average time/residue: 0.1049
  time to fit residues: 20.2108
Evaluate side-chains
  111 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 95
  time to evaluate  : 0.587 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  617 GLU
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  593 VAL
Chi-restraints excluded: chain C residue  640 VAL
Chi-restraints excluded: chain C residue  688 THR
Chi-restraints excluded: chain C residue  788 VAL
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain D residue  249 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 3 optimal weight:   20.0000
   chunk 151 optimal weight:    0.7980
   chunk 156 optimal weight:    0.8980
   chunk 91 optimal weight:    0.0470
   chunk 36 optimal weight:    4.9990
   chunk 88 optimal weight:    0.0050
   chunk 113 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 166 optimal weight:    5.9990
   chunk 158 optimal weight:    3.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.5492

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 207 HIS
D  10 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.108349 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.087591 restraints weight = 35540.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.090177 restraints weight = 20298.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.091901 restraints weight = 14219.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.093055 restraints weight = 11334.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.093804 restraints weight = 9753.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8083
moved from start:          0.1307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16729  Z= 0.127
  Angle     :  0.599   7.454  23040  Z= 0.328
  Chirality :  0.044   0.374   2517
  Planarity :  0.004   0.044   2602
  Dihedral  : 22.051 175.127   3050
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  7.91 %
    Favored  : 92.03 %
  Rotamer:
    Outliers :  1.22 %
    Allowed  : 10.80 %
    Favored  : 87.98 %
  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: -0.88 (0.21), residues: 1745
  helix:  1.06 (0.23), residues: 543
  sheet: -0.71 (0.30), residues: 340
  loop : -1.63 (0.22), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 828 
 TYR   0.023   0.001   TYR A 559 
 PHE   0.015   0.001   PHE A 936 
 TRP   0.011   0.001   TRP C 893 
 HIS   0.012   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.13 (16721)
  covalent geometry    : angle       0.59710 /  0.33 (23036)
  hydrogen bonds       : bond        0.04361 /  4.93 (  656)
  hydrogen bonds       : angle       5.12260 /  6.72 ( 1822)
  metal coordination   : bond        0.00624 /  0.76 (    8)
  metal coordination   : angle       3.55502 /  5.50 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 0.405 
Fit side-chains
REVERT: A  602 MET cc_start: 0.6304 (mtp) cc_final: 0.5939 (mtp)
REVERT: A  761 ARG cc_start: 0.7657 (ttp80) cc_final: 0.7204 (tmm-80)
REVERT: A  974 MET cc_start: 0.8032 (mtp) cc_final: 0.7807 (mtm)
REVERT: C  568 MET cc_start: 0.7941 (mmm) cc_final: 0.7739 (mmm)
REVERT: D   52 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7244 (pp30)
REVERT: D  138 TYR cc_start: 0.6920 (OUTLIER) cc_final: 0.6461 (t80)
  outliers start: 19
  outliers final: 11
  residues processed: 119
  average time/residue: 0.1070
  time to fit residues: 20.6038
Evaluate side-chains
  108 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 95
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  578 MET
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain D residue   52 GLN
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain D residue  249 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 63 optimal weight:    3.9990
   chunk 106 optimal weight:    9.9990
   chunk 31 optimal weight:    0.9980
   chunk 136 optimal weight:    0.8980
   chunk 114 optimal weight:    3.9990
   chunk 102 optimal weight:   10.0000
   chunk 93 optimal weight:    2.9990
   chunk 36 optimal weight:    0.6980
   chunk 0 optimal weight:   20.0000
   chunk 163 optimal weight:    8.9990
   chunk 120 optimal weight:    2.9990
   overall best weight:    1.7184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 505 ASN
D  10 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.106461 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.085645 restraints weight = 35631.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.088143 restraints weight = 20599.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.089836 restraints weight = 14559.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.090930 restraints weight = 11637.741|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.091642 restraints weight = 10080.213|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1506

