Starting phenix.real_space_refine
on Thu Aug  6 00:07:41 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9mna_48418/08_2026/9mna_48418.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9mna_48418/08_2026/9mna_48418.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9mna_48418/08_2026/9mna_48418.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9mna_48418/08_2026/9mna_48418.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9mna_48418/08_2026/9mna_48418.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9mna_48418/08_2026/9mna_48418.map"
  }
  resolution = 3.77
  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=   0.002 sd=   0.034
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P      72      5.49       5
     Mg      1      5.21       5
     S      58      5.16       5
     C    7501      2.51       5
     N    2132      2.21       5
     O    2312      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 12076
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 1617
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 202, 1617
          Classifications: {'peptide': 202}
          Incomplete info: {'truncation_to_alanine': 13}
          Link IDs: {'PTRANS': 5, 'TRANS': 196}
          Chain breaks: 1
          Unresolved chain link angles: 1
          Unresolved non-hydrogen bonds: 54
          Unresolved non-hydrogen angles: 63
          Unresolved non-hydrogen dihedrals: 46
          Unresolved non-hydrogen chiralities: 2
          Planarities with less than four sites: {'ARG:plan': 3, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 1518
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 198, 1518
          Classifications: {'peptide': 198}
          Incomplete info: {'truncation_to_alanine': 26}
          Link IDs: {'PTRANS': 5, 'TRANS': 192}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 113
          Unresolved non-hydrogen angles: 133
          Unresolved non-hydrogen dihedrals: 98
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'ARG:plan': 5, 'ASP:plan': 3, 'GLU:plan': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 63
    Chain: "E"
      Number of atoms: 7479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 983, 7479
          Classifications: {'peptide': 983}
          Modifications used: {'COO': 1}
          Incomplete info: {'truncation_to_alanine': 88}
          Link IDs: {'PTRANS': 65, 'TRANS': 917}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 375
          Unresolved non-hydrogen angles: 451
          Unresolved non-hydrogen dihedrals: 312
          Unresolved non-hydrogen chiralities: 7
          Planarities with less than four sites: {'GLN:plan1': 14, 'ASP:plan': 10, 'HIS:plan': 3, 'ARG:plan': 17, 'PHE:plan': 2, 'GLU:plan': 14, 'TYR:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 264
    Chain: "N"
      Number of atoms: 619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 619
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "T"
      Number of atoms: 611
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 30, 611
          Classifications: {'DNA': 30}
          Link IDs: {'rna3p': 29}
    Chain: "R"
      Number of atoms: 200
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 200
          Classifications: {'RNA': 9}
          Modifications used: {'rna3p_pur': 8}
          Link IDs: {'rna3p': 8}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.40, per 1000 atoms: 0.20
  Number of scatterers: 12076
  At special positions: 0
  Unit cell: (95.6824, 127.09, 119.055, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      58     16.00
     P      72     15.00
     Mg      1     11.99
     O    2312      8.00
     N    2132      7.00
     C    7501      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: 0.93
  Conformation dependent library (CDL) restraints added in 435.8 milliseconds
  

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2646

  Finding SS restraints...
    Secondary structure from input PDB file:
      61 helices and 11 sheets defined
      57.8% alpha, 6.4% beta
      21 base pairs and 45 stacking pairs defined.
    Time for finding SS restraints: 0.93
  Creating SS restraints...
