Starting phenix.real_space_refine
on Wed Mar  4 13:13:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6upk_20840/03_2026/6upk_20840.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6upk_20840/03_2026/6upk_20840.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6upk_20840/03_2026/6upk_20840.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6upk_20840/03_2026/6upk_20840.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6upk_20840/03_2026/6upk_20840.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6upk_20840/03_2026/6upk_20840.map"
  }
  resolution = 4.9
  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=   0.005 sd=   0.025
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: 5
    Type Number    sf(0)   Gaussians
     P     144      5.49       5
     S      44      5.16       5
     C    8349      2.51       5
     N    2497      2.21       5
     O    2827      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 15 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: 13861
  Number of models: 1
  Model: ""
    Number of chains: 13
    Chain: "A"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 76, 619
          Classifications: {'peptide': 76}
          Link IDs: {'PTRANS': 2, 'TRANS': 73}
    Chain: "B"
      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: "C"
      Number of atoms: 833
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 108, 833
          Classifications: {'peptide': 108}
          Link IDs: {'PTRANS': 5, 'TRANS': 102}
    Chain: "D"
      Number of atoms: 736
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 94, 736
          Classifications: {'peptide': 94}
          Link IDs: {'PTRANS': 2, 'TRANS': 91}
    Chain: "E"
      Number of atoms: 807
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 98, 807
          Classifications: {'peptide': 98}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 3, 'TRANS': 94}
    Chain: "F"
      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: "G"
      Number of atoms: 915
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 112, 915
          Classifications: {'peptide': 112}
          Link IDs: {'PTRANS': 8, 'TRANS': 103}
          Chain breaks: 2
    Chain: "G"
      Number of atoms: 2241
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 276, 2241
          Classifications: {'peptide': 276}
          Incomplete info: {'truncation_to_alanine': 6}
          Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 264}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 12
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 6
          Planarities with less than four sites: {'UNK:plan-1': 6}
          Unresolved non-hydrogen planarities: 6
    Chain: "G"
      Number of atoms: 175
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 35, 175
          Classifications: {'peptide': 35}
          Incomplete info: {'truncation_to_alanine': 35}
          Link IDs: {'TRANS': 34}
          Unresolved non-hydrogen bonds: 70
          Unresolved non-hydrogen angles: 105
          Unresolved non-hydrogen dihedrals: 35
          Planarities with less than four sites: {'UNK:plan-1': 35}
          Unresolved non-hydrogen planarities: 35
    Chain: "H"
      Number of atoms: 1364
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 167, 1358
          Classifications: {'peptide': 167}
          Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 160}
          Chain breaks: 1
      Conformer: "B"
        Number of residues, atoms: 167, 1358
          Classifications: {'peptide': 167}
          Link IDs: {'CIS': 2, 'PTRANS': 4, 'TRANS': 160}
          Chain breaks: 1
          bond proxies already assigned to first conformer: 1379
    Chain: "H"
      Number of atoms: 1962
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 244, 1956
          Classifications: {'peptide': 244}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 232}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'UNK:plan-1': 13, 'GLU:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 29
      Conformer: "B"
        Number of residues, atoms: 244, 1956
          Classifications: {'peptide': 244}
          Incomplete info: {'truncation_to_alanine': 17}
          Link IDs: {'CIS': 1, 'PCIS': 3, 'PTRANS': 7, 'TRANS': 232}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 42
          Unresolved non-hydrogen angles: 59
          Unresolved non-hydrogen dihedrals: 25
          Planarities with less than four sites: {'UNK:plan-1': 13, 'GLU:plan': 2, 'GLN:plan1': 2}
          Unresolved non-hydrogen planarities: 29
          bond proxies already assigned to first conformer: 1994
    Chain: "I"
      Number of atoms: 1466
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1466
          Classifications: {'DNA': 72}
          Link IDs: {'rna3p': 71}
    Chain: "J"
      Number of atoms: 1486
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 72, 1486
          Classifications: {'DNA': 72}
          Link IDs: {'rna3p': 71}
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N  ASER H  86 " occ=0.66
      ... (10 atoms not shown)
      pdb=" OG BSER H  86 " occ=0.34
    residue:
      pdb=" N  ACYS H 207 " occ=0.61
      ... (10 atoms not shown)
      pdb=" SG BCYS H 207 " occ=0.39
  Time building chain proxies: 3.50, per 1000 atoms: 0.25
  Number of scatterers: 13861
  At special positions: 0
  Unit cell: (95.4045, 120.659, 165.555, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      44     16.00
     P     144     15.00
     O    2827      8.00
     N    2497      7.00
     C    8349      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
  Links applied
    TRANS
      " UNK G 634 " - " LYS G 633 "
      " UNK G 926 " - " LEU G 925 "
      " UNK H 172 " - " GLN H 171 "
  Time building additional restraints: 1.40
  Conformation dependent library (CDL) restraints added in 580.9 milliseconds
  