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  16729  Z= 0.190
  Angle     :  0.630   8.624  23040  Z= 0.342
  Chirality :  0.045   0.367   2517
  Planarity :  0.004   0.046   2602
  Dihedral  : 22.137 175.741   3050
  Min Nonbonded Distance : 1.990

Molprobity Statistics.
  All-atom Clashscore : 8.56
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.94 %
    Favored  : 91.00 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 11.12 %
    Favored  : 87.08 %
  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: -0.96 (0.21), residues: 1745
  helix:  0.99 (0.23), residues: 544
  sheet: -0.80 (0.30), residues: 341
  loop : -1.66 (0.21), residues: 860

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 471 
 TYR   0.030   0.002   TYR A 559 
 PHE   0.020   0.001   PHE A 916 
 TRP   0.010   0.001   TRP C 893 
 HIS   0.008   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00425 /  0.19 (16721)
  covalent geometry    : angle       0.62751 /  0.34 (23036)
  hydrogen bonds       : bond        0.04699 /  5.27 (  656)
  hydrogen bonds       : angle       5.04405 /  6.62 ( 1822)
  metal coordination   : bond        0.01270 /  1.44 (    8)
  metal coordination   : angle       4.32966 /  6.16 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 96
  time to evaluate  : 0.585 
Fit side-chains
REVERT: A  602 MET cc_start: 0.6584 (mtp) cc_final: 0.5977 (mtp)
REVERT: A  604 ASP cc_start: 0.7938 (t0) cc_final: 0.7558 (t0)
REVERT: A  761 ARG cc_start: 0.7773 (ttp80) cc_final: 0.7264 (tmm-80)
REVERT: A  974 MET cc_start: 0.8086 (mtp) cc_final: 0.7877 (mtt)
REVERT: C  568 MET cc_start: 0.8077 (mmm) cc_final: 0.7726 (mmm)
REVERT: D   52 GLN cc_start: 0.7465 (OUTLIER) cc_final: 0.7067 (pp30)
REVERT: D   74 TYR cc_start: 0.8248 (m-10) cc_final: 0.8047 (m-10)
REVERT: D  110 MET cc_start: 0.8336 (mmt) cc_final: 0.8131 (mmt)
REVERT: D  138 TYR cc_start: 0.7080 (OUTLIER) cc_final: 0.6443 (t80)
  outliers start: 28
  outliers final: 21
  residues processed: 117
  average time/residue: 0.1139
  time to fit residues: 21.3779
Evaluate side-chains
  116 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 93
  time to evaluate  : 0.439 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  617 GLU
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  578 MET
Chi-restraints excluded: chain C residue  593 VAL
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  715 VAL
Chi-restraints excluded: chain C residue  883 MET
Chi-restraints excluded: chain D residue   52 GLN
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain D residue  249 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 180 optimal weight:   10.0000
   chunk 30 optimal weight:    4.9990
   chunk 3 optimal weight:   20.0000
   chunk 146 optimal weight:    0.1980
   chunk 9 optimal weight:    0.5980
   chunk 135 optimal weight:    0.6980
   chunk 169 optimal weight:    2.9990
   chunk 77 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 18 optimal weight:    5.9990
   chunk 31 optimal weight:    0.7980
   overall best weight:    1.0582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  10 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.107504 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.086708 restraints weight = 35553.835|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.089264 restraints weight = 20383.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.090965 restraints weight = 14332.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.092089 restraints weight = 11441.199|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.092776 restraints weight = 9878.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3379
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.1564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16729  Z= 0.142
  Angle     :  0.598   8.304  23040  Z= 0.325
  Chirality :  0.044   0.371   2517
  Planarity :  0.004   0.044   2602
  Dihedral  : 22.095 175.828   3050
  Min Nonbonded Distance : 2.006

Molprobity Statistics.
  All-atom Clashscore : 8.34
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.08 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 11.95 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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: -0.86 (0.21), residues: 1745
  helix:  1.10 (0.23), residues: 544
  sheet: -0.75 (0.30), residues: 340
  loop : -1.62 (0.22), residues: 861

