Starting phenix.real_space_refine
on Wed Mar  4 19:18:00 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7at8_11910/03_2026/7at8_11910.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7at8_11910/03_2026/7at8_11910.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7at8_11910/03_2026/7at8_11910.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7at8_11910/03_2026/7at8_11910.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7at8_11910/03_2026/7at8_11910.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7at8_11910/03_2026/7at8_11910.map"
  }
  resolution = 4.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.002
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     Zn      7      6.06       5
     P     310      5.49       5
     S      55      5.16       5
     C    9053      2.51       5
     N    2945      2.21       5
     O    3581      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 21 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15951
  Number of models: 1
  Model: ""
    Number of chains: 14
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 619
          Classifications: {'peptide': 72}
          Link IDs: {'PTRANS': 2, 'TRANS': 69}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 1851
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 239, 1851
          Classifications: {'peptide': 239}
          Incomplete info: {'truncation_to_alanine': 15}
          Link IDs: {'PTRANS': 10, 'TRANS': 228}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 32
          Unresolved non-hydrogen angles: 47
          Unresolved non-hydrogen dihedrals: 17
          Planarities with less than four sites: {'UNK:plan-1': 13, 'ASN:plan1': 1, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 19
    Chain: "C"
      Number of atoms: 1024
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 124, 1024
          Classifications: {'peptide': 124}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 3, 'TRANS': 120}
          Unresolved non-hydrogen bonds: 8
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 8
    Chain: "D"
      Number of atoms: 911
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 113, 911
          Classifications: {'peptide': 113}
          Link IDs: {'PTRANS': 5, 'TRANS': 107}
    Chain: "E"
      Number of atoms: 638
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 80, 638
          Classifications: {'peptide': 80}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 78}
    Chain: "F"
      Number of atoms: 795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 795
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 5, 'TRANS': 97}
    Chain: "G"
      Number of atoms: 745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 95, 745
          Classifications: {'peptide': 95}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 2, 'TRANS': 92}
    Chain: "H"
      Number of atoms: 791
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 96, 791
          Classifications: {'peptide': 96}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 92}
    Chain: "I"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 78, 619
          Classifications: {'peptide': 78}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 76}
    Chain: "J"
      Number of atoms: 809
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 809
          Classifications: {'peptide': 105}
          Link IDs: {'PTRANS': 5, 'TRANS': 99}
    Chain: "K"
      Number of atoms: 726
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 726
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 2, 'TRANS': 90}
    Chain: "T"
      Number of atoms: 3176
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 3176
          Classifications: {'DNA': 156}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 155}
    Chain: "U"
      Number of atoms: 3214
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 156, 3214
          Classifications: {'DNA': 156}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 155}
    Chain: "A"
      Number of atoms: 33
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 33
          Unusual residues: {' ZN': 7}
          Classifications: {'peptide': 1, 'undetermined': 7}
          Link IDs: {None: 7}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    222  SG  CYS A 286      42.792  44.930  98.704  1.00172.70           S
  ATOM    250  SG  CYS A 289      39.019  44.911  98.087  0.99172.87           S
  ATOM    296  SG  CYS A 294      41.047  41.721  97.546  0.87165.55           S
  ATOM    815  SG  CYS A 548      59.081  55.951  95.973  1.00224.51           S
  ATOM    908  SG  CYS A 561      56.647  54.817  93.302  1.00185.75           S
  ATOM    958  SG  CYS A 567      55.456  57.195  95.986  1.00196.50           S
  ATOM    985  SG  CYS A 571      57.977  58.482  93.473  1.00189.83           S
  ATOM    760  SG  CYS A 541      56.817  52.987  96.687  1.00200.99           S
  ATOM    815  SG  CYS A 548      59.081  55.951  95.973  1.00224.51           S
  ATOM    841  SG  CYS A 552      60.285  52.403  95.140  1.00211.70           S
  ATOM    760  SG  CYS A 541      56.817  52.987  96.687  1.00200.99           S
  ATOM    854  SG  CYS A 554      56.701  51.050  93.445  0.93198.28           S
  ATOM    908  SG  CYS A 561      56.647  54.817  93.302  1.00185.75           S
  ATOM    943  SG  CYS A 565      53.618  52.936  94.782  1.00180.30           S
  ATOM   1087  SG  CYS A 584      42.028  59.705  77.412  1.00141.94           S
  ATOM   1197  SG  CYS A 598      42.846  57.761  80.573  1.00148.79           S
  ATOM   1255  SG  CYS A 606      40.534  60.860  80.840  1.00151.54           S
  ATOM   1351  SG  CYS A 619      39.256  57.835  79.458  1.00148.68           S
  ATOM   1041  SG  CYS A 578      44.356  61.108  80.066  1.00152.37           S
  ATOM   1139  SG  CYS A 591      46.636  58.342  81.480  1.00155.72           S
  ATOM   1197  SG  CYS A 598      42.846  57.761  80.573  1.00148.79           S
  ATOM   1234  SG  CYS A 603      44.045  59.728  83.596  1.00143.87           S
  ATOM   1041  SG  CYS A 578      44.356  61.108  80.066  1.00152.37           S
  ATOM   1058  SG  CYS A 580      44.717  62.660  76.821  1.00142.11           S
  ATOM   1087  SG  CYS A 584      42.028  59.705  77.412  1.00141.94           S
  ATOM   1126  SG  CYS A 589      45.819  59.144  77.101  1.00147.49           S

  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   ALA D  31 " occ=0.00
      ... (3 atoms not shown)
      pdb=" CB  ALA D  31 " occ=0.00
    residue:
      pdb=" N   THR D  32 " occ=0.00
      ... (5 atoms not shown)
      pdb=" CG2 THR D  32 " occ=0.00
  Time building chain proxies: 3.25, per 1000 atoms: 0.20
  Number of scatterers: 15951
  At special positions: 0
  Unit cell: (130.95, 171.108, 144.918, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      7     29.99
     S      55     16.00
     P     310     15.00
     O    3581      8.00
     N    2945      7.00
     C    9053      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: 1.44
  Conformation dependent library (CDL) restraints added in 347.8 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" ND1 HIS A 297 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 289 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 286 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 294 "
      pdb="  ZN A1002 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 548 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 567 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 571 "
        pdb="ZN    ZN A1002 " - pdb=" SG  CYS A 561 "
      pdb="  ZN A1003 "
        pdb="ZN    ZN A1003 " - pdb=" NE2 HIS A 543 "
        pdb="ZN    ZN A1003 " - pdb=" SG  CYS A 548 "
        pdb="ZN    ZN A1003 " - pdb=" SG  CYS A 541 "
        pdb="ZN    ZN A1003 " - pdb=" SG  CYS A 552 "
      pdb="  ZN A1004 "
        pdb="ZN    ZN A1004 " - pdb=" SG  CYS A 541 "
        pdb="ZN    ZN A1004 " - pdb=" SG  CYS A 554 "
        pdb="ZN    ZN A1004 " - pdb=" SG  CYS A 561 "
        pdb="ZN    ZN A1004 " - pdb=" SG  CYS A 565 "
      pdb="  ZN A1005 "
        pdb="ZN    ZN A1005 " - pdb=" SG  CYS A 619 "
        pdb="ZN    ZN A1005 " - pdb=" SG  CYS A 606 "
        pdb="ZN    ZN A1005 " - pdb=" SG  CYS A 598 "
        pdb="ZN    ZN A1005 " - pdb=" SG  CYS A 584 "
      pdb="  ZN A1006 "
        pdb="ZN    ZN A1006 " - pdb=" SG  CYS A 603 "
        pdb="ZN    ZN A1006 " - pdb=" SG  CYS A 598 "
        pdb="ZN    ZN A1006 " - pdb=" SG  CYS A 578 "
        pdb="ZN    ZN A1006 " - pdb=" SG  CYS A 591 "
      pdb="  ZN A1007 "
        pdb="ZN    ZN A1007 " - pdb=" SG  CYS A 578 "
        pdb="ZN    ZN A1007 " - pdb=" SG  CYS A 589 "
        pdb="ZN    ZN A1007 " - pdb=" SG  CYS A 580 "
        pdb="ZN    ZN A1007 " - pdb=" SG  CYS A 584 "
      Number of angles added : 36