    Processing helix  chain 'A' and resid 149 through 155
    Processing helix  chain 'A' and resid 160 through 166
      removed outlier: 3.846A  pdb=" N   LEU A 164 " --> pdb=" O   GLU A 160 " (cutoff:3.500A)
      removed outlier: 4.316A  pdb=" N   ALA A 166 " --> pdb=" O   GLU A 162 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 221
    Processing helix  chain 'A' and resid 243 through 260
    Processing helix  chain 'A' and resid 264 through 269
    Processing helix  chain 'A' and resid 278 through 285
      removed outlier: 4.115A  pdb=" N   PHE A 285 " --> pdb=" O   VAL A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 296 through 305
    Processing helix  chain 'A' and resid 321 through 335
      removed outlier: 3.791A  pdb=" N   SER A 331 " --> pdb=" O   GLN A 327 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 354
      removed outlier: 3.582A  pdb=" N   ASP A 342 " --> pdb=" O   GLU A 338 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   SER A 343 " --> pdb=" O   GLU A 339 " (cutoff:3.500A)
      removed outlier: 4.048A  pdb=" N   LEU A 344 " --> pdb=" O   LEU A 340 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LEU A 345 " --> pdb=" O   TYR A 341 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   ALA A 354 " --> pdb=" O   PHE A 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 160 through 166
    Processing helix  chain 'B' and resid 208 through 222
      removed outlier: 3.526A  pdb=" N   TYR B 212 " --> pdb=" O   SER B 208 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   SER B 218 " --> pdb=" O   GLU B 214 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 261
    Processing helix  chain 'B' and resid 278 through 286
      removed outlier: 3.550A  pdb=" N   LYS B 283 " --> pdb=" O   ASN B 279 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   HIS B 284 " --> pdb=" O   ALA B 280 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 296 through 304
    Processing helix  chain 'B' and resid 318 through 332
      removed outlier: 4.260A  pdb=" N   VAL B 323 " --> pdb=" O   SER B 319 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   HIS B 324 " --> pdb=" O   ASP B 320 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 337 through 341
      removed outlier: 4.458A  pdb=" N   LEU B 340 " --> pdb=" O   VAL B 337 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 342 through 355
      removed outlier: 3.563A  pdb=" N   ALA B 347 " --> pdb=" O   SER B 343 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   ILE B 348 " --> pdb=" O   LEU B 344 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLU B 352 " --> pdb=" O   ILE B 348 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   LEU B 353 " --> pdb=" O   ALA B 349 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 221 through 236
      removed outlier: 4.123A  pdb=" N   LEU E 234 " --> pdb=" O   PHE E 230 " (cutoff:3.500A)
      removed outlier: 3.894A  pdb=" N   LEU E 235 " --> pdb=" O   LYS E 231 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 238 through 252
      removed outlier: 3.627A  pdb=" N   HIS E 244 " --> pdb=" O   PRO E 240 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   LEU E 245 " --> pdb=" O   LEU E 241 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   GLN E 252 " --> pdb=" O   VAL E 248 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 252 through 257
      removed outlier: 3.582A  pdb=" N   LYS E 257 " --> pdb=" O   ARG E 253 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 263 through 274
      removed outlier: 3.564A  pdb=" N   GLN E 274 " --> pdb=" O   GLY E 270 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 278 through 291
      removed outlier: 4.190A  pdb=" N   TYR E 282 " --> pdb=" O   LYS E 278 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 295 through 307
    Processing helix  chain 'E' and resid 315 through 325
    Processing helix  chain 'E' and resid 326 through 328
      No H-bonds generated for 'chain 'E' and resid 326 through 328'
    Processing helix  chain 'E' and resid 332 through 337
    Processing helix  chain 'E' and resid 340 through 355