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 529 
 TYR   0.027   0.001   TYR A 559 
 PHE   0.013   0.001   PHE A 916 
 TRP   0.010   0.001   TRP C 893 
 HIS   0.011   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00301 /  0.14 (16721)
  covalent geometry    : angle       0.59592 /  0.33 (23036)
  hydrogen bonds       : bond        0.04311 /  4.85 (  656)
  hydrogen bonds       : angle       4.91363 /  6.46 ( 1822)
  metal coordination   : bond        0.00829 /  0.96 (    8)
  metal coordination   : angle       3.48004 /  5.03 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 93
  time to evaluate  : 0.594 
Fit side-chains
REVERT: A  602 MET cc_start: 0.6497 (mtp) cc_final: 0.6258 (mtp)
REVERT: A  604 ASP cc_start: 0.7839 (t0) cc_final: 0.7444 (t0)
REVERT: A  757 TYR cc_start: 0.8284 (t80) cc_final: 0.7997 (t80)
REVERT: A  936 PHE cc_start: 0.7746 (OUTLIER) cc_final: 0.7259 (m-10)
REVERT: C  568 MET cc_start: 0.8000 (mmm) cc_final: 0.7638 (mmm)
REVERT: C  858 MET cc_start: 0.8592 (mmt) cc_final: 0.8194 (mmm)
REVERT: D   52 GLN cc_start: 0.7431 (OUTLIER) cc_final: 0.7023 (pp30)
REVERT: D   74 TYR cc_start: 0.8215 (m-10) cc_final: 0.7970 (m-10)
REVERT: D  138 TYR cc_start: 0.6883 (OUTLIER) cc_final: 0.6280 (t80)
  outliers start: 31
  outliers final: 21
  residues processed: 115
  average time/residue: 0.0991
  time to fit residues: 18.9256
Evaluate side-chains
  116 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 92
  time to evaluate  : 0.593 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  617 GLU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  897 CYS
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  578 MET
Chi-restraints excluded: chain C residue  593 VAL
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  688 THR
Chi-restraints excluded: chain D residue   52 GLN
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain D residue  249 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 176 optimal weight:    5.9990
   chunk 68 optimal weight:    5.9990
   chunk 104 optimal weight:    3.9990
   chunk 79 optimal weight:    6.9990
   chunk 19 optimal weight:    9.9990
   chunk 137 optimal weight:    0.9990
   chunk 181 optimal weight:   20.0000
   chunk 52 optimal weight:    0.7980
   chunk 151 optimal weight:    0.0030
   chunk 91 optimal weight:    0.0770
   chunk 42 optimal weight:    3.9990
   overall best weight:    1.1752