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2576

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 16 sheets defined
      39.6% alpha, 17.8% beta
      65 base pairs and 102 stacking pairs defined.
    Time for finding SS restraints: 2.26
  Creating SS restraints...
    Processing helix  chain 'A' and resid 63 through 79
      removed outlier: 3.921A  pdb=" N   PHE A  67 " --> pdb=" O   ARG A  63 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A  70 " --> pdb=" O   PRO A  66 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   ALA A  75 " --> pdb=" O   VAL A  71 " (cutoff:3.500A)
      removed outlier: 4.418A  pdb=" N   GLN A  76 " --> pdb=" O   ARG A  72 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   ASP A  77 " --> pdb=" O   GLU A  73 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   PHE A  78 " --> pdb=" O   ILE A  74 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 85 through 114
      removed outlier: 3.872A  pdb=" N   VAL A  89 " --> pdb=" O   GLN A  85 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   MET A  90 " --> pdb=" O   SER A  86 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ALA A  91 " --> pdb=" O   SER A  87 " (cutoff:3.500A)
      removed outlier: 3.954A  pdb=" N   GLY A 102 " --> pdb=" O   ALA A  98 " (cutoff:3.500A)
      removed outlier: 5.401A  pdb=" N   LEU A 103 " --> pdb=" O   TYR A  99 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   ASP A 106 " --> pdb=" O   GLY A 102 " (cutoff:3.500A)
      removed outlier: 4.360A  pdb=" N   THR A 107 " --> pdb=" O   LEU A 103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 120 through 131
      removed outlier: 3.650A  pdb=" N   ILE A 124 " --> pdb=" O   MET A 120 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   ALA A 127 " --> pdb=" O   ASP A 123 " (cutoff:3.500A)
      removed outlier: 3.710A  pdb=" N   ARG A 128 " --> pdb=" O   ILE A 124 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   ARG A 129 " --> pdb=" O   GLN A 125 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 25 through 29
    Processing helix  chain 'B' and resid 30 through 41
    Processing helix  chain 'B' and resid 48 through 77
      removed outlier: 4.211A  pdb=" N   GLU B  52 " --> pdb=" O   GLY B  48 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   ARG B  55 " --> pdb=" O   TYR B  51 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLY B  56 " --> pdb=" O   GLU B  52 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL B  57 " --> pdb=" O   GLU B  53 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   ASN B  64 " --> pdb=" O   VAL B  60 " (cutoff:3.500A)
      removed outlier: 4.027A  pdb=" N   VAL B  65 " --> pdb=" O   PHE B  61 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   ALA B  69 " --> pdb=" O   VAL B  65 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 82 through 94
      removed outlier: 3.970A  pdb=" N   VAL B  86 " --> pdb=" O   THR B  82 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 26 through 38
      removed outlier: 3.557A  pdb=" N   LYS C  36 " --> pdb=" O   ARG C  32 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   GLY C  37 " --> pdb=" O   LEU C  33 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 45 through 74
      removed outlier: 4.137A  pdb=" N   VAL C  49 " --> pdb=" O   ALA C  45 " (cutoff:3.500A)
      removed outlier: 3.606A  pdb=" N   LEU C  51 " --> pdb=" O   ALA C  47 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   ALA C  60 " --> pdb=" O   GLU C  56 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 81 through 87
    Processing helix  chain 'C' and resid 91 through 97
    Processing helix  chain 'C' and resid 112 through 116
    Processing helix  chain 'D' and resid 40 through 45
    Processing helix  chain 'D' and resid 55 through 84
      removed outlier: 3.763A  pdb=" N   ASN D  67 " --> pdb=" O   ASN D  63 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE D  69 " --> pdb=" O   PHE D  65 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   ARG D  72 " --> pdb=" O   ASP D  68 " (cutoff:3.500A)
      removed outlier: 3.919A  pdb=" N   GLU D  76 " --> pdb=" O   ARG D  72 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 90 through 102
      removed outlier: 3.756A  pdb=" N   ALA D  97 " --> pdb=" O   GLU D  93 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 103 through 124
    Processing helix  chain 'E' and resid 44 through 57
      removed outlier: 4.205A  pdb=" N   LYS E  56 " --> pdb=" O   ARG E  52 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   SER E  57 " --> pdb=" O   ARG E  53 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 64 through 79
      removed outlier: 4.191A  pdb=" N   LEU E  70 " --> pdb=" O   PRO E  66 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASP E  77 " --> pdb=" O   GLU E  73 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   PHE E  78 " --> pdb=" O   ILE E  74 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 85 through 115
      removed outlier: 3.925A  pdb=" N   VAL E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   GLU E  97 " --> pdb=" O   GLN E  93 " (cutoff:3.500A)
      removed outlier: 3.927A  pdb=" N   GLY E 102 " --> pdb=" O   ALA E  98 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   LEU E 103 " --> pdb=" O   TYR E  99 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 121 through 132
      removed outlier: 4.655A  pdb=" N   GLN E 125 " --> pdb=" O   PRO E 121 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 24 through 29
      removed outlier: 3.940A  pdb=" N   ILE F  29 " --> pdb=" O   ILE F  26 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 30 through 41
    Processing helix  chain 'F' and resid 49 through 76
      removed outlier: 4.244A  pdb=" N   GLU F  53 " --> pdb=" O   LEU F  49 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   PHE F  61 " --> pdb=" O   VAL F  57 " (cutoff:3.500A)
      removed outlier: 4.161A  pdb=" N   ASP F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.583A  pdb=" N   THR F  73 " --> pdb=" O   ALA F  69 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 83 through 94
      removed outlier: 3.685A  pdb=" N   VAL F  87 " --> pdb=" O   ALA F  83 " (cutoff:3.500A)
      removed outlier: 3.743A  pdb=" N   TYR F  88 " --> pdb=" O   MET F  84 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 617 through 636
      removed outlier: 4.396A  pdb=" N   ILE G 624 " --> pdb=" O   ASN G 620 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   ILE G 625 " --> pdb=" O   ALA G 621 " (cutoff:3.500A)
      removed outlier: 4.430A  pdb=" N   LYS G 626 " --> pdb=" O   PHE G 622 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   GLU G 627 " --> pdb=" O   ARG G 623 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   VAL G 628 " --> pdb=" O   ILE G 624 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 763 through 788
      removed outlier: 3.635A  pdb=" N   GLN G 767 " --> pdb=" O   LEU G 763 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   LYS G 775 " --> pdb=" O   GLU G 771 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LEU G 776 " --> pdb=" O   MET G 772 " (cutoff:3.500A)
      removed outlier: 4.399A  pdb=" N   ALA G 779 " --> pdb=" O   LYS G 775 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 878 through 890
    Processing helix  chain 'G' and resid 901 through 910
    Processing helix  chain 'G' and resid 916 through 924
      removed outlier: 3.717A  pdb=" N   GLY G 920 " --> pdb=" O   PHE G 917 " (cutoff:3.500A)
      removed outlier: 5.365A  pdb=" N   GLY G 921 " --> pdb=" O   GLU G 918 " (cutoff:3.500A)
      removed outlier: 5.989A  pdb=" N   TRP G 922 " --> pdb=" O   GLN G 919 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 80 through 90
      removed outlier: 4.258A  pdb=" N  ASER H  86 " --> pdb=" O   PHE H  82 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 176 through 180
      removed outlier: 3.549A  pdb=" N   UNK H 180 " --> pdb=" O   UNK H 177 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 292 through 299
    Processing helix  chain 'H' and resid 309 through 323
      removed outlier: 3.796A  pdb=" N   SER H 315 " --> pdb=" O   TYR H 311 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   VAL H 317 " --> pdb=" O   MET H 313 " (cutoff:3.500A)
    Processing helix  chain 'H' and resid 334 through 338
    Processing helix  chain 'H' and resid 407 through 421
    Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84
      removed outlier: 7.269A  pdb=" N   ARG A  83 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'C' and resid 77 through 78
    Processing sheet with id=AA3, first strand: chain 'E' and resid 83 through 84
      removed outlier: 6.917A  pdb=" N   ARG E  83 " --> pdb=" O   VAL F  81 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'G' and resid 530 through 532
      removed outlier: 3.722A  pdb=" N   TYR G 530 " --> pdb=" O   ILE G 539 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'G' and resid 554 through 562
      removed outlier: 6.642A  pdb=" N   GLU G 597 " --> pdb=" O   VAL H 163 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   VAL H 163 " --> pdb=" O   GLU G 597 " (cutoff:3.500A)
      removed outlier: 6.717A  pdb=" N   THR G 599 " --> pdb=" O   MET H 161 " (cutoff:3.500A)
      removed outlier: 3.643A  pdb=" N   VAL H 163 " --> pdb=" O   LEU H 148 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   THR H 140 " --> pdb=" O   THR H 147 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLN H 138 " --> pdb=" O   GLU H 149 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'G' and resid 698 through 700
      removed outlier: 3.585A  pdb=" N   GLY G 686 " --> pdb=" O   HIS G 683 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   LEU G 665 " --> pdb=" O   GLY G 678 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   LEU G 680 " --> pdb=" O   LYS G 663 " (cutoff:3.500A)
      removed outlier: 6.369A  pdb=" N   LYS G 663 " --> pdb=" O   LEU G 680 " (cutoff:3.500A)
      removed outlier: 7.555A  pdb=" N   ALA G 682 " --> pdb=" O   LYS G 661 " (cutoff:3.500A)
      removed outlier: 6.268A  pdb=" N   LYS G 661 " --> pdb=" O   ALA G 682 " (cutoff:3.500A)
      removed outlier: 9.532A  pdb=" N   ASP G 664 " --> pdb=" O   GLU G 743 " (cutoff:3.500A)
      removed outlier: 5.493A  pdb=" N   GLU G 743 " --> pdb=" O   ASP G 664 " (cutoff:3.500A)
      removed outlier: 8.173A  pdb=" N   ARG G 734 " --> pdb=" O   ASN G 726 " (cutoff:3.500A)
      removed outlier: 8.648A  pdb=" N   ASN G 726 " --> pdb=" O   ARG G 734 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   THR G 736 " --> pdb=" O   LEU G 724 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL G 738 " --> pdb=" O   PHE G 722 " (cutoff:3.500A)
      removed outlier: 6.709A  pdb=" N   VAL G 719 " --> pdb=" O   PHE G 709 " (cutoff:3.500A)
      removed outlier: 4.209A  pdb=" N   PHE G 709 " --> pdb=" O   VAL G 719 " (cutoff:3.500A)
      removed outlier: 6.703A  pdb=" N   HIS G 721 " --> pdb=" O   ALA G 707 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA G 707 " --> pdb=" O   HIS G 721 " (cutoff:3.500A)
      removed outlier: 6.504A  pdb=" N   HIS G 723 " --> pdb=" O   LYS G 705 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'G' and resid 806 through 808
      removed outlier: 3.501A  pdb=" N   PHE G 833 " --> pdb=" O   ASN G 826 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'G' and resid 870 through 874
      removed outlier: 6.770A  pdb=" N   MET G 870 " --> pdb=" O   ILE G 859 " (cutoff:3.500A)
      removed outlier: 7.389A  pdb=" N   ILE G 859 " --> pdb=" O   MET G 870 " (cutoff:3.500A)
      removed outlier: 5.618A  pdb=" N   ASN G 872 " --> pdb=" O   MET G 857 " (cutoff:3.500A)
      removed outlier: 6.997A  pdb=" N   MET G 857 " --> pdb=" O   ASN G 872 " (cutoff:3.500A)
      removed outlier: 8.760A  pdb=" N   THR G 894 " --> pdb=" O   GLU G 841 " (cutoff:3.500A)
      removed outlier: 5.895A  pdb=" N   ILE G 843 " --> pdb=" O   THR G 894 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'H' and resid 6 through 7
    Processing sheet with id=AB1, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.597A  pdb=" N   ASP H  75 " --> pdb=" O   TYR H  11 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   LEU H  62 " --> pdb=" O   TYR H  74 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   LYS H  63 " --> pdb=" O   ILE H  52 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   ILE H  52 " --> pdb=" O   LYS H  63 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'H' and resid 111 through 114
      removed outlier: 4.698A  pdb=" N   LEU H 119 " --> pdb=" O   GLU H 130 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   GLU H 130 " --> pdb=" O   LEU H 119 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   PHE H 121 " --> pdb=" O   VAL H 128 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'H' and resid 200 through 201
      removed outlier: 3.676A  pdb=" N   CYS H 200 " --> pdb=" O   ILE H 218 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'H' and resid 200 through 201
      removed outlier: 3.676A  pdb=" N   CYS H 200 " --> pdb=" O   ILE H 218 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'H' and resid 239 through 246
      removed outlier: 6.507A  pdb=" N   SER H 258 " --> pdb=" O   LEU H 240 " (cutoff:3.500A)
      removed outlier: 5.798A  pdb=" N   LEU H 242 " --> pdb=" O   VAL H 256 " (cutoff:3.500A)
      removed outlier: 7.871A  pdb=" N   VAL H 256 " --> pdb=" O   LEU H 242 " (cutoff:3.500A)
      removed outlier: 5.177A  pdb=" N   LEU H 244 " --> pdb=" O   PHE H 254 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   PHE H 254 " --> pdb=" O   LEU H 244 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   GLN H 252 " --> pdb=" O   PRO H 246 " (cutoff:3.500A)
      removed outlier: 5.951A  pdb=" N   HIS H 271 " --> pdb=" O   LEU H 259 " (cutoff:3.500A)
      removed outlier: 9.554A  pdb=" N   ARG H 269 " --> pdb=" O   PRO H 261 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'H' and resid 342 through 344
    Processing sheet with id=AB7, first strand: chain 'H' and resid 400 through 406
      removed outlier: 6.520A  pdb=" N   PHE H 389 " --> pdb=" O   SER H 405 " (cutoff:3.500A)
      removed outlier: 7.841A  pdb=" N   LYS H 426 " --> pdb=" O   SER H 375 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL H 377 " --> pdb=" O   LYS H 426 " (cutoff:3.500A)

