Starting phenix.real_space_refine
on Sat Sep 12 16:12:45 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7z03_14403/09_2026/7z03_14403.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7z03_14403/09_2026/7z03_14403.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7z03_14403/09_2026/7z03_14403.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7z03_14403/09_2026/7z03_14403.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7z03_14403/09_2026/7z03_14403.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7z03_14403/09_2026/7z03_14403.map"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7z03_14403/09_2026/7z03_14403.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7z03_14403/09_2026/7z03_14403.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 4287 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 7
    Type Number    sf(0)   Gaussians
     Mn      4      7.51       5
     P      82      5.49       5
     Mg      2      5.21       5
     S      34      5.16       5
     C    8173      2.51       5
     N    2365      2.21       5
     O    2736      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 23 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13396
  Number of models: 1
  Model: ""
    Number of chains: 10
    Chain: "C"
      Number of atoms: 2916
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2916
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 7, 'TRANS': 366}
          Chain breaks: 1
    Chain: "D"
      Number of atoms: 2914
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 374, 2914
          Classifications: {'peptide': 374}
          Link IDs: {'PTRANS': 7, 'TRANS': 366}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 3010
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 381, 3010
          Classifications: {'peptide': 381}
          Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 360}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 2897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 368, 2897
          Classifications: {'peptide': 368}
          Link IDs: {'PTRANS': 20, 'TRANS': 347}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 806
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
    Chain: "F"
      Number of atoms: 793
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 39, 793
          Classifications: {'DNA': 39}
          Link IDs: {'rna3p': 38}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Residues with excluded nonbonded symmetry interactions: 22
    residue:
      pdb=" N   GLY A 284 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY A 284 " occ=0.50
    residue:
      pdb=" N   ALA A 287 " occ=0.60
      ... (3 atoms not shown)
      pdb=" CB  ALA A 287 " occ=0.60
    residue:
      pdb=" N   THR A 290 " occ=0.70
      ... (5 atoms not shown)
      pdb=" CG2 THR A 290 " occ=0.70
    residue:
      pdb=" N   ALA A 291 " occ=0.60
      ... (3 atoms not shown)
      pdb=" CB  ALA A 291 " occ=0.60
    residue:
      pdb=" N   GLN A 292 " occ=0.70
      ... (7 atoms not shown)
      pdb=" NE2 GLN A 292 " occ=0.70
    residue:
      pdb=" N   LEU A 293 " occ=0.80
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 293 " occ=0.80
    residue:
      pdb=" N   PRO A 303 " occ=0.61
      ... (5 atoms not shown)
      pdb=" CD  PRO A 303 " occ=0.61
    residue:
      pdb=" N   PRO A 304 " occ=0.68
      ... (5 atoms not shown)
      pdb=" CD  PRO A 304 " occ=0.68
    residue:
      pdb=" N   VAL A 305 " occ=0.88
      ... (5 atoms not shown)
      pdb=" CG2 VAL A 305 " occ=0.88
    residue:
      pdb=" N   TRP A 306 " occ=0.97
      ... (12 atoms not shown)
      pdb=" CH2 TRP A 306 " occ=0.97
    residue:
      pdb=" N   LEU A 307 " occ=0.87
      ... (6 atoms not shown)
      pdb=" CD2 LEU A 307 " occ=0.87
    residue:
      pdb=" N   ILE A 309 " occ=0.89
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 309 " occ=0.89
    ... (remaining 10 not shown)
  Time building chain proxies: 3.21, per 1000 atoms: 0.24
  Number of scatterers: 13396
  At special positions: 0
  Unit cell: (108.018, 118.608, 136.611, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Mn      4     24.99
     S      34     16.00
     P      82     15.00
     Mg      2     11.99
     O    2736      8.00
     N    2365      7.00
     C    8173      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 581.9 milliseconds
  

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2812

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 17 sheets defined
      43.4% alpha, 17.9% beta
      39 base pairs and 67 stacking pairs defined.
    Time for finding SS restraints: 1.63
  Creating SS restraints...
    Processing helix  chain 'C' and resid 42 through 56
      removed outlier: 3.831A  pdb=" N   LEU C  47 " --> pdb=" O   LYS C  43 " (cutoff:3.500A)
      removed outlier: 3.620A  pdb=" N   ILE C  50 " --> pdb=" O   LEU C  46 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 101 through 104
    Processing helix  chain 'C' and resid 128 through 141
    Processing helix  chain 'C' and resid 143 through 151
      removed outlier: 4.345A  pdb=" N   ARG C 149 " --> pdb=" O   GLY C 145 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 159 through 164
    Processing helix  chain 'C' and resid 165 through 178
    Processing helix  chain 'C' and resid 180 through 201
    Processing helix  chain 'C' and resid 876 through 887
    Processing helix  chain 'C' and resid 889 through 891
      No H-bonds generated for 'chain 'C' and resid 889 through 891'
    Processing helix  chain 'C' and resid 892 through 900
    Processing helix  chain 'C' and resid 900 through 919
      removed outlier: 3.591A  pdb=" N   LEU C 910 " --> pdb=" O   ASN C 906 " (cutoff:3.500A)
      removed outlier: 4.312A  pdb=" N   ARG C 917 " --> pdb=" O   GLN C 913 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 947 through 951
      removed outlier: 3.544A  pdb=" N   THR C 950 " --> pdb=" O   ASP C 947 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   LEU C 951 " --> pdb=" O   THR C 948 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 947 through 951'
    Processing helix  chain 'C' and resid 952 through 970
    Processing helix  chain 'C' and resid 985 through 989
      removed outlier: 3.801A  pdb=" N   THR C 988 " --> pdb=" O   GLY C 985 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 990 through 1006
      removed outlier: 3.615A  pdb=" N   ASP C 995 " --> pdb=" O   SER C 991 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1017 through 1024
    Processing helix  chain 'C' and resid 1042 through 1046
    Processing helix  chain 'D' and resid 42 through 56
      removed outlier: 3.865A  pdb=" N   LEU D  47 " --> pdb=" O   LYS D  43 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 101 through 104
    Processing helix  chain 'D' and resid 128 through 141
    Processing helix  chain 'D' and resid 143 through 151
      removed outlier: 4.263A  pdb=" N   ARG D 149 " --> pdb=" O   GLY D 145 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 165 through 178
      removed outlier: 3.741A  pdb=" N   LEU D 172 " --> pdb=" O   GLU D 168 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 180 through 199
      removed outlier: 3.634A  pdb=" N   GLN D 184 " --> pdb=" O   GLU D 180 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   GLU D 199 " --> pdb=" O   SER D 195 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 875 through 887
    Processing helix  chain 'D' and resid 889 through 891
      No H-bonds generated for 'chain 'D' and resid 889 through 891'
    Processing helix  chain 'D' and resid 892 through 900
      removed outlier: 3.665A  pdb=" N   ARG D 896 " --> pdb=" O   GLY D 892 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 900 through 919
      removed outlier: 4.507A  pdb=" N   ARG D 917 " --> pdb=" O   GLN D 913 " (cutoff:3.500A)
      removed outlier: 3.599A  pdb=" N   LEU D 918 " --> pdb=" O   GLN D 914 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 949 through 951
      No H-bonds generated for 'chain 'D' and resid 949 through 951'
    Processing helix  chain 'D' and resid 952 through 971
      removed outlier: 4.052A  pdb=" N   VAL D 971 " --> pdb=" O   LEU D 967 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 990 through 1006
      removed outlier: 4.528A  pdb=" N   THR D 996 " --> pdb=" O   GLU D 992 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1018 through 1024
      removed outlier: 4.107A  pdb=" N   GLU D1022 " --> pdb=" O   GLU D1018 " (cutoff:3.500A)
      removed outlier: 3.639A  pdb=" N   ARG D1023 " --> pdb=" O   ALA D1019 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 1043 through 1046
    Processing helix  chain 'A' and resid 20 through 39
    Processing helix  chain 'A' and resid 56 through 70
    Processing helix  chain 'A' and resid 86 through 93
      removed outlier: 4.365A  pdb=" N   SER A  93 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 93 through 99
      removed outlier: 3.836A  pdb=" N   PHE A  99 " --> pdb=" O   ASP A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 138
      removed outlier: 3.650A  pdb=" N   ILE A 137 " --> pdb=" O   ARG A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 145 through 173
      removed outlier: 3.598A  pdb=" N   GLN A 150 " --> pdb=" O   GLY A 146 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 212
    Processing helix  chain 'A' and resid 245 through 249
    Processing helix  chain 'A' and resid 285 through 294
    Processing helix  chain 'A' and resid 295 through 297
      No H-bonds generated for 'chain 'A' and resid 295 through 297'
    Processing helix  chain 'A' and resid 319 through 328
      removed outlier: 3.527A  pdb=" N   LYS A 323 " --> pdb=" O   ASP A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 361 through 372
      removed outlier: 3.582A  pdb=" N   LEU A 372 " --> pdb=" O   ARG A 368 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 376 through 394
      removed outlier: 3.888A  pdb=" N   GLN A 381 " --> pdb=" O   GLU A 377 " (cutoff:3.500A)
      removed outlier: 5.473A  pdb=" N   ARG A 382 " --> pdb=" O   SER A 378 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 20 through 39
      removed outlier: 3.750A  pdb=" N   TRP B  30 " --> pdb=" O   ALA B  26 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 56 through 74
      removed outlier: 3.573A  pdb=" N   ARG B  60 " --> pdb=" O   PRO B  56 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   GLN B  71 " --> pdb=" O   VAL B  67 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   GLN B  72 " --> pdb=" O   VAL B  68 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   THR B  73 " --> pdb=" O   ASN B  69 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 93 through 99
      removed outlier: 4.084A  pdb=" N   PHE B  99 " --> pdb=" O   ASP B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 133 through 137
    Processing helix  chain 'B' and resid 154 through 173
    Processing helix  chain 'B' and resid 208 through 212
      removed outlier: 3.744A  pdb=" N   PHE B 212 " --> pdb=" O   ALA B 209 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 245 through 249
      removed outlier: 3.600A  pdb=" N   GLU B 248 " --> pdb=" O   SER B 245 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   CYS B 249 " --> pdb=" O   PHE B 246 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 245 through 249'
    Processing helix  chain 'B' and resid 285 through 293
      removed outlier: 3.518A  pdb=" N   ALA B 291 " --> pdb=" O   ALA B 287 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 294 through 297
    Processing helix  chain 'B' and resid 316 through 329
      removed outlier: 4.583A  pdb=" N   ARG B 322 " --> pdb=" O   HIS B 318 " (cutoff:3.500A)
      removed outlier: 3.945A  pdb=" N   LYS B 323 " --> pdb=" O   ASP B 319 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 361 through 373
      removed outlier: 3.841A  pdb=" N   LEU B 372 " --> pdb=" O   ARG B 368 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 395
      removed outlier: 4.529A  pdb=" N   ARG B 382 " --> pdb=" O   SER B 378 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 14 through 21
      removed outlier: 6.561A  pdb=" N   GLY C  16 " --> pdb=" O   ASN C  10 " (cutoff:3.500A)
      removed outlier: 6.463A  pdb=" N   GLU C  84 " --> pdb=" O   LEU C   4 " (cutoff:3.500A)
      removed outlier: 4.593A  pdb=" N   LEU C   6 " --> pdb=" O   GLU C  82 " (cutoff:3.500A)
      removed outlier: 6.791A  pdb=" N   GLU C  82 " --> pdb=" O   LEU C   6 " (cutoff:3.500A)
      removed outlier: 4.483A  pdb=" N   LEU C   8 " --> pdb=" O   LEU C  80 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU C  80 " --> pdb=" O   LEU C   8 " (cutoff:3.500A)
      removed outlier: 5.210A  pdb=" N   ASN C  10 " --> pdb=" O   GLU C  78 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   GLU C  78 " --> pdb=" O   ASN C  10 " (cutoff:3.500A)
      removed outlier: 6.566A  pdb=" N   LEU C 116 " --> pdb=" O   LEU C 125 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 152 through 153
      removed outlier: 6.522A  pdb=" N   LEU C 980 " --> pdb=" O   GLY C1012 " (cutoff:3.500A)
      removed outlier: 8.074A  pdb=" N   ILE C1014 " --> pdb=" O   LEU C 980 " (cutoff:3.500A)
      removed outlier: 7.055A  pdb=" N   LEU C 982 " --> pdb=" O   ILE C1014 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 922 through 926
    Processing sheet with id=AA4, first strand: chain 'C' and resid 1031 through 1032
    Processing sheet with id=AA5, first strand: chain 'D' and resid 14 through 21
      removed outlier: 6.610A  pdb=" N   GLY D  16 " --> pdb=" O   ASN D  10 " (cutoff:3.500A)
      removed outlier: 6.226A  pdb=" N   ILE D   3 " --> pdb=" O   GLU D  86 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   GLU D  86 " --> pdb=" O   ILE D   3 " (cutoff:3.500A)
      removed outlier: 6.429A  pdb=" N   LEU D  11 " --> pdb=" O   GLU D  78 " (cutoff:3.500A)
      removed outlier: 11.406A  pdb=" N   GLU D  78 " --> pdb=" O   LEU D  11 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   LEU D 116 " --> pdb=" O   LEU D 125 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'D' and resid 152 through 153
      removed outlier: 6.132A  pdb=" N   PHE D  33 " --> pdb=" O   VAL D1013 " (cutoff:3.500A)
      removed outlier: 6.844A  pdb=" N   ALA D  34 " --> pdb=" O   ILE D1028 " (cutoff:3.500A)
      removed outlier: 7.089A  pdb=" N   VAL D1030 " --> pdb=" O   ALA D  34 " (cutoff:3.500A)
      removed outlier: 6.310A  pdb=" N   THR D  36 " --> pdb=" O   VAL D1030 " (cutoff:3.500A)
      removed outlier: 8.101A  pdb=" N   LYS D1032 " --> pdb=" O   THR D  36 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'D' and resid 924 through 926
    Processing sheet with id=AA8, first strand: chain 'A' and resid 102 through 105
      removed outlier: 6.429A  pdb=" N   LEU A  77 " --> pdb=" O   THR A 103 " (cutoff:3.500A)
      removed outlier: 7.962A  pdb=" N   VAL A 105 " --> pdb=" O   LEU A  77 " (cutoff:3.500A)
      removed outlier: 6.494A  pdb=" N   VAL A  79 " --> pdb=" O   VAL A 105 " (cutoff:3.500A)
      removed outlier: 6.105A  pdb=" N   ILE A  43 " --> pdb=" O   VAL A  78 " (cutoff:3.500A)
      removed outlier: 7.626A  pdb=" N   LEU A  80 " --> pdb=" O   ILE A  43 " (cutoff:3.500A)
      removed outlier: 6.624A  pdb=" N   VAL A  45 " --> pdb=" O   LEU A  80 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   ARG A   2 " --> pdb=" O   ALA A  42 " (cutoff:3.500A)
      removed outlier: 8.297A  pdb=" N   ILE A  44 " --> pdb=" O   ARG A   2 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   LEU A   4 " --> pdb=" O   ILE A  44 " (cutoff:3.500A)
      removed outlier: 7.523A  pdb=" N   ALA A  46 " --> pdb=" O   LEU A   4 " (cutoff:3.500A)
      removed outlier: 7.497A  pdb=" N   THR A   6 " --> pdb=" O   ALA A  46 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   VAL A 255 " --> pdb=" O   ASN A 270 " (cutoff:3.500A)
      removed outlier: 4.948A  pdb=" N   ASN A 270 " --> pdb=" O   VAL A 255 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LEU A 257 " --> pdb=" O   VAL A 268 " (cutoff:3.500A)
      removed outlier: 4.674A  pdb=" N   VAL A 268 " --> pdb=" O   LEU A 257 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   THR A 259 " --> pdb=" O   GLU A 266 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 14 through 15
    Processing sheet with id=AB1, first strand: chain 'A' and resid 114 through 116
    Processing sheet with id=AB2, first strand: chain 'A' and resid 180 through 182
      removed outlier: 6.827A  pdb=" N   ALA A 181 " --> pdb=" O   ALA A 219 " (cutoff:3.500A)
      removed outlier: 5.755A  pdb=" N   VAL A 235 " --> pdb=" O   ILE A 229 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ILE A 229 " --> pdb=" O   VAL A 235 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 279 through 284
      removed outlier: 6.754A  pdb=" N   VAL A 305 " --> pdb=" O   VAL A 333 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   VAL A 335 " --> pdb=" O   VAL A 305 " (cutoff:3.500A)
      removed outlier: 6.406A  pdb=" N   LEU A 307 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   LEU A 337 " --> pdb=" O   LEU A 307 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 102 through 105
      removed outlier: 6.580A  pdb=" N   LEU B  77 " --> pdb=" O   THR B 103 " (cutoff:3.500A)
      removed outlier: 8.048A  pdb=" N   VAL B 105 " --> pdb=" O   LEU B  77 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   VAL B  79 " --> pdb=" O   VAL B 105 " (cutoff:3.500A)
      removed outlier: 6.684A  pdb=" N   ILE B  43 " --> pdb=" O   VAL B  78 " (cutoff:3.500A)
      removed outlier: 8.250A  pdb=" N   LEU B  80 " --> pdb=" O   ILE B  43 " (cutoff:3.500A)
      removed outlier: 6.994A  pdb=" N   VAL B  45 " --> pdb=" O   LEU B  80 " (cutoff:3.500A)
      removed outlier: 6.838A  pdb=" N   ARG B   2 " --> pdb=" O   ALA B  42 " (cutoff:3.500A)
      removed outlier: 8.204A  pdb=" N   ILE B  44 " --> pdb=" O   ARG B   2 " (cutoff:3.500A)
      removed outlier: 6.547A  pdb=" N   LEU B   4 " --> pdb=" O   ILE B  44 " (cutoff:3.500A)
      removed outlier: 7.742A  pdb=" N   ALA B  46 " --> pdb=" O   LEU B   4 " (cutoff:3.500A)
      removed outlier: 7.702A  pdb=" N   THR B   6 " --> pdb=" O   ALA B  46 " (cutoff:3.500A)
      removed outlier: 6.393A  pdb=" N   VAL B 255 " --> pdb=" O   ASN B 270 " (cutoff:3.500A)
      removed outlier: 4.658A  pdb=" N   ASN B 270 " --> pdb=" O   VAL B 255 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU B 257 " --> pdb=" O   VAL B 268 " (cutoff:3.500A)
      removed outlier: 4.876A  pdb=" N   VAL B 268 " --> pdb=" O   LEU B 257 " (cutoff:3.500A)
      removed outlier: 6.857A  pdb=" N   THR B 259 " --> pdb=" O   GLU B 266 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'B' and resid 14 through 15
    Processing sheet with id=AB6, first strand: chain 'B' and resid 114 through 116
    Processing sheet with id=AB7, first strand: chain 'B' and resid 180 through 183
      removed outlier: 6.518A  pdb=" N   ALA B 181 " --> pdb=" O   ALA B 219 " (cutoff:3.500A)
      removed outlier: 6.713A  pdb=" N   ILE B 218 " --> pdb=" O   ARG B 236 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 279 through 284
      removed outlier: 3.587A  pdb=" N   GLY B 284 " --> pdb=" O   GLU B 310 " (cutoff:3.500A)
      removed outlier: 9.377A  pdb=" N   VAL B 305 " --> pdb=" O   VAL B 335 " (cutoff:3.500A)
      removed outlier: 8.737A  pdb=" N   LEU B 337 " --> pdb=" O   VAL B 305 " (cutoff:3.500A)
      removed outlier: 6.448A  pdb=" N   LEU B 307 " --> pdb=" O   LEU B 337 " (cutoff:3.500A)
      removed outlier: 8.081A  pdb=" N   ARG B 339 " --> pdb=" O   LEU B 307 " (cutoff:3.500A)
      removed outlier: 6.217A  pdb=" N   ILE B 309 " --> pdb=" O   ARG B 339 " (cutoff:3.500A)