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.107106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3275 r_free = 0.3275 target = 0.086413 restraints weight = 35108.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.088953 restraints weight = 20067.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.090664 restraints weight = 14066.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3369 r_free = 0.3369 target = 0.091802 restraints weight = 11183.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.092540 restraints weight = 9631.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8104
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16729  Z= 0.150
  Angle     :  0.612  14.411  23040  Z= 0.329
  Chirality :  0.044   0.369   2517
  Planarity :  0.004   0.045   2602
  Dihedral  : 22.108 175.979   3050
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 8.63
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.14 %
    Favored  : 91.81 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.08 %
    Favored  : 85.60 %
  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: -0.84 (0.21), residues: 1745
  helix:  1.13 (0.23), residues: 544
  sheet: -0.70 (0.30), residues: 339
  loop : -1.64 (0.21), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 137 
 TYR   0.028   0.001   TYR A 559 
 PHE   0.017   0.001   PHE A 916 
 TRP   0.010   0.001   TRP C 893 
 HIS   0.010   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00326 /  0.15 (16721)
  covalent geometry    : angle       0.60999 /  0.33 (23036)
  hydrogen bonds       : bond        0.04344 /  4.88 (  656)
  hydrogen bonds       : angle       4.86452 /  6.40 ( 1822)
  metal coordination   : bond        0.00924 /  1.07 (    8)
  metal coordination   : angle       3.59082 /  5.08 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 92
  time to evaluate  : 0.677 
Fit side-chains
REVERT: A  602 MET cc_start: 0.6550 (mtp) cc_final: 0.6265 (mtp)
REVERT: A  604 ASP cc_start: 0.7803 (t0) cc_final: 0.7362 (t0)
REVERT: A  936 PHE cc_start: 0.7788 (OUTLIER) cc_final: 0.7032 (m-80)
REVERT: A 1003 MET cc_start: 0.7541 (mmm) cc_final: 0.7323 (mmm)
REVERT: C  568 MET cc_start: 0.8006 (mmm) cc_final: 0.7648 (mmm)
REVERT: C  726 ILE cc_start: 0.8008 (OUTLIER) cc_final: 0.7790 (pt)
REVERT: D   52 GLN cc_start: 0.7387 (OUTLIER) cc_final: 0.6985 (pp30)
REVERT: D   74 TYR cc_start: 0.8229 (m-10) cc_final: 0.8028 (m-10)
REVERT: D  138 TYR cc_start: 0.6869 (OUTLIER) cc_final: 0.6226 (t80)
  outliers start: 36
  outliers final: 25
  residues processed: 121
  average time/residue: 0.1104
  time to fit residues: 22.1784
Evaluate side-chains
  119 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 90
  time to evaluate  : 0.527 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  617 GLU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  936 PHE
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  578 MET
Chi-restraints excluded: chain C residue  593 VAL
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  688 THR
Chi-restraints excluded: chain C residue  715 VAL
Chi-restraints excluded: chain C residue  726 ILE
Chi-restraints excluded: chain D residue   52 GLN
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain D residue  249 CYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 46 optimal weight:    0.6980
   chunk 35 optimal weight:    5.9990
   chunk 82 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   chunk 87 optimal weight:    0.7980
   chunk 162 optimal weight:    6.9990
   chunk 71 optimal weight:    3.9990
   chunk 105 optimal weight:    0.6980
   chunk 60 optimal weight:    1.9990
   chunk 127 optimal weight:    4.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.107743 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.087055 restraints weight = 35326.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.089607 restraints weight = 20265.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.091323 restraints weight = 14233.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.092440 restraints weight = 11368.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.093188 restraints weight = 9820.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.3386
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.1681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  16729  Z= 0.139
  Angle     :  0.605  14.461  23040  Z= 0.325
  Chirality :  0.044   0.370   2517
  Planarity :  0.004   0.045   2602
  Dihedral  : 22.090 173.577   3050
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 8.31
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  8.08 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 12.28 %
    Favored  : 85.41 %
  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: -0.81 (0.21), residues: 1745
  helix:  1.16 (0.23), residues: 544
  sheet: -0.68 (0.30), residues: 339
  loop : -1.64 (0.22), residues: 862