    436 hydrogen bonds defined for protein.
    1231 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      152 hydrogen bonds
      244 hydrogen bond angles
      0 basepair planarities
      65 basepair parallelities
      102 stacking parallelities
  Total time for adding SS restraints: 3.72

  Time building geometry restraints manager: 1.79 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3383
        1.33 -     1.45: 3635
        1.45 -     1.57: 7041
        1.57 -     1.70: 286
        1.70 -     1.82: 73
  Bond restraints: 14418
  Sorted by residual:
  bond pdb=" CA  GLU H 299 "
       pdb=" C   GLU H 299 "
    ideal  model  delta    sigma   weight residual
    1.523  1.558 -0.034 1.34e-02 5.57e+03 6.56e+00
  bond pdb=" N   ASP H 101 "
       pdb=" CA  ASP H 101 "
    ideal  model  delta    sigma   weight residual
    1.458  1.499 -0.041 1.90e-02 2.77e+03 4.58e+00
  bond pdb=" C   TYR H  93 "
       pdb=" N   ARG H  94 "
    ideal  model  delta    sigma   weight residual
    1.333  1.306  0.028 1.43e-02 4.89e+03 3.74e+00
  bond pdb=" C   LYS H 100 "
       pdb=" N   ASP H 101 "
    ideal  model  delta    sigma   weight residual
    1.329  1.354 -0.025 1.40e-02 5.10e+03 3.29e+00
  bond pdb=" N   GLU H 299 "
       pdb=" CA  GLU H 299 "
    ideal  model  delta    sigma   weight residual
    1.457  1.480 -0.023 1.29e-02 6.01e+03 3.13e+00
  ... (remaining 14413 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.25: 19345
        2.25 -     4.50: 640
        4.50 -     6.75: 66
        6.75 -     9.00: 10
        9.00 -    11.26: 6
  Bond angle restraints: 20067
  Sorted by residual:
  angle pdb=" N   TYR H  93 "
        pdb=" CA  TYR H  93 "
        pdb=" C   TYR H  93 "
      ideal   model   delta    sigma   weight residual
     111.75  122.51  -10.76 1.28e+00 6.10e-01 7.07e+01
  angle pdb=" N   ILE G 586 "
        pdb=" CA  ILE G 586 "
        pdb=" C   ILE G 586 "
      ideal   model   delta    sigma   weight residual
     111.91  105.33    6.58 8.90e-01 1.26e+00 5.46e+01
  angle pdb=" N   THR H 170 "
        pdb=" CA  THR H 170 "
        pdb=" C   THR H 170 "
      ideal   model   delta    sigma   weight residual
     111.28  102.21    9.07 1.35e+00 5.49e-01 4.51e+01
  angle pdb=" N   TYR E  41 "
        pdb=" CA  TYR E  41 "
        pdb=" C   TYR E  41 "
      ideal   model   delta    sigma   weight residual
     110.50  119.93   -9.43 1.41e+00 5.03e-01 4.47e+01
  angle pdb=" C   LYS H 100 "
        pdb=" N   ASP H 101 "
        pdb=" CA  ASP H 101 "
      ideal   model   delta    sigma   weight residual
     121.70  132.96  -11.26 1.80e+00 3.09e-01 3.91e+01
  ... (remaining 20062 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    27.34: 7400
       27.34 -    54.68: 770
       54.68 -    82.01: 148
       82.01 -   109.35: 3
      109.35 -   136.69: 2
  Dihedral angle restraints: 8323
    sinusoidal: 4337
      harmonic: 3986
  Sorted by residual:
  dihedral pdb=" CA  PHE H 165 "
           pdb=" C   PHE H 165 "
           pdb=" N   TYR H 166 "
           pdb=" CA  TYR H 166 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  151.69   28.31     0      5.00e+00 4.00e-02 3.21e+01
  dihedral pdb=" CA  TYR H  11 "
           pdb=" C   TYR H  11 "
           pdb=" N   GLN H  12 "
           pdb=" CA  GLN H  12 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.04   27.96     0      5.00e+00 4.00e-02 3.13e+01
  dihedral pdb=" CA  PHE H  89 "
           pdb=" C   PHE H  89 "
           pdb=" N   LYS H  90 "
           pdb=" CA  LYS H  90 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -152.38  -27.62     0      5.00e+00 4.00e-02 3.05e+01
  ... (remaining 8320 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.097: 2085
       0.097 -    0.193: 152
       0.193 -    0.290: 8
       0.290 -    0.386: 2
       0.386 -    0.482: 2
  Chirality restraints: 2249
  Sorted by residual:
  chirality pdb=" CB  VAL H 362 "
            pdb=" CA  VAL H 362 "
            pdb=" CG1 VAL H 362 "
            pdb=" CG2 VAL H 362 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.15   -0.48 2.00e-01 2.50e+01 5.82e+00
  chirality pdb=" CA  TYR H  93 "
            pdb=" N   TYR H  93 "
            pdb=" C   TYR H  93 "
            pdb=" CB  TYR H  93 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.12    0.39 2.00e-01 2.50e+01 3.79e+00
  chirality pdb=" CB  ILE G 718 "
            pdb=" CA  ILE G 718 "
            pdb=" CG1 ILE G 718 "
            pdb=" CG2 ILE G 718 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.28    0.36 2.00e-01 2.50e+01 3.24e+00
  ... (remaining 2246 not shown)

  Planarity restraints: 2064
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  VAL H 167 "   -0.020 2.00e-02 2.50e+03   4.05e-02 1.64e+01
        pdb=" C   VAL H 167 "    0.070 2.00e-02 2.50e+03
        pdb=" O   VAL H 167 "   -0.026 2.00e-02 2.50e+03
        pdb=" N   PRO H 168 "   -0.024 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS H  92 "   -0.018 2.00e-02 2.50e+03   3.73e-02 1.39e+01
        pdb=" C   HIS H  92 "    0.064 2.00e-02 2.50e+03
        pdb=" O   HIS H  92 "   -0.024 2.00e-02 2.50e+03
        pdb=" N   TYR H  93 "   -0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR D  40 "   -0.023 2.00e-02 2.50e+03   1.88e-02 7.10e+00
        pdb=" CG  TYR D  40 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TYR D  40 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TYR D  40 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE1 TYR D  40 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE2 TYR D  40 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR D  40 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR D  40 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 2061 not shown)

  Histogram of nonbonded interaction distances:
        1.57 -     2.24: 27
        2.24 -     2.90: 5241
        2.90 -     3.57: 21765
        3.57 -     4.23: 36651
        4.23 -     4.90: 54899
  Nonbonded interactions: 118583
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS G 626 "
            pdb=" OP1  DT I  -6 "
     model   vdw
     1.570 3.120
  nonbonded pdb=" NE2 GLN H 267 "
            pdb=" OP1  DC J   1 "
     model   vdw
     1.571 3.120
  nonbonded pdb=" CG  GLN H 267 "
            pdb=" OP1  DC J   1 "
     model   vdw
     1.687 3.440
  nonbonded pdb=" NH1 ARG E  40 "
            pdb=" N2   DG J  -8 "
     model   vdw
     1.734 3.200
  nonbonded pdb=" CD  GLN H 267 "
            pdb=" OP1  DC J   1 "
     model   vdw
     1.833 3.270
  ... (remaining 118578 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = (chain 'F' and resid 25 through 102)
}