    519 hydrogen bonds defined for protein.
    1470 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      102 hydrogen bonds
      204 hydrogen bond angles
      0 basepair planarities
      39 basepair parallelities
      67 stacking parallelities
  Total time for adding SS restraints: 2.76

  Time building geometry restraints manager: 1.51 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4039
        1.34 -     1.46: 2454
        1.46 -     1.57: 7091
        1.57 -     1.69: 160
        1.69 -     1.81: 52
  Bond restraints: 13796
  Sorted by residual:
  bond pdb=" C4  ADP D1101 "
       pdb=" C5  ADP D1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" C4  ADP C1101 "
       pdb=" C5  ADP C1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.381  0.109 2.00e-02 2.50e+03 2.98e+01
  bond pdb=" C5  ADP D1101 "
       pdb=" C6  ADP D1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.407  0.083 2.00e-02 2.50e+03 1.74e+01
  bond pdb=" C5  ADP C1101 "
       pdb=" C6  ADP C1101 "
    ideal  model  delta    sigma   weight residual
    1.490  1.408  0.082 2.00e-02 2.50e+03 1.69e+01
  bond pdb=" N   ILE A 223 "
       pdb=" CA  ILE A 223 "
    ideal  model  delta    sigma   weight residual
    1.458  1.495 -0.037 1.17e-02 7.31e+03 1.01e+01
  ... (remaining 13791 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.69: 18826
        2.69 -     5.37: 195
        5.37 -     8.06: 18
        8.06 -    10.75: 6
       10.75 -    13.44: 4
  Bond angle restraints: 19049
  Sorted by residual:
  angle pdb=" C   ASN D  12 "
        pdb=" CA  ASN D  12 "
        pdb=" CB  ASN D  12 "
      ideal   model   delta    sigma   weight residual
     116.54  109.97    6.57 1.15e+00 7.56e-01 3.26e+01
  angle pdb=" CA  GLY A 221 "
        pdb=" C   GLY A 221 "
        pdb=" O   GLY A 221 "
      ideal   model   delta    sigma   weight residual
     121.61  115.82    5.79 1.05e+00 9.07e-01 3.04e+01
  angle pdb=" CA  GLY B 221 "
        pdb=" C   GLY B 221 "
        pdb=" O   GLY B 221 "
      ideal   model   delta    sigma   weight residual
     121.78  117.04    4.74 9.10e-01 1.21e+00 2.71e+01
  angle pdb=" N3   DT F  33 "
        pdb=" C4   DT F  33 "
        pdb=" O4   DT F  33 "
      ideal   model   delta    sigma   weight residual
     119.90  122.69   -2.79 6.00e-01 2.78e+00 2.17e+01
  angle pdb=" PA  ADP C1101 "
        pdb=" O3A ADP C1101 "
        pdb=" PB  ADP C1101 "
      ideal   model   delta    sigma   weight residual
     120.50  133.94  -13.44 3.00e+00 1.11e-01 2.01e+01
  ... (remaining 19044 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.46: 7608
       34.46 -    68.93: 442
       68.93 -   103.39: 19
      103.39 -   137.85: 5
      137.85 -   172.32: 2
  Dihedral angle restraints: 8076
    sinusoidal: 3741
      harmonic: 4335
  Sorted by residual:
  dihedral pdb=" C5' ADP D1101 "
           pdb=" O5' ADP D1101 "
           pdb=" PA  ADP D1101 "
           pdb=" O2A ADP D1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   66.10 -126.09     1      2.00e+01 2.50e-03 3.81e+01
  dihedral pdb=" O2A ADP D1101 "
           pdb=" O3A ADP D1101 "
           pdb=" PA  ADP D1101 "
           pdb=" PB  ADP D1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   65.40 -125.40     1      2.00e+01 2.50e-03 3.79e+01
  dihedral pdb=" O1B ADP D1101 "
           pdb=" O3A ADP D1101 "
           pdb=" PB  ADP D1101 "
           pdb=" PA  ADP D1101 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   57.79 -117.80     1      2.00e+01 2.50e-03 3.52e+01
  ... (remaining 8073 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.058: 1822
       0.058 -    0.115: 335
       0.115 -    0.173: 29
       0.173 -    0.231: 3
       0.231 -    0.288: 4
  Chirality restraints: 2193
  Sorted by residual:
  chirality pdb=" CA  TYR A 237 "
            pdb=" N   TYR A 237 "
            pdb=" C   TYR A 237 "
            pdb=" CB  TYR A 237 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.80   -0.29 2.00e-01 2.50e+01 2.08e+00
  chirality pdb=" C3' ADP C1101 "
            pdb=" C2' ADP C1101 "
            pdb=" C4' ADP C1101 "
            pdb=" O3' ADP C1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.76    0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" C3' ADP D1101 "
            pdb=" C2' ADP D1101 "
            pdb=" C4' ADP D1101 "
            pdb=" O3' ADP D1101 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.51   -2.75    0.24 2.00e-01 2.50e+01 1.44e+00
  ... (remaining 2190 not shown)

  Planarity restraints: 2183
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR D  58 "    0.032 5.00e-02 4.00e+02   4.80e-02 3.68e+00
        pdb=" N   PRO D  59 "   -0.083 5.00e-02 4.00e+02
        pdb=" CA  PRO D  59 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO D  59 "    0.027 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A  47 "   -0.007 2.00e-02 2.50e+03   1.38e-02 1.91e+00
        pdb=" C   GLY A  47 "    0.024 2.00e-02 2.50e+03
        pdb=" O   GLY A  47 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   ASP A  48 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA D  41 "    0.007 2.00e-02 2.50e+03   1.33e-02 1.76e+00
        pdb=" C   ALA D  41 "   -0.023 2.00e-02 2.50e+03
        pdb=" O   ALA D  41 "    0.008 2.00e-02 2.50e+03
        pdb=" N   GLY D  42 "    0.008 2.00e-02 2.50e+03
  ... (remaining 2180 not shown)

  Histogram of nonbonded interaction distances:
        1.50 -     2.18: 12
        2.18 -     2.86: 4464
        2.86 -     3.54: 18886
        3.54 -     4.22: 31260
        4.22 -     4.90: 53778
  Nonbonded interactions: 108400
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP A  48 "
            pdb="MN    MN A 501 "
     model   vdw
     1.498 2.320
  nonbonded pdb=" OD2 ASP A  48 "
            pdb="MN    MN A 502 "
     model   vdw
     1.600 2.320
  nonbonded pdb=" ND2 ASN A  83 "
            pdb=" OP2  DC F  55 "
     model   vdw
     1.761 3.120
  nonbonded pdb=" OD1 ASN B  83 "
            pdb="MN    MN B 502 "
     model   vdw
     1.806 2.320
  nonbonded pdb=" O3B ADP C1101 "
            pdb="MG    MG C1102 "
     model   vdw
     1.816 2.170
  ... (remaining 108395 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 1 through 137 or resid 153 through 343 or resid 356 throug \ 
h 502))
  selection = (chain 'B' and (resid 1 through 189 or resid 204 through 502))
}
ncs_group {
  reference = (chain 'C' and (resid 1 through 200 or resid 875 through 1102))
  selection = (chain 'D' and (resid 1 through 200 or resid 875 through 1102))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=0.99
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.860
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.050
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.950
  Find NCS groups from input model:        0.260
  Set up NCS constraints:                  0.030
  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:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6386
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   0.109  13796  Z= 0.335
  Angle     :  0.740  13.436  19049  Z= 0.482
  Chirality :  0.045   0.288   2193
  Planarity :  0.003   0.048   2183
  Dihedral  : 18.983 172.318   5264
  Min Nonbonded Distance : 1.498

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.31 %
    Favored  : 99.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.23), residues: 1479
  helix:  1.66 (0.23), residues: 547
  sheet:  0.38 (0.34), residues: 231
  loop : -0.29 (0.25), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG D 976 
 TYR   0.014   0.001   TYR C 882 
 PHE   0.014   0.001   PHE C 895 
 TRP   0.010   0.001   TRP A   9 
 HIS   0.009   0.001   HIS A 392 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00467 /  0.33 (13796)
  covalent geometry    : angle       0.73972 /  0.48 (19049)
  hydrogen bonds       : bond        0.14864 /  9.65 (  621)
  hydrogen bonds       : angle       5.72061 /  4.00 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  599 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 598
  time to evaluate  : 0.479 
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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  189 VAL cc_start: 0.8396 (t) cc_final: 0.8014 (t)
REVERT: C  193 HIS cc_start: 0.7134 (t70) cc_final: 0.6664 (t70)
REVERT: C 1033 ILE cc_start: 0.6499 (mm) cc_final: 0.6244 (mp)
REVERT: D   52 LEU cc_start: 0.7449 (tp) cc_final: 0.7075 (tp)
REVERT: A   93 SER cc_start: 0.7255 (m) cc_final: 0.6489 (p)
REVERT: B  246 PHE cc_start: 0.6214 (m-80) cc_final: 0.5719 (m-10)
REVERT: B  306 TRP cc_start: 0.7409 (m-10) cc_final: 0.6825 (m-10)
  outliers start: 1
  outliers final: 1
  residues processed: 598
  average time/residue: 0.1272
  time to fit residues: 108.1359
Evaluate side-chains
  396 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 395
  time to evaluate  : 0.406 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  185 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    0.4980
   chunk 10 optimal weight:    4.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    0.0670
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    6.9990
   chunk 149 optimal weight:    9.9990
   overall best weight:    1.0720