  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2264

  Finding SS restraints...
    Secondary structure from input PDB file:
      49 helices and 13 sheets defined
      61.0% alpha, 4.7% beta
      150 base pairs and 257 stacking pairs defined.
    Time for finding SS restraints: 2.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 144 through 153
      removed outlier: 3.521A  pdb=" N   TYR A 153 " --> pdb=" O   LEU A 149 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 442 through 453
      removed outlier: 3.736A  pdb=" N   GLY A 450 " --> pdb=" O   ARG A 446 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   THR A 451 " --> pdb=" O   VAL A 447 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 455 through 462
      removed outlier: 3.673A  pdb=" N   ARG A 461 " --> pdb=" O   CYS A 457 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 470 through 479
    Processing helix  chain 'A' and resid 493 through 504
    Processing helix  chain 'A' and resid 552 through 557
    Processing helix  chain 'A' and resid 589 through 594
    Processing helix  chain 'A' and resid 622 through 627
    Processing helix  chain 'A' and resid 666 through 679
      removed outlier: 3.545A  pdb=" N   ASP A 670 " --> pdb=" O   GLN A 666 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   VAL A 675 " --> pdb=" O   ARG A 671 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 700 through 705
    Processing helix  chain 'C' and resid 589 through 602
      removed outlier: 4.055A  pdb=" N   ARG C 593 " --> pdb=" O   PRO C 589 " (cutoff:3.500A)
      removed outlier: 3.640A  pdb=" N   GLU C 594 " --> pdb=" O   GLU C 590 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 608 through 625
      removed outlier: 4.377A  pdb=" N   MET C 614 " --> pdb=" O   GLU C 610 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 630 through 650
      removed outlier: 4.426A  pdb=" N   HIS C 634 " --> pdb=" O   ASN C 630 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   VAL C 640 " --> pdb=" O   CYS C 636 " (cutoff:3.500A)
      removed outlier: 6.275A  pdb=" N   GLN C 645 " --> pdb=" O   GLU C 641 " (cutoff:3.500A)
      removed outlier: 5.341A  pdb=" N   LYS C 646 " --> pdb=" O   ASN C 642 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 652 through 666
    Processing helix  chain 'C' and resid 671 through 684
      removed outlier: 3.920A  pdb=" N   ASP C 675 " --> pdb=" O   ILE C 671 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   MET C 684 " --> pdb=" O   LYS C 680 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 44 through 57
    Processing helix  chain 'D' and resid 63 through 79
      removed outlier: 3.878A  pdb=" N   PHE D  67 " --> pdb=" O   ARG D  63 " (cutoff:3.500A)
      removed outlier: 3.699A  pdb=" N   ASP D  77 " --> pdb=" O   GLU D  73 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   PHE D  78 " --> pdb=" O   ILE D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 85 through 114
    Processing helix  chain 'D' and resid 120 through 131
    Processing helix  chain 'E' and resid 24 through 29
      removed outlier: 3.693A  pdb=" N   ILE E  29 " --> pdb=" O   ILE E  26 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 30 through 42
    Processing helix  chain 'E' and resid 49 through 76
      removed outlier: 4.479A  pdb=" N   GLU E  53 " --> pdb=" O   LEU E  49 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 82 through 93
      removed outlier: 3.950A  pdb=" N   VAL E  86 " --> pdb=" O   THR E  82 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 17 through 22
    Processing helix  chain 'F' and resid 26 through 37
      removed outlier: 3.685A  pdb=" N   VAL F  30 " --> pdb=" O   PRO F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 45 through 73
      removed outlier: 4.538A  pdb=" N   VAL F  49 " --> pdb=" O   ALA F  45 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 79 through 90
      removed outlier: 3.553A  pdb=" N   ASP F  90 " --> pdb=" O   ALA F  86 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 97
    Processing helix  chain 'G' and resid 34 through 46
    Processing helix  chain 'G' and resid 52 through 81
    Processing helix  chain 'G' and resid 87 through 99
      removed outlier: 3.563A  pdb=" N   ILE G  91 " --> pdb=" O   THR G  87 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 100 through 121
      removed outlier: 3.863A  pdb=" N   ALA G 121 " --> pdb=" O   LYS G 117 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 44 through 57
    Processing helix  chain 'H' and resid 63 through 79
      removed outlier: 3.943A  pdb=" N   PHE H  67 " --> pdb=" O   ARG H  63 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASP H  77 " --> pdb=" O   GLU H  73 " (cutoff:3.500A)
      removed outlier: 4.156A  pdb=" N   PHE H  78 " --> pdb=" O   ILE H  74 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 85 through 114
    Processing helix  chain 'H' and resid 120 through 131
    Processing helix  chain 'I' and resid 25 through 29
      removed outlier: 3.704A  pdb=" N   ILE I  29 " --> pdb=" O   ILE I  26 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 30 through 42
    Processing helix  chain 'I' and resid 49 through 76
      removed outlier: 4.390A  pdb=" N   GLU I  53 " --> pdb=" O   LEU I  49 " (cutoff:3.500A)
    Processing helix  chain 'I' and resid 82 through 93
      removed outlier: 3.920A  pdb=" N   VAL I  86 " --> pdb=" O   THR I  82 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 16 through 22
    Processing helix  chain 'J' and resid 26 through 37
      removed outlier: 3.623A  pdb=" N   VAL J  30 " --> pdb=" O   PRO J  26 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 46 through 73
    Processing helix  chain 'J' and resid 79 through 90
      removed outlier: 3.669A  pdb=" N   ASP J  90 " --> pdb=" O   ALA J  86 " (cutoff:3.500A)
    Processing helix  chain 'J' and resid 91 through 97
    Processing helix  chain 'K' and resid 34 through 46
    Processing helix  chain 'K' and resid 52 through 81
    Processing helix  chain 'K' and resid 87 through 99
      removed outlier: 3.591A  pdb=" N   ILE K  91 " --> pdb=" O   THR K  87 " (cutoff:3.500A)
    Processing helix  chain 'K' and resid 100 through 121
      removed outlier: 3.817A  pdb=" N   ALA K 121 " --> pdb=" O   LYS K 117 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 114 through 115
      removed outlier: 5.761A  pdb=" N   SER A 114 " --> pdb=" O   GLY A 699 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 120 through 121
      removed outlier: 6.204A  pdb=" N   PHE A 120 " --> pdb=" O   ILE A 663 " (cutoff:3.500A)
      removed outlier: 8.231A  pdb=" N   SER A 665 " --> pdb=" O   PHE A 120 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 285 through 286
    Processing sheet with id=AA4, first strand: chain 'A' and resid 632 through 636
    Processing sheet with id=AA5, first strand: chain 'A' and resid 655 through 658
      removed outlier: 6.780A  pdb=" N   PHE A 655 " --> pdb=" O   ALA A 730 " (cutoff:3.500A)
      removed outlier: 6.216A  pdb=" N   ALA A 730 " --> pdb=" O   PHE A 655 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 83 through 84
      removed outlier: 6.991A  pdb=" N   ARG D  83 " --> pdb=" O   VAL E  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'E' and resid 97 through 98
    Processing sheet with id=AA8, first strand: chain 'F' and resid 42 through 43
      removed outlier: 7.645A  pdb=" N   ARG F  42 " --> pdb=" O   ILE G  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'F' and resid 77 through 78
      removed outlier: 3.648A  pdb=" N   ILE F  78 " --> pdb=" O   GLY G  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA9
    Processing sheet with id=AB1, first strand: chain 'F' and resid 100 through 102
      removed outlier: 6.782A  pdb=" N   THR F 101 " --> pdb=" O   TYR I  98 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB1
    Processing sheet with id=AB2, first strand: chain 'H' and resid 83 through 84
      removed outlier: 7.563A  pdb=" N   ARG H  83 " --> pdb=" O   VAL I  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB2
    Processing sheet with id=AB3, first strand: chain 'J' and resid 42 through 43
      removed outlier: 7.602A  pdb=" N   ARG J  42 " --> pdb=" O   ILE K  86 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'J' and resid 77 through 78
      removed outlier: 3.616A  pdb=" N   ILE J  78 " --> pdb=" O   GLY K  50 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB4

    517 hydrogen bonds defined for protein.
    1524 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      383 hydrogen bonds
      766 hydrogen bond angles
      0 basepair planarities
      150 basepair parallelities
      257 stacking parallelities
  Total time for adding SS restraints: 3.54

  Time building geometry restraints manager: 1.92 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: 3729
        1.33 -     1.45: 4551
        1.45 -     1.57: 7896
        1.57 -     1.69: 620
        1.69 -     1.81: 80
  Bond restraints: 16876
  Sorted by residual:
  bond pdb=" N   ASN C 607 "
       pdb=" CA  ASN C 607 "
    ideal  model  delta    sigma   weight residual
    1.457  1.499 -0.042 1.29e-02 6.01e+03 1.06e+01
  bond pdb=" N   VAL C 581 "
       pdb=" CA  VAL C 581 "
    ideal  model  delta    sigma   weight residual
    1.459  1.499 -0.040 1.25e-02 6.40e+03 1.01e+01
  bond pdb=" C2  SAH A1008 "
       pdb=" N3  SAH A1008 "
    ideal  model  delta    sigma   weight residual
    1.322  1.383 -0.061 2.00e-02 2.50e+03 9.24e+00
  bond pdb=" N   VAL A 755 "
       pdb=" CA  VAL A 755 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.16e+00
  bond pdb=" N   LYS A 753 "
       pdb=" CA  LYS A 753 "
    ideal  model  delta    sigma   weight residual
    1.457  1.488 -0.031 1.06e-02 8.90e+03 8.81e+00
  ... (remaining 16871 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 23574
        2.01 -     4.01: 513
        4.01 -     6.02: 22
        6.02 -     8.03: 6
        8.03 -    10.04: 4
  Bond angle restraints: 24119
  Sorted by residual:
  angle pdb=" N   ASP C 585 "
        pdb=" CA  ASP C 585 "
        pdb=" C   ASP C 585 "
      ideal   model   delta    sigma   weight residual
     109.56  102.09    7.47 1.84e+00 2.95e-01 1.65e+01
  angle pdb=" O3'  DA U -66 "
        pdb=" P    DT U -65 "
        pdb=" O5'  DT U -65 "
      ideal   model   delta    sigma   weight residual
     104.00   97.94    6.06 1.50e+00 4.44e-01 1.63e+01
  angle pdb=" C   ASN C 607 "
        pdb=" N   GLU C 608 "
        pdb=" CA  GLU C 608 "
      ideal   model   delta    sigma   weight residual
     121.54  129.23   -7.69 1.91e+00 2.74e-01 1.62e+01
  angle pdb=" CA  LEU A 752 "
        pdb=" C   LEU A 752 "
        pdb=" O   LEU A 752 "
      ideal   model   delta    sigma   weight residual
     122.63  118.03    4.60 1.29e+00 6.01e-01 1.27e+01
  angle pdb=" C   GLU C 580 "
        pdb=" N   VAL C 581 "
        pdb=" CA  VAL C 581 "
      ideal   model   delta    sigma   weight residual
     121.97  128.19   -6.22 1.80e+00 3.09e-01 1.19e+01
  ... (remaining 24114 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.23: 6869
       18.23 -    36.46: 1167
       36.46 -    54.69: 1069
       54.69 -    72.91: 240
       72.91 -    91.14: 12
  Dihedral angle restraints: 9357
    sinusoidal: 5864
      harmonic: 3493
  Sorted by residual:
  dihedral pdb=" CA  PHE C 603 "
           pdb=" C   PHE C 603 "
           pdb=" N   SER C 604 "
           pdb=" CA  SER C 604 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.22   20.78     0      5.00e+00 4.00e-02 1.73e+01
  dihedral pdb=" CA  ASN C 562 "
           pdb=" C   ASN C 562 "
           pdb=" N   ARG C 563 "
           pdb=" CA  ARG C 563 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.75   18.25     0      5.00e+00 4.00e-02 1.33e+01
  dihedral pdb=" CA  ILE C 627 "
           pdb=" C   ILE C 627 "
           pdb=" N   ALA C 628 "
           pdb=" CA  ALA C 628 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.11  -15.89     0      5.00e+00 4.00e-02 1.01e+01
  ... (remaining 9354 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 2192
       0.047 -    0.095: 447
       0.095 -    0.142: 58
       0.142 -    0.189: 7
       0.189 -    0.237: 2
  Chirality restraints: 2706
  Sorted by residual:
  chirality pdb=" CA  VAL C 606 "
            pdb=" N   VAL C 606 "
            pdb=" C   VAL C 606 "
            pdb=" CB  VAL C 606 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.68   -0.24 2.00e-01 2.50e+01 1.40e+00
  chirality pdb=" CA  ARG A 745 "
            pdb=" N   ARG A 745 "
            pdb=" C   ARG A 745 "
            pdb=" CB  ARG A 745 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.32    0.19 2.00e-01 2.50e+01 9.28e-01
  chirality pdb=" C3' SAH A1008 "
            pdb=" C2' SAH A1008 "
            pdb=" C4' SAH A1008 "
            pdb=" O3' SAH A1008 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.71   -2.52   -0.19 2.00e-01 2.50e+01 8.89e-01
  ... (remaining 2703 not shown)

  Planarity restraints: 1989
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC U -27 "   -0.032 2.00e-02 2.50e+03   2.96e-02 1.97e+01
        pdb=" N1   DC U -27 "    0.072 2.00e-02 2.50e+03
        pdb=" C2   DC U -27 "   -0.038 2.00e-02 2.50e+03
        pdb=" O2   DC U -27 "    0.010 2.00e-02 2.50e+03
        pdb=" N3   DC U -27 "    0.005 2.00e-02 2.50e+03
        pdb=" C4   DC U -27 "   -0.001 2.00e-02 2.50e+03
        pdb=" N4   DC U -27 "   -0.002 2.00e-02 2.50e+03
        pdb=" C5   DC U -27 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6   DC U -27 "   -0.006 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DC U  41 "    0.028 2.00e-02 2.50e+03   2.82e-02 1.79e+01
        pdb=" N1   DC U  41 "   -0.067 2.00e-02 2.50e+03
        pdb=" C2   DC U  41 "    0.041 2.00e-02 2.50e+03
        pdb=" O2   DC U  41 "   -0.012 2.00e-02 2.50e+03
        pdb=" N3   DC U  41 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4   DC U  41 "    0.001 2.00e-02 2.50e+03
        pdb=" N4   DC U  41 "    0.003 2.00e-02 2.50e+03
        pdb=" C5   DC U  41 "    0.003 2.00e-02 2.50e+03
        pdb=" C6   DC U  41 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'  DT U  14 "    0.032 2.00e-02 2.50e+03   2.67e-02 1.78e+01
        pdb=" N1   DT U  14 "   -0.070 2.00e-02 2.50e+03
        pdb=" C2   DT U  14 "    0.034 2.00e-02 2.50e+03
        pdb=" O2   DT U  14 "   -0.007 2.00e-02 2.50e+03
        pdb=" N3   DT U  14 "   -0.002 2.00e-02 2.50e+03
        pdb=" C4   DT U  14 "    0.001 2.00e-02 2.50e+03
        pdb=" O4   DT U  14 "    0.001 2.00e-02 2.50e+03
        pdb=" C5   DT U  14 "    0.003 2.00e-02 2.50e+03
        pdb=" C7   DT U  14 "    0.007 2.00e-02 2.50e+03
        pdb=" C6   DT U  14 "    0.001 2.00e-02 2.50e+03
  ... (remaining 1986 not shown)