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=0.32 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:             0.850
  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:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.050
  Set scattering table:                    0.040
  Process input model:                     17.390
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.780
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.076  14421  Z= 0.266
  Angle     :  0.939  11.256  20076  Z= 0.553
  Chirality :  0.053   0.482   2249
  Planarity :  0.007   0.064   2061
  Dihedral  : 20.423 136.691   5738
  Min Nonbonded Distance : 1.570

Molprobity Statistics.
  All-atom Clashscore : 20.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -3.94 (0.19), residues: 1292
  helix: -2.50 (0.17), residues: 446
  sheet: -3.00 (0.34), residues: 169
  loop : -2.58 (0.20), residues: 677

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG D  79 
 TYR   0.046   0.004   TYR D  40 
 PHE   0.037   0.003   PHE H 222 
 TRP   0.024   0.003   TRP G 902 
 HIS   0.009   0.002   HIS H 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00541 (14418)
  covalent geometry    : angle       0.93929 (20067)
  hydrogen bonds       : bond        0.18724 (  587)
  hydrogen bonds       : angle       8.33307 ( 1475)
  link_TRANS           : bond        0.00336 (    3)
  link_TRANS           : angle       0.74565 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 134
  time to evaluate  : 0.404 
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   97 GLU cc_start: 0.9866 (mt-10) cc_final: 0.9598 (mp0)
REVERT: A   99 TYR cc_start: 0.9380 (t80) cc_final: 0.8876 (t80)
REVERT: A  129 ARG cc_start: 0.9575 (mtt180) cc_final: 0.9007 (ttm110)
REVERT: B   50 ILE cc_start: 0.9300 (mm) cc_final: 0.8839 (mm)
REVERT: B   61 PHE cc_start: 0.9595 (t80) cc_final: 0.9337 (t80)
REVERT: B   68 ASP cc_start: 0.9072 (p0) cc_final: 0.8815 (p0)
REVERT: D   37 TYR cc_start: 0.9109 (m-80) cc_final: 0.8849 (m-80)
REVERT: D   82 HIS cc_start: 0.9774 (t-90) cc_final: 0.9522 (m90)
REVERT: E   67 PHE cc_start: 0.9506 (t80) cc_final: 0.9134 (t80)
REVERT: E   94 GLU cc_start: 0.9712 (tp30) cc_final: 0.9452 (tt0)
REVERT: F   84 MET cc_start: 0.9609 (mmp) cc_final: 0.9406 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 134
  average time/residue: 0.1272
  time to fit residues: 23.9687
Evaluate side-chains
  91 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 91
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
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:   20.0000
   chunk 107 optimal weight:   20.0000
   chunk 10 optimal weight:    0.9980
   chunk 66 optimal weight:   20.0000
   chunk 130 optimal weight:    3.9990
   chunk 124 optimal weight:   10.0000
   chunk 103 optimal weight:    0.3980
   chunk 77 optimal weight:    7.9990
   chunk 122 optimal weight:    9.9990
   chunk 91 optimal weight:   20.0000
   chunk 55 optimal weight:    5.9990
   overall best weight:    3.8786

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 125 GLN
B  64 ASN
** B  75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  68 ASN
C 110 ASN
E  85 GLN
E  93 GLN
F  25 ASN
G 585 ASN
G 604 ASN
G 619 GLN
H  12 GLN
** H  60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H 144 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.048860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3049 r_free = 0.3049 target = 0.037949 restraints weight = 448595.104|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.039664 restraints weight = 177389.083|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.039768 restraints weight = 80899.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.039930 restraints weight = 59311.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.040104 restraints weight = 51235.214|
|-----------------------------------------------------------------------------|
r_work (final): 0.2625
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2587
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2587 r_free = 0.2587    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.32   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2584 r_free = 0.2584    target_work(ls_wunit_k1) = 0.027         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2584
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.2249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14421  Z= 0.197
  Angle     :  0.667  10.865  20076  Z= 0.375
  Chirality :  0.041   0.230   2249
  Planarity :  0.006   0.059   2061
  Dihedral  : 26.029 139.253   3072
  Min Nonbonded Distance : 1.948

Molprobity Statistics.
  All-atom Clashscore : 19.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.00 %
    Favored  : 98.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -2.71 (0.21), residues: 1292
  helix: -0.84 (0.21), residues: 478
  sheet: -2.70 (0.36), residues: 162
  loop : -2.30 (0.22), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F  67 
 TYR   0.019   0.002   TYR D  40 
 PHE   0.015   0.002   PHE H 415 
 TRP   0.021   0.002   TRP G 902 
 HIS   0.005   0.001   HIS F  75 

Details of bonding type rmsd
  covalent geometry    : bond        0.00410 (14418)
  covalent geometry    : angle       0.66732 (20067)
  hydrogen bonds       : bond        0.08440 (  587)
  hydrogen bonds       : angle       6.25796 ( 1475)
  link_TRANS           : bond        0.00203 (    3)
  link_TRANS           : angle       0.73331 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 119
  time to evaluate  : 0.470 
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   67 PHE cc_start: 0.9627 (t80) cc_final: 0.9287 (t80)
REVERT: A   99 TYR cc_start: 0.9039 (t80) cc_final: 0.8601 (t80)
REVERT: A  128 ARG cc_start: 0.9734 (mtp180) cc_final: 0.9510 (ttm110)
REVERT: B   61 PHE cc_start: 0.9278 (t80) cc_final: 0.8827 (t80)
REVERT: B   63 GLU cc_start: 0.9264 (pt0) cc_final: 0.8832 (pt0)
REVERT: B   68 ASP cc_start: 0.8737 (p0) cc_final: 0.8017 (p0)
REVERT: C   50 TYR cc_start: 0.9174 (t80) cc_final: 0.8724 (t80)
REVERT: E   62 ILE cc_start: 0.9092 (mm) cc_final: 0.8806 (mm)
REVERT: E   67 PHE cc_start: 0.9240 (t80) cc_final: 0.8163 (t80)
REVERT: E   93 GLN cc_start: 0.9588 (tt0) cc_final: 0.8956 (tp40)
REVERT: E   94 GLU cc_start: 0.9730 (tp30) cc_final: 0.9364 (tt0)
REVERT: G  870 MET cc_start: 0.7042 (tpt) cc_final: 0.6752 (tpp)
REVERT: G  906 MET cc_start: 0.7922 (mmt) cc_final: 0.7333 (mmp)
REVERT: H  253 MET cc_start: 0.9119 (mmp) cc_final: 0.8832 (mmm)
  outliers start: 0
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1288
  time to fit residues: 21.9854
Evaluate side-chains
  87 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 22 optimal weight:    7.9990
   chunk 144 optimal weight:    8.9990
   chunk 132 optimal weight:    8.9990
   chunk 21 optimal weight:    6.9990
   chunk 109 optimal weight:    8.9990
   chunk 95 optimal weight:    0.9980
   chunk 133 optimal weight:    7.9990
   chunk 58 optimal weight:    3.9990
   chunk 14 optimal weight:    9.9990
   chunk 17 optimal weight:   10.0000
   chunk 113 optimal weight:    7.9990
   overall best weight:    5.5988

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  89 ASN
** E  85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** H  60 HIS ** 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 = 0.3025 r_free = 0.3025 target = 0.044651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.032795 restraints weight = 496898.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 51)----------------|
| r_work = 0.2894 r_free = 0.2894 target = 0.034379 restraints weight = 167918.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.035357 restraints weight = 83709.282|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.2955 r_free = 0.2955 target = 0.035946 restraints weight = 51637.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.2973 r_free = 0.2973 target = 0.036368 restraints weight = 36559.993|
|-----------------------------------------------------------------------------|
r_work (final): 0.2514
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2537
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2537 r_free = 0.2537    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2536 r_free = 0.2536    target_work(ls_wunit_k1) = 0.025         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2536
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8075
moved from start:          0.3493