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 137 
 TYR   0.029   0.001   TYR A 757 
 PHE   0.015   0.001   PHE A 916 
 TRP   0.010   0.001   TRP C 893 
 HIS   0.012   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00296 /  0.14 (16721)
  covalent geometry    : angle       0.60342 /  0.33 (23036)
  hydrogen bonds       : bond        0.04233 /  4.76 (  656)
  hydrogen bonds       : angle       4.81185 /  6.34 ( 1822)
  metal coordination   : bond        0.00809 /  0.94 (    8)
  metal coordination   : angle       3.33282 /  4.65 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 91
  time to evaluate  : 0.584 
Fit side-chains
REVERT: A  602 MET cc_start: 0.6557 (mtp) cc_final: 0.6314 (mtp)
REVERT: A  604 ASP cc_start: 0.7736 (t0) cc_final: 0.7320 (t0)
REVERT: C  568 MET cc_start: 0.8000 (mmm) cc_final: 0.7744 (mmm)
REVERT: C  726 ILE cc_start: 0.7979 (OUTLIER) cc_final: 0.7764 (pt)
REVERT: D   22 MET cc_start: 0.8419 (mtt) cc_final: 0.8077 (mtp)
REVERT: D   52 GLN cc_start: 0.7425 (OUTLIER) cc_final: 0.6895 (pp30)
REVERT: D   74 TYR cc_start: 0.8264 (m-10) cc_final: 0.8061 (m-10)
REVERT: D  138 TYR cc_start: 0.6841 (OUTLIER) cc_final: 0.6090 (t80)
REVERT: D  209 SER cc_start: 0.7897 (p) cc_final: 0.7560 (p)
  outliers start: 36
  outliers final: 27
  residues processed: 120
  average time/residue: 0.1078
  time to fit residues: 21.5898
Evaluate side-chains
  119 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 89
  time to evaluate  : 0.612 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  617 GLU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  897 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  578 MET
Chi-restraints excluded: chain C residue  593 VAL
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  688 THR
Chi-restraints excluded: chain C residue  715 VAL
Chi-restraints excluded: chain C residue  726 ILE
Chi-restraints excluded: chain C residue  883 MET
Chi-restraints excluded: chain D residue   52 GLN
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain D residue  249 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 0 optimal weight:   20.0000
   chunk 86 optimal weight:    9.9990
   chunk 73 optimal weight:    4.9990
   chunk 79 optimal weight:    6.9990
   chunk 109 optimal weight:    0.0980
   chunk 37 optimal weight:    2.9990
   chunk 63 optimal weight:    0.8980
   chunk 180 optimal weight:    9.9990
   chunk 61 optimal weight:    1.9990
   chunk 30 optimal weight:    0.8980
   chunk 120 optimal weight:    0.9980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.107670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.087044 restraints weight = 35237.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.089611 restraints weight = 19986.208|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.091332 restraints weight = 13961.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.092473 restraints weight = 11092.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3393 r_free = 0.3393 target = 0.093221 restraints weight = 9544.943|
|-----------------------------------------------------------------------------|
r_work (final): 0.3391
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8086
moved from start:          0.1737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  16729  Z= 0.138
  Angle     :  0.611  15.518  23040  Z= 0.327
  Chirality :  0.044   0.369   2517
  Planarity :  0.004   0.046   2602
  Dihedral  : 22.093 173.804   3050
  Min Nonbonded Distance : 2.011