  Histogram of nonbonded interaction distances:
        1.76 -     2.39: 27
        2.39 -     3.02: 8377
        3.02 -     3.65: 26442
        3.65 -     4.27: 38411
        4.27 -     4.90: 57802
  Nonbonded interactions: 131059
  Sorted by model distance:
  nonbonded pdb=" O   LYS A 615 "
            pdb=" NH1 ARG A 626 "
     model   vdw
     1.763 3.120
  nonbonded pdb=" OG1 THR G  29 "
            pdb=" OP1  DT T  30 "
     model   vdw
     2.036 3.040
  nonbonded pdb=" C   LYS A 615 "
            pdb=" NH1 ARG A 626 "
     model   vdw
     2.068 3.350
  nonbonded pdb=" OD1 ASP C 675 "
            pdb=" N   LYS C 676 "
     model   vdw
     2.123 3.120
  nonbonded pdb=" OE2 GLU A 658 "
            pdb=" NE  ARG A 725 "
     model   vdw
     2.209 3.120
  ... (remaining 131054 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 'E' and resid 25 through 102)
  selection = chain 'I'
}
ncs_group {
  reference = chain 'F'
  selection = (chain 'J' and resid 16 through 118)
}
ncs_group {
  reference = (chain 'G' and resid 29 through 121)
  selection = chain 'K'
}

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=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.180
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     18.420
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.020
  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:1.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   22.420
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
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      :  0.004   0.061  16904  Z= 0.217
  Angle     :  0.664  10.036  24155  Z= 0.411
  Chirality :  0.038   0.237   2706
  Planarity :  0.004   0.030   1989
  Dihedral  : 24.584  91.143   7093
  Min Nonbonded Distance : 1.763

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.35 %
    Allowed  :  2.25 %
    Favored  : 97.40 %
  Rotamer:
    Outliers :  0.40 %
    Allowed  :  1.29 %
    Favored  : 98.32 %
  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: -0.95 (0.23), residues: 1155
  helix:  0.52 (0.19), residues: 677
  sheet: -2.90 (1.27), residues: 14
  loop : -2.36 (0.24), residues: 464

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG C 593 
 TYR   0.011   0.001   TYR K  37 
 PHE   0.006   0.001   PHE C 603 
 TRP   0.006   0.001   TRP C 617 
 HIS   0.008   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00403 (16876)
  covalent geometry    : angle       0.64859 (24119)
  hydrogen bonds       : bond        0.10391 (  900)
  hydrogen bonds       : angle       4.21913 ( 2290)
  metal coordination   : bond        0.00551 (   28)
  metal coordination   : angle       3.76391 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  453 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 449
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  696 THR cc_start: 0.6129 (m) cc_final: 0.5893 (p)
REVERT: A  719 MET cc_start: 0.7885 (tpp) cc_final: 0.7678 (tpp)
REVERT: C  632 MET cc_start: 0.8165 (mmp) cc_final: 0.7864 (mmp)
REVERT: C  649 LYS cc_start: 0.8627 (mmtt) cc_final: 0.8414 (mmtm)
REVERT: D   45 THR cc_start: 0.7940 (m) cc_final: 0.7601 (m)
REVERT: D   50 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8683 (pt0)
REVERT: D   86 SER cc_start: 0.8499 (p) cc_final: 0.7937 (m)
REVERT: D   90 MET cc_start: 0.8481 (mmt) cc_final: 0.8190 (mmp)
REVERT: D   93 GLN cc_start: 0.9194 (tt0) cc_final: 0.8714 (tt0)
REVERT: D   97 GLU cc_start: 0.9092 (mt-10) cc_final: 0.8822 (mt-10)
REVERT: D   99 TYR cc_start: 0.8382 (t80) cc_final: 0.7238 (t80)
REVERT: D  103 LEU cc_start: 0.9100 (tp) cc_final: 0.8843 (tt)
REVERT: D  107 THR cc_start: 0.9501 (m) cc_final: 0.9081 (m)
REVERT: D  125 GLN cc_start: 0.9183 (mt0) cc_final: 0.8559 (mm110)
REVERT: E   74 GLU cc_start: 0.8874 (mt-10) cc_final: 0.8415 (tp30)
REVERT: E   79 LYS cc_start: 0.8489 (mtpp) cc_final: 0.8196 (mmtm)
REVERT: F   61 GLU cc_start: 0.8943 (tp30) cc_final: 0.8499 (tp30)
REVERT: F   85 LEU cc_start: 0.9350 (mt) cc_final: 0.9149 (mt)
REVERT: F   90 ASP cc_start: 0.8123 (t0) cc_final: 0.7472 (t70)
REVERT: F   95 LYS cc_start: 0.9273 (ttmt) cc_final: 0.9056 (tmtt)
REVERT: F   97 LEU cc_start: 0.9398 (mt) cc_final: 0.9047 (mp)
REVERT: G   37 TYR cc_start: 0.8042 (m-80) cc_final: 0.7096 (m-80)
REVERT: G   40 LYS cc_start: 0.9065 (mttt) cc_final: 0.8826 (mmtp)
REVERT: G   64 ASN cc_start: 0.8973 (m-40) cc_final: 0.8575 (t0)
REVERT: G   91 ILE cc_start: 0.9486 (mm) cc_final: 0.9163 (tt)
REVERT: G  102 GLU cc_start: 0.7164 (tp30) cc_final: 0.6753 (tp30)
REVERT: H   41 TYR cc_start: 0.7768 (m-80) cc_final: 0.7411 (m-80)
REVERT: H   79 LYS cc_start: 0.7791 (tttm) cc_final: 0.7543 (mptt)
REVERT: H   80 THR cc_start: 0.7915 (t) cc_final: 0.7154 (t)
REVERT: H  120 MET cc_start: 0.7660 (mtt) cc_final: 0.7055 (mtt)
REVERT: I   49 LEU cc_start: 0.9027 (mt) cc_final: 0.8389 (mm)
REVERT: I   55 ARG cc_start: 0.8886 (mtt90) cc_final: 0.8609 (mtm180)
REVERT: I   68 ASP cc_start: 0.8528 (m-30) cc_final: 0.8294 (m-30)
REVERT: J   39 TYR cc_start: 0.8113 (m-80) cc_final: 0.7380 (m-80)
REVERT: J   56 GLU cc_start: 0.8599 (tt0) cc_final: 0.8375 (tt0)
REVERT: J   68 ASN cc_start: 0.7348 (m-40) cc_final: 0.6957 (m-40)
REVERT: J   89 ASN cc_start: 0.8737 (m-40) cc_final: 0.8401 (t0)
REVERT: J   92 GLU cc_start: 0.7144 (mt-10) cc_final: 0.5803 (mt-10)
REVERT: J   94 ASN cc_start: 0.8746 (t0) cc_final: 0.7875 (m-40)
REVERT: J   95 LYS cc_start: 0.8987 (tttt) cc_final: 0.8634 (ttpt)
REVERT: K   92 GLN cc_start: 0.8800 (tt0) cc_final: 0.8328 (tm-30)
  outliers start: 4
  outliers final: 1
  residues processed: 453
  average time/residue: 0.1644
  time to fit residues: 101.8487
Evaluate side-chains
  241 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 240
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 98 optimal weight:    2.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    0.0970
   chunk 66 optimal weight:    0.9980
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0270
   chunk 77 optimal weight:    0.9980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    1.9990
   overall best weight:    0.8238

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

Flipped N/Q/H residues before XYZ refinement:
C 620 HIS
C 624 HIS
** C 631 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  68 GLN
E  93 GLN
F  73 ASN
G  46 HIS
H  68 GLN
K  79 HIS
** K  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.070022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.055746 restraints weight = 91044.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.057166 restraints weight = 50895.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.058097 restraints weight = 34362.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.058713 restraints weight = 26486.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.059078 restraints weight = 22365.331|
|-----------------------------------------------------------------------------|
r_work (final): 0.3255
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3255
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3255 r_free = 0.3255    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       12 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3253 r_free = 0.3253    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.3253
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.3112