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065  14421  Z= 0.258
  Angle     :  0.718  10.844  20076  Z= 0.404
  Chirality :  0.043   0.246   2249
  Planarity :  0.006   0.065   2061
  Dihedral  : 26.500 141.448   3072
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 28.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.23 %
    Favored  : 92.77 %
  Rotamer:
    Outliers :  0.26 %
    Allowed  :  2.70 %
    Favored  : 97.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -2.30 (0.22), residues: 1292
  helix: -0.33 (0.22), residues: 478
  sheet: -2.79 (0.35), residues: 174
  loop : -2.09 (0.23), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG G 569 
 TYR   0.026   0.002   TYR B  72 
 PHE   0.017   0.002   PHE H 403 
 TRP   0.019   0.003   TRP G 902 
 HIS   0.011   0.002   HIS H 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00535 (14418)
  covalent geometry    : angle       0.71810 (20067)
  hydrogen bonds       : bond        0.08930 (  587)
  hydrogen bonds       : angle       6.30763 ( 1475)
  link_TRANS           : bond        0.00226 (    3)
  link_TRANS           : angle       0.59963 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 104
  time to evaluate  : 0.497 
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   99 TYR cc_start: 0.9539 (t80) cc_final: 0.8837 (t80)
REVERT: A  110 CYS cc_start: 0.9305 (m) cc_final: 0.8887 (m)
REVERT: B   68 ASP cc_start: 0.8928 (p0) cc_final: 0.8723 (p0)
REVERT: C   50 TYR cc_start: 0.9508 (t80) cc_final: 0.8919 (t80)
REVERT: D   59 MET cc_start: 0.9541 (ttm) cc_final: 0.9199 (mtp)
REVERT: E   67 PHE cc_start: 0.9308 (t80) cc_final: 0.8847 (t80)
REVERT: E   94 GLU cc_start: 0.9767 (tp30) cc_final: 0.9439 (tt0)
REVERT: F   84 MET cc_start: 0.9729 (mpp) cc_final: 0.9488 (mpp)
REVERT: H  289 MET cc_start: 0.8880 (mpp) cc_final: 0.8609 (mpp)
  outliers start: 3
  outliers final: 2
  residues processed: 107
  average time/residue: 0.1128
  time to fit residues: 17.8198
Evaluate side-chains
  73 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 71
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 64 optimal weight:    7.9990
   chunk 80 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 106 optimal weight:    6.9990
   chunk 139 optimal weight:    6.9990
   chunk 56 optimal weight:    0.8980
   chunk 33 optimal weight:    0.0670
   chunk 118 optimal weight:   10.0000
   chunk 23 optimal weight:    7.9990
   chunk 18 optimal weight:    5.9990
   chunk 123 optimal weight:    0.6980
   overall best weight:    1.6720

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B  93 GLN
D  82 HIS
E  85 GLN
E  93 GLN
H  60 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2843 r_free = 0.2843 target = 0.034451 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2462 r_free = 0.2462 target = 0.022105 restraints weight = 439730.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.2522 r_free = 0.2522 target = 0.023616 restraints weight = 186771.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.024647 restraints weight = 108085.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.2591 r_free = 0.2591 target = 0.025332 restraints weight = 72816.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 62)----------------|
| r_work = 0.2608 r_free = 0.2608 target = 0.025829 restraints weight = 54041.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.2542
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2517
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2517 r_free = 0.2517    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2517 r_free = 0.2517    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2517
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8340
moved from start:          0.3645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  14421  Z= 0.132
  Angle     :  0.581   7.684  20076  Z= 0.328
  Chirality :  0.040   0.210   2249
  Planarity :  0.004   0.063   2061
  Dihedral  : 26.412 138.323   3072
  Min Nonbonded Distance : 2.022

Molprobity Statistics.
  All-atom Clashscore : 16.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.39 %
    Favored  : 98.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -1.65 (0.23), residues: 1292
  helix:  0.36 (0.23), residues: 487
  sheet: -2.31 (0.38), residues: 165
  loop : -1.94 (0.23), residues: 640

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG G 569 
 TYR   0.014   0.001   TYR D  42 
 PHE   0.017   0.001   PHE F  61 
 TRP   0.018   0.002   TRP G 922 
 HIS   0.011   0.001   HIS A 113 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (14418)
  covalent geometry    : angle       0.58057 (20067)
  hydrogen bonds       : bond        0.07820 (  587)
  hydrogen bonds       : angle       5.43913 ( 1475)
  link_TRANS           : bond        0.00160 (    3)
  link_TRANS           : angle       0.61049 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 128
  time to evaluate  : 0.465 
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   67 PHE cc_start: 0.9645 (t80) cc_final: 0.9342 (t80)
REVERT: A   96 CYS cc_start: 0.9755 (t) cc_final: 0.9435 (t)
REVERT: A   97 GLU cc_start: 0.9730 (mt-10) cc_final: 0.9491 (mm-30)
REVERT: A  110 CYS cc_start: 0.9484 (m) cc_final: 0.9282 (m)
REVERT: A  122 LYS cc_start: 0.9220 (ttpt) cc_final: 0.8761 (ptmt)
REVERT: A  129 ARG cc_start: 0.9778 (mtt180) cc_final: 0.9438 (mmp80)
REVERT: B   68 ASP cc_start: 0.8863 (p0) cc_final: 0.8217 (p0)
REVERT: D   37 TYR cc_start: 0.8403 (m-80) cc_final: 0.7914 (m-80)
REVERT: D   54 ILE cc_start: 0.9692 (mp) cc_final: 0.9372 (tp)
REVERT: D   59 MET cc_start: 0.9453 (ttm) cc_final: 0.9120 (mtm)
REVERT: D  106 LEU cc_start: 0.9820 (tt) cc_final: 0.9603 (tt)
REVERT: E   62 ILE cc_start: 0.9212 (mm) cc_final: 0.8729 (mm)
REVERT: E   67 PHE cc_start: 0.9132 (t80) cc_final: 0.8884 (t80)
REVERT: E   93 GLN cc_start: 0.9531 (tt0) cc_final: 0.8492 (tp-100)
REVERT: E   94 GLU cc_start: 0.9749 (tp30) cc_final: 0.9238 (tt0)
REVERT: F   84 MET cc_start: 0.9622 (mpp) cc_final: 0.9375 (mpp)
REVERT: G  906 MET cc_start: 0.7597 (mmt) cc_final: 0.7184 (mmp)
REVERT: H  253 MET cc_start: 0.9008 (mmp) cc_final: 0.8693 (mmp)
REVERT: H  289 MET cc_start: 0.8901 (mpp) cc_final: 0.8661 (mpp)
  outliers start: 0
  outliers final: 0
  residues processed: 128
  average time/residue: 0.1281
  time to fit residues: 23.6465
Evaluate side-chains
  89 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 89
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 2 optimal weight:    0.0470
   chunk 129 optimal weight:   10.0000
   chunk 108 optimal weight:    4.9990
   chunk 43 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   chunk 87 optimal weight:    1.9990
   chunk 76 optimal weight:    5.9990
   chunk 81 optimal weight:    0.5980
   chunk 143 optimal weight:    7.9990
   chunk 139 optimal weight:    7.9990
   chunk 74 optimal weight:    9.9990
   overall best weight:    1.7082

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

Flipped N/Q/H residues before XYZ refinement:
B  93 GLN
E  85 GLN
F  27 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.047000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.036500 restraints weight = 402301.698|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3012 r_free = 0.3012 target = 0.037827 restraints weight = 146668.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.039037 restraints weight = 70319.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3052 r_free = 0.3052 target = 0.039184 restraints weight = 36320.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.039321 restraints weight = 41403.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.2604
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2569
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2569 r_free = 0.2569    target_work(ls_wunit_k1) = 0.026         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2569
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8298
moved from start:          0.3929

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14421  Z= 0.132
  Angle     :  0.575   7.533  20076  Z= 0.324
  Chirality :  0.039   0.202   2249
  Planarity :  0.004   0.052   2061
  Dihedral  : 26.336 138.794   3072
  Min Nonbonded Distance : 2.009

Molprobity Statistics.
  All-atom Clashscore : 16.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.74 %
    Favored  : 95.26 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  1.13 %
    Favored  : 98.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -1.45 (0.23), residues: 1292
  helix:  0.55 (0.24), residues: 485
  sheet: -2.14 (0.38), residues: 165
  loop : -1.86 (0.23), residues: 642