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C1005 ASN
** D  10 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D1016 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 222 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 227 GLN
** A 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B  84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 234 HIS
** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.088166 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.059544 restraints weight = 43392.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.062023 restraints weight = 25073.462|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3220 r_free = 0.3220 target = 0.063754 restraints weight = 17221.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.065016 restraints weight = 13153.878|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3262 r_free = 0.3262 target = 0.065901 restraints weight = 10771.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3214
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3214
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3214 r_free = 0.3214    target_work(ls_wunit_k1) = 0.064         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:        4 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3181 r_free = 0.3181    target_work(ls_wunit_k1) = 0.062         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 15 (20 function evaluations)
r_final: 0.3181
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7784
moved from start:          0.3549

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.076  13796  Z= 0.206
  Angle     :  0.888  17.393  19049  Z= 0.430
  Chirality :  0.051   0.304   2193
  Planarity :  0.006   0.095   2183
  Dihedral  : 21.292 176.024   2467
  Min Nonbonded Distance : 1.932

Molprobity Statistics.
  All-atom Clashscore : 19.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.64 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 18.92 %
    Favored  : 77.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.38 (0.22), residues: 1479
  helix:  1.26 (0.22), residues: 541
  sheet:  0.05 (0.32), residues: 267
  loop : -0.42 (0.25), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 146 
 TYR   0.041   0.004   TYR A  16 
 PHE   0.038   0.003   PHE C 895 
 TRP   0.037   0.003   TRP C 880 
 HIS   0.009   0.002   HIS B 222 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00438 /  0.21 (13796)
  covalent geometry    : angle       0.88810 /  0.43 (19049)
  hydrogen bonds       : bond        0.05427 /  3.55 (  621)
  hydrogen bonds       : angle       5.11501 /  3.51 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  484 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 442
  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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   12 ASN cc_start: 0.9371 (m-40) cc_final: 0.9108 (m-40)
REVERT: C   74 ARG cc_start: 0.8888 (mmp80) cc_final: 0.8146 (mmp-170)
REVERT: C   82 GLU cc_start: 0.8507 (tt0) cc_final: 0.8265 (tm-30)
REVERT: C   85 PHE cc_start: 0.9516 (p90) cc_final: 0.9239 (p90)
REVERT: C   95 PHE cc_start: 0.8744 (OUTLIER) cc_final: 0.8170 (t80)
REVERT: C  135 LEU cc_start: 0.9643 (OUTLIER) cc_final: 0.9377 (mm)
REVERT: C  189 VAL cc_start: 0.9517 (t) cc_final: 0.8841 (t)
REVERT: C  880 TRP cc_start: 0.9117 (m100) cc_final: 0.8141 (m100)
REVERT: C  882 TYR cc_start: 0.8283 (m-80) cc_final: 0.8080 (m-80)
REVERT: C  893 ASP cc_start: 0.8616 (m-30) cc_final: 0.8213 (m-30)
REVERT: C  895 PHE cc_start: 0.9019 (t80) cc_final: 0.8297 (t80)
REVERT: C  902 LEU cc_start: 0.9196 (mm) cc_final: 0.8466 (tp)
REVERT: C  904 LEU cc_start: 0.9783 (tp) cc_final: 0.9531 (pp)
REVERT: C  906 ASN cc_start: 0.9175 (m110) cc_final: 0.8648 (m-40)
REVERT: C  921 ARG cc_start: 0.8623 (ttt180) cc_final: 0.8257 (ttt-90)
REVERT: C  932 LEU cc_start: 0.8716 (mt) cc_final: 0.8342 (mm)
REVERT: C  955 GLU cc_start: 0.9195 (mp0) cc_final: 0.8959 (mp0)
REVERT: C  973 HIS cc_start: 0.9252 (p90) cc_final: 0.8959 (p90)
REVERT: C 1045 PHE cc_start: 0.8897 (m-80) cc_final: 0.8132 (m-80)
REVERT: D   12 ASN cc_start: 0.9247 (m-40) cc_final: 0.8777 (t0)
REVERT: D   55 TYR cc_start: 0.8520 (m-10) cc_final: 0.7884 (m-10)
REVERT: D   84 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8650 (mm-30)
REVERT: D   92 TYR cc_start: 0.8487 (OUTLIER) cc_final: 0.7672 (m-10)
REVERT: D  165 LYS cc_start: 0.9474 (mmmt) cc_final: 0.9157 (mmmm)
REVERT: D  184 GLN cc_start: 0.9301 (mp10) cc_final: 0.8872 (mp10)
REVERT: D  188 MET cc_start: 0.9059 (ptp) cc_final: 0.8739 (ttm)
REVERT: D  896 ARG cc_start: 0.8413 (ttm110) cc_final: 0.7751 (mtm110)
REVERT: D  914 GLN cc_start: 0.9507 (tp40) cc_final: 0.9070 (tp-100)
REVERT: D  919 HIS cc_start: 0.8118 (t-170) cc_final: 0.7820 (t70)
REVERT: D  941 GLN cc_start: 0.9121 (mt0) cc_final: 0.8733 (pt0)
REVERT: D  989 LEU cc_start: 0.9699 (mt) cc_final: 0.9310 (tp)
REVERT: D 1011 ILE cc_start: 0.9485 (pt) cc_final: 0.8822 (mm)
REVERT: D 1016 HIS cc_start: 0.7958 (m-70) cc_final: 0.7726 (m170)
REVERT: A    9 TRP cc_start: 0.9643 (m-10) cc_final: 0.9387 (m-10)
REVERT: A   10 HIS cc_start: 0.9189 (m-70) cc_final: 0.8752 (m-70)
REVERT: A   18 LYS cc_start: 0.9145 (mmmt) cc_final: 0.8663 (mmtm)
REVERT: A   65 ARG cc_start: 0.9136 (tpm170) cc_final: 0.8877 (tpp-160)
REVERT: A   93 SER cc_start: 0.9512 (m) cc_final: 0.8823 (p)
REVERT: A  149 LYS cc_start: 0.9656 (mttm) cc_final: 0.9200 (mttt)
REVERT: A  212 PHE cc_start: 0.8141 (m-80) cc_final: 0.7806 (m-80)
REVERT: A  232 MET cc_start: 0.9174 (mmm) cc_final: 0.8893 (mpp)
REVERT: A  253 LYS cc_start: 0.8231 (mmmm) cc_final: 0.7792 (mmmm)
REVERT: A  366 PHE cc_start: 0.9050 (t80) cc_final: 0.8632 (t80)
REVERT: B   15 PHE cc_start: 0.8748 (t80) cc_final: 0.7965 (t80)
REVERT: B   16 TYR cc_start: 0.8300 (m-80) cc_final: 0.8019 (m-10)
REVERT: B   18 LYS cc_start: 0.8644 (mtmm) cc_final: 0.7811 (ptpt)
REVERT: B   62 LEU cc_start: 0.9656 (OUTLIER) cc_final: 0.9245 (mm)
REVERT: B   65 ARG cc_start: 0.9361 (mtp85) cc_final: 0.9019 (ptp-110)
REVERT: B   75 CYS cc_start: 0.8129 (m) cc_final: 0.7625 (m)
REVERT: B  207 PHE cc_start: 0.8200 (t80) cc_final: 0.7181 (t80)
REVERT: B  225 ARG cc_start: 0.8926 (ttm170) cc_final: 0.8437 (ttm110)
REVERT: B  271 LEU cc_start: 0.9043 (mm) cc_final: 0.8799 (mm)
REVERT: B  282 LEU cc_start: 0.8591 (mt) cc_final: 0.8266 (mt)
REVERT: B  317 LEU cc_start: 0.9313 (tp) cc_final: 0.8850 (tp)
REVERT: B  321 GLN cc_start: 0.9101 (mt0) cc_final: 0.8676 (mt0)
REVERT: B  366 PHE cc_start: 0.9246 (t80) cc_final: 0.8958 (t80)
  outliers start: 42
  outliers final: 22
  residues processed: 455
  average time/residue: 0.1098
  time to fit residues: 74.6954
Evaluate side-chains
  414 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 388
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   95 PHE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  135 LEU
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue   92 TYR
Chi-restraints excluded: chain D residue  103 ASN
Chi-restraints excluded: chain D residue  116 LEU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue 1041 LEU
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  182 THR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  200 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 130 optimal weight:    2.9990
   chunk 123 optimal weight:    4.9990
   chunk 78 optimal weight:    0.0970
   chunk 74 optimal weight:    0.8980
   chunk 140 optimal weight:    4.9990
   chunk 30 optimal weight:    0.9980
   chunk 149 optimal weight:    9.9990
   chunk 4 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 50 optimal weight:    4.9990
   chunk 88 optimal weight:    0.9990
   overall best weight:    1.1982

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D1016 HIS
** B 318 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 = 0.3591 r_free = 0.3591 target = 0.084350 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.056989 restraints weight = 44370.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.059273 restraints weight = 25549.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.060831 restraints weight = 17565.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.061993 restraints weight = 13447.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3213 r_free = 0.3213 target = 0.062795 restraints weight = 10993.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3166
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3166
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3166 r_free = 0.3166    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       15 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 7 (14 function evaluations)
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7871
moved from start:          0.4195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  13796  Z= 0.191
  Angle     :  0.845  14.543  19049  Z= 0.409
  Chirality :  0.050   0.420   2193
  Planarity :  0.004   0.053   2183
  Dihedral  : 21.272 179.529   2467
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 19.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 21.98 %
    Favored  : 74.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.22), residues: 1479
  helix:  1.07 (0.22), residues: 548
  sheet: -0.12 (0.31), residues: 284
  loop : -0.43 (0.25), residues: 647

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 197 
 TYR   0.028   0.003   TYR B 217 
 PHE   0.025   0.003   PHE C 895 
 TRP   0.026   0.003   TRP B 296 
 HIS   0.021   0.002   HIS A 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00401 /  0.19 (13796)
  covalent geometry    : angle       0.84478 /  0.41 (19049)
  hydrogen bonds       : bond        0.04902 /  3.25 (  621)
  hydrogen bonds       : angle       4.93486 /  3.39 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  447 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 398
  time to evaluate  : 0.574 
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: C   12 ASN cc_start: 0.9394 (m-40) cc_final: 0.9070 (m-40)
REVERT: C   45 THR cc_start: 0.9766 (m) cc_final: 0.9541 (p)
REVERT: C   72 MET cc_start: 0.8281 (ppp) cc_final: 0.7496 (ppp)
REVERT: C   74 ARG cc_start: 0.8846 (mmp80) cc_final: 0.8507 (mmp80)
REVERT: C   82 GLU cc_start: 0.8424 (tt0) cc_final: 0.8207 (tm-30)
REVERT: C   85 PHE cc_start: 0.9524 (p90) cc_final: 0.9293 (p90)
REVERT: C   95 PHE cc_start: 0.8958 (OUTLIER) cc_final: 0.8432 (t80)
REVERT: C  135 LEU cc_start: 0.9637 (mm) cc_final: 0.9431 (mm)
REVERT: C  193 HIS cc_start: 0.9212 (t70) cc_final: 0.8237 (t70)
REVERT: C  884 ASN cc_start: 0.9022 (t0) cc_final: 0.8383 (m110)
REVERT: C  893 ASP cc_start: 0.8734 (m-30) cc_final: 0.8313 (m-30)
REVERT: C  895 PHE cc_start: 0.9049 (t80) cc_final: 0.8409 (t80)
REVERT: C  897 LYS cc_start: 0.9385 (mtmt) cc_final: 0.8923 (mmtp)
REVERT: C  902 LEU cc_start: 0.9156 (mm) cc_final: 0.8399 (tp)
REVERT: C  906 ASN cc_start: 0.9201 (m110) cc_final: 0.8682 (m110)
REVERT: C  921 ARG cc_start: 0.8698 (ttt180) cc_final: 0.8280 (ttt-90)
REVERT: C  973 HIS cc_start: 0.9228 (p90) cc_final: 0.8904 (p90)
REVERT: D    4 LEU cc_start: 0.9119 (pp) cc_final: 0.8647 (mp)
REVERT: D   12 ASN cc_start: 0.9337 (m-40) cc_final: 0.8934 (t0)
REVERT: D   92 TYR cc_start: 0.8571 (m-80) cc_final: 0.8178 (m-10)
REVERT: D  165 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9142 (mmmm)
REVERT: D  184 GLN cc_start: 0.9315 (mp10) cc_final: 0.8838 (mp10)
REVERT: D  188 MET cc_start: 0.9036 (ptp) cc_final: 0.8781 (ttm)
REVERT: D  197 ARG cc_start: 0.9464 (tpt90) cc_final: 0.9100 (tpt90)
REVERT: D  896 ARG cc_start: 0.8549 (ttm110) cc_final: 0.8148 (ttp-110)
REVERT: D  914 GLN cc_start: 0.9468 (tp40) cc_final: 0.9104 (tp-100)
REVERT: D  919 HIS cc_start: 0.8195 (t-170) cc_final: 0.7817 (t70)
REVERT: D  941 GLN cc_start: 0.9165 (mt0) cc_final: 0.8756 (pt0)
REVERT: D  989 LEU cc_start: 0.9692 (mt) cc_final: 0.9277 (tp)
REVERT: D 1038 TYR cc_start: 0.8688 (m-10) cc_final: 0.8231 (m-10)
REVERT: A    1 MET cc_start: 0.7498 (OUTLIER) cc_final: 0.7178 (ttm)
REVERT: A   18 LYS cc_start: 0.9272 (mmmt) cc_final: 0.8896 (mmtm)
REVERT: A   65 ARG cc_start: 0.9123 (tpm170) cc_final: 0.8839 (tpp-160)
REVERT: A   93 SER cc_start: 0.9509 (m) cc_final: 0.8922 (p)
REVERT: A  149 LYS cc_start: 0.9708 (mttm) cc_final: 0.9203 (mttm)
REVERT: A  212 PHE cc_start: 0.8211 (m-80) cc_final: 0.7914 (m-80)
REVERT: A  253 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7794 (mmmm)
REVERT: A  306 TRP cc_start: 0.8830 (m-10) cc_final: 0.8274 (m-10)
REVERT: A  357 LEU cc_start: 0.9271 (mp) cc_final: 0.9050 (mp)
REVERT: A  366 PHE cc_start: 0.9114 (t80) cc_final: 0.8561 (t80)
REVERT: B   15 PHE cc_start: 0.8883 (t80) cc_final: 0.7958 (t80)
REVERT: B   16 TYR cc_start: 0.8293 (m-80) cc_final: 0.8045 (m-10)
REVERT: B   18 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8484 (ptpt)
REVERT: B   33 GLU cc_start: 0.9454 (tt0) cc_final: 0.9196 (mt-10)
REVERT: B   62 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9068 (mm)
REVERT: B   65 ARG cc_start: 0.9354 (mtp85) cc_final: 0.9098 (ptp-110)
REVERT: B   75 CYS cc_start: 0.8180 (m) cc_final: 0.7639 (m)
REVERT: B  169 CYS cc_start: 0.9561 (OUTLIER) cc_final: 0.9350 (p)
REVERT: B  207 PHE cc_start: 0.9140 (t80) cc_final: 0.8263 (t80)
REVERT: B  282 LEU cc_start: 0.8813 (mt) cc_final: 0.8591 (mp)
REVERT: B  321 GLN cc_start: 0.9120 (mt0) cc_final: 0.8443 (tp-100)
REVERT: B  366 PHE cc_start: 0.9269 (t80) cc_final: 0.8913 (t80)
  outliers start: 49
  outliers final: 34
  residues processed: 415
  average time/residue: 0.1101
  time to fit residues: 68.4469
Evaluate side-chains
  417 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 379
  time to evaluate  : 0.482 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   32 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   95 PHE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  970 LEU
Chi-restraints excluded: chain C residue  976 ARG
Chi-restraints excluded: chain C residue  982 LEU
Chi-restraints excluded: chain C residue  986 PHE
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  149 ARG
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  906 ASN
Chi-restraints excluded: chain D residue  993 THR
Chi-restraints excluded: chain D residue  994 LEU
Chi-restraints excluded: chain D residue 1041 LEU
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain A residue  161 TYR
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  335 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   79 VAL
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  169 CYS
Chi-restraints excluded: chain B residue  200 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 67 optimal weight:    5.9990
   chunk 65 optimal weight:    0.6980
   chunk 41 optimal weight:    4.9990
   chunk 58 optimal weight:    5.9990
   chunk 59 optimal weight:    3.9990
   chunk 8 optimal weight:    0.0980
   chunk 139 optimal weight:    3.9990
   chunk 97 optimal weight:    5.9990
   chunk 77 optimal weight:    4.9990
   chunk 70 optimal weight:    3.9990
   chunk 81 optimal weight:    5.9990
   overall best weight:    2.5586