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.72 %
    Favored  : 85.35 %
  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: -0.80 (0.21), residues: 1745
  helix:  1.22 (0.23), residues: 542
  sheet: -0.67 (0.30), residues: 339
  loop : -1.66 (0.22), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 137 
 TYR   0.027   0.001   TYR A 757 
 PHE   0.016   0.001   PHE C 641 
 TRP   0.009   0.001   TRP C 893 
 HIS   0.010   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 (16721)
  covalent geometry    : angle       0.60985 /  0.33 (23036)
  hydrogen bonds       : bond        0.04215 /  4.73 (  656)
  hydrogen bonds       : angle       4.77533 /  6.31 ( 1822)
  metal coordination   : bond        0.00751 /  0.86 (    8)
  metal coordination   : angle       3.17945 /  4.29 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.597 
Fit side-chains
REVERT: A  604 ASP cc_start: 0.7658 (t0) cc_final: 0.7360 (t0)
REVERT: A  883 MET cc_start: 0.8430 (tpp) cc_final: 0.8057 (tpt)
REVERT: A 1003 MET cc_start: 0.7268 (mmm) cc_final: 0.6933 (tpt)
REVERT: C  568 MET cc_start: 0.7999 (mmm) cc_final: 0.7727 (mmm)
REVERT: C  726 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7669 (pt)
REVERT: D   22 MET cc_start: 0.8411 (mtt) cc_final: 0.8102 (mtp)
REVERT: D   52 GLN cc_start: 0.7421 (OUTLIER) cc_final: 0.6882 (pp30)
REVERT: D  138 TYR cc_start: 0.6817 (OUTLIER) cc_final: 0.6075 (t80)
REVERT: D  209 SER cc_start: 0.7851 (p) cc_final: 0.7549 (p)
  outliers start: 30
  outliers final: 27
  residues processed: 115
  average time/residue: 0.1111
  time to fit residues: 21.0436
Evaluate side-chains
  120 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.591 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  617 GLU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  806 LYS
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  897 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  578 MET
Chi-restraints excluded: chain C residue  593 VAL
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  688 THR
Chi-restraints excluded: chain C residue  715 VAL
Chi-restraints excluded: chain C residue  726 ILE
Chi-restraints excluded: chain D residue   52 GLN
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  138 TYR
Chi-restraints excluded: chain D residue  249 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 145 optimal weight:    5.9990
   chunk 10 optimal weight:    0.9990
   chunk 81 optimal weight:    0.9980
   chunk 118 optimal weight:    0.8980
   chunk 35 optimal weight:    5.9990
   chunk 173 optimal weight:    3.9990
   chunk 76 optimal weight:    6.9990
   chunk 120 optimal weight:    0.9990
   chunk 146 optimal weight:    0.0030
   chunk 125 optimal weight:    0.7980
   chunk 72 optimal weight:    0.9990
   overall best weight:    0.7392

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.108674 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.088066 restraints weight = 35237.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.090660 restraints weight = 20049.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.092395 restraints weight = 14027.446|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.093562 restraints weight = 11133.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 46)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.094322 restraints weight = 9561.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8068
moved from start:          0.1790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  16729  Z= 0.128
  Angle     :  0.611  16.115  23040  Z= 0.325
  Chirality :  0.044   0.370   2517
  Planarity :  0.004   0.045   2602
  Dihedral  : 22.062 173.954   3050
  Min Nonbonded Distance : 2.020

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.79 %
    Favored  : 92.21 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.98 %
    Favored  : 85.09 %
  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: -0.77 (0.21), residues: 1745
  helix:  1.23 (0.23), residues: 542
  sheet: -0.64 (0.31), residues: 339
  loop : -1.64 (0.22), residues: 864

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG D 137 
 TYR   0.034   0.001   TYR A 757 
 PHE   0.016   0.001   PHE C 641 
 TRP   0.009   0.001   TRP C 893 
 HIS   0.009   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.13 (16721)
  covalent geometry    : angle       0.60939 /  0.32 (23036)
  hydrogen bonds       : bond        0.04077 /  4.57 (  656)
  hydrogen bonds       : angle       4.72120 /  6.26 ( 1822)
  metal coordination   : bond        0.00596 /  0.69 (    8)
  metal coordination   : angle       2.87000 /  3.58 (    4)