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 128 
 TYR   0.028   0.002   TYR B  72 
 PHE   0.011   0.001   PHE H 415 
 TRP   0.016   0.002   TRP G 922 
 HIS   0.005   0.001   HIS H 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (14418)
  covalent geometry    : angle       0.57540 (20067)
  hydrogen bonds       : bond        0.07590 (  587)
  hydrogen bonds       : angle       5.25445 ( 1475)
  link_TRANS           : bond        0.00149 (    3)
  link_TRANS           : angle       0.58960 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 118
  time to evaluate  : 0.498 
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   67 PHE cc_start: 0.9578 (t80) cc_final: 0.9266 (t80)
REVERT: A   96 CYS cc_start: 0.9721 (t) cc_final: 0.9388 (t)
REVERT: A   97 GLU cc_start: 0.9708 (mt-10) cc_final: 0.9448 (mm-30)
REVERT: A  110 CYS cc_start: 0.9416 (m) cc_final: 0.9207 (m)
REVERT: A  122 LYS cc_start: 0.9431 (ttpt) cc_final: 0.8957 (ptmt)
REVERT: D   37 TYR cc_start: 0.8601 (m-80) cc_final: 0.7981 (m-80)
REVERT: D   54 ILE cc_start: 0.9686 (mp) cc_final: 0.9400 (tp)
REVERT: D   59 MET cc_start: 0.9476 (ttm) cc_final: 0.9106 (mtp)
REVERT: E   62 ILE cc_start: 0.9225 (mm) cc_final: 0.8728 (mm)
REVERT: E   67 PHE cc_start: 0.9059 (t80) cc_final: 0.8822 (t80)
REVERT: E   93 GLN cc_start: 0.9496 (tt0) cc_final: 0.8555 (tp-100)
REVERT: E   94 GLU cc_start: 0.9711 (tp30) cc_final: 0.9193 (tt0)
REVERT: F   63 GLU cc_start: 0.9740 (mp0) cc_final: 0.9532 (mp0)
REVERT: G  906 MET cc_start: 0.7028 (mmt) cc_final: 0.6614 (mmp)
REVERT: H  253 MET cc_start: 0.8980 (mmp) cc_final: 0.8132 (mtt)
REVERT: H  289 MET cc_start: 0.8832 (mpp) cc_final: 0.8613 (mpp)
REVERT: H  313 MET cc_start: 0.9188 (ttm) cc_final: 0.8835 (mtp)
  outliers start: 1
  outliers final: 1
  residues processed: 119
  average time/residue: 0.1369
  time to fit residues: 23.2764
Evaluate side-chains
  88 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 87
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 93 optimal weight:    5.9990
   chunk 12 optimal weight:   10.0000
   chunk 122 optimal weight:    1.9990
   chunk 142 optimal weight:    7.9990
   chunk 5 optimal weight:    0.7980
   chunk 104 optimal weight:    9.9990
   chunk 139 optimal weight:    7.9990
   chunk 3 optimal weight:    0.9990
   chunk 20 optimal weight:    8.9990
   chunk 143 optimal weight:    8.9990
   chunk 71 optimal weight:   30.0000
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN
E 125 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2803 r_free = 0.2803 target = 0.032898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2427 r_free = 0.2427 target = 0.021179 restraints weight = 430744.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.2484 r_free = 0.2484 target = 0.022577 restraints weight = 189082.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.2522 r_free = 0.2522 target = 0.023525 restraints weight = 111390.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.2548 r_free = 0.2548 target = 0.024185 restraints weight = 75878.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 49)----------------|
| r_work = 0.2563 r_free = 0.2563 target = 0.024635 restraints weight = 56608.614|
|-----------------------------------------------------------------------------|
r_work (final): 0.2466
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2479
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2479 r_free = 0.2479    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2479 r_free = 0.2479    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2479
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.4349

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  14421  Z= 0.182
  Angle     :  0.615   7.415  20076  Z= 0.346
  Chirality :  0.040   0.196   2249
  Planarity :  0.005   0.058   2061
  Dihedral  : 26.611 139.981   3072
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 23.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  1.91 %
    Favored  : 97.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -1.55 (0.23), residues: 1292
  helix:  0.41 (0.23), residues: 478
  sheet: -2.19 (0.38), residues: 165
  loop : -1.83 (0.23), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG E 129 
 TYR   0.019   0.002   TYR B  88 
 PHE   0.013   0.002   PHE H 403 
 TRP   0.016   0.002   TRP G 922 
 HIS   0.007   0.001   HIS H 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 (14418)
  covalent geometry    : angle       0.61526 (20067)
  hydrogen bonds       : bond        0.07882 (  587)
  hydrogen bonds       : angle       5.40602 ( 1475)
  link_TRANS           : bond        0.00163 (    3)
  link_TRANS           : angle       0.57001 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 106
  time to evaluate  : 0.486 
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   67 PHE cc_start: 0.9551 (t80) cc_final: 0.9195 (t80)
REVERT: A   96 CYS cc_start: 0.9846 (t) cc_final: 0.9575 (t)
REVERT: A   97 GLU cc_start: 0.9797 (mt-10) cc_final: 0.9502 (mm-30)
REVERT: A  110 CYS cc_start: 0.9470 (m) cc_final: 0.9241 (m)
REVERT: A  122 LYS cc_start: 0.9410 (ttpt) cc_final: 0.9006 (ptmt)
REVERT: B   68 ASP cc_start: 0.9223 (p0) cc_final: 0.8959 (p0)
REVERT: D   37 TYR cc_start: 0.9009 (m-80) cc_final: 0.8267 (m-10)
REVERT: E   93 GLN cc_start: 0.9531 (tt0) cc_final: 0.8455 (tp-100)
REVERT: E   94 GLU cc_start: 0.9790 (tp30) cc_final: 0.9350 (tt0)
REVERT: F   84 MET cc_start: 0.9741 (mpp) cc_final: 0.9416 (mpp)
REVERT: G  559 MET cc_start: 0.9117 (tmm) cc_final: 0.8677 (tmm)
REVERT: G  870 MET cc_start: 0.7533 (tpt) cc_final: 0.7313 (tpp)
REVERT: H   18 MET cc_start: 0.8504 (mmm) cc_final: 0.8290 (mmm)
REVERT: H  253 MET cc_start: 0.9000 (mmp) cc_final: 0.8179 (mtt)
REVERT: H  289 MET cc_start: 0.8833 (mpp) cc_final: 0.8626 (mpp)
REVERT: H  313 MET cc_start: 0.9213 (ttm) cc_final: 0.8879 (mtp)
  outliers start: 2
  outliers final: 1
  residues processed: 107
  average time/residue: 0.1454
  time to fit residues: 21.6852
Evaluate side-chains
  77 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 76
  time to evaluate  : 0.445 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 105 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 80 optimal weight:    6.9990
   chunk 78 optimal weight:    7.9990
   chunk 117 optimal weight:    9.9990
   chunk 12 optimal weight:    6.9990
   chunk 84 optimal weight:    8.9990
   chunk 38 optimal weight:    5.9990
   chunk 26 optimal weight:   20.0000
   chunk 122 optimal weight:    9.9990
   chunk 114 optimal weight:    2.9990
   overall best weight:    5.5990

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

Flipped N/Q/H residues before XYZ refinement:
C  89 ASN
E  85 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2789 r_free = 0.2789 target = 0.031715 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2419 r_free = 0.2419 target = 0.020548 restraints weight = 283811.520|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.2473 r_free = 0.2473 target = 0.021733 restraints weight = 140018.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.2508 r_free = 0.2508 target = 0.022569 restraints weight = 87508.645|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.2533 r_free = 0.2533 target = 0.023179 restraints weight = 61914.058|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2550 r_free = 0.2550 target = 0.023590 restraints weight = 47510.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.2436
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2436
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2436 r_free = 0.2436    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2436 r_free = 0.2436    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2436
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8441
moved from start:          0.4818

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042  14421  Z= 0.249
  Angle     :  0.690   8.891  20076  Z= 0.388
  Chirality :  0.042   0.196   2249
  Planarity :  0.006   0.069   2061
  Dihedral  : 27.048 141.100   3072
  Min Nonbonded Distance : 1.910