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.063  16904  Z= 0.192
  Angle     :  0.663  25.809  24155  Z= 0.356
  Chirality :  0.036   0.175   2706
  Planarity :  0.004   0.059   1989
  Dihedral  : 28.928  92.128   4740
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 9.96
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.12 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  0.30 %
    Allowed  :  3.07 %
    Favored  : 96.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.24), residues: 1155
  helix:  1.38 (0.19), residues: 683
  sheet: -2.88 (1.21), residues: 14
  loop : -1.67 (0.27), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG H  42 
 TYR   0.022   0.001   TYR F  39 
 PHE   0.013   0.001   PHE A 456 
 TRP   0.009   0.002   TRP C 591 
 HIS   0.018   0.002   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00414 (16876)
  covalent geometry    : angle       0.60966 (24119)
  hydrogen bonds       : bond        0.04278 (  900)
  hydrogen bonds       : angle       3.55333 ( 2290)
  metal coordination   : bond        0.01454 (   28)
  metal coordination   : angle       6.80162 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  299 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 296
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  696 THR cc_start: 0.7776 (m) cc_final: 0.7523 (p)
REVERT: C  603 PHE cc_start: 0.5975 (m-80) cc_final: 0.5034 (m-80)
REVERT: C  614 MET cc_start: 0.6887 (mtp) cc_final: 0.6583 (mtm)
REVERT: C  657 MET cc_start: 0.5320 (tpp) cc_final: 0.5049 (mmp)
REVERT: C  672 MET cc_start: 0.8263 (ppp) cc_final: 0.7442 (ppp)
REVERT: C  673 SER cc_start: 0.9043 (m) cc_final: 0.8485 (m)
REVERT: D   60 LEU cc_start: 0.8529 (mt) cc_final: 0.8062 (mt)
REVERT: D   86 SER cc_start: 0.9035 (p) cc_final: 0.8666 (p)
REVERT: D   93 GLN cc_start: 0.9452 (tt0) cc_final: 0.9072 (tp40)
REVERT: D  120 MET cc_start: 0.8781 (mmp) cc_final: 0.8565 (mmm)
REVERT: D  125 GLN cc_start: 0.8980 (mt0) cc_final: 0.8727 (mm110)
REVERT: E   74 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8489 (tp30)
REVERT: E   79 LYS cc_start: 0.8522 (mtpp) cc_final: 0.8231 (mmtm)
REVERT: F   29 ARG cc_start: 0.7105 (mtp85) cc_final: 0.5891 (ttm170)
REVERT: F   38 ASN cc_start: 0.7783 (t0) cc_final: 0.7356 (t0)
REVERT: F   56 GLU cc_start: 0.9387 (tt0) cc_final: 0.9013 (mt-10)
REVERT: F   61 GLU cc_start: 0.8990 (tp30) cc_final: 0.8488 (tp30)
REVERT: F   90 ASP cc_start: 0.8241 (t0) cc_final: 0.7579 (t70)
REVERT: G   40 LYS cc_start: 0.9227 (mttt) cc_final: 0.8892 (mmtp)
REVERT: G   64 ASN cc_start: 0.8981 (m-40) cc_final: 0.8687 (t0)
REVERT: G   80 TYR cc_start: 0.8633 (m-10) cc_final: 0.8306 (m-80)
REVERT: G   81 ASN cc_start: 0.8818 (t0) cc_final: 0.8486 (t0)
REVERT: G   90 GLU cc_start: 0.9042 (mp0) cc_final: 0.8672 (mp0)
REVERT: G   91 ILE cc_start: 0.9439 (mm) cc_final: 0.9166 (tt)
REVERT: H   46 VAL cc_start: 0.9225 (t) cc_final: 0.8772 (t)
REVERT: H   84 PHE cc_start: 0.8322 (m-80) cc_final: 0.8030 (m-10)
REVERT: H  105 GLU cc_start: 0.8573 (tp30) cc_final: 0.8046 (tp30)
REVERT: H  107 THR cc_start: 0.9437 (m) cc_final: 0.9220 (m)
REVERT: H  120 MET cc_start: 0.7761 (mtt) cc_final: 0.7115 (mmm)
REVERT: I   37 LEU cc_start: 0.9364 (mt) cc_final: 0.9129 (mt)
REVERT: I   43 VAL cc_start: 0.9404 (t) cc_final: 0.9089 (p)
REVERT: I   53 GLU cc_start: 0.9097 (pp20) cc_final: 0.8873 (pp20)
REVERT: J   39 TYR cc_start: 0.8745 (m-80) cc_final: 0.7987 (m-80)
REVERT: J   56 GLU cc_start: 0.8632 (tt0) cc_final: 0.8280 (tt0)
REVERT: J   64 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8038 (tp30)
REVERT: J   68 ASN cc_start: 0.7879 (m-40) cc_final: 0.7288 (m-40)
REVERT: J   89 ASN cc_start: 0.8853 (m-40) cc_final: 0.8487 (t0)
REVERT: J   92 GLU cc_start: 0.7278 (mt-10) cc_final: 0.7022 (mt-10)
REVERT: J   94 ASN cc_start: 0.8686 (t0) cc_final: 0.7650 (m-40)
REVERT: J   95 LYS cc_start: 0.9074 (tttt) cc_final: 0.8829 (ttpt)
REVERT: J  112 GLN cc_start: 0.9144 (mm-40) cc_final: 0.8727 (mp10)
REVERT: K   70 ILE cc_start: 0.9477 (mm) cc_final: 0.9220 (mm)
REVERT: K   90 GLU cc_start: 0.9519 (mp0) cc_final: 0.8818 (mp0)
REVERT: K   92 GLN cc_start: 0.8933 (tt0) cc_final: 0.8412 (tm-30)
  outliers start: 3
  outliers final: 1
  residues processed: 297
  average time/residue: 0.1353
  time to fit residues: 57.8030
Evaluate side-chains
  219 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 218
  time to evaluate  : 0.424 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 144 optimal weight:    2.9990
   chunk 123 optimal weight:    2.9990
   chunk 10 optimal weight:    2.9990
   chunk 87 optimal weight:    3.9990
   chunk 125 optimal weight:    2.9990
   chunk 90 optimal weight:    0.5980
   chunk 64 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 113 optimal weight:    0.5980
   chunk 82 optimal weight:    0.0980
   chunk 136 optimal weight:    2.9990
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
C 620 HIS
D  85 GLN
E  93 GLN
G  46 HIS
H  68 GLN
H  85 GLN
** K  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.069692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.055529 restraints weight = 92724.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.056958 restraints weight = 51845.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.057902 restraints weight = 35120.605|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.058516 restraints weight = 27171.137|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.058873 restraints weight = 22981.509|
|-----------------------------------------------------------------------------|
r_work (final): 0.3254
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3254
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3254 r_free = 0.3254    target_work(ls_wunit_k1) = 0.058         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.3254
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7994
moved from start:          0.3786

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.094  16904  Z= 0.155
  Angle     :  0.598  22.629  24155  Z= 0.331
  Chirality :  0.034   0.138   2706
  Planarity :  0.004   0.049   1989
  Dihedral  : 28.996  92.087   4740
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  2.68 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.46 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.25), residues: 1155
  helix:  1.67 (0.20), residues: 688
  sheet: -1.22 (1.54), residues: 10
  loop : -1.50 (0.28), residues: 457

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG I  67 
 TYR   0.009   0.001   TYR F  57 
 PHE   0.011   0.001   PHE H  78 
 TRP   0.010   0.001   TRP C 591 
 HIS   0.006   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 (16876)
  covalent geometry    : angle       0.55975 (24119)
  hydrogen bonds       : bond        0.03676 (  900)
  hydrogen bonds       : angle       3.35310 ( 2290)
  metal coordination   : bond        0.01873 (   28)
  metal coordination   : angle       5.47456 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 280
  time to evaluate  : 0.458 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  687 LEU cc_start: 0.9096 (tp) cc_final: 0.8699 (tp)
REVERT: A  696 THR cc_start: 0.7606 (m) cc_final: 0.7281 (p)
REVERT: C  590 GLU cc_start: 0.9113 (pm20) cc_final: 0.8480 (mm-30)
REVERT: C  603 PHE cc_start: 0.5617 (m-80) cc_final: 0.4707 (m-80)
REVERT: C  616 LEU cc_start: 0.8430 (mt) cc_final: 0.8208 (mt)
REVERT: C  637 MET cc_start: 0.8322 (mmt) cc_final: 0.7970 (ppp)
REVERT: C  657 MET cc_start: 0.5778 (tpp) cc_final: 0.5538 (tpp)
REVERT: C  663 MET cc_start: 0.5274 (mtm) cc_final: 0.5055 (mtp)
REVERT: D   86 SER cc_start: 0.8969 (p) cc_final: 0.8707 (p)
REVERT: D   93 GLN cc_start: 0.9248 (tt0) cc_final: 0.8178 (tt0)
REVERT: D   97 GLU cc_start: 0.8706 (mt-10) cc_final: 0.7492 (mt-10)
REVERT: D   99 TYR cc_start: 0.8844 (t80) cc_final: 0.8388 (t80)
REVERT: D  125 GLN cc_start: 0.9007 (mt0) cc_final: 0.8717 (mm110)
REVERT: E   63 GLU cc_start: 0.8631 (tp30) cc_final: 0.8326 (tp30)
REVERT: E   74 GLU cc_start: 0.8894 (mt-10) cc_final: 0.8476 (tp30)
REVERT: E   79 LYS cc_start: 0.8502 (mtpp) cc_final: 0.8228 (mmtm)
REVERT: E   95 ARG cc_start: 0.6825 (mtp85) cc_final: 0.6019 (mmt180)
REVERT: F   56 GLU cc_start: 0.9417 (tt0) cc_final: 0.9066 (mt-10)
REVERT: F   57 TYR cc_start: 0.9131 (t80) cc_final: 0.8619 (t80)
REVERT: F   61 GLU cc_start: 0.9036 (tp30) cc_final: 0.8556 (tp30)
REVERT: F   90 ASP cc_start: 0.8382 (t0) cc_final: 0.7663 (t70)
REVERT: G   40 LYS cc_start: 0.9224 (mttt) cc_final: 0.8880 (mmtp)
REVERT: G   56 MET cc_start: 0.8677 (tpp) cc_final: 0.8356 (tpp)
REVERT: G   64 ASN cc_start: 0.8942 (m-40) cc_final: 0.8697 (t0)
REVERT: G  105 LYS cc_start: 0.9244 (mtmt) cc_final: 0.9034 (mtmm)
REVERT: H   46 VAL cc_start: 0.9455 (t) cc_final: 0.9141 (t)
REVERT: H   80 THR cc_start: 0.7944 (t) cc_final: 0.7612 (t)
REVERT: H   82 LEU cc_start: 0.8177 (tp) cc_final: 0.7952 (tp)
REVERT: H   90 MET cc_start: 0.8868 (mmp) cc_final: 0.8512 (ptp)
REVERT: H  105 GLU cc_start: 0.8555 (tp30) cc_final: 0.8117 (tp30)
REVERT: H  107 THR cc_start: 0.9517 (m) cc_final: 0.9019 (p)
REVERT: H  120 MET cc_start: 0.8064 (mtt) cc_final: 0.7156 (mmm)
REVERT: I   43 VAL cc_start: 0.9474 (t) cc_final: 0.9192 (p)
REVERT: I   79 LYS cc_start: 0.8385 (mmmm) cc_final: 0.8149 (mmmt)
REVERT: J   39 TYR cc_start: 0.8692 (m-80) cc_final: 0.8411 (m-80)
REVERT: J   56 GLU cc_start: 0.8558 (tt0) cc_final: 0.8201 (mt-10)
REVERT: J   64 GLU cc_start: 0.8904 (tm-30) cc_final: 0.8387 (tp30)
REVERT: J   68 ASN cc_start: 0.7881 (m-40) cc_final: 0.7583 (m-40)
REVERT: J   87 VAL cc_start: 0.9627 (m) cc_final: 0.9370 (m)
REVERT: J   89 ASN cc_start: 0.8838 (m-40) cc_final: 0.8569 (t0)
REVERT: J   94 ASN cc_start: 0.8721 (t0) cc_final: 0.7688 (m-40)
REVERT: J   95 LYS cc_start: 0.9094 (tttt) cc_final: 0.8825 (ttpt)
REVERT: K   49 THR cc_start: 0.8436 (m) cc_final: 0.7851 (p)
REVERT: K   56 MET cc_start: 0.8921 (tpp) cc_final: 0.8692 (tpp)
REVERT: K   90 GLU cc_start: 0.9505 (mp0) cc_final: 0.8905 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1326
  time to fit residues: 53.8731
Evaluate side-chains
  209 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 209
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 132 optimal weight:    2.9990
   chunk 89 optimal weight:    0.7980
   chunk 54 optimal weight:    0.9990
   chunk 134 optimal weight:    2.9990
   chunk 73 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 101 optimal weight:    1.9990
   chunk 93 optimal weight:    0.7980
   chunk 48 optimal weight:    2.9990
   chunk 47 optimal weight:    0.9990
   chunk 65 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
C 620 HIS
D  68 GLN
E  93 GLN
H  68 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.067227 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.052934 restraints weight = 92553.795|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.054294 restraints weight = 51875.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.055207 restraints weight = 35408.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.055768 restraints weight = 27522.965|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3198 r_free = 0.3198 target = 0.056152 restraints weight = 23457.545|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.4590