    Processing helix  chain 'E' and resid 392 through 409
      removed outlier: 3.659A  pdb=" N   ALA E 409 " --> pdb=" O   HIS E 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 424 through 462
      removed outlier: 4.012A  pdb=" N   TYR E 461 " --> pdb=" O   GLU E 457 " (cutoff:3.500A)
      removed outlier: 4.073A  pdb=" N   GLU E 462 " --> pdb=" O   ARG E 458 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 467 through 472
    Processing helix  chain 'E' and resid 475 through 489
      removed outlier: 3.517A  pdb=" N   VAL E 479 " --> pdb=" O   ASP E 475 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 496 through 521
      removed outlier: 4.449A  pdb=" N   GLN E 517 " --> pdb=" O   VAL E 513 " (cutoff:3.500A)
      removed outlier: 4.619A  pdb=" N   ARG E 518 " --> pdb=" O   VAL E 514 " (cutoff:3.500A)
      removed outlier: 4.182A  pdb=" N   VAL E 519 " --> pdb=" O   GLN E 515 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 521 through 534
      removed outlier: 3.853A  pdb=" N   ALA E 525 " --> pdb=" O   GLY E 521 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 535 through 537
      No H-bonds generated for 'chain 'E' and resid 535 through 537'
    Processing helix  chain 'E' and resid 548 through 555
      removed outlier: 3.759A  pdb=" N   TRP E 553 " --> pdb=" O   PRO E 549 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 568 through 587
    Processing helix  chain 'E' and resid 624 through 634
    Processing helix  chain 'E' and resid 678 through 687
      removed outlier: 3.721A  pdb=" N   LEU E 684 " --> pdb=" O   HIS E 680 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 692 through 704
    Processing helix  chain 'E' and resid 711 through 723
      removed outlier: 3.663A  pdb=" N   ALA E 723 " --> pdb=" O   GLN E 719 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 726 through 730
      removed outlier: 3.599A  pdb=" N   LEU E 729 " --> pdb=" O   CYS E 726 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 751 through 789
      removed outlier: 3.540A  pdb=" N   GLU E 778 " --> pdb=" O   SER E 774 " (cutoff:3.500A)
      removed outlier: 3.967A  pdb=" N   LEU E 785 " --> pdb=" O   TYR E 781 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 818 through 824
    Processing helix  chain 'E' and resid 837 through 850
      removed outlier: 3.656A  pdb=" N   LEU E 841 " --> pdb=" O   GLY E 837 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 856 through 867
    Processing helix  chain 'E' and resid 867 through 877
    Processing helix  chain 'E' and resid 890 through 906
    Processing helix  chain 'E' and resid 925 through 934
    Processing helix  chain 'E' and resid 954 through 974
      removed outlier: 3.561A  pdb=" N   GLY E 958 " --> pdb=" O   ASP E 954 " (cutoff:3.500A)
      removed outlier: 3.741A  pdb=" N   GLN E 969 " --> pdb=" O   VAL E 965 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 975 through 982
      removed outlier: 4.043A  pdb=" N   GLN E 979 " --> pdb=" O   MET E 975 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   VAL E 980 " --> pdb=" O   ARG E 976 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 986 through 998
      removed outlier: 3.666A  pdb=" N   VAL E 990 " --> pdb=" O   THR E 986 " (cutoff:3.500A)
      removed outlier: 5.191A  pdb=" N   GLN E 992 " --> pdb=" O   LYS E 988 " (cutoff:3.500A)
      removed outlier: 5.572A  pdb=" N   THR E 993 " --> pdb=" O   VAL E 989 " (cutoff:3.500A)
      removed outlier: 4.104A  pdb=" N   VAL E 998 " --> pdb=" O   VAL E 994 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1002 through 1017
      removed outlier: 3.573A  pdb=" N   GLN E1009 " --> pdb=" O   GLY E1005 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   GLU E1011 " --> pdb=" O   ARG E1007 " (cutoff:3.500A)
      removed outlier: 3.972A  pdb=" N   LYS E1012 " --> pdb=" O   LEU E1008 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   ARG E1013 " --> pdb=" O   GLN E1009 " (cutoff:3.500A)
      removed outlier: 3.994A  pdb=" N   LEU E1014 " --> pdb=" O   ILE E1010 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1025 through 1033