Molprobity Statistics.
  All-atom Clashscore : 29.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.85 %
    Favored  : 92.15 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.52 %
    Favored  : 99.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -1.84 (0.22), residues: 1292
  helix:  0.05 (0.23), residues: 474
  sheet: -2.37 (0.37), residues: 170
  loop : -1.87 (0.23), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG E 128 
 TYR   0.024   0.002   TYR B  72 
 PHE   0.017   0.002   PHE H 403 
 TRP   0.016   0.002   TRP G 902 
 HIS   0.010   0.002   HIS H 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00518 (14418)
  covalent geometry    : angle       0.69033 (20067)
  hydrogen bonds       : bond        0.08656 (  587)
  hydrogen bonds       : angle       5.85359 ( 1475)
  link_TRANS           : bond        0.00204 (    3)
  link_TRANS           : angle       0.56167 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 98
  time to evaluate  : 0.426 
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: A   67 PHE cc_start: 0.9523 (t80) cc_final: 0.9111 (t80)
REVERT: A   96 CYS cc_start: 0.9828 (t) cc_final: 0.9399 (t)
REVERT: A   97 GLU cc_start: 0.9801 (mt-10) cc_final: 0.9439 (mm-30)
REVERT: A  110 CYS cc_start: 0.9459 (m) cc_final: 0.9230 (m)
REVERT: A  122 LYS cc_start: 0.9505 (ttpt) cc_final: 0.9048 (ptmt)
REVERT: B   59 LYS cc_start: 0.9626 (pptt) cc_final: 0.9380 (pptt)
REVERT: B   61 PHE cc_start: 0.9280 (t80) cc_final: 0.9015 (t80)
REVERT: B   72 TYR cc_start: 0.9251 (m-80) cc_final: 0.8983 (m-10)
REVERT: D   59 MET cc_start: 0.9480 (ttm) cc_final: 0.9259 (mtp)
REVERT: D   65 PHE cc_start: 0.9794 (t80) cc_final: 0.9474 (t80)
REVERT: E   93 GLN cc_start: 0.9509 (tt0) cc_final: 0.9201 (tt0)
REVERT: E   94 GLU cc_start: 0.9744 (tp30) cc_final: 0.9295 (tt0)
REVERT: F   62 LEU cc_start: 0.9816 (mt) cc_final: 0.9578 (mt)
REVERT: F   63 GLU cc_start: 0.9754 (mp0) cc_final: 0.9534 (mp0)
REVERT: G  870 MET cc_start: 0.7777 (tpt) cc_final: 0.7476 (tpp)
REVERT: H   18 MET cc_start: 0.8606 (mmm) cc_final: 0.8385 (mmm)
REVERT: H  253 MET cc_start: 0.8837 (mmp) cc_final: 0.8042 (mtt)
REVERT: H  289 MET cc_start: 0.8878 (mpp) cc_final: 0.8612 (mpp)
REVERT: H  313 MET cc_start: 0.9207 (ttm) cc_final: 0.8858 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 98
  average time/residue: 0.1260
  time to fit residues: 17.9966
Evaluate side-chains
  70 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 70
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 81 optimal weight:    7.9990
   chunk 5 optimal weight:    7.9990
   chunk 50 optimal weight:   20.0000
   chunk 55 optimal weight:    4.9990
   chunk 13 optimal weight:    0.8980
   chunk 51 optimal weight:    0.5980
   chunk 115 optimal weight:    2.9990
   chunk 68 optimal weight:    8.9990
   chunk 123 optimal weight:    2.9990
   chunk 12 optimal weight:    9.9990
   chunk 42 optimal weight:    4.9990
   overall best weight:    2.4986

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2828 r_free = 0.2828 target = 0.032924 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2438 r_free = 0.2438 target = 0.020880 restraints weight = 383649.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.2499 r_free = 0.2499 target = 0.022327 restraints weight = 159927.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2541 r_free = 0.2541 target = 0.023325 restraints weight = 92988.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.2571 r_free = 0.2571 target = 0.024066 restraints weight = 63001.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.2590 r_free = 0.2590 target = 0.024555 restraints weight = 46606.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.2482
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2482
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2482 r_free = 0.2482    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2482 r_free = 0.2482    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2482
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8388
moved from start:          0.4893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  14421  Z= 0.150
  Angle     :  0.595   7.436  20076  Z= 0.336
  Chirality :  0.040   0.194   2249
  Planarity :  0.005   0.061   2061
  Dihedral  : 26.916 137.884   3072
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 20.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -1.45 (0.23), residues: 1292
  helix:  0.48 (0.23), residues: 479
  sheet: -2.14 (0.38), residues: 168
  loop : -1.77 (0.23), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG E 128 
 TYR   0.021   0.002   TYR B  72 
 PHE   0.018   0.001   PHE B  61 
 TRP   0.018   0.002   TRP G 922 
 HIS   0.006   0.001   HIS H 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (14418)
  covalent geometry    : angle       0.59501 (20067)
  hydrogen bonds       : bond        0.07483 (  587)
  hydrogen bonds       : angle       5.31930 ( 1475)
  link_TRANS           : bond        0.00160 (    3)
  link_TRANS           : angle       0.58517 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 107
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9507 (t80) cc_final: 0.9104 (t80)
REVERT: A   96 CYS cc_start: 0.9815 (t) cc_final: 0.9513 (t)
REVERT: A   97 GLU cc_start: 0.9754 (mt-10) cc_final: 0.9509 (mm-30)
REVERT: A  122 LYS cc_start: 0.9407 (ttpt) cc_final: 0.8918 (ptmt)
REVERT: A  128 ARG cc_start: 0.9759 (ptt-90) cc_final: 0.9396 (ptt90)
REVERT: A  129 ARG cc_start: 0.9764 (mtt180) cc_final: 0.9544 (mmp80)
REVERT: B   44 LYS cc_start: 0.8643 (tmtt) cc_final: 0.8412 (tptp)
REVERT: B   59 LYS cc_start: 0.9622 (pptt) cc_final: 0.9409 (ptmm)
REVERT: B   68 ASP cc_start: 0.9104 (p0) cc_final: 0.8887 (p0)
REVERT: B   72 TYR cc_start: 0.9260 (m-80) cc_final: 0.8951 (m-10)
REVERT: D   59 MET cc_start: 0.9510 (ttm) cc_final: 0.9224 (mtm)
REVERT: D   65 PHE cc_start: 0.9778 (t80) cc_final: 0.9575 (t80)
REVERT: E   93 GLN cc_start: 0.9483 (tt0) cc_final: 0.8358 (tp-100)
REVERT: E   94 GLU cc_start: 0.9728 (tp30) cc_final: 0.9280 (tt0)
REVERT: F   84 MET cc_start: 0.9606 (mpp) cc_final: 0.9383 (mpp)
REVERT: G  559 MET cc_start: 0.9226 (tmm) cc_final: 0.8746 (tmm)
REVERT: H  253 MET cc_start: 0.8893 (mmp) cc_final: 0.8074 (mtt)
REVERT: H  289 MET cc_start: 0.8861 (mpp) cc_final: 0.8615 (mpp)
REVERT: H  313 MET cc_start: 0.9205 (ttm) cc_final: 0.8823 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 107
  average time/residue: 0.1244
  time to fit residues: 19.5869
Evaluate side-chains
  77 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.451 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 134 optimal weight:    8.9990
   chunk 121 optimal weight:    7.9990
   chunk 71 optimal weight:   50.0000
   chunk 78 optimal weight:    9.9990
   chunk 64 optimal weight:    7.9990
   chunk 29 optimal weight:    3.9990
   chunk 40 optimal weight:    6.9990
   chunk 123 optimal weight:    9.9990
   chunk 5 optimal weight:    8.9990
   chunk 109 optimal weight:    7.9990
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2780 r_free = 0.2780 target = 0.031388 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.2386 r_free = 0.2386 target = 0.019767 restraints weight = 389296.783|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2448 r_free = 0.2448 target = 0.021128 restraints weight = 165691.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.2488 r_free = 0.2488 target = 0.022059 restraints weight = 97084.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.2515 r_free = 0.2515 target = 0.022730 restraints weight = 66394.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2534 r_free = 0.2534 target = 0.023198 restraints weight = 49791.833|
|-----------------------------------------------------------------------------|
r_work (final): 0.2427
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2427
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2427 r_free = 0.2427    target_work(ls_wunit_k1) = 0.022         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2427
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.5202

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038  14421  Z= 0.245
  Angle     :  0.684   7.928  20076  Z= 0.386
  Chirality :  0.042   0.198   2249
  Planarity :  0.005   0.058   2061
  Dihedral  : 27.220 139.976   3072
  Min Nonbonded Distance : 1.900