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
D 110 GLN
** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 110 HIS
** A 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 380 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.081028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3032 r_free = 0.3032 target = 0.054104 restraints weight = 46940.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.056250 restraints weight = 27330.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.057760 restraints weight = 18890.048|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.058818 restraints weight = 14531.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.059586 restraints weight = 12040.448|
|-----------------------------------------------------------------------------|
r_work (final): 0.3121
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3123
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3123 r_free = 0.3123    target_work(ls_wunit_k1) = 0.059         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3123
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8017
moved from start:          0.4695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.065  13796  Z= 0.295
  Angle     :  0.842  14.157  19049  Z= 0.422
  Chirality :  0.050   0.527   2193
  Planarity :  0.004   0.053   2183
  Dihedral  : 21.321 176.294   2467
  Min Nonbonded Distance : 1.759

Molprobity Statistics.
  All-atom Clashscore : 21.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.97 %
    Favored  : 97.03 %
  Rotamer:
    Outliers :  5.49 %
    Allowed  : 22.61 %
    Favored  : 71.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.22), residues: 1479
  helix:  0.90 (0.22), residues: 548
  sheet: -0.13 (0.31), residues: 285
  loop : -0.43 (0.25), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  74 
 TYR   0.040   0.003   TYR C 882 
 PHE   0.022   0.003   PHE C 898 
 TRP   0.024   0.003   TRP B 296 
 HIS   0.020   0.002   HIS A 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00574 /  0.29 (13796)
  covalent geometry    : angle       0.84249 /  0.42 (19049)
  hydrogen bonds       : bond        0.05160 /  3.45 (  621)
  hydrogen bonds       : angle       5.17259 /  3.56 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  459 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 70
    poor density    : 389
  time to evaluate  : 0.514 
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: C   12 ASN cc_start: 0.9410 (m-40) cc_final: 0.8905 (t0)
REVERT: C   27 PHE cc_start: 0.9121 (m-10) cc_final: 0.8871 (m-80)
REVERT: C   45 THR cc_start: 0.9687 (m) cc_final: 0.9451 (p)
REVERT: C  134 GLU cc_start: 0.9560 (mt-10) cc_final: 0.9343 (pp20)
REVERT: C  135 LEU cc_start: 0.9709 (mm) cc_final: 0.8266 (mm)
REVERT: C  190 PHE cc_start: 0.8799 (t80) cc_final: 0.8195 (t80)
REVERT: C  193 HIS cc_start: 0.9148 (t70) cc_final: 0.8000 (t-170)
REVERT: C  880 TRP cc_start: 0.8959 (m100) cc_final: 0.8295 (m100)
REVERT: C  884 ASN cc_start: 0.8986 (t0) cc_final: 0.8061 (m110)
REVERT: C  893 ASP cc_start: 0.8800 (m-30) cc_final: 0.8431 (m-30)
REVERT: C  897 LYS cc_start: 0.9403 (mtmt) cc_final: 0.8968 (mmtp)
REVERT: C  902 LEU cc_start: 0.9168 (mm) cc_final: 0.8393 (tp)
REVERT: C  906 ASN cc_start: 0.9259 (m110) cc_final: 0.8708 (m110)
REVERT: C  973 HIS cc_start: 0.9261 (p90) cc_final: 0.9053 (p90)
REVERT: C 1045 PHE cc_start: 0.9122 (m-80) cc_final: 0.8298 (m-80)
REVERT: D   12 ASN cc_start: 0.9287 (m-40) cc_final: 0.8707 (t0)
REVERT: D   72 MET cc_start: 0.8249 (ttt) cc_final: 0.7445 (tpt)
REVERT: D  139 LEU cc_start: 0.9479 (mm) cc_final: 0.9256 (mm)
REVERT: D  155 GLN cc_start: 0.8801 (pm20) cc_final: 0.8487 (pm20)
REVERT: D  165 LYS cc_start: 0.9486 (mmmt) cc_final: 0.9149 (mmmm)
REVERT: D  184 GLN cc_start: 0.9306 (mp10) cc_final: 0.9083 (mt0)
REVERT: D  188 MET cc_start: 0.9063 (ptp) cc_final: 0.8813 (ttm)
REVERT: D  884 ASN cc_start: 0.8866 (t0) cc_final: 0.8633 (t0)
REVERT: D  914 GLN cc_start: 0.9437 (tp40) cc_final: 0.9103 (tm-30)
REVERT: D  919 HIS cc_start: 0.8358 (t-170) cc_final: 0.7905 (t70)
REVERT: D  941 GLN cc_start: 0.9195 (mt0) cc_final: 0.8745 (mm-40)
REVERT: D  975 THR cc_start: 0.9174 (m) cc_final: 0.8818 (p)
REVERT: D  983 ASP cc_start: 0.8059 (t0) cc_final: 0.7234 (t0)
REVERT: D  989 LEU cc_start: 0.9662 (mt) cc_final: 0.9349 (tp)
REVERT: A    1 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7188 (ttm)
REVERT: A   18 LYS cc_start: 0.9376 (mmmt) cc_final: 0.9016 (mmtm)
REVERT: A   65 ARG cc_start: 0.9141 (tpm170) cc_final: 0.8872 (tpm170)
REVERT: A   93 SER cc_start: 0.9559 (m) cc_final: 0.9050 (p)
REVERT: A  149 LYS cc_start: 0.9720 (mttm) cc_final: 0.9291 (mttm)
REVERT: A  212 PHE cc_start: 0.8165 (m-80) cc_final: 0.7888 (m-80)
REVERT: A  232 MET cc_start: 0.9270 (mmm) cc_final: 0.8958 (mpp)
REVERT: A  244 LEU cc_start: 0.9341 (mt) cc_final: 0.9072 (mt)
REVERT: A  306 TRP cc_start: 0.8745 (m-10) cc_final: 0.8350 (m-10)
REVERT: A  360 LEU cc_start: 0.8605 (mm) cc_final: 0.8373 (mm)
REVERT: A  366 PHE cc_start: 0.9061 (t80) cc_final: 0.8418 (t80)
REVERT: B   15 PHE cc_start: 0.8936 (t80) cc_final: 0.7638 (t80)
REVERT: B   16 TYR cc_start: 0.8488 (m-80) cc_final: 0.8019 (m-80)
REVERT: B   18 LYS cc_start: 0.8818 (mtmm) cc_final: 0.8430 (ptpt)
REVERT: B   33 GLU cc_start: 0.9457 (tt0) cc_final: 0.9203 (mt-10)
REVERT: B   62 LEU cc_start: 0.9585 (OUTLIER) cc_final: 0.9120 (mm)
REVERT: B   65 ARG cc_start: 0.9371 (mtp85) cc_final: 0.9017 (ptp-110)
REVERT: B   75 CYS cc_start: 0.8324 (m) cc_final: 0.8038 (m)
REVERT: B  127 CYS cc_start: 0.8840 (m) cc_final: 0.8573 (m)
REVERT: B  131 PHE cc_start: 0.7470 (t80) cc_final: 0.6890 (t80)
REVERT: B  132 LEU cc_start: 0.9063 (tp) cc_final: 0.8509 (tt)
REVERT: B  165 TYR cc_start: 0.9583 (t80) cc_final: 0.9355 (t80)
REVERT: B  282 LEU cc_start: 0.8874 (mt) cc_final: 0.8559 (mp)
REVERT: B  321 GLN cc_start: 0.9153 (mt0) cc_final: 0.8676 (mt0)
REVERT: B  357 LEU cc_start: 0.9411 (tp) cc_final: 0.8921 (pp)
REVERT: B  366 PHE cc_start: 0.9301 (t80) cc_final: 0.8915 (t80)
REVERT: B  373 GLU cc_start: 0.8935 (tp30) cc_final: 0.8626 (tp30)
  outliers start: 70
  outliers final: 50
  residues processed: 412
  average time/residue: 0.1101
  time to fit residues: 67.6055
Evaluate side-chains
  407 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 355
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   95 PHE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  123 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  965 LEU
Chi-restraints excluded: chain C residue  970 LEU
Chi-restraints excluded: chain C residue  976 ARG
Chi-restraints excluded: chain C residue  981 PHE
Chi-restraints excluded: chain C residue  986 PHE
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   56 HIS
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  116 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain D residue  149 ARG
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  906 ASN
Chi-restraints excluded: chain D residue  993 THR
Chi-restraints excluded: chain D residue  994 LEU
Chi-restraints excluded: chain D residue 1011 ILE
Chi-restraints excluded: chain D residue 1014 ILE
Chi-restraints excluded: chain D residue 1030 VAL
Chi-restraints excluded: chain D residue 1036 LEU
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  101 ASN
Chi-restraints excluded: chain A residue  127 CYS
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  140 SER
Chi-restraints excluded: chain A residue  157 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  275 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 22 optimal weight:    5.9990
   chunk 65 optimal weight:    0.9990
   chunk 60 optimal weight:    2.9990
   chunk 99 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 96 optimal weight:    0.7980
   chunk 111 optimal weight:   10.0000
   chunk 25 optimal weight:    0.4980
   chunk 91 optimal weight:    0.8980
   chunk 7 optimal weight:    4.9990
   chunk 31 optimal weight:    2.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 193 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.083303 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3086 r_free = 0.3086 target = 0.056202 restraints weight = 45635.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.058471 restraints weight = 26087.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3171 r_free = 0.3171 target = 0.060074 restraints weight = 17883.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3194 r_free = 0.3194 target = 0.061208 restraints weight = 13645.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.062016 restraints weight = 11223.841|
|-----------------------------------------------------------------------------|
r_work (final): 0.3162
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3164
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3164 r_free = 0.3164    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3164
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.4940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.090  13796  Z= 0.171
  Angle     :  0.846  13.982  19049  Z= 0.403
  Chirality :  0.050   0.508   2193
  Planarity :  0.004   0.052   2183
  Dihedral  : 21.276 171.713   2467
  Min Nonbonded Distance : 1.887