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.142  16904  Z= 0.190
  Angle     :  0.622  19.009  24155  Z= 0.346
  Chirality :  0.035   0.200   2706
  Planarity :  0.004   0.051   1989
  Dihedral  : 29.220  93.758   4740
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 11.92
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.07 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.36 %
    Favored  : 96.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.25), residues: 1155
  helix:  1.55 (0.20), residues: 697
  sheet: -0.92 (1.70), residues: 10
  loop : -1.31 (0.29), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 593 
 TYR   0.015   0.001   TYR A 453 
 PHE   0.010   0.001   PHE A 290 
 TRP   0.013   0.002   TRP A 612 
 HIS   0.006   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00409 (16876)
  covalent geometry    : angle       0.58891 (24119)
  hydrogen bonds       : bond        0.04353 (  900)
  hydrogen bonds       : angle       3.43983 ( 2290)
  metal coordination   : bond        0.02741 (   28)
  metal coordination   : angle       5.21501 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  264 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 263
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  444 MET cc_start: 0.2630 (ptm) cc_final: 0.2386 (tmm)
REVERT: A  687 LEU cc_start: 0.8997 (tp) cc_final: 0.8607 (tp)
REVERT: A  696 THR cc_start: 0.8231 (m) cc_final: 0.7970 (p)
REVERT: C  590 GLU cc_start: 0.9046 (pm20) cc_final: 0.8464 (mm-30)
REVERT: C  603 PHE cc_start: 0.5369 (m-80) cc_final: 0.5015 (m-10)
REVERT: C  616 LEU cc_start: 0.8519 (mt) cc_final: 0.8306 (mt)
REVERT: C  637 MET cc_start: 0.8459 (mmt) cc_final: 0.8088 (ppp)
REVERT: C  663 MET cc_start: 0.6044 (mtm) cc_final: 0.5706 (mtp)
REVERT: D   50 GLU cc_start: 0.8662 (tp30) cc_final: 0.8404 (tp30)
REVERT: D   90 MET cc_start: 0.8636 (mmp) cc_final: 0.8015 (mmp)
REVERT: D   93 GLN cc_start: 0.9056 (tt0) cc_final: 0.7989 (tt0)
REVERT: D   94 GLU cc_start: 0.8186 (mp0) cc_final: 0.7786 (mp0)
REVERT: D   97 GLU cc_start: 0.8737 (mt-10) cc_final: 0.7611 (mt-10)
REVERT: D   99 TYR cc_start: 0.9072 (t80) cc_final: 0.8580 (t80)
REVERT: D  107 THR cc_start: 0.9374 (m) cc_final: 0.9086 (p)
REVERT: D  125 GLN cc_start: 0.8915 (mt0) cc_final: 0.8689 (mm110)
REVERT: E   63 GLU cc_start: 0.8774 (tp30) cc_final: 0.8574 (tp30)
REVERT: E   74 GLU cc_start: 0.8949 (mt-10) cc_final: 0.8563 (tp30)
REVERT: E   88 TYR cc_start: 0.8341 (m-10) cc_final: 0.7827 (m-10)
REVERT: E   95 ARG cc_start: 0.6922 (mtp85) cc_final: 0.6275 (mmt180)
REVERT: E   98 TYR cc_start: 0.9007 (m-10) cc_final: 0.8770 (m-10)
REVERT: F   50 TYR cc_start: 0.8314 (t80) cc_final: 0.7760 (t80)
REVERT: F   56 GLU cc_start: 0.9338 (tt0) cc_final: 0.8994 (mt-10)
REVERT: F   57 TYR cc_start: 0.8859 (t80) cc_final: 0.8481 (t80)
REVERT: F   61 GLU cc_start: 0.9006 (tp30) cc_final: 0.8550 (tp30)
REVERT: F   90 ASP cc_start: 0.8718 (t0) cc_final: 0.8260 (t70)
REVERT: F   97 LEU cc_start: 0.9247 (mp) cc_final: 0.9045 (mp)
REVERT: G   40 LYS cc_start: 0.9334 (mttt) cc_final: 0.9024 (mmtp)
REVERT: G   64 ASN cc_start: 0.9123 (m-40) cc_final: 0.8751 (t0)
REVERT: G   90 GLU cc_start: 0.9068 (mp0) cc_final: 0.8762 (mp0)
REVERT: G  102 GLU cc_start: 0.7903 (tp30) cc_final: 0.7548 (tp30)
REVERT: H   46 VAL cc_start: 0.9349 (t) cc_final: 0.9012 (t)
REVERT: H   80 THR cc_start: 0.7760 (t) cc_final: 0.7509 (p)
REVERT: H  105 GLU cc_start: 0.8553 (tp30) cc_final: 0.8182 (tp30)
REVERT: H  107 THR cc_start: 0.9499 (m) cc_final: 0.9005 (p)
REVERT: H  120 MET cc_start: 0.7937 (mtt) cc_final: 0.7612 (mtm)
REVERT: H  123 ASP cc_start: 0.8934 (m-30) cc_final: 0.8453 (m-30)
REVERT: H  130 ILE cc_start: 0.9060 (mm) cc_final: 0.8833 (mm)
REVERT: I   43 VAL cc_start: 0.9566 (t) cc_final: 0.9363 (p)
REVERT: I   63 GLU cc_start: 0.8876 (tp30) cc_final: 0.8578 (tp30)
REVERT: J   41 GLU cc_start: 0.8454 (tp30) cc_final: 0.8190 (tp30)
REVERT: J   56 GLU cc_start: 0.8480 (tt0) cc_final: 0.8232 (tt0)
REVERT: J   64 GLU cc_start: 0.9225 (tm-30) cc_final: 0.8450 (tm-30)
REVERT: J   68 ASN cc_start: 0.8273 (m-40) cc_final: 0.7755 (m-40)
REVERT: J   89 ASN cc_start: 0.8851 (m-40) cc_final: 0.8463 (t0)
REVERT: J   92 GLU cc_start: 0.7715 (mt-10) cc_final: 0.7237 (mt-10)
REVERT: J   94 ASN cc_start: 0.8713 (t0) cc_final: 0.8191 (m-40)
REVERT: J   95 LYS cc_start: 0.9254 (tttt) cc_final: 0.8797 (ttpt)
REVERT: J   99 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7646 (mmt180)
REVERT: K   49 THR cc_start: 0.7648 (m) cc_final: 0.7255 (p)
REVERT: K   61 SER cc_start: 0.9313 (t) cc_final: 0.8861 (t)
REVERT: K   70 ILE cc_start: 0.9549 (mm) cc_final: 0.9308 (mm)
REVERT: K   90 GLU cc_start: 0.9511 (mp0) cc_final: 0.8943 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 264
  average time/residue: 0.1246
  time to fit residues: 48.3245
Evaluate side-chains
  216 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 216
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 31 optimal weight:    0.0670
   chunk 107 optimal weight:    0.9990
   chunk 133 optimal weight:    2.9990
   chunk 132 optimal weight:    2.9990
   chunk 135 optimal weight:    2.9990
   chunk 61 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 85 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 109 optimal weight:    1.9990
   chunk 100 optimal weight:    0.6980
   overall best weight:    0.9524

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

Flipped N/Q/H residues before XYZ refinement:
C 620 HIS
** D  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  68 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.066184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.052078 restraints weight = 92053.134|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.053383 restraints weight = 53006.848|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3144 r_free = 0.3144 target = 0.054259 restraints weight = 36656.469|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.054823 restraints weight = 28708.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.055124 restraints weight = 24528.579|
|-----------------------------------------------------------------------------|
r_work (final): 0.3158
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3158
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3158 r_free = 0.3158    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       14 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3157 r_free = 0.3157    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.3157
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.5070

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.218  16904  Z= 0.194
  Angle     :  0.618  13.127  24155  Z= 0.347
  Chirality :  0.036   0.181   2706
  Planarity :  0.004   0.054   1989
  Dihedral  : 29.296  94.734   4740
  Min Nonbonded Distance : 2.111

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.33 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  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 (0.25), residues: 1155
  helix:  1.63 (0.20), residues: 692
  sheet: -0.74 (1.72), residues: 10
  loop : -1.18 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  63 
 TYR   0.012   0.001   TYR J  39 
 PHE   0.016   0.002   PHE A 290 
 TRP   0.007   0.001   TRP A 612 
 HIS   0.013   0.001   HIS A 297 

Details of bonding type rmsd
  covalent geometry    : bond        0.00416 (16876)
  covalent geometry    : angle       0.59433 (24119)
  hydrogen bonds       : bond        0.04160 (  900)
  hydrogen bonds       : angle       3.45302 ( 2290)
  metal coordination   : bond        0.04179 (   28)
  metal coordination   : angle       4.46434 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 249
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.8277 (tmm) cc_final: 0.8066 (tmm)
REVERT: A  444 MET cc_start: 0.3093 (ptm) cc_final: 0.2843 (tmm)
REVERT: A  453 TYR cc_start: 0.7177 (m-10) cc_final: 0.6521 (p90)
REVERT: A  687 LEU cc_start: 0.9134 (tp) cc_final: 0.8678 (tp)
REVERT: A  696 THR cc_start: 0.8050 (m) cc_final: 0.7805 (p)
REVERT: C  603 PHE cc_start: 0.5552 (m-80) cc_final: 0.5202 (m-10)
REVERT: C  637 MET cc_start: 0.8497 (mmt) cc_final: 0.8085 (ppp)
REVERT: C  663 MET cc_start: 0.5499 (mtm) cc_final: 0.4878 (mtp)
REVERT: D   50 GLU cc_start: 0.8721 (tp30) cc_final: 0.8451 (tp30)
REVERT: D   93 GLN cc_start: 0.9170 (tt0) cc_final: 0.8017 (tt0)
REVERT: D   97 GLU cc_start: 0.8783 (mt-10) cc_final: 0.8209 (mt-10)
REVERT: D   99 TYR cc_start: 0.9106 (t80) cc_final: 0.8308 (t80)
REVERT: E   63 GLU cc_start: 0.8733 (tp30) cc_final: 0.8468 (tp30)
REVERT: E   74 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8611 (tp30)
REVERT: E   88 TYR cc_start: 0.8423 (m-10) cc_final: 0.7682 (m-10)
REVERT: E   98 TYR cc_start: 0.9155 (m-10) cc_final: 0.8806 (m-10)
REVERT: F   61 GLU cc_start: 0.8975 (tp30) cc_final: 0.8412 (tp30)
REVERT: G   40 LYS cc_start: 0.9202 (mttt) cc_final: 0.8946 (mttm)
REVERT: G   56 MET cc_start: 0.8729 (tpp) cc_final: 0.8467 (tpp)
REVERT: G   64 ASN cc_start: 0.9168 (m-40) cc_final: 0.8713 (t0)
REVERT: G   90 GLU cc_start: 0.9089 (mp0) cc_final: 0.8640 (mp0)
REVERT: H  105 GLU cc_start: 0.8617 (tp30) cc_final: 0.8154 (tp30)
REVERT: H  107 THR cc_start: 0.9490 (m) cc_final: 0.8996 (p)
REVERT: H  123 ASP cc_start: 0.8952 (m-30) cc_final: 0.8646 (m-30)
REVERT: I   63 GLU cc_start: 0.9053 (tp30) cc_final: 0.8821 (tp30)
REVERT: J   39 TYR cc_start: 0.9005 (m-80) cc_final: 0.8642 (m-80)
REVERT: J   41 GLU cc_start: 0.8431 (tp30) cc_final: 0.8171 (tp30)
REVERT: J   56 GLU cc_start: 0.8519 (tt0) cc_final: 0.8271 (tt0)
REVERT: J   64 GLU cc_start: 0.9315 (tm-30) cc_final: 0.8760 (tm-30)
REVERT: J   68 ASN cc_start: 0.8302 (m-40) cc_final: 0.7858 (m-40)
REVERT: J   94 ASN cc_start: 0.8733 (t0) cc_final: 0.8221 (m-40)
REVERT: J   95 LYS cc_start: 0.9288 (tttt) cc_final: 0.8711 (tppt)
REVERT: J   99 ARG cc_start: 0.7943 (mpt180) cc_final: 0.7492 (mmt180)
REVERT: K   49 THR cc_start: 0.7358 (m) cc_final: 0.6983 (p)
REVERT: K   90 GLU cc_start: 0.9488 (mp0) cc_final: 0.9066 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 249
  average time/residue: 0.1285
  time to fit residues: 46.8569
Evaluate side-chains
  200 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 84 optimal weight:    0.6980
   chunk 86 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 42 optimal weight:    0.7980
   chunk 133 optimal weight:    2.9990
   chunk 102 optimal weight:    0.9980
   chunk 128 optimal weight:    2.9990
   chunk 12 optimal weight:    0.0060
   chunk 94 optimal weight:    0.7980
   chunk 21 optimal weight:    2.9990
   chunk 122 optimal weight:    2.9990
   overall best weight:    0.6596