    Processing helix  chain 'E' and resid 1035 through 1044
      removed outlier: 4.317A  pdb=" N   SER E1039 " --> pdb=" O   GLN E1035 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1046 through 1065
    Processing helix  chain 'E' and resid 1112 through 1117
      removed outlier: 3.604A  pdb=" N   ASN E1117 " --> pdb=" O   ARG E1113 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1119 through 1141
      removed outlier: 5.553A  pdb=" N   HIS E1125 " --> pdb=" O   PRO E1121 " (cutoff:3.500A)
      removed outlier: 4.087A  pdb=" N   SER E1126 " --> pdb=" O   ASN E1122 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1159 through 1177
      removed outlier: 3.894A  pdb=" N   GLU E1177 " --> pdb=" O   ARG E1173 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1178 through 1192
    Processing helix  chain 'E' and resid 1197 through 1209
      removed outlier: 3.625A  pdb=" N   LEU E1204 " --> pdb=" O   GLU E1200 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 1218 through 1225
      removed outlier: 3.550A  pdb=" N   GLN E1221 " --> pdb=" O   ASP E1218 " (cutoff:3.500A)
      removed outlier: 3.610A  pdb=" N   LYS E1223 " --> pdb=" O   GLU E1220 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 191 through 197
      removed outlier: 6.472A  pdb=" N   HIS A 184 " --> pdb=" O   LEU A 192 " (cutoff:3.500A)
      removed outlier: 4.687A  pdb=" N   TRP A 194 " --> pdb=" O   TRP A 182 " (cutoff:3.500A)
      removed outlier: 7.198A  pdb=" N   TRP A 182 " --> pdb=" O   TRP A 194 " (cutoff:3.500A)
      removed outlier: 4.713A  pdb=" N   GLN A 196 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   ILE A 180 " --> pdb=" O   GLN A 196 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   ALA A 181 " --> pdb=" O   VAL A 174 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   ILE A 170 " --> pdb=" O   LEU A 185 " (cutoff:3.500A)
      removed outlier: 6.700A  pdb=" N   ILE A 171 " --> pdb=" O   VAL A 230 " (cutoff:3.500A)
      removed outlier: 8.402A  pdb=" N   GLU A 232 " --> pdb=" O   ILE A 171 " (cutoff:3.500A)
      removed outlier: 8.651A  pdb=" N   ILE A 173 " --> pdb=" O   GLU A 232 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   TYR A 229 " --> pdb=" O   LEU A 274 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   MET A 276 " --> pdb=" O   TYR A 229 " (cutoff:3.500A)
      removed outlier: 6.860A  pdb=" N   LEU A 231 " --> pdb=" O   MET A 276 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 288 through 289
    Processing sheet with id=AA3, first strand: chain 'B' and resid 191 through 196
      removed outlier: 3.818A  pdb=" N   ASP B 193 " --> pdb=" O   HIS B 184 " (cutoff:3.500A)
      removed outlier: 4.009A  pdb=" N   VAL B 174 " --> pdb=" O   ALA B 181 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   ALA B 183 " --> pdb=" O   SER B 172 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE B 171 " --> pdb=" O   PHE B 228 " (cutoff:3.500A)
      removed outlier: 3.913A  pdb=" N   VAL B 230 " --> pdb=" O   ILE B 171 " (cutoff:3.500A)
      removed outlier: 7.706A  pdb=" N   PHE B 175 " --> pdb=" O   GLU B 232 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   LEU B 274 " --> pdb=" O   TYR B 229 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 412 through 415
    Processing sheet with id=AA5, first strand: chain 'E' and resid 588 through 590
    Processing sheet with id=AA6, first strand: chain 'E' and resid 606 through 609
    Processing sheet with id=AA7, first strand: chain 'E' and resid 707 through 709
    Processing sheet with id=AA8, first strand: chain 'E' and resid 798 through 800
    Processing sheet with id=AA9, first strand: chain 'E' and resid 831 through 832
      removed outlier: 3.726A  pdb=" N   ARG E 831 " --> pdb=" O   SER E 915 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 919 through 922
      removed outlier: 3.641A  pdb=" N   VAL E1147 " --> pdb=" O   TRP E1154 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'E' and resid 1069 through 1071

    539 hydrogen bonds defined for protein.