Molprobity Statistics.
  All-atom Clashscore : 19.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.43 %
    Favored  : 97.57 %
  Rotamer:
    Outliers :  4.08 %
    Allowed  : 25.12 %
    Favored  : 70.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.16 (0.22), residues: 1479
  helix:  0.86 (0.22), residues: 548
  sheet:  0.13 (0.32), residues: 267
  loop : -0.44 (0.25), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D 197 
 TYR   0.036   0.003   TYR D  55 
 PHE   0.021   0.002   PHE B  27 
 TRP   0.023   0.003   TRP A 296 
 HIS   0.016   0.001   HIS A 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00368 /  0.17 (13796)
  covalent geometry    : angle       0.84628 /  0.40 (19049)
  hydrogen bonds       : bond        0.04744 /  3.20 (  621)
  hydrogen bonds       : angle       4.94701 /  3.41 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  434 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 382
  time to evaluate  : 0.495 
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: C   12 ASN cc_start: 0.9397 (m-40) cc_final: 0.8847 (t0)
REVERT: C   27 PHE cc_start: 0.9128 (m-10) cc_final: 0.8870 (m-80)
REVERT: C   45 THR cc_start: 0.9668 (m) cc_final: 0.9398 (p)
REVERT: C  135 LEU cc_start: 0.9709 (mm) cc_final: 0.9390 (mm)
REVERT: C  142 LEU cc_start: 0.9149 (pp) cc_final: 0.8728 (tt)
REVERT: C  193 HIS cc_start: 0.9059 (t70) cc_final: 0.8270 (t-90)
REVERT: C  197 ARG cc_start: 0.9455 (tpt90) cc_final: 0.9244 (tpm170)
REVERT: C  880 TRP cc_start: 0.9003 (m100) cc_final: 0.8140 (m100)
REVERT: C  884 ASN cc_start: 0.8966 (t0) cc_final: 0.8190 (m110)
REVERT: C  893 ASP cc_start: 0.8798 (m-30) cc_final: 0.8398 (m-30)
REVERT: C  895 PHE cc_start: 0.9016 (t80) cc_final: 0.8323 (t80)
REVERT: C  897 LYS cc_start: 0.9327 (mtmt) cc_final: 0.8935 (mmtp)
REVERT: C  902 LEU cc_start: 0.9121 (mm) cc_final: 0.8352 (tp)
REVERT: C  906 ASN cc_start: 0.9171 (m110) cc_final: 0.8659 (m110)
REVERT: C  973 HIS cc_start: 0.9194 (p90) cc_final: 0.8864 (p90)
REVERT: C  984 GLU cc_start: 0.8162 (tp30) cc_final: 0.7589 (tp30)
REVERT: C 1029 LYS cc_start: 0.9052 (OUTLIER) cc_final: 0.8768 (mppt)
REVERT: C 1045 PHE cc_start: 0.9124 (m-80) cc_final: 0.8776 (m-80)
REVERT: D   12 ASN cc_start: 0.9241 (m-40) cc_final: 0.8656 (t0)
REVERT: D   72 MET cc_start: 0.8031 (ttt) cc_final: 0.7229 (tpt)
REVERT: D  155 GLN cc_start: 0.8758 (pm20) cc_final: 0.8412 (pm20)
REVERT: D  165 LYS cc_start: 0.9495 (mmmt) cc_final: 0.9151 (mmmm)
REVERT: D  184 GLN cc_start: 0.9332 (mp10) cc_final: 0.9103 (mt0)
REVERT: D  188 MET cc_start: 0.9004 (ptp) cc_final: 0.8804 (ttm)
REVERT: D  894 LYS cc_start: 0.9286 (ttpt) cc_final: 0.9039 (ptmt)
REVERT: D  896 ARG cc_start: 0.8509 (ttm110) cc_final: 0.7778 (mtm110)
REVERT: D  910 LEU cc_start: 0.9586 (OUTLIER) cc_final: 0.9355 (mp)
REVERT: D  914 GLN cc_start: 0.9430 (tp40) cc_final: 0.9199 (tm-30)
REVERT: D  919 HIS cc_start: 0.8079 (t-170) cc_final: 0.7658 (t70)
REVERT: D  941 GLN cc_start: 0.9114 (mt0) cc_final: 0.8859 (mm-40)
REVERT: D  975 THR cc_start: 0.9191 (m) cc_final: 0.8836 (p)
REVERT: D  983 ASP cc_start: 0.8129 (t0) cc_final: 0.7192 (t0)
REVERT: D  989 LEU cc_start: 0.9654 (mt) cc_final: 0.9309 (tp)
REVERT: A    1 MET cc_start: 0.7414 (OUTLIER) cc_final: 0.7087 (ttm)
REVERT: A   18 LYS cc_start: 0.9385 (mmmt) cc_final: 0.9032 (mmtm)
REVERT: A   58 TYR cc_start: 0.9215 (p90) cc_final: 0.8835 (p90)
REVERT: A   65 ARG cc_start: 0.9127 (tpm170) cc_final: 0.8826 (tpm170)
REVERT: A   93 SER cc_start: 0.9535 (m) cc_final: 0.9115 (p)
REVERT: A  149 LYS cc_start: 0.9684 (mttm) cc_final: 0.9242 (mttm)
REVERT: A  212 PHE cc_start: 0.8225 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  244 LEU cc_start: 0.9310 (mt) cc_final: 0.9044 (mt)
REVERT: A  306 TRP cc_start: 0.8937 (m-10) cc_final: 0.8370 (m-10)
REVERT: A  366 PHE cc_start: 0.9016 (t80) cc_final: 0.8368 (t80)
REVERT: B   15 PHE cc_start: 0.8946 (t80) cc_final: 0.7563 (t80)
REVERT: B   16 TYR cc_start: 0.8474 (m-80) cc_final: 0.7949 (m-80)
REVERT: B   33 GLU cc_start: 0.9432 (tt0) cc_final: 0.8834 (tm-30)
REVERT: B   65 ARG cc_start: 0.9310 (mtp85) cc_final: 0.9021 (mtm-85)
REVERT: B   75 CYS cc_start: 0.8369 (m) cc_final: 0.8100 (m)
REVERT: B  127 CYS cc_start: 0.8739 (m) cc_final: 0.8500 (m)
REVERT: B  253 LYS cc_start: 0.8327 (mmmt) cc_final: 0.7643 (mmtm)
REVERT: B  271 LEU cc_start: 0.9132 (OUTLIER) cc_final: 0.8879 (mm)
REVERT: B  321 GLN cc_start: 0.9066 (mt0) cc_final: 0.8221 (mt0)
REVERT: B  325 GLN cc_start: 0.9378 (mt0) cc_final: 0.9114 (pt0)
REVERT: B  357 LEU cc_start: 0.9373 (tp) cc_final: 0.8889 (pp)
REVERT: B  366 PHE cc_start: 0.9234 (t80) cc_final: 0.8521 (t80)
REVERT: B  387 PHE cc_start: 0.9418 (t80) cc_final: 0.9151 (t80)
  outliers start: 52
  outliers final: 38
  residues processed: 398
  average time/residue: 0.1076
  time to fit residues: 64.5045
Evaluate side-chains
  409 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 367
  time to evaluate  : 0.505 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   95 PHE
Chi-restraints excluded: chain C residue  111 VAL
Chi-restraints excluded: chain C residue  123 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue  970 LEU
Chi-restraints excluded: chain C residue  976 ARG
Chi-restraints excluded: chain C residue 1020 MET
Chi-restraints excluded: chain C residue 1029 LYS
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  906 ASN
Chi-restraints excluded: chain D residue  910 LEU
Chi-restraints excluded: chain D residue  993 THR
Chi-restraints excluded: chain D residue  994 LEU
Chi-restraints excluded: chain D residue 1011 ILE
Chi-restraints excluded: chain D residue 1014 ILE
Chi-restraints excluded: chain A residue    1 MET
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 129 optimal weight:    8.9990
   chunk 36 optimal weight:    0.6980
   chunk 17 optimal weight:    0.9980
   chunk 12 optimal weight:    0.5980
   chunk 58 optimal weight:    5.9990
   chunk 137 optimal weight:    5.9990
   chunk 15 optimal weight:    0.9990
   chunk 90 optimal weight:    0.9990
   chunk 54 optimal weight:    0.9980
   chunk 91 optimal weight:    0.0670
   chunk 150 optimal weight:   10.0000
   overall best weight:    0.6718

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 193 HIS
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 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 = 0.3604 r_free = 0.3604 target = 0.083723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.056623 restraints weight = 45634.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.058921 restraints weight = 25916.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.060550 restraints weight = 17671.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.061674 restraints weight = 13445.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3221 r_free = 0.3221 target = 0.062444 restraints weight = 11043.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3173
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3173
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3173 r_free = 0.3173    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3173
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.5109

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  13796  Z= 0.148
  Angle     :  0.849  15.188  19049  Z= 0.397
  Chirality :  0.050   0.448   2193
  Planarity :  0.004   0.051   2183
  Dihedral  : 21.226 168.386   2467
  Min Nonbonded Distance : 1.914

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  4.71 %
    Allowed  : 26.37 %
    Favored  : 68.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.22 (0.22), residues: 1479
  helix:  0.86 (0.22), residues: 543
  sheet:  0.21 (0.32), residues: 265
  loop : -0.37 (0.25), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 197 
 TYR   0.025   0.002   TYR D  55 
 PHE   0.023   0.003   PHE C 898 
 TRP   0.025   0.002   TRP A 296 
 HIS   0.012   0.001   HIS A 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00313 /  0.15 (13796)
  covalent geometry    : angle       0.84932 /  0.40 (19049)
  hydrogen bonds       : bond        0.04552 /  3.06 (  621)
  hydrogen bonds       : angle       4.92535 /  3.39 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  442 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 60
    poor density    : 382
  time to evaluate  : 0.511 
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: C   12 ASN cc_start: 0.9399 (m-40) cc_final: 0.8880 (t0)
REVERT: C   27 PHE cc_start: 0.9145 (m-10) cc_final: 0.8876 (m-80)
REVERT: C   45 THR cc_start: 0.9682 (m) cc_final: 0.9431 (p)
REVERT: C  135 LEU cc_start: 0.9700 (mm) cc_final: 0.9361 (mm)
REVERT: C  193 HIS cc_start: 0.9083 (t-170) cc_final: 0.8306 (t-90)
REVERT: C  880 TRP cc_start: 0.8979 (m100) cc_final: 0.8287 (m100)
REVERT: C  884 ASN cc_start: 0.8880 (t0) cc_final: 0.8086 (m110)
REVERT: C  895 PHE cc_start: 0.9152 (t80) cc_final: 0.8375 (t80)
REVERT: C  897 LYS cc_start: 0.9332 (mtmt) cc_final: 0.8852 (mmtp)
REVERT: C  902 LEU cc_start: 0.9081 (mm) cc_final: 0.8287 (tp)
REVERT: C  906 ASN cc_start: 0.9172 (m110) cc_final: 0.8668 (m110)
REVERT: C  919 HIS cc_start: 0.8407 (t70) cc_final: 0.8131 (t70)
REVERT: C  984 GLU cc_start: 0.8090 (tp30) cc_final: 0.7506 (tp30)
REVERT: C 1029 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8749 (mppt)
REVERT: C 1045 PHE cc_start: 0.9121 (m-80) cc_final: 0.8843 (m-80)
REVERT: D   12 ASN cc_start: 0.9232 (m-40) cc_final: 0.8668 (t0)
REVERT: D   72 MET cc_start: 0.7971 (ttt) cc_final: 0.7191 (tpt)
REVERT: D  155 GLN cc_start: 0.8783 (pm20) cc_final: 0.8419 (pm20)
REVERT: D  162 LEU cc_start: 0.9493 (OUTLIER) cc_final: 0.9261 (mm)
REVERT: D  165 LYS cc_start: 0.9491 (mmmt) cc_final: 0.9146 (mmmm)
REVERT: D  184 GLN cc_start: 0.9327 (mp10) cc_final: 0.9025 (mp10)
REVERT: D  894 LYS cc_start: 0.9302 (ttpt) cc_final: 0.9034 (ptmt)
REVERT: D  896 ARG cc_start: 0.8472 (ttm110) cc_final: 0.7751 (mtm110)
REVERT: D  910 LEU cc_start: 0.9607 (OUTLIER) cc_final: 0.9376 (mp)
REVERT: D  914 GLN cc_start: 0.9422 (tp40) cc_final: 0.9209 (tm-30)
REVERT: D  919 HIS cc_start: 0.7992 (t-170) cc_final: 0.7554 (t70)
REVERT: D  941 GLN cc_start: 0.9252 (mt0) cc_final: 0.8915 (mm-40)
REVERT: D  983 ASP cc_start: 0.8217 (t0) cc_final: 0.7156 (t0)
REVERT: D  989 LEU cc_start: 0.9639 (OUTLIER) cc_final: 0.9299 (tp)
REVERT: A   18 LYS cc_start: 0.9425 (mmmt) cc_final: 0.9133 (mmtm)
REVERT: A   40 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8274 (p)
REVERT: A   58 TYR cc_start: 0.9210 (p90) cc_final: 0.8865 (p90)
REVERT: A   65 ARG cc_start: 0.9137 (tpm170) cc_final: 0.8852 (tpm170)
REVERT: A   93 SER cc_start: 0.9535 (m) cc_final: 0.9172 (p)
REVERT: A  149 LYS cc_start: 0.9677 (mttm) cc_final: 0.9231 (mttm)
REVERT: A  212 PHE cc_start: 0.8269 (m-80) cc_final: 0.8002 (m-80)
REVERT: A  232 MET cc_start: 0.9223 (mmm) cc_final: 0.8858 (mpp)
REVERT: A  244 LEU cc_start: 0.9294 (mt) cc_final: 0.9057 (mt)
REVERT: A  253 LYS cc_start: 0.8143 (mmmm) cc_final: 0.7730 (mmmm)
REVERT: A  286 LEU cc_start: 0.9791 (pt) cc_final: 0.9589 (tt)
REVERT: A  306 TRP cc_start: 0.8815 (m-10) cc_final: 0.8287 (m-10)
REVERT: A  366 PHE cc_start: 0.9036 (t80) cc_final: 0.8360 (t80)
REVERT: B   15 PHE cc_start: 0.8940 (t80) cc_final: 0.7608 (t80)
REVERT: B   16 TYR cc_start: 0.8528 (m-80) cc_final: 0.7991 (m-80)
REVERT: B   18 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8542 (ptpt)
REVERT: B   33 GLU cc_start: 0.9422 (tt0) cc_final: 0.8820 (tm-30)
REVERT: B   62 LEU cc_start: 0.9544 (OUTLIER) cc_final: 0.8960 (mm)
REVERT: B   65 ARG cc_start: 0.9303 (mtp85) cc_final: 0.9082 (ptp-110)
REVERT: B   75 CYS cc_start: 0.8472 (m) cc_final: 0.8205 (m)
REVERT: B  113 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8667 (tm-30)
REVERT: B  127 CYS cc_start: 0.8744 (m) cc_final: 0.8509 (m)
REVERT: B  220 LEU cc_start: 0.9444 (mt) cc_final: 0.9142 (mm)
REVERT: B  271 LEU cc_start: 0.9141 (OUTLIER) cc_final: 0.8866 (mm)
REVERT: B  321 GLN cc_start: 0.9000 (mt0) cc_final: 0.8449 (mt0)
REVERT: B  357 LEU cc_start: 0.9429 (tp) cc_final: 0.8934 (pp)
REVERT: B  366 PHE cc_start: 0.9256 (t80) cc_final: 0.8464 (t80)
REVERT: B  387 PHE cc_start: 0.9426 (t80) cc_final: 0.9146 (t80)
  outliers start: 60
  outliers final: 39
  residues processed: 403
  average time/residue: 0.1049
  time to fit residues: 63.9088
Evaluate side-chains
  408 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 362
  time to evaluate  : 0.464 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   95 PHE
Chi-restraints excluded: chain C residue  123 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue  970 LEU
Chi-restraints excluded: chain C residue  976 ARG
Chi-restraints excluded: chain C residue 1020 MET
Chi-restraints excluded: chain C residue 1029 LYS
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  910 LEU
Chi-restraints excluded: chain D residue  982 LEU
Chi-restraints excluded: chain D residue  989 LEU
Chi-restraints excluded: chain D residue  993 THR
Chi-restraints excluded: chain D residue  994 LEU
Chi-restraints excluded: chain D residue 1014 ILE
Chi-restraints excluded: chain A residue   40 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   43 ILE
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 134 optimal weight:    0.6980
   chunk 6 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 105 optimal weight:    0.3980
   chunk 36 optimal weight:    2.9990
   chunk 89 optimal weight:    4.9990
   chunk 131 optimal weight:    0.7980
   chunk 61 optimal weight:    0.6980
   chunk 153 optimal weight:    9.9990
   chunk 1 optimal weight:    2.9990
   overall best weight:    0.9182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.083367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.056356 restraints weight = 46021.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.058666 restraints weight = 26375.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.060243 restraints weight = 18042.535|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.061413 restraints weight = 13755.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3215 r_free = 0.3215 target = 0.062180 restraints weight = 11274.961|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3170
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3170 r_free = 0.3170    target_work(ls_wunit_k1) = 0.061         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3170
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8001
moved from start:          0.5292