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

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

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3490 Ramachandran restraints generated.
    1745 Oldfield, 0 Emsley, 1745 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 91
  time to evaluate  : 0.495 
Fit side-chains
REVERT: A  604 ASP cc_start: 0.7581 (t0) cc_final: 0.7362 (t0)
REVERT: A  757 TYR cc_start: 0.8283 (t80) cc_final: 0.7816 (t80)
REVERT: A  847 MET cc_start: 0.5554 (ttt) cc_final: 0.5339 (ttm)
REVERT: A 1003 MET cc_start: 0.7158 (mmm) cc_final: 0.6829 (tpt)
REVERT: C  568 MET cc_start: 0.7989 (mmm) cc_final: 0.7781 (mmm)
REVERT: C  726 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7664 (pt)
REVERT: D   22 MET cc_start: 0.8423 (mtt) cc_final: 0.8128 (mtp)
REVERT: D   52 GLN cc_start: 0.7402 (OUTLIER) cc_final: 0.6848 (pp30)
REVERT: D  138 TYR cc_start: 0.6740 (OUTLIER) cc_final: 0.6274 (t80)
REVERT: D  209 SER cc_start: 0.7816 (p) cc_final: 0.7518 (p)
  outliers start: 30
  outliers final: 27
  residues processed: 115
  average time/residue: 0.1002
  time to fit residues: 19.1142
Evaluate side-chains
  120 residues out of total 1556 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 90
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  472 VAL
Chi-restraints excluded: chain A residue  532 VAL
Chi-restraints excluded: chain A residue  559 TYR
Chi-restraints excluded: chain A residue  563 LEU
Chi-restraints excluded: chain A residue  605 VAL
Chi-restraints excluded: chain A residue  617 GLU
Chi-restraints excluded: chain A residue  623 SER
Chi-restraints excluded: chain A residue  626 VAL
Chi-restraints excluded: chain A residue  769 VAL
Chi-restraints excluded: chain A residue  806 LYS
Chi-restraints excluded: chain A residue  841 MET
Chi-restraints excluded: chain A residue  897 CYS
Chi-restraints excluded: chain B residue   28 VAL
Chi-restraints excluded: chain B residue   67 CYS
Chi-restraints excluded: chain B residue  107 ILE
Chi-restraints excluded: chain B residue  144 VAL
Chi-restraints excluded: chain B residue  272 VAL
Chi-restraints excluded: chain B residue  274 VAL
Chi-restraints excluded: chain B residue  329 LEU
Chi-restraints excluded: chain B residue  341 THR
Chi-restraints excluded: chain C residue  485 TYR
Chi-restraints excluded: chain C residue  578 MET
Chi-restraints excluded: chain C residue  593 VAL
Chi-restraints excluded: chain C residue  626 VAL
Chi-restraints excluded: chain C residue  688 THR
Chi-restraints excluded: chain C residue  726 ILE
Chi-restraints excluded: chain C residue  883 MET
Chi-restraints excluded: chain D residue   52 GLN
Chi-restraints excluded: chain D residue  128 ASP
Chi-restraints excluded: chain D residue  138 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 158 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0020
   chunk 131 optimal weight:    2.9990
   chunk 135 optimal weight:    1.9990
   chunk 121 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 173 optimal weight:    4.9990
   chunk 63 optimal weight:    0.5980
   chunk 65 optimal weight:    0.8980
   chunk 81 optimal weight:    5.9990
   overall best weight:    0.6588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B  23 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 100 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.109180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.088788 restraints weight = 35080.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.091307 restraints weight = 20296.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.092994 restraints weight = 14339.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.094128 restraints weight = 11475.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.094864 restraints weight = 9900.710|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8059
moved from start:          0.1825

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  16729  Z= 0.123
  Angle     :  0.596  15.987  23040  Z= 0.317
  Chirality :  0.043   0.370   2517
  Planarity :  0.004   0.045   2602
  Dihedral  : 22.036 174.079   3050
  Min Nonbonded Distance : 2.015

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.68 %
    Favored  : 92.32 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 12.98 %
    Favored  : 85.03 %
  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: -0.71 (0.21), residues: 1745
  helix:  1.29 (0.23), residues: 542
  sheet: -0.55 (0.31), residues: 330
  loop : -1.63 (0.22), residues: 873

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 558 
 TYR   0.029   0.001   TYR A 757 
 PHE   0.019   0.001   PHE C 641 
 TRP   0.011   0.001   TRP C 893 
 HIS   0.008   0.001   HIS D 140 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 (16721)
  covalent geometry    : angle       0.59459 /  0.32 (23036)
  hydrogen bonds       : bond        0.03975 /  4.45 (  656)
  hydrogen bonds       : angle       4.65526 /  6.19 ( 1822)
  metal coordination   : bond        0.00589 /  0.69 (    8)
  metal coordination   : angle       2.88808 /  3.27 (    4)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2194.81 seconds
wall clock time: 39 minutes 1.47 seconds (2341.47 seconds total)