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

Flipped N/Q/H residues before XYZ refinement:
H  68 GLN
** K  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.066709 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3092 r_free = 0.3092 target = 0.052533 restraints weight = 91577.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.053909 restraints weight = 51093.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3157 r_free = 0.3157 target = 0.054824 restraints weight = 34689.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3175 r_free = 0.3175 target = 0.055408 restraints weight = 26872.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.055821 restraints weight = 22768.652|
|-----------------------------------------------------------------------------|
r_work (final): 0.3176
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3176
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3176 r_free = 0.3176    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.3176
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.5305

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.186  16904  Z= 0.167
  Angle     :  0.607  19.094  24155  Z= 0.340
  Chirality :  0.035   0.175   2706
  Planarity :  0.004   0.056   1989
  Dihedral  : 29.285  95.110   4740
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.98 %
    Favored  : 95.93 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.08 %
    Favored  : 97.92 %
  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:  0.92 (0.25), residues: 1155
  helix:  1.71 (0.20), residues: 690
  sheet: -0.62 (1.75), residues: 10
  loop : -1.12 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H 128 
 TYR   0.012   0.001   TYR C 565 
 PHE   0.008   0.001   PHE A 290 
 TRP   0.008   0.001   TRP C 591 
 HIS   0.006   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 (16876)
  covalent geometry    : angle       0.57909 (24119)
  hydrogen bonds       : bond        0.03857 (  900)
  hydrogen bonds       : angle       3.46024 ( 2290)
  metal coordination   : bond        0.03546 (   28)
  metal coordination   : angle       4.75111 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  256 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 256
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.8312 (tmm) cc_final: 0.8034 (tmm)
REVERT: A  687 LEU cc_start: 0.9124 (tp) cc_final: 0.8645 (tp)
REVERT: A  696 THR cc_start: 0.8024 (m) cc_final: 0.7771 (p)
REVERT: C  590 GLU cc_start: 0.8896 (pm20) cc_final: 0.8426 (mm-30)
REVERT: C  603 PHE cc_start: 0.5610 (m-80) cc_final: 0.5037 (m-80)
REVERT: C  637 MET cc_start: 0.8589 (mmt) cc_final: 0.8075 (ppp)
REVERT: C  663 MET cc_start: 0.5307 (mtm) cc_final: 0.4909 (mtp)
REVERT: D   50 GLU cc_start: 0.8878 (tp30) cc_final: 0.8611 (tp30)
REVERT: D   90 MET cc_start: 0.8719 (mmp) cc_final: 0.8231 (mmp)
REVERT: D   93 GLN cc_start: 0.9160 (tt0) cc_final: 0.8315 (tt0)
REVERT: D   97 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8256 (mt-10)
REVERT: D   99 TYR cc_start: 0.9041 (t80) cc_final: 0.8199 (t80)
REVERT: E   63 GLU cc_start: 0.8705 (tp30) cc_final: 0.8497 (tp30)
REVERT: E   74 GLU cc_start: 0.8978 (mt-10) cc_final: 0.8588 (tp30)
REVERT: E   88 TYR cc_start: 0.8365 (m-10) cc_final: 0.7661 (m-10)
REVERT: F   50 TYR cc_start: 0.8253 (t80) cc_final: 0.7872 (t80)
REVERT: F   61 GLU cc_start: 0.8918 (tp30) cc_final: 0.8345 (tp30)
REVERT: F   95 LYS cc_start: 0.8664 (pptt) cc_final: 0.8408 (tmmt)
REVERT: F   97 LEU cc_start: 0.9402 (mp) cc_final: 0.9197 (mp)
REVERT: G   31 LYS cc_start: 0.8687 (tmtt) cc_final: 0.8387 (tptp)
REVERT: G   64 ASN cc_start: 0.9119 (m-40) cc_final: 0.8656 (t0)
REVERT: H   46 VAL cc_start: 0.9297 (t) cc_final: 0.8932 (t)
REVERT: H  105 GLU cc_start: 0.8665 (tp30) cc_final: 0.8216 (tp30)
REVERT: H  107 THR cc_start: 0.9490 (m) cc_final: 0.9019 (p)
REVERT: H  123 ASP cc_start: 0.8781 (m-30) cc_final: 0.8456 (m-30)
REVERT: I   63 GLU cc_start: 0.8806 (tp30) cc_final: 0.8447 (tp30)
REVERT: J   39 TYR cc_start: 0.9154 (m-80) cc_final: 0.8841 (m-80)
REVERT: J   41 GLU cc_start: 0.8434 (tp30) cc_final: 0.8142 (tp30)
REVERT: J   64 GLU cc_start: 0.9323 (tm-30) cc_final: 0.8561 (tm-30)
REVERT: J   68 ASN cc_start: 0.8344 (m-40) cc_final: 0.7722 (m-40)
REVERT: J   94 ASN cc_start: 0.8632 (t0) cc_final: 0.8110 (m-40)
REVERT: J   95 LYS cc_start: 0.9221 (tttt) cc_final: 0.8603 (tppt)
REVERT: J   99 ARG cc_start: 0.7934 (mpt180) cc_final: 0.7473 (mmt180)
REVERT: K   49 THR cc_start: 0.7258 (m) cc_final: 0.6859 (p)
REVERT: K   90 GLU cc_start: 0.9539 (mp0) cc_final: 0.8963 (mp0)
REVERT: K  103 LEU cc_start: 0.9263 (tp) cc_final: 0.9035 (mm)
  outliers start: 0
  outliers final: 0
  residues processed: 256
  average time/residue: 0.1290
  time to fit residues: 48.3943
Evaluate side-chains
  204 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.454 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 60 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 100 optimal weight:    0.5980
   chunk 131 optimal weight:    2.9990
   chunk 90 optimal weight:    0.8980
   chunk 11 optimal weight:    7.9990
   chunk 42 optimal weight:    0.8980
   chunk 101 optimal weight:    2.9990
   chunk 108 optimal weight:    0.9990
   overall best weight:    0.8582

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

Flipped N/Q/H residues before XYZ refinement:
** D  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  24 GLN
H  68 GLN
H  76 GLN
** K  81 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 = 0.3450 r_free = 0.3450 target = 0.065428 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.051632 restraints weight = 90211.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.052933 restraints weight = 51778.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.053801 restraints weight = 35519.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.054311 restraints weight = 27661.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.054711 restraints weight = 23750.174|
|-----------------------------------------------------------------------------|
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3151
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3151 r_free = 0.3151    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.3151
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8121
moved from start:          0.5720

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.168  16904  Z= 0.185
  Angle     :  0.630  20.751  24155  Z= 0.351
  Chirality :  0.036   0.180   2706
  Planarity :  0.004   0.055   1989
  Dihedral  : 29.359  97.132   4740
  Min Nonbonded Distance : 2.165

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.24 %
    Favored  : 95.67 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  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 (0.25), residues: 1155
  helix:  1.64 (0.20), residues: 690
  sheet: -0.43 (1.68), residues: 10
  loop : -1.11 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG H 129 
 TYR   0.011   0.001   TYR E  98 
 PHE   0.013   0.001   PHE A 290 
 TRP   0.006   0.001   TRP C 591 
 HIS   0.006   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (16876)
  covalent geometry    : angle       0.59808 (24119)
  hydrogen bonds       : bond        0.04189 (  900)
  hydrogen bonds       : angle       3.55812 ( 2290)
  metal coordination   : bond        0.03218 (   28)
  metal coordination   : angle       5.14848 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.394 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.8438 (tmm) cc_final: 0.8150 (tmm)
REVERT: A  687 LEU cc_start: 0.9201 (tp) cc_final: 0.8765 (tp)
REVERT: A  696 THR cc_start: 0.8083 (m) cc_final: 0.7825 (p)
REVERT: C  594 GLU cc_start: 0.8380 (mm-30) cc_final: 0.8090 (mp0)
REVERT: C  603 PHE cc_start: 0.4891 (m-80) cc_final: 0.4565 (m-80)
REVERT: C  637 MET cc_start: 0.8725 (mmt) cc_final: 0.8242 (ppp)
REVERT: C  663 MET cc_start: 0.6219 (mtm) cc_final: 0.5608 (mtp)
REVERT: C  683 GLU cc_start: 0.7133 (mp0) cc_final: 0.6895 (pm20)
REVERT: D   50 GLU cc_start: 0.8819 (tp30) cc_final: 0.8487 (tp30)
REVERT: D   90 MET cc_start: 0.8395 (mmp) cc_final: 0.8122 (mmp)
REVERT: D   94 GLU cc_start: 0.8655 (pm20) cc_final: 0.8410 (pm20)
REVERT: D   99 TYR cc_start: 0.9141 (t80) cc_final: 0.8267 (t80)
REVERT: D  120 MET cc_start: 0.8989 (mmm) cc_final: 0.8611 (mmm)
REVERT: E   63 GLU cc_start: 0.8821 (tp30) cc_final: 0.8589 (tp30)
REVERT: E   74 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8658 (tp30)
REVERT: E   88 TYR cc_start: 0.8417 (m-10) cc_final: 0.7741 (m-10)
REVERT: F   57 TYR cc_start: 0.8985 (t80) cc_final: 0.8658 (t80)
REVERT: F   61 GLU cc_start: 0.8903 (tp30) cc_final: 0.8551 (tp30)
REVERT: F   97 LEU cc_start: 0.9464 (mp) cc_final: 0.9260 (mp)
REVERT: G   31 LYS cc_start: 0.8635 (tmtt) cc_final: 0.8422 (tptp)
REVERT: G   40 LYS cc_start: 0.8590 (mtpt) cc_final: 0.8329 (mmtp)
REVERT: G   56 MET cc_start: 0.8842 (tpp) cc_final: 0.8501 (tpp)
REVERT: G   64 ASN cc_start: 0.9212 (m-40) cc_final: 0.8778 (t0)
REVERT: G  105 LYS cc_start: 0.9007 (ptmm) cc_final: 0.8766 (ptpp)
REVERT: H   46 VAL cc_start: 0.9280 (t) cc_final: 0.8928 (t)
REVERT: H   59 GLU cc_start: 0.7663 (pm20) cc_final: 0.7417 (pm20)
REVERT: H   76 GLN cc_start: 0.8389 (mt0) cc_final: 0.7899 (mp10)
REVERT: H  105 GLU cc_start: 0.8731 (tp30) cc_final: 0.8339 (tp30)
REVERT: H  107 THR cc_start: 0.9473 (m) cc_final: 0.8996 (p)
REVERT: H  115 LYS cc_start: 0.8556 (tmtt) cc_final: 0.8126 (mmmm)
REVERT: H  123 ASP cc_start: 0.8881 (m-30) cc_final: 0.8510 (m-30)
REVERT: I   63 GLU cc_start: 0.8967 (tp30) cc_final: 0.8398 (tp30)
REVERT: J   24 GLN cc_start: 0.8943 (mm110) cc_final: 0.8205 (mp10)
REVERT: J   38 ASN cc_start: 0.9540 (m-40) cc_final: 0.9223 (m-40)
REVERT: J   39 TYR cc_start: 0.9309 (m-80) cc_final: 0.9029 (m-80)
REVERT: J   41 GLU cc_start: 0.8514 (tp30) cc_final: 0.8217 (tp30)
REVERT: J   56 GLU cc_start: 0.8356 (tt0) cc_final: 0.7662 (tt0)
REVERT: J   90 ASP cc_start: 0.8736 (t0) cc_final: 0.8329 (t70)
REVERT: J   94 ASN cc_start: 0.8710 (t0) cc_final: 0.8173 (m-40)
REVERT: J   95 LYS cc_start: 0.9212 (tttt) cc_final: 0.8872 (ttpt)
REVERT: J   99 ARG cc_start: 0.8058 (mpt180) cc_final: 0.7508 (mmt180)
REVERT: K   49 THR cc_start: 0.7112 (m) cc_final: 0.6796 (p)
REVERT: K   70 ILE cc_start: 0.9719 (mm) cc_final: 0.9513 (mm)
REVERT: K   90 GLU cc_start: 0.9504 (mp0) cc_final: 0.9073 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1266
  time to fit residues: 45.8210
Evaluate side-chains
  199 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 122 optimal weight:    2.9990
   chunk 144 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 42 optimal weight:    0.5980
   chunk 13 optimal weight:    0.3980
   chunk 1 optimal weight:    4.9990
   chunk 111 optimal weight:    0.4980
   chunk 35 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 45 optimal weight:    0.0970
   overall best weight:    0.4978