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  13796  Z= 0.155
  Angle     :  0.831  14.254  19049  Z= 0.393
  Chirality :  0.049   0.505   2193
  Planarity :  0.004   0.058   2183
  Dihedral  : 21.197 166.688   2467
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 17.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.57 %
    Favored  : 97.43 %
  Rotamer:
    Outliers :  3.85 %
    Allowed  : 28.26 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.22), residues: 1479
  helix:  0.84 (0.22), residues: 543
  sheet:  0.10 (0.32), residues: 275
  loop : -0.24 (0.26), residues: 661

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D 197 
 TYR   0.023   0.002   TYR C  55 
 PHE   0.042   0.003   PHE B  27 
 TRP   0.029   0.002   TRP A 296 
 HIS   0.010   0.001   HIS A 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00329 /  0.16 (13796)
  covalent geometry    : angle       0.83107 /  0.39 (19049)
  hydrogen bonds       : bond        0.04455 /  2.99 (  621)
  hydrogen bonds       : angle       4.87021 /  3.36 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  422 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 373
  time to evaluate  : 0.481 
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: C   12 ASN cc_start: 0.9447 (m-40) cc_final: 0.8905 (t0)
REVERT: C   27 PHE cc_start: 0.9163 (m-80) cc_final: 0.8865 (m-80)
REVERT: C   45 THR cc_start: 0.9669 (m) cc_final: 0.9442 (p)
REVERT: C   74 ARG cc_start: 0.8313 (ttt180) cc_final: 0.8108 (ttm170)
REVERT: C   76 THR cc_start: 0.8834 (OUTLIER) cc_final: 0.8440 (p)
REVERT: C  135 LEU cc_start: 0.9694 (mm) cc_final: 0.9362 (mm)
REVERT: C  142 LEU cc_start: 0.9055 (pp) cc_final: 0.8662 (tt)
REVERT: C  193 HIS cc_start: 0.9099 (t-170) cc_final: 0.8299 (t-90)
REVERT: C  197 ARG cc_start: 0.9495 (tpt90) cc_final: 0.9280 (tpm170)
REVERT: C  880 TRP cc_start: 0.9003 (m100) cc_final: 0.8009 (m100)
REVERT: C  884 ASN cc_start: 0.8858 (t0) cc_final: 0.8047 (m110)
REVERT: C  895 PHE cc_start: 0.9071 (t80) cc_final: 0.8339 (t80)
REVERT: C  897 LYS cc_start: 0.9328 (mtmt) cc_final: 0.8917 (mmtp)
REVERT: C  902 LEU cc_start: 0.9084 (mm) cc_final: 0.8298 (tp)
REVERT: C  906 ASN cc_start: 0.9144 (m110) cc_final: 0.8623 (m-40)
REVERT: C  919 HIS cc_start: 0.8441 (t70) cc_final: 0.8113 (t70)
REVERT: C  984 GLU cc_start: 0.8047 (tp30) cc_final: 0.7477 (tp30)
REVERT: C 1036 LEU cc_start: 0.9213 (mp) cc_final: 0.8707 (mt)
REVERT: C 1045 PHE cc_start: 0.9172 (m-80) cc_final: 0.8812 (m-80)
REVERT: D   12 ASN cc_start: 0.9225 (m-40) cc_final: 0.8665 (t0)
REVERT: D   72 MET cc_start: 0.7943 (ttt) cc_final: 0.7154 (tpt)
REVERT: D  155 GLN cc_start: 0.8803 (pm20) cc_final: 0.8424 (pm20)
REVERT: D  162 LEU cc_start: 0.9510 (OUTLIER) cc_final: 0.9268 (mm)
REVERT: D  165 LYS cc_start: 0.9488 (mmmt) cc_final: 0.9140 (mmmm)
REVERT: D  188 MET cc_start: 0.8979 (ttm) cc_final: 0.8538 (tmm)
REVERT: D  894 LYS cc_start: 0.9283 (ttpt) cc_final: 0.9030 (ptmt)
REVERT: D  896 ARG cc_start: 0.8432 (ttm110) cc_final: 0.7700 (mtm110)
REVERT: D  910 LEU cc_start: 0.9622 (OUTLIER) cc_final: 0.9400 (mp)
REVERT: D  919 HIS cc_start: 0.7957 (t-170) cc_final: 0.7572 (t70)
REVERT: D  941 GLN cc_start: 0.9241 (mt0) cc_final: 0.9027 (mm-40)
REVERT: D  983 ASP cc_start: 0.8159 (t0) cc_final: 0.6986 (t0)
REVERT: D  989 LEU cc_start: 0.9641 (mt) cc_final: 0.9307 (tp)
REVERT: D 1038 TYR cc_start: 0.8460 (m-10) cc_final: 0.8106 (m-10)
REVERT: A   58 TYR cc_start: 0.9237 (p90) cc_final: 0.8905 (p90)
REVERT: A   65 ARG cc_start: 0.9139 (tpm170) cc_final: 0.8852 (tpm170)
REVERT: A   93 SER cc_start: 0.9543 (m) cc_final: 0.9244 (p)
REVERT: A  212 PHE cc_start: 0.8211 (m-80) cc_final: 0.7966 (m-80)
REVERT: A  232 MET cc_start: 0.9246 (mmm) cc_final: 0.8941 (mpp)
REVERT: A  244 LEU cc_start: 0.9294 (mt) cc_final: 0.9041 (mt)
REVERT: A  286 LEU cc_start: 0.9800 (pt) cc_final: 0.9586 (tt)
REVERT: A  306 TRP cc_start: 0.8894 (m-10) cc_final: 0.8348 (m-10)
REVERT: A  366 PHE cc_start: 0.9052 (t80) cc_final: 0.8366 (t80)
REVERT: B   15 PHE cc_start: 0.8949 (t80) cc_final: 0.7585 (t80)
REVERT: B   16 TYR cc_start: 0.8565 (m-80) cc_final: 0.8033 (m-80)
REVERT: B   18 LYS cc_start: 0.8875 (mtmm) cc_final: 0.8466 (ptpt)
REVERT: B   33 GLU cc_start: 0.9412 (tt0) cc_final: 0.9126 (pt0)
REVERT: B   62 LEU cc_start: 0.9535 (OUTLIER) cc_final: 0.8982 (mm)
REVERT: B   65 ARG cc_start: 0.9302 (mtp85) cc_final: 0.8964 (ptp-110)
REVERT: B   75 CYS cc_start: 0.8518 (m) cc_final: 0.8263 (m)
REVERT: B  113 GLN cc_start: 0.8882 (tp-100) cc_final: 0.8674 (tm-30)
REVERT: B  127 CYS cc_start: 0.8780 (m) cc_final: 0.8568 (m)
REVERT: B  271 LEU cc_start: 0.9176 (OUTLIER) cc_final: 0.8907 (mm)
REVERT: B  321 GLN cc_start: 0.9002 (mt0) cc_final: 0.8146 (mt0)
REVERT: B  325 GLN cc_start: 0.9376 (mt0) cc_final: 0.9086 (pt0)
REVERT: B  357 LEU cc_start: 0.9443 (tp) cc_final: 0.8973 (pp)
REVERT: B  366 PHE cc_start: 0.9269 (t80) cc_final: 0.8530 (t80)
REVERT: B  387 PHE cc_start: 0.9433 (t80) cc_final: 0.9138 (t80)
  outliers start: 49
  outliers final: 39
  residues processed: 389
  average time/residue: 0.1109
  time to fit residues: 64.3117
Evaluate side-chains
  413 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 369
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   95 PHE
Chi-restraints excluded: chain C residue  123 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue  970 LEU
Chi-restraints excluded: chain C residue  976 ARG
Chi-restraints excluded: chain C residue  998 LEU
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  910 LEU
Chi-restraints excluded: chain D residue  982 LEU
Chi-restraints excluded: chain D residue  993 THR
Chi-restraints excluded: chain D residue  994 LEU
Chi-restraints excluded: chain D residue 1014 ILE
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  132 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  311 ILE
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 133 optimal weight:    0.0050
   chunk 139 optimal weight:    0.8980
   chunk 49 optimal weight:    7.9990
   chunk 145 optimal weight:    4.9990
   chunk 32 optimal weight:    0.8980
   chunk 114 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 112 optimal weight:    5.9990
   chunk 66 optimal weight:    3.9990
   chunk 92 optimal weight:    2.9990
   chunk 91 optimal weight:    1.9990
   overall best weight:    1.3598

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 379 GLN
** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 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 = 0.3579 r_free = 0.3579 target = 0.082285 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.055084 restraints weight = 46124.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3112 r_free = 0.3112 target = 0.057341 restraints weight = 26658.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.058936 restraints weight = 18366.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 21)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.060032 restraints weight = 14041.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.060843 restraints weight = 11582.485|
|-----------------------------------------------------------------------------|
r_work (final): 0.3155
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3156
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       18 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3156 r_free = 0.3156    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3156
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.5508