Molprobity Statistics.
  All-atom Clashscore : 28.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.15 %
    Favored  : 92.85 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.61 %
    Favored  : 99.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -1.67 (0.22), residues: 1292
  helix:  0.21 (0.23), residues: 479
  sheet: -2.27 (0.38), residues: 170
  loop : -1.81 (0.23), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  39 
 TYR   0.023   0.002   TYR B  72 
 PHE   0.018   0.002   PHE B  61 
 TRP   0.018   0.002   TRP G 902 
 HIS   0.011   0.001   HIS H 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00508 (14418)
  covalent geometry    : angle       0.68437 (20067)
  hydrogen bonds       : bond        0.08358 (  587)
  hydrogen bonds       : angle       5.77896 ( 1475)
  link_TRANS           : bond        0.00196 (    3)
  link_TRANS           : angle       0.54557 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 95
  time to evaluate  : 0.459 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9465 (t80) cc_final: 0.9062 (t80)
REVERT: A   96 CYS cc_start: 0.9837 (t) cc_final: 0.9446 (t)
REVERT: A   97 GLU cc_start: 0.9792 (mt-10) cc_final: 0.9462 (mm-30)
REVERT: A  110 CYS cc_start: 0.9473 (m) cc_final: 0.8833 (t)
REVERT: B   59 LYS cc_start: 0.9636 (pptt) cc_final: 0.9383 (pptt)
REVERT: B   68 ASP cc_start: 0.9172 (p0) cc_final: 0.8940 (p0)
REVERT: B   72 TYR cc_start: 0.9246 (m-80) cc_final: 0.8946 (m-10)
REVERT: D   65 PHE cc_start: 0.9798 (t80) cc_final: 0.9515 (t80)
REVERT: D   99 ARG cc_start: 0.9239 (mmt180) cc_final: 0.8674 (mtt-85)
REVERT: E   93 GLN cc_start: 0.9473 (tt0) cc_final: 0.9159 (tt0)
REVERT: E   94 GLU cc_start: 0.9729 (tp30) cc_final: 0.9265 (tt0)
REVERT: H   18 MET cc_start: 0.8589 (mmm) cc_final: 0.8112 (mmp)
REVERT: H  253 MET cc_start: 0.8859 (mmp) cc_final: 0.8195 (mtt)
REVERT: H  289 MET cc_start: 0.8845 (mpp) cc_final: 0.8587 (mpp)
REVERT: H  313 MET cc_start: 0.9221 (ttm) cc_final: 0.8880 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 95
  average time/residue: 0.1220
  time to fit residues: 16.9997
Evaluate side-chains
  69 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 69
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    7.9990
   chunk 82 optimal weight:    2.9990
   chunk 70 optimal weight:    9.9990
   chunk 86 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 131 optimal weight:   10.0000
   chunk 24 optimal weight:    0.6980
   chunk 129 optimal weight:    9.9990
   chunk 139 optimal weight:    6.9990
   chunk 50 optimal weight:   20.0000
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2829 r_free = 0.2829 target = 0.032847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2432 r_free = 0.2432 target = 0.020672 restraints weight = 418402.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2497 r_free = 0.2497 target = 0.022153 restraints weight = 166386.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2540 r_free = 0.2540 target = 0.023194 restraints weight = 95293.696|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.2569 r_free = 0.2569 target = 0.023938 restraints weight = 63909.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2589 r_free = 0.2589 target = 0.024450 restraints weight = 47163.341|
|-----------------------------------------------------------------------------|
r_work (final): 0.2484
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2484
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2484 r_free = 0.2484    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2484 r_free = 0.2484    target_work(ls_wunit_k1) = 0.023         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2484
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8381
moved from start:          0.5227

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  14421  Z= 0.145
  Angle     :  0.613   8.813  20076  Z= 0.344
  Chirality :  0.041   0.192   2249
  Planarity :  0.005   0.061   2061
  Dihedral  : 27.101 137.529   3072
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.26 %
    Favored  : 99.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    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: -1.38 (0.23), residues: 1292
  helix:  0.53 (0.23), residues: 478
  sheet: -2.01 (0.39), residues: 168
  loop : -1.74 (0.23), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG G 569 
 TYR   0.021   0.002   TYR B  72 
 PHE   0.011   0.001   PHE H 121 
 TRP   0.019   0.002   TRP G 922 
 HIS   0.005   0.001   HIS H 247 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (14418)
  covalent geometry    : angle       0.61288 (20067)
  hydrogen bonds       : bond        0.07547 (  587)
  hydrogen bonds       : angle       5.34259 ( 1475)
  link_TRANS           : bond        0.00160 (    3)
  link_TRANS           : angle       0.56245 (    9)

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

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

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2584 Ramachandran restraints generated.
    1292 Oldfield, 0 Emsley, 1292 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 103
  time to evaluate  : 0.485 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   67 PHE cc_start: 0.9467 (t80) cc_final: 0.9061 (t80)
REVERT: A   96 CYS cc_start: 0.9822 (t) cc_final: 0.9517 (t)
REVERT: A   97 GLU cc_start: 0.9762 (mt-10) cc_final: 0.9531 (mm-30)
REVERT: A  110 CYS cc_start: 0.9523 (m) cc_final: 0.8873 (t)
REVERT: A  122 LYS cc_start: 0.9551 (ttpt) cc_final: 0.9080 (ptmt)
REVERT: B   59 LYS cc_start: 0.9640 (pptt) cc_final: 0.9425 (ptmm)
REVERT: B   68 ASP cc_start: 0.9099 (p0) cc_final: 0.8847 (p0)
REVERT: B   72 TYR cc_start: 0.9259 (m-80) cc_final: 0.8948 (m-10)
REVERT: C   50 TYR cc_start: 0.9337 (t80) cc_final: 0.9075 (t80)
REVERT: D   54 ILE cc_start: 0.9683 (mp) cc_final: 0.9399 (tp)
REVERT: D   59 MET cc_start: 0.9531 (ttm) cc_final: 0.9134 (mtm)
REVERT: D   82 HIS cc_start: 0.9415 (m90) cc_final: 0.9182 (m90)
REVERT: E   93 GLN cc_start: 0.9430 (tt0) cc_final: 0.8309 (tp-100)
REVERT: E   94 GLU cc_start: 0.9735 (tp30) cc_final: 0.9338 (tt0)
REVERT: F   84 MET cc_start: 0.9601 (mpp) cc_final: 0.9337 (mpp)
REVERT: G  559 MET cc_start: 0.9184 (tmm) cc_final: 0.8709 (tmm)
REVERT: G  870 MET cc_start: 0.7698 (tpt) cc_final: 0.7480 (tpp)
REVERT: H  253 MET cc_start: 0.8914 (mmp) cc_final: 0.8180 (mtt)
REVERT: H  289 MET cc_start: 0.8874 (mpp) cc_final: 0.8632 (mpp)
REVERT: H  313 MET cc_start: 0.9222 (ttm) cc_final: 0.8819 (mtp)
  outliers start: 0
  outliers final: 0
  residues processed: 103
  average time/residue: 0.1182
  time to fit residues: 18.1590
Evaluate side-chains
  77 residues out of total 1150 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.484 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 145
   random chunks:
   chunk 21 optimal weight:    0.7980
   chunk 62 optimal weight:   30.0000
   chunk 75 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 3 optimal weight:    0.8980
   chunk 37 optimal weight:    8.9990
   chunk 52 optimal weight:    7.9990
   chunk 49 optimal weight:    0.3980
   chunk 82 optimal weight:    7.9990
   chunk 135 optimal weight:   10.0000
   chunk 90 optimal weight:   30.0000
   overall best weight:    3.2184

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

Flipped N/Q/H residues before XYZ refinement:
E  85 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.032247 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2389 r_free = 0.2389 target = 0.019939 restraints weight = 337380.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.2446 r_free = 0.2446 target = 0.021221 restraints weight = 161054.537|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.2484 r_free = 0.2484 target = 0.022098 restraints weight = 99300.744|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.2510 r_free = 0.2510 target = 0.022743 restraints weight = 70163.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.2528 r_free = 0.2528 target = 0.023193 restraints weight = 53977.937|
|-----------------------------------------------------------------------------|
r_work (final): 0.2422
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.2504
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.2504 r_free = 0.2504    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.2504 r_free = 0.2504    target_work(ls_wunit_k1) = 0.024         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        1 |
|-----------------------------------------------------------------------------|
r_final: 0.2504
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8190
moved from start:          0.5329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039  14421  Z= 0.172
  Angle     :  0.620   8.381  20076  Z= 0.351
  Chirality :  0.040   0.193   2249
  Planarity :  0.005   0.058   2061
  Dihedral  : 27.103 137.762   3072
  Min Nonbonded Distance : 1.937

Molprobity Statistics.
  All-atom Clashscore : 22.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.43 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 10.64 %
    Cis-general     : 0.24 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.39 (0.23), residues: 1292
  helix:  0.52 (0.23), residues: 478
  sheet: -2.05 (0.39), residues: 168
  loop : -1.74 (0.23), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B  39 
 TYR   0.022   0.002   TYR B  72 
 PHE   0.018   0.002   PHE B  61 
 TRP   0.019   0.002   TRP G 922 
 HIS   0.005   0.001   HIS H 224 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (14418)
  covalent geometry    : angle       0.61992 (20067)
  hydrogen bonds       : bond        0.07521 (  587)
  hydrogen bonds       : angle       5.39889 ( 1475)
  link_TRANS           : bond        0.00154 (    3)
  link_TRANS           : angle       0.56639 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2373.00 seconds
wall clock time: 41 minutes 59.32 seconds (2519.32 seconds total)