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

Flipped N/Q/H residues before XYZ refinement:
** E  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  68 GLN
** K  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.066723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.052842 restraints weight = 91825.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.054201 restraints weight = 51487.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.055101 restraints weight = 34794.771|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.055654 restraints weight = 27002.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.056054 restraints weight = 22967.672|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3187
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3187 r_free = 0.3187    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.3187
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8084
moved from start:          0.5857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.131  16904  Z= 0.152
  Angle     :  0.599  16.653  24155  Z= 0.336
  Chirality :  0.035   0.176   2706
  Planarity :  0.004   0.056   1989
  Dihedral  : 29.284  96.946   4740
  Min Nonbonded Distance : 2.194

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.55 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.59 %
    Favored  : 99.41 %
  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:  1.05 (0.26), residues: 1155
  helix:  1.81 (0.20), residues: 689
  sheet: -0.64 (1.55), residues: 10
  loop : -1.05 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG I  55 
 TYR   0.009   0.001   TYR E  98 
 PHE   0.010   0.001   PHE A 290 
 TRP   0.004   0.001   TRP A 113 
 HIS   0.006   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (16876)
  covalent geometry    : angle       0.57479 (24119)
  hydrogen bonds       : bond        0.03698 (  900)
  hydrogen bonds       : angle       3.38440 ( 2290)
  metal coordination   : bond        0.02509 (   28)
  metal coordination   : angle       4.37155 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.407 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.8434 (tmm) cc_final: 0.8022 (tmm)
REVERT: A  680 MET cc_start: 0.8193 (mmm) cc_final: 0.7329 (mtp)
REVERT: A  687 LEU cc_start: 0.9202 (tp) cc_final: 0.8776 (tp)
REVERT: A  696 THR cc_start: 0.8328 (m) cc_final: 0.8107 (p)
REVERT: C  614 MET cc_start: 0.6906 (mtp) cc_final: 0.6619 (mtm)
REVERT: C  637 MET cc_start: 0.8711 (mmt) cc_final: 0.8288 (ppp)
REVERT: C  663 MET cc_start: 0.6133 (mtm) cc_final: 0.5744 (mtp)
REVERT: C  684 MET cc_start: 0.3883 (tpp) cc_final: 0.3610 (tpt)
REVERT: D   50 GLU cc_start: 0.8942 (tp30) cc_final: 0.8652 (tp30)
REVERT: D   93 GLN cc_start: 0.9199 (tt0) cc_final: 0.8072 (tm-30)
REVERT: D   97 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8081 (mt-10)
REVERT: D   99 TYR cc_start: 0.8953 (t80) cc_final: 0.8013 (t80)
REVERT: D  105 GLU cc_start: 0.7996 (pp20) cc_final: 0.7636 (pp20)
REVERT: D  120 MET cc_start: 0.8885 (mmm) cc_final: 0.8410 (mmm)
REVERT: E   88 TYR cc_start: 0.8615 (m-10) cc_final: 0.7891 (m-10)
REVERT: F   50 TYR cc_start: 0.8041 (t80) cc_final: 0.7680 (t80)
REVERT: F   57 TYR cc_start: 0.8921 (t80) cc_final: 0.8713 (t80)
REVERT: F   61 GLU cc_start: 0.8899 (tp30) cc_final: 0.8521 (tp30)
REVERT: G   48 ASP cc_start: 0.8346 (t0) cc_final: 0.8114 (t0)
REVERT: G   64 ASN cc_start: 0.9138 (m-40) cc_final: 0.8657 (t0)
REVERT: G  105 LYS cc_start: 0.8837 (ptmm) cc_final: 0.8413 (ptpp)
REVERT: H   46 VAL cc_start: 0.9390 (t) cc_final: 0.9083 (t)
REVERT: H   59 GLU cc_start: 0.7485 (pm20) cc_final: 0.7268 (pm20)
REVERT: H   76 GLN cc_start: 0.8101 (mt0) cc_final: 0.7764 (pt0)
REVERT: H  105 GLU cc_start: 0.8765 (tp30) cc_final: 0.8207 (tp30)
REVERT: H  107 THR cc_start: 0.9452 (m) cc_final: 0.8968 (t)
REVERT: H  115 LYS cc_start: 0.8576 (tmtt) cc_final: 0.8224 (mmmt)
REVERT: H  131 ARG cc_start: 0.9102 (mtt180) cc_final: 0.8847 (tpp80)
REVERT: I   39 ARG cc_start: 0.9064 (mpt180) cc_final: 0.8744 (mpt180)
REVERT: I   63 GLU cc_start: 0.8932 (tp30) cc_final: 0.8357 (tp30)
REVERT: J   24 GLN cc_start: 0.8817 (mm110) cc_final: 0.8124 (mp10)
REVERT: J   38 ASN cc_start: 0.9527 (m-40) cc_final: 0.9248 (m-40)
REVERT: J   39 TYR cc_start: 0.9314 (m-80) cc_final: 0.9051 (m-80)
REVERT: J   41 GLU cc_start: 0.8460 (tp30) cc_final: 0.8192 (tp30)
REVERT: J   94 ASN cc_start: 0.8737 (t0) cc_final: 0.8125 (m-40)
REVERT: J   95 LYS cc_start: 0.9180 (tttt) cc_final: 0.8819 (ttpt)
REVERT: J   99 ARG cc_start: 0.7936 (mpt180) cc_final: 0.7528 (mmt180)
REVERT: K   49 THR cc_start: 0.7054 (m) cc_final: 0.6797 (p)
REVERT: K   90 GLU cc_start: 0.9572 (mp0) cc_final: 0.9277 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1335
  time to fit residues: 50.1844
Evaluate side-chains
  208 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 208
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 31 optimal weight:    0.0870
   chunk 1 optimal weight:    5.9990
   chunk 111 optimal weight:    0.9990
   chunk 10 optimal weight:    1.9990
   chunk 52 optimal weight:    0.8980
   chunk 74 optimal weight:    0.5980
   chunk 128 optimal weight:    3.9990
   chunk 123 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   overall best weight:    0.9162

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

Flipped N/Q/H residues before XYZ refinement:
C 634 HIS
** D  68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
H  68 GLN
J  68 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.065223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.051321 restraints weight = 92841.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3096 r_free = 0.3096 target = 0.052588 restraints weight = 53713.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.053453 restraints weight = 37167.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.053970 restraints weight = 29064.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 52)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.054371 restraints weight = 24919.994|
|-----------------------------------------------------------------------------|
r_work (final): 0.3137
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3138
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3138 r_free = 0.3138    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3137 r_free = 0.3137    target_work(ls_wunit_k1) = 0.054         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.3137
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8141
moved from start:          0.6158