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  13796  Z= 0.180
  Angle     :  0.829  13.807  19049  Z= 0.397
  Chirality :  0.049   0.421   2193
  Planarity :  0.004   0.052   2183
  Dihedral  : 21.188 166.227   2467
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 18.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.11 %
    Favored  : 96.89 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 27.94 %
    Favored  : 67.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.23), residues: 1479
  helix:  0.88 (0.22), residues: 540
  sheet: -0.04 (0.30), residues: 289
  loop : -0.18 (0.27), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG D  74 
 TYR   0.020   0.002   TYR B 237 
 PHE   0.046   0.003   PHE B  27 
 TRP   0.037   0.002   TRP A 296 
 HIS   0.008   0.001   HIS A 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00374 /  0.18 (13796)
  covalent geometry    : angle       0.82920 /  0.40 (19049)
  hydrogen bonds       : bond        0.04429 /  2.97 (  621)
  hydrogen bonds       : angle       4.92107 /  3.39 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  423 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 57
    poor density    : 366
  time to evaluate  : 0.484 
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: C   12 ASN cc_start: 0.9456 (m-40) cc_final: 0.8891 (t0)
REVERT: C   27 PHE cc_start: 0.9187 (m-80) cc_final: 0.8874 (m-80)
REVERT: C   45 THR cc_start: 0.9662 (m) cc_final: 0.9445 (p)
REVERT: C   74 ARG cc_start: 0.8417 (ttt180) cc_final: 0.8007 (ttt180)
REVERT: C   76 THR cc_start: 0.8825 (OUTLIER) cc_final: 0.8416 (p)
REVERT: C  127 ASP cc_start: 0.8957 (p0) cc_final: 0.8539 (m-30)
REVERT: C  131 ASP cc_start: 0.9135 (t0) cc_final: 0.8427 (t0)
REVERT: C  135 LEU cc_start: 0.9703 (mm) cc_final: 0.9319 (mm)
REVERT: C  142 LEU cc_start: 0.9007 (pp) cc_final: 0.8562 (tt)
REVERT: C  155 GLN cc_start: 0.8296 (pm20) cc_final: 0.7669 (pm20)
REVERT: C  193 HIS cc_start: 0.9107 (t-170) cc_final: 0.8179 (t-90)
REVERT: C  197 ARG cc_start: 0.9517 (tpt90) cc_final: 0.9283 (tpm170)
REVERT: C  880 TRP cc_start: 0.8987 (m100) cc_final: 0.8263 (m100)
REVERT: C  884 ASN cc_start: 0.8794 (t0) cc_final: 0.7963 (m110)
REVERT: C  895 PHE cc_start: 0.9161 (t80) cc_final: 0.8327 (t80)
REVERT: C  897 LYS cc_start: 0.9331 (mtmt) cc_final: 0.8880 (mmtp)
REVERT: C  902 LEU cc_start: 0.9071 (mm) cc_final: 0.8250 (tp)
REVERT: C  906 ASN cc_start: 0.9189 (m110) cc_final: 0.8639 (m110)
REVERT: C  919 HIS cc_start: 0.8409 (t70) cc_final: 0.8086 (t70)
REVERT: C  983 ASP cc_start: 0.8081 (t0) cc_final: 0.7386 (t0)
REVERT: C  984 GLU cc_start: 0.8016 (tp30) cc_final: 0.7419 (tp30)
REVERT: C 1045 PHE cc_start: 0.9219 (m-80) cc_final: 0.8868 (m-80)
REVERT: D   12 ASN cc_start: 0.9222 (m-40) cc_final: 0.8671 (t0)
REVERT: D   75 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.8242 (p0)
REVERT: D  155 GLN cc_start: 0.8788 (pm20) cc_final: 0.8530 (pm20)
REVERT: D  162 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9295 (mm)
REVERT: D  188 MET cc_start: 0.8958 (ttm) cc_final: 0.8492 (tmm)
REVERT: D  894 LYS cc_start: 0.9263 (ttpt) cc_final: 0.8996 (ptmt)
REVERT: D  896 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8156 (ttp-110)
REVERT: D  910 LEU cc_start: 0.9636 (OUTLIER) cc_final: 0.9426 (mp)
REVERT: D  919 HIS cc_start: 0.8102 (t-170) cc_final: 0.7679 (t70)
REVERT: D  941 GLN cc_start: 0.9225 (mt0) cc_final: 0.8980 (mm-40)
REVERT: D  949 ARG cc_start: 0.8939 (mmm160) cc_final: 0.8636 (mmp80)
REVERT: D  983 ASP cc_start: 0.8162 (t0) cc_final: 0.7015 (t70)
REVERT: D  989 LEU cc_start: 0.9626 (OUTLIER) cc_final: 0.9287 (tp)
REVERT: D 1038 TYR cc_start: 0.8474 (m-10) cc_final: 0.8180 (m-10)
REVERT: A   58 TYR cc_start: 0.9249 (p90) cc_final: 0.8931 (p90)
REVERT: A   65 ARG cc_start: 0.9146 (tpm170) cc_final: 0.8851 (tpm170)
REVERT: A   93 SER cc_start: 0.9543 (m) cc_final: 0.9297 (p)
REVERT: A  180 ILE cc_start: 0.9670 (OUTLIER) cc_final: 0.9424 (tp)
REVERT: A  212 PHE cc_start: 0.8281 (m-80) cc_final: 0.8050 (m-80)
REVERT: A  232 MET cc_start: 0.9283 (mmm) cc_final: 0.8880 (mpp)
REVERT: A  244 LEU cc_start: 0.9287 (mt) cc_final: 0.9015 (mt)
REVERT: A  253 LYS cc_start: 0.8161 (mmmm) cc_final: 0.7512 (mtpp)
REVERT: A  306 TRP cc_start: 0.8837 (m-10) cc_final: 0.8305 (m-10)
REVERT: A  366 PHE cc_start: 0.9082 (t80) cc_final: 0.8256 (t80)
REVERT: A  387 PHE cc_start: 0.9439 (t80) cc_final: 0.9154 (t80)
REVERT: B   15 PHE cc_start: 0.8956 (t80) cc_final: 0.7588 (t80)
REVERT: B   16 TYR cc_start: 0.8605 (m-80) cc_final: 0.8028 (m-80)
REVERT: B   18 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8473 (ptpt)
REVERT: B   33 GLU cc_start: 0.9442 (tt0) cc_final: 0.9231 (pt0)
REVERT: B   62 LEU cc_start: 0.9531 (OUTLIER) cc_final: 0.8976 (mm)
REVERT: B   65 ARG cc_start: 0.9296 (mtp85) cc_final: 0.8964 (ptp-110)
REVERT: B   75 CYS cc_start: 0.8503 (m) cc_final: 0.7089 (t)
REVERT: B  113 GLN cc_start: 0.8894 (tp-100) cc_final: 0.8693 (tm-30)
REVERT: B  127 CYS cc_start: 0.8836 (m) cc_final: 0.8608 (m)
REVERT: B  260 PHE cc_start: 0.9130 (m-80) cc_final: 0.8892 (m-80)
REVERT: B  271 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8921 (mm)
REVERT: B  321 GLN cc_start: 0.9040 (mt0) cc_final: 0.8519 (mt0)
REVERT: B  325 GLN cc_start: 0.9370 (mt0) cc_final: 0.8932 (tm-30)
REVERT: B  357 LEU cc_start: 0.9445 (tp) cc_final: 0.9048 (pp)
REVERT: B  366 PHE cc_start: 0.9276 (t80) cc_final: 0.8484 (t80)
REVERT: B  387 PHE cc_start: 0.9432 (t80) cc_final: 0.9068 (t80)
  outliers start: 57
  outliers final: 41
  residues processed: 388
  average time/residue: 0.1102
  time to fit residues: 63.9081
Evaluate side-chains
  402 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 353
  time to evaluate  : 0.476 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue   80 LEU
Chi-restraints excluded: chain C residue   95 PHE
Chi-restraints excluded: chain C residue  123 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue  970 LEU
Chi-restraints excluded: chain C residue  976 ARG
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue    4 LEU
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  910 LEU
Chi-restraints excluded: chain D residue  982 LEU
Chi-restraints excluded: chain D residue  989 LEU
Chi-restraints excluded: chain D residue  993 THR
Chi-restraints excluded: chain D residue 1011 ILE
Chi-restraints excluded: chain D residue 1014 ILE
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue   78 VAL
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 70 optimal weight:    0.0070
   chunk 148 optimal weight:   50.0000
   chunk 152 optimal weight:   10.0000
   chunk 63 optimal weight:    2.9990
   chunk 40 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9980
   chunk 100 optimal weight:    1.9990
   chunk 125 optimal weight:    0.1980
   chunk 77 optimal weight:    0.8980
   chunk 58 optimal weight:    6.9990
   overall best weight:    0.8200

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C  63 ASN
C 919 HIS
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 HIS
** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.082937 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.055578 restraints weight = 46050.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.057852 restraints weight = 26464.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.059445 restraints weight = 18161.935|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.060595 restraints weight = 13885.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.061362 restraints weight = 11419.973|
|-----------------------------------------------------------------------------|
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3171
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       17 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3171 r_free = 0.3171    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3171
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8025
moved from start:          0.5635

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  13796  Z= 0.149
  Angle     :  0.857  13.843  19049  Z= 0.400
  Chirality :  0.050   0.418   2193
  Planarity :  0.004   0.062   2183
  Dihedral  : 21.185 166.515   2467
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 17.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.77 %
    Favored  : 97.23 %
  Rotamer:
    Outliers :  3.69 %
    Allowed  : 29.36 %
    Favored  : 66.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.32 (0.23), residues: 1479
  helix:  0.90 (0.23), residues: 536
  sheet: -0.10 (0.30), residues: 292
  loop : -0.08 (0.27), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG D 197 
 TYR   0.019   0.002   TYR C  55 
 PHE   0.051   0.002   PHE B  27 
 TRP   0.042   0.002   TRP A 296 
 HIS   0.009   0.001   HIS C  56 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 (13796)
  covalent geometry    : angle       0.85669 /  0.40 (19049)
  hydrogen bonds       : bond        0.04289 /  2.87 (  621)
  hydrogen bonds       : angle       4.95214 /  3.39 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  417 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 370
  time to evaluate  : 0.451 
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: C   12 ASN cc_start: 0.9461 (m-40) cc_final: 0.8951 (t0)
REVERT: C   27 PHE cc_start: 0.9179 (m-80) cc_final: 0.8863 (m-80)
REVERT: C   45 THR cc_start: 0.9641 (m) cc_final: 0.9401 (p)
REVERT: C   48 ASP cc_start: 0.9304 (m-30) cc_final: 0.9101 (m-30)
REVERT: C   55 TYR cc_start: 0.8712 (m-80) cc_final: 0.8508 (m-10)
REVERT: C   76 THR cc_start: 0.8872 (OUTLIER) cc_final: 0.8435 (p)
REVERT: C  127 ASP cc_start: 0.8891 (p0) cc_final: 0.8486 (m-30)
REVERT: C  131 ASP cc_start: 0.9137 (t0) cc_final: 0.8499 (t0)
REVERT: C  135 LEU cc_start: 0.9695 (mm) cc_final: 0.9399 (mm)
REVERT: C  155 GLN cc_start: 0.8301 (pm20) cc_final: 0.7617 (pm20)
REVERT: C  193 HIS cc_start: 0.9100 (t-170) cc_final: 0.8179 (t-90)
REVERT: C  197 ARG cc_start: 0.9531 (tpt90) cc_final: 0.9316 (tpm170)
REVERT: C  880 TRP cc_start: 0.9027 (m100) cc_final: 0.7982 (m100)
REVERT: C  884 ASN cc_start: 0.8776 (t0) cc_final: 0.7805 (m110)
REVERT: C  895 PHE cc_start: 0.9068 (t80) cc_final: 0.8193 (t80)
REVERT: C  897 LYS cc_start: 0.9330 (mtmt) cc_final: 0.8933 (mmtp)
REVERT: C  902 LEU cc_start: 0.9031 (mm) cc_final: 0.8297 (tp)
REVERT: C  904 LEU cc_start: 0.9749 (tp) cc_final: 0.9462 (pp)
REVERT: C  906 ASN cc_start: 0.9134 (m110) cc_final: 0.8572 (m110)
REVERT: C  983 ASP cc_start: 0.7908 (t0) cc_final: 0.7211 (t0)
REVERT: C  984 GLU cc_start: 0.7934 (tp30) cc_final: 0.7363 (tp30)
REVERT: C 1045 PHE cc_start: 0.9216 (m-80) cc_final: 0.8850 (m-80)
REVERT: D   12 ASN cc_start: 0.9255 (m-40) cc_final: 0.8705 (t0)
REVERT: D   72 MET cc_start: 0.7861 (ttt) cc_final: 0.7198 (tpt)
REVERT: D   75 ASP cc_start: 0.8486 (OUTLIER) cc_final: 0.8278 (p0)
REVERT: D  155 GLN cc_start: 0.8810 (pm20) cc_final: 0.8579 (pm20)
REVERT: D  162 LEU cc_start: 0.9513 (OUTLIER) cc_final: 0.9305 (mm)
REVERT: D  165 LYS cc_start: 0.9487 (mmmt) cc_final: 0.9141 (mmmm)
REVERT: D  188 MET cc_start: 0.8967 (ttm) cc_final: 0.8481 (tmm)
REVERT: D  894 LYS cc_start: 0.9295 (ttpt) cc_final: 0.9039 (ptmt)
REVERT: D  896 ARG cc_start: 0.8456 (ttm110) cc_final: 0.8111 (ttp-110)
REVERT: D  910 LEU cc_start: 0.9627 (OUTLIER) cc_final: 0.9422 (mp)
REVERT: D  919 HIS cc_start: 0.8079 (t-170) cc_final: 0.7680 (t70)
REVERT: D  949 ARG cc_start: 0.8931 (mmm160) cc_final: 0.8618 (mmp80)
REVERT: D  983 ASP cc_start: 0.8207 (t0) cc_final: 0.7076 (t70)
REVERT: D  989 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9234 (tp)
REVERT: D 1020 MET cc_start: 0.9369 (pmm) cc_final: 0.9067 (pmm)
REVERT: D 1038 TYR cc_start: 0.8474 (m-10) cc_final: 0.8180 (m-10)
REVERT: A    1 MET cc_start: 0.7650 (tpp) cc_final: 0.6909 (mmt)
REVERT: A   18 LYS cc_start: 0.9515 (mmmt) cc_final: 0.9240 (mmtm)
REVERT: A   58 TYR cc_start: 0.9232 (p90) cc_final: 0.8909 (p90)
REVERT: A   65 ARG cc_start: 0.9151 (tpm170) cc_final: 0.8853 (tpm170)
REVERT: A   93 SER cc_start: 0.9522 (m) cc_final: 0.9312 (p)
REVERT: A  149 LYS cc_start: 0.9686 (mttm) cc_final: 0.9355 (mttm)
REVERT: A  180 ILE cc_start: 0.9669 (OUTLIER) cc_final: 0.9441 (tp)
REVERT: A  212 PHE cc_start: 0.8298 (m-80) cc_final: 0.8078 (m-80)
REVERT: A  232 MET cc_start: 0.9267 (mmm) cc_final: 0.8889 (mpp)
REVERT: A  244 LEU cc_start: 0.9283 (mt) cc_final: 0.9001 (mt)
REVERT: A  253 LYS cc_start: 0.8117 (mmmm) cc_final: 0.7508 (mtpp)
REVERT: A  306 TRP cc_start: 0.8862 (m-10) cc_final: 0.8287 (m-10)
REVERT: A  366 PHE cc_start: 0.9075 (t80) cc_final: 0.8218 (t80)
REVERT: A  387 PHE cc_start: 0.9427 (t80) cc_final: 0.9115 (t80)
REVERT: B   15 PHE cc_start: 0.8965 (t80) cc_final: 0.7568 (t80)
REVERT: B   16 TYR cc_start: 0.8607 (m-80) cc_final: 0.8029 (m-80)
REVERT: B   18 LYS cc_start: 0.8887 (mtmm) cc_final: 0.8393 (ptpt)
REVERT: B   33 GLU cc_start: 0.9431 (tt0) cc_final: 0.9218 (pt0)
REVERT: B   62 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.8974 (mm)
REVERT: B   65 ARG cc_start: 0.9300 (mtp85) cc_final: 0.8962 (ptp-110)
REVERT: B   75 CYS cc_start: 0.8488 (m) cc_final: 0.7198 (t)
REVERT: B   97 MET cc_start: 0.9189 (mmm) cc_final: 0.8905 (ppp)
REVERT: B  127 CYS cc_start: 0.8811 (m) cc_final: 0.8585 (m)
REVERT: B  253 LYS cc_start: 0.8175 (mmmt) cc_final: 0.7892 (mmtt)
REVERT: B  271 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8944 (mm)
REVERT: B  321 GLN cc_start: 0.9019 (mt0) cc_final: 0.8069 (mt0)
REVERT: B  325 GLN cc_start: 0.9345 (mt0) cc_final: 0.9048 (pt0)
REVERT: B  357 LEU cc_start: 0.9467 (tp) cc_final: 0.9083 (pp)
REVERT: B  366 PHE cc_start: 0.9261 (t80) cc_final: 0.8485 (t80)
REVERT: B  387 PHE cc_start: 0.9357 (t80) cc_final: 0.9012 (t80)
  outliers start: 47
  outliers final: 37
  residues processed: 388
  average time/residue: 0.1071
  time to fit residues: 62.2696
Evaluate side-chains
  401 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 356
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  123 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue  970 LEU
Chi-restraints excluded: chain C residue  976 ARG
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   75 ASP
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  162 LEU
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  910 LEU
Chi-restraints excluded: chain D residue  989 LEU
Chi-restraints excluded: chain D residue 1014 ILE
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain D residue 1030 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  153 LEU
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 119 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 48 optimal weight:    4.9990
   chunk 85 optimal weight:    3.9990
   chunk 25 optimal weight:    0.6980
   chunk 127 optimal weight:    5.9990
   chunk 56 optimal weight:    0.7980
   chunk 84 optimal weight:    0.6980
   chunk 13 optimal weight:    3.9990
   chunk 102 optimal weight:    3.9990
   chunk 30 optimal weight:    0.9990
   overall best weight:    1.0384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C  63 ASN
** D  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 HIS
** B   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.082734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.055577 restraints weight = 45795.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3128 r_free = 0.3128 target = 0.057817 restraints weight = 26606.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.059411 restraints weight = 18375.979|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.060496 restraints weight = 14069.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.061287 restraints weight = 11631.197|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3168
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3168 r_free = 0.3168    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3168
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8041
moved from start:          0.5743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13796  Z= 0.160
  Angle     :  0.869  17.052  19049  Z= 0.405
  Chirality :  0.051   0.439   2193
  Planarity :  0.004   0.075   2183
  Dihedral  : 21.197 167.001   2467
  Min Nonbonded Distance : 1.878

Molprobity Statistics.
  All-atom Clashscore : 18.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  3.92 %
    Allowed  : 29.59 %
    Favored  : 66.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.23), residues: 1479
  helix:  0.86 (0.23), residues: 536
  sheet: -0.13 (0.30), residues: 292
  loop : -0.11 (0.27), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 197 
 TYR   0.021   0.002   TYR A 160 
 PHE   0.043   0.002   PHE B  27 
 TRP   0.045   0.002   TRP A 296 
 HIS   0.022   0.001   HIS A 164 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00339 /  0.16 (13796)
  covalent geometry    : angle       0.86890 /  0.41 (19049)
  hydrogen bonds       : bond        0.04344 /  2.91 (  621)
  hydrogen bonds       : angle       4.98862 /  3.44 ( 1674)

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

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

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2958 Ramachandran restraints generated.
    1479 Oldfield, 0 Emsley, 1479 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  408 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 358
  time to evaluate  : 0.487 
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: C    2 LYS cc_start: 0.9340 (tppp) cc_final: 0.9132 (tppt)
REVERT: C   12 ASN cc_start: 0.9480 (m-40) cc_final: 0.8977 (t0)
REVERT: C   27 PHE cc_start: 0.9193 (m-80) cc_final: 0.8961 (m-10)
REVERT: C   45 THR cc_start: 0.9641 (m) cc_final: 0.9399 (p)
REVERT: C   48 ASP cc_start: 0.9307 (m-30) cc_final: 0.9097 (m-30)
REVERT: C   76 THR cc_start: 0.8860 (OUTLIER) cc_final: 0.8441 (p)
REVERT: C  127 ASP cc_start: 0.8917 (p0) cc_final: 0.8546 (m-30)
REVERT: C  131 ASP cc_start: 0.9172 (t0) cc_final: 0.8537 (t0)
REVERT: C  135 LEU cc_start: 0.9722 (mm) cc_final: 0.9370 (mm)
REVERT: C  155 GLN cc_start: 0.8317 (pm20) cc_final: 0.7631 (pm20)
REVERT: C  193 HIS cc_start: 0.9107 (t-170) cc_final: 0.8191 (t-90)
REVERT: C  197 ARG cc_start: 0.9537 (tpt90) cc_final: 0.9323 (tpm170)
REVERT: C  880 TRP cc_start: 0.8962 (m100) cc_final: 0.8268 (m100)
REVERT: C  884 ASN cc_start: 0.8784 (t0) cc_final: 0.7821 (m110)
REVERT: C  895 PHE cc_start: 0.9083 (t80) cc_final: 0.8206 (t80)
REVERT: C  897 LYS cc_start: 0.9320 (mtmt) cc_final: 0.8913 (mmtp)
REVERT: C  902 LEU cc_start: 0.9031 (mm) cc_final: 0.8197 (tp)
REVERT: C  906 ASN cc_start: 0.9155 (m110) cc_final: 0.8595 (m110)
REVERT: C  983 ASP cc_start: 0.7880 (t0) cc_final: 0.7151 (t0)
REVERT: C  984 GLU cc_start: 0.7907 (tp30) cc_final: 0.7319 (tp30)
REVERT: C 1045 PHE cc_start: 0.9250 (m-80) cc_final: 0.8946 (m-80)
REVERT: D   12 ASN cc_start: 0.9270 (m-40) cc_final: 0.8734 (t0)
REVERT: D   72 MET cc_start: 0.7862 (ttt) cc_final: 0.7139 (tpt)
REVERT: D  155 GLN cc_start: 0.8810 (pm20) cc_final: 0.8582 (pm20)
REVERT: D  165 LYS cc_start: 0.9484 (mmmt) cc_final: 0.9146 (mmmm)
REVERT: D  188 MET cc_start: 0.8975 (ttm) cc_final: 0.8478 (tmm)
REVERT: D  894 LYS cc_start: 0.9287 (ttpt) cc_final: 0.9037 (ptmt)
REVERT: D  896 ARG cc_start: 0.8496 (ttm110) cc_final: 0.8129 (ttp-110)
REVERT: D  910 LEU cc_start: 0.9640 (OUTLIER) cc_final: 0.9432 (mp)
REVERT: D  919 HIS cc_start: 0.8162 (t-170) cc_final: 0.7749 (t70)
REVERT: D  949 ARG cc_start: 0.8935 (mmm160) cc_final: 0.8623 (mmp80)
REVERT: D  983 ASP cc_start: 0.8227 (t0) cc_final: 0.7081 (t70)
REVERT: D  989 LEU cc_start: 0.9615 (OUTLIER) cc_final: 0.9264 (tp)
REVERT: D 1020 MET cc_start: 0.9340 (pmm) cc_final: 0.9006 (pmm)
REVERT: D 1038 TYR cc_start: 0.8512 (m-10) cc_final: 0.8234 (m-10)
REVERT: A    1 MET cc_start: 0.7647 (tpp) cc_final: 0.7000 (mmt)
REVERT: A   18 LYS cc_start: 0.9528 (mmmt) cc_final: 0.9260 (mmtm)
REVERT: A   58 TYR cc_start: 0.9238 (p90) cc_final: 0.8919 (p90)
REVERT: A   65 ARG cc_start: 0.9151 (tpm170) cc_final: 0.8855 (tpm170)
REVERT: A  149 LYS cc_start: 0.9697 (mttm) cc_final: 0.9353 (mttm)
REVERT: A  180 ILE cc_start: 0.9663 (OUTLIER) cc_final: 0.9432 (tp)
REVERT: A  212 PHE cc_start: 0.8337 (m-80) cc_final: 0.8110 (m-80)
REVERT: A  232 MET cc_start: 0.9313 (mmm) cc_final: 0.8916 (mpp)
REVERT: A  244 LEU cc_start: 0.9307 (mt) cc_final: 0.9035 (mt)
REVERT: A  253 LYS cc_start: 0.8113 (mmmm) cc_final: 0.7490 (mtpp)
REVERT: A  306 TRP cc_start: 0.8879 (m-10) cc_final: 0.8308 (m-10)
REVERT: A  366 PHE cc_start: 0.9079 (t80) cc_final: 0.8229 (t80)
REVERT: A  387 PHE cc_start: 0.9435 (t80) cc_final: 0.9112 (t80)
REVERT: B   15 PHE cc_start: 0.8967 (t80) cc_final: 0.7866 (t80)
REVERT: B   18 LYS cc_start: 0.8880 (mtmm) cc_final: 0.8455 (ptpt)
REVERT: B   33 GLU cc_start: 0.9436 (tt0) cc_final: 0.9231 (pt0)
REVERT: B   62 LEU cc_start: 0.9522 (OUTLIER) cc_final: 0.8963 (mm)
REVERT: B   65 ARG cc_start: 0.9299 (mtp85) cc_final: 0.8960 (ptp-110)
REVERT: B   75 CYS cc_start: 0.8554 (m) cc_final: 0.7222 (t)
REVERT: B   97 MET cc_start: 0.9185 (mmm) cc_final: 0.8950 (ppp)
REVERT: B   99 PHE cc_start: 0.8900 (m-80) cc_final: 0.8655 (m-80)
REVERT: B  127 CYS cc_start: 0.8810 (m) cc_final: 0.8583 (m)
REVERT: B  165 TYR cc_start: 0.9470 (t80) cc_final: 0.9222 (t80)
REVERT: B  253 LYS cc_start: 0.8176 (mmmt) cc_final: 0.7907 (mmtt)
REVERT: B  260 PHE cc_start: 0.9051 (m-80) cc_final: 0.8746 (m-80)
REVERT: B  271 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8953 (mm)
REVERT: B  321 GLN cc_start: 0.9009 (mt0) cc_final: 0.8496 (mt0)
REVERT: B  325 GLN cc_start: 0.9380 (mt0) cc_final: 0.8919 (tm-30)
REVERT: B  357 LEU cc_start: 0.9476 (tp) cc_final: 0.9092 (pp)
REVERT: B  366 PHE cc_start: 0.9262 (t80) cc_final: 0.8504 (t80)
REVERT: B  387 PHE cc_start: 0.9365 (t80) cc_final: 0.9030 (t80)
  outliers start: 50
  outliers final: 38
  residues processed: 377
  average time/residue: 0.1056
  time to fit residues: 59.7927
Evaluate side-chains
  399 residues out of total 1274 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 355
  time to evaluate  : 0.303 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue   14 LEU
Chi-restraints excluded: chain C residue   46 LEU
Chi-restraints excluded: chain C residue   63 ASN
Chi-restraints excluded: chain C residue   76 THR
Chi-restraints excluded: chain C residue  123 LYS
Chi-restraints excluded: chain C residue  129 VAL
Chi-restraints excluded: chain C residue  200 LEU
Chi-restraints excluded: chain C residue  967 LEU
Chi-restraints excluded: chain C residue  976 ARG
Chi-restraints excluded: chain C residue  998 LEU
Chi-restraints excluded: chain C residue 1030 VAL
Chi-restraints excluded: chain D residue   32 LEU
Chi-restraints excluded: chain D residue   35 ILE
Chi-restraints excluded: chain D residue   58 THR
Chi-restraints excluded: chain D residue   80 LEU
Chi-restraints excluded: chain D residue  124 ILE
Chi-restraints excluded: chain D residue  154 SER
Chi-restraints excluded: chain D residue  189 VAL
Chi-restraints excluded: chain D residue  887 ILE
Chi-restraints excluded: chain D residue  910 LEU
Chi-restraints excluded: chain D residue  989 LEU
Chi-restraints excluded: chain D residue  993 THR
Chi-restraints excluded: chain D residue 1014 ILE
Chi-restraints excluded: chain D residue 1026 VAL
Chi-restraints excluded: chain A residue   49 VAL
Chi-restraints excluded: chain A residue   96 ILE
Chi-restraints excluded: chain A residue  115 LEU
Chi-restraints excluded: chain A residue  164 HIS
Chi-restraints excluded: chain A residue  180 ILE
Chi-restraints excluded: chain A residue  185 LEU
Chi-restraints excluded: chain A residue  255 VAL
Chi-restraints excluded: chain A residue  257 LEU
Chi-restraints excluded: chain A residue  275 VAL
Chi-restraints excluded: chain A residue  336 LEU
Chi-restraints excluded: chain B residue   44 ILE
Chi-restraints excluded: chain B residue   62 LEU
Chi-restraints excluded: chain B residue  104 VAL
Chi-restraints excluded: chain B residue  114 ILE
Chi-restraints excluded: chain B residue  157 ILE
Chi-restraints excluded: chain B residue  182 THR
Chi-restraints excluded: chain B residue  200 TYR
Chi-restraints excluded: chain B residue  271 LEU
Chi-restraints excluded: chain B residue  275 VAL
Chi-restraints excluded: chain B residue  309 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 154
   random chunks:
   chunk 59 optimal weight:    0.5980
   chunk 18 optimal weight:    4.9990
   chunk 44 optimal weight:    0.0970
   chunk 113 optimal weight:    5.9990
   chunk 4 optimal weight:    1.9990
   chunk 50 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 22 optimal weight:    1.9990
   chunk 69 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    0.9384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** C  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 919 HIS
** D  56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 884 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 164 HIS
** B   5 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 224 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 318 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3587 r_free = 0.3587 target = 0.082683 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3075 r_free = 0.3075 target = 0.055428 restraints weight = 46060.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.057691 restraints weight = 26536.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3159 r_free = 0.3159 target = 0.059296 restraints weight = 18243.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.060421 restraints weight = 13940.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.061246 restraints weight = 11461.526|
|-----------------------------------------------------------------------------|
r_work (final): 0.3169
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3169
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       19 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3169 r_free = 0.3169    target_work(ls_wunit_k1) = 0.060         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       20 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3169
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.5776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13796  Z= 0.154
  Angle     :  0.867  16.700  19049  Z= 0.405
  Chirality :  0.050   0.420   2193
  Planarity :  0.004   0.074   2183
  Dihedral  : 21.202 167.189   2467
  Min Nonbonded Distance : 1.881

Molprobity Statistics.
  All-atom Clashscore : 18.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.25 %
    Favored  : 96.75 %
  Rotamer:
    Outliers :  3.38 %
    Allowed  : 29.91 %
    Favored  : 66.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.85 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.23), residues: 1479
  helix:  0.89 (0.23), residues: 535
  sheet: -0.14 (0.30), residues: 292
  loop : -0.12 (0.27), residues: 652

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG D 197 
 TYR   0.019   0.002   TYR C  55 
 PHE   0.040   0.002   PHE A  27 
 TRP   0.042   0.002   TRP A 296 
 HIS   0.008   0.001   HIS A 385 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.15 (13796)
  covalent geometry    : angle       0.86737 /  0.40 (19049)
  hydrogen bonds       : bond        0.04276 /  2.86 (  621)
  hydrogen bonds       : angle       5.00950 /  3.45 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2822.08 seconds
wall clock time: 49 minutes 35.89 seconds (2975.89 seconds total)