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.129  16904  Z= 0.193
  Angle     :  0.641  17.677  24155  Z= 0.357
  Chirality :  0.036   0.178   2706
  Planarity :  0.004   0.054   1989
  Dihedral  : 29.418  99.671   4740
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 13.43
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.50 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.09 %
    Favored  : 98.81 %
  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:  0.91 (0.25), residues: 1155
  helix:  1.65 (0.20), residues: 689
  sheet: -0.71 (1.48), residues: 10
  loop : -1.03 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E  23 
 TYR   0.014   0.001   TYR C 565 
 PHE   0.009   0.001   PHE C 639 
 TRP   0.006   0.001   TRP C 591 
 HIS   0.005   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00424 (16876)
  covalent geometry    : angle       0.61311 (24119)
  hydrogen bonds       : bond        0.04260 (  900)
  hydrogen bonds       : angle       3.58327 ( 2290)
  metal coordination   : bond        0.02495 (   28)
  metal coordination   : angle       4.90194 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  253 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 252
  time to evaluate  : 0.432 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.8426 (tmm) cc_final: 0.8121 (tmm)
REVERT: A  453 TYR cc_start: 0.7288 (m-10) cc_final: 0.6601 (p90)
REVERT: A  687 LEU cc_start: 0.9201 (tp) cc_final: 0.8783 (tp)
REVERT: A  696 THR cc_start: 0.8170 (m) cc_final: 0.7878 (p)
REVERT: C  590 GLU cc_start: 0.9088 (pm20) cc_final: 0.8467 (mt-10)
REVERT: C  591 TRP cc_start: 0.8878 (p-90) cc_final: 0.8597 (p-90)
REVERT: C  603 PHE cc_start: 0.5670 (m-80) cc_final: 0.5455 (m-80)
REVERT: C  612 GLU cc_start: 0.7656 (tp30) cc_final: 0.7425 (tp30)
REVERT: C  614 MET cc_start: 0.7772 (mtp) cc_final: 0.7451 (mtm)
REVERT: C  663 MET cc_start: 0.6013 (mtm) cc_final: 0.5579 (mtp)
REVERT: D   50 GLU cc_start: 0.8836 (tp30) cc_final: 0.8511 (tp30)
REVERT: D   93 GLN cc_start: 0.9141 (tt0) cc_final: 0.8284 (tt0)
REVERT: D   97 GLU cc_start: 0.8858 (mt-10) cc_final: 0.8294 (mt-10)
REVERT: D   99 TYR cc_start: 0.9100 (t80) cc_final: 0.8226 (t80)
REVERT: D  105 GLU cc_start: 0.8077 (pp20) cc_final: 0.7544 (pp20)
REVERT: D  120 MET cc_start: 0.8893 (mmm) cc_final: 0.8688 (mmm)
REVERT: E   88 TYR cc_start: 0.8425 (m-10) cc_final: 0.7787 (m-10)
REVERT: F   50 TYR cc_start: 0.8332 (t80) cc_final: 0.8112 (t80)
REVERT: F   61 GLU cc_start: 0.8943 (tp30) cc_final: 0.8526 (tp30)
REVERT: F   97 LEU cc_start: 0.9485 (mp) cc_final: 0.9271 (mp)
REVERT: G   31 LYS cc_start: 0.8571 (tmtt) cc_final: 0.8338 (tptp)
REVERT: G   40 LYS cc_start: 0.8385 (mtpt) cc_final: 0.8141 (mmtp)
REVERT: G   48 ASP cc_start: 0.8425 (t0) cc_final: 0.8183 (t0)
REVERT: G   56 MET cc_start: 0.8698 (tpp) cc_final: 0.8327 (tpp)
REVERT: G   64 ASN cc_start: 0.9074 (m-40) cc_final: 0.8714 (t0)
REVERT: G  102 GLU cc_start: 0.7561 (tp30) cc_final: 0.7107 (tp30)
REVERT: G  105 LYS cc_start: 0.8888 (ptmm) cc_final: 0.8400 (mtmt)
REVERT: H   46 VAL cc_start: 0.9372 (t) cc_final: 0.9104 (t)
REVERT: H   59 GLU cc_start: 0.7744 (pm20) cc_final: 0.7391 (pm20)
REVERT: H   76 GLN cc_start: 0.8153 (mt0) cc_final: 0.7762 (pt0)
REVERT: H   81 ASP cc_start: 0.8623 (m-30) cc_final: 0.8388 (m-30)
REVERT: H  105 GLU cc_start: 0.8915 (tp30) cc_final: 0.8286 (tp30)
REVERT: H  115 LYS cc_start: 0.8552 (tmtt) cc_final: 0.8279 (mmmm)
REVERT: H  123 ASP cc_start: 0.8821 (m-30) cc_final: 0.8608 (m-30)
REVERT: H  131 ARG cc_start: 0.9054 (mtt180) cc_final: 0.8708 (tpp80)
REVERT: I   63 GLU cc_start: 0.8923 (tp30) cc_final: 0.8315 (tp30)
REVERT: J   41 GLU cc_start: 0.8579 (tp30) cc_final: 0.8263 (tp30)
REVERT: J   56 GLU cc_start: 0.8691 (tt0) cc_final: 0.8112 (tm-30)
REVERT: J   94 ASN cc_start: 0.9008 (t0) cc_final: 0.8440 (m-40)
REVERT: J   95 LYS cc_start: 0.9197 (tttt) cc_final: 0.8893 (ttpt)
REVERT: J   99 ARG cc_start: 0.8064 (mpt180) cc_final: 0.7568 (mmt180)
REVERT: K   49 THR cc_start: 0.6983 (m) cc_final: 0.6779 (p)
REVERT: K   70 ILE cc_start: 0.9701 (mm) cc_final: 0.9497 (mm)
REVERT: K   90 GLU cc_start: 0.9523 (mp0) cc_final: 0.9142 (mp0)
  outliers start: 1
  outliers final: 0
  residues processed: 252
  average time/residue: 0.1343
  time to fit residues: 48.9277
Evaluate side-chains
  198 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 198
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 62 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0770
   chunk 26 optimal weight:    2.9990
   chunk 143 optimal weight:    3.9990
   chunk 27 optimal weight:    0.6980
   chunk 25 optimal weight:    5.9990
   chunk 16 optimal weight:    6.9990
   chunk 84 optimal weight:    0.0170
   chunk 14 optimal weight:    0.9980
   chunk 124 optimal weight:    2.9990
   chunk 24 optimal weight:    0.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
H  68 GLN
** K  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.066196 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3089 r_free = 0.3089 target = 0.052393 restraints weight = 92625.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.053704 restraints weight = 52896.628|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.054591 restraints weight = 36347.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.055122 restraints weight = 28317.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.055507 restraints weight = 24195.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.3171
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.055         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8107
moved from start:          0.6254

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.119  16904  Z= 0.159
  Angle     :  0.620  14.828  24155  Z= 0.347
  Chirality :  0.035   0.172   2706
  Planarity :  0.004   0.056   1989
  Dihedral  : 29.346  99.870   4740
  Min Nonbonded Distance : 2.205

Molprobity Statistics.
  All-atom Clashscore : 12.09
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  3.64 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.49 %
    Favored  : 99.51 %
  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:  0.97 (0.25), residues: 1155
  helix:  1.69 (0.20), residues: 690
  sheet: -0.66 (1.52), residues: 10
  loop : -0.99 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG E  23 
 TYR   0.010   0.001   TYR C 565 
 PHE   0.008   0.001   PHE E 100 
 TRP   0.012   0.001   TRP C 591 
 HIS   0.006   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00346 (16876)
  covalent geometry    : angle       0.60059 (24119)
  hydrogen bonds       : bond        0.03809 (  900)
  hydrogen bonds       : angle       3.43820 ( 2290)
  metal coordination   : bond        0.02336 (   28)
  metal coordination   : angle       4.05130 (   36)

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

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

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2310 Ramachandran restraints generated.
    1155 Oldfield, 0 Emsley, 1155 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  260 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 260
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  121 MET cc_start: 0.8271 (tmm) cc_final: 0.7852 (tmm)
REVERT: A  687 LEU cc_start: 0.9167 (tp) cc_final: 0.8789 (tp)
REVERT: A  696 THR cc_start: 0.8356 (m) cc_final: 0.8128 (p)
REVERT: C  590 GLU cc_start: 0.9106 (pm20) cc_final: 0.8473 (mt-10)
REVERT: C  591 TRP cc_start: 0.8885 (p-90) cc_final: 0.8635 (p-90)
REVERT: C  616 LEU cc_start: 0.8280 (mt) cc_final: 0.7987 (mt)
REVERT: C  663 MET cc_start: 0.5917 (mtm) cc_final: 0.5490 (mtp)
REVERT: D   50 GLU cc_start: 0.8969 (tp30) cc_final: 0.8666 (tp30)
REVERT: D   99 TYR cc_start: 0.9054 (t80) cc_final: 0.8033 (t80)
REVERT: D  105 GLU cc_start: 0.7903 (pp20) cc_final: 0.7578 (pp20)
REVERT: D  120 MET cc_start: 0.9002 (mmm) cc_final: 0.8424 (mmm)
REVERT: E   63 GLU cc_start: 0.8814 (tp30) cc_final: 0.8599 (tp30)
REVERT: E   88 TYR cc_start: 0.8367 (m-10) cc_final: 0.7708 (m-10)
REVERT: F   50 TYR cc_start: 0.8082 (t80) cc_final: 0.7709 (t80)
REVERT: F   57 TYR cc_start: 0.8980 (t80) cc_final: 0.8755 (t80)
REVERT: F   61 GLU cc_start: 0.8839 (tp30) cc_final: 0.8488 (tp30)
REVERT: G   31 LYS cc_start: 0.8554 (tmtt) cc_final: 0.8312 (tptp)
REVERT: G   56 MET cc_start: 0.8498 (tpp) cc_final: 0.8169 (tpp)
REVERT: G   64 ASN cc_start: 0.9033 (m-40) cc_final: 0.8693 (t0)
REVERT: G  105 LYS cc_start: 0.8847 (ptmm) cc_final: 0.8413 (ptpp)
REVERT: H   46 VAL cc_start: 0.9406 (t) cc_final: 0.9110 (t)
REVERT: H   59 GLU cc_start: 0.7674 (pm20) cc_final: 0.7324 (pm20)
REVERT: H   76 GLN cc_start: 0.8137 (mt0) cc_final: 0.7717 (pt0)
REVERT: H  105 GLU cc_start: 0.8958 (tp30) cc_final: 0.8491 (tp30)
REVERT: H  107 THR cc_start: 0.9476 (m) cc_final: 0.8954 (p)
REVERT: H  115 LYS cc_start: 0.8684 (tmtt) cc_final: 0.8355 (mmmt)
REVERT: H  123 ASP cc_start: 0.8759 (m-30) cc_final: 0.8498 (m-30)
REVERT: H  131 ARG cc_start: 0.9059 (mtt180) cc_final: 0.8707 (tpp80)
REVERT: I   63 GLU cc_start: 0.8873 (tp30) cc_final: 0.8296 (tp30)
REVERT: J   24 GLN cc_start: 0.8811 (mm110) cc_final: 0.8134 (mp10)
REVERT: J   41 GLU cc_start: 0.8509 (tp30) cc_final: 0.8200 (tp30)
REVERT: J   56 GLU cc_start: 0.8828 (tt0) cc_final: 0.8174 (tt0)
REVERT: J   94 ASN cc_start: 0.9079 (t0) cc_final: 0.8422 (m-40)
REVERT: J   95 LYS cc_start: 0.9148 (tttt) cc_final: 0.8847 (ttpt)
REVERT: J   99 ARG cc_start: 0.7958 (mpt180) cc_final: 0.7554 (mmt180)
REVERT: K   49 THR cc_start: 0.6980 (m) cc_final: 0.6750 (p)
REVERT: K   70 ILE cc_start: 0.9646 (mm) cc_final: 0.9445 (mm)
REVERT: K   90 GLU cc_start: 0.9583 (mp0) cc_final: 0.9276 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 260
  average time/residue: 0.1307
  time to fit residues: 48.7327
Evaluate side-chains
  213 residues out of total 1015 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 135 optimal weight:    2.9990
   chunk 80 optimal weight:    2.9990
   chunk 91 optimal weight:    0.1980
   chunk 35 optimal weight:    2.9990
   chunk 99 optimal weight:    0.0870
   chunk 50 optimal weight:    0.5980
   chunk 11 optimal weight:    6.9990
   chunk 69 optimal weight:    0.8980
   chunk 124 optimal weight:    2.9990
   chunk 129 optimal weight:    2.9990
   chunk 107 optimal weight:    0.0370
   overall best weight:    0.3636

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

Flipped N/Q/H residues before XYZ refinement:
C 634 HIS
H  68 GLN
** K  81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.067103 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3116 r_free = 0.3116 target = 0.053378 restraints weight = 92744.062|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.054716 restraints weight = 53080.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.055620 restraints weight = 36506.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.056182 restraints weight = 28467.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.056537 restraints weight = 24235.814|
|-----------------------------------------------------------------------------|
r_work (final): 0.3197
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3197
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3197 r_free = 0.3197    target_work(ls_wunit_k1) = 0.056         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
r_final: 0.3197
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.6357

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.108  16904  Z= 0.150
  Angle     :  0.619  13.351  24155  Z= 0.347
  Chirality :  0.035   0.202   2706
  Planarity :  0.004   0.057   1989
  Dihedral  : 29.284 100.806   4740
  Min Nonbonded Distance : 2.183

Molprobity Statistics.
  All-atom Clashscore : 12.13
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.33 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  0.49 %
    Favored  : 99.41 %
  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:  0.96 (0.26), residues: 1155
  helix:  1.66 (0.20), residues: 690
  sheet: -0.49 (1.51), residues: 10
  loop : -0.94 (0.31), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG E  23 
 TYR   0.011   0.001   TYR A 292 
 PHE   0.013   0.001   PHE H 104 
 TRP   0.017   0.002   TRP C 591 
 HIS   0.006   0.001   HIS I  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (16876)
  covalent geometry    : angle       0.60158 (24119)
  hydrogen bonds       : bond        0.03724 (  900)
  hydrogen bonds       : angle       3.43308 ( 2290)
  metal coordination   : bond        0.02100 (   28)
  metal coordination   : angle       3.77828 (   36)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2673.01 seconds
wall clock time: 46 minutes 39.35 seconds (2799.35 seconds total)