    1584 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      51 hydrogen bonds
      102 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      45 stacking parallelities
  Total time for adding SS restraints: 2.39

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2664
        1.33 -     1.45: 2991
        1.45 -     1.57: 6614
        1.57 -     1.69: 139
        1.69 -     1.82: 93
  Bond restraints: 12501
  Sorted by residual:
  bond pdb=" C3'  DA N  45 "
       pdb=" O3'  DA N  45 "
    ideal  model  delta    sigma   weight residual
    1.435  1.505 -0.070 1.30e-02 5.92e+03 2.88e+01
  bond pdb=" C1'  DT T  11 "
       pdb=" N1   DT T  11 "
    ideal  model  delta    sigma   weight residual
    1.468  1.526 -0.058 1.40e-02 5.10e+03 1.72e+01
  bond pdb=" C3'  DA N  43 "
       pdb=" O3'  DA N  43 "
    ideal  model  delta    sigma   weight residual
    1.435  1.487 -0.052 1.30e-02 5.92e+03 1.63e+01
  bond pdb=" C3'  DA N  37 "
       pdb=" C2'  DA N  37 "
    ideal  model  delta    sigma   weight residual
    1.516  1.545 -0.029 8.00e-03 1.56e+04 1.28e+01
  bond pdb=" C1'  DT T  10 "
       pdb=" N1   DT T  10 "
    ideal  model  delta    sigma   weight residual
    1.468  1.517 -0.049 1.40e-02 5.10e+03 1.24e+01
  ... (remaining 12496 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.68: 16921
        2.68 -     5.36: 340
        5.36 -     8.05: 42
        8.05 -    10.73: 9
       10.73 -    13.41: 2
  Bond angle restraints: 17314
  Sorted by residual:
  angle pdb=" N   ASP E1151 "
        pdb=" CA  ASP E1151 "
        pdb=" C   ASP E1151 "
      ideal   model   delta    sigma   weight residual
     113.23  106.58    6.65 1.22e+00 6.72e-01 2.97e+01
  angle pdb=" O4'  DA N  40 "
        pdb=" C4'  DA N  40 "
        pdb=" C3'  DA N  40 "
      ideal   model   delta    sigma   weight residual
     106.00  102.81    3.19 6.00e-01 2.78e+00 2.82e+01
  angle pdb=" C   LYS B 222 "
        pdb=" N   MET B 223 "
        pdb=" CA  MET B 223 "
      ideal   model   delta    sigma   weight residual
     121.20  127.89   -6.69 1.40e+00 5.10e-01 2.28e+01
  angle pdb=" C3'  DA N  45 "
        pdb=" O3'  DA N  45 "
        pdb=" P    DA N  46 "
      ideal   model   delta    sigma   weight residual
     119.70  125.39   -5.69 1.20e+00 6.94e-01 2.25e+01
  angle pdb=" C   HIS E1150 "
        pdb=" N   ASP E1151 "
        pdb=" CA  ASP E1151 "
      ideal   model   delta    sigma   weight residual
     123.47  130.44   -6.97 1.53e+00 4.27e-01 2.08e+01
  ... (remaining 17309 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.50: 6948
       35.50 -    71.00: 386
       71.00 -   106.50: 8
      106.50 -   141.99: 0
      141.99 -   177.49: 5
  Dihedral angle restraints: 7347
    sinusoidal: 3288
      harmonic: 4059
  Sorted by residual:
  dihedral pdb=" CA  SER E1148 "
           pdb=" C   SER E1148 "
           pdb=" N   VAL E1149 "
           pdb=" CA  VAL E1149 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.61   27.39     0      5.00e+00 4.00e-02 3.00e+01
  dihedral pdb=" CA  MET A 288 "
           pdb=" C   MET A 288 "
           pdb=" N   ILE A 289 "
           pdb=" CA  ILE A 289 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  153.08   26.92     0      5.00e+00 4.00e-02 2.90e+01
  dihedral pdb=" CA  GLU E1023 "
           pdb=" C   GLU E1023 "
           pdb=" N   PHE E1024 "
           pdb=" CA  PHE E1024 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.38   25.62     0      5.00e+00 4.00e-02 2.63e+01
  ... (remaining 7344 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 1701
       0.069 -    0.139: 254
       0.139 -    0.208: 30
       0.208 -    0.278: 6
       0.278 -    0.347: 1
  Chirality restraints: 1992
  Sorted by residual:
  chirality pdb=" CG  LEU A 185 "
            pdb=" CB  LEU A 185 "
            pdb=" CD1 LEU A 185 "
            pdb=" CD2 LEU A 185 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.24   -0.35 2.00e-01 2.50e+01 3.01e+00
  chirality pdb=" CB  VAL E 543 "
            pdb=" CA  VAL E 543 "
            pdb=" CG1 VAL E 543 "
            pdb=" CG2 VAL E 543 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.38   -0.25 2.00e-01 2.50e+01 1.52e+00
  chirality pdb=" CG  LEU E 234 "
            pdb=" CB  LEU E 234 "
            pdb=" CD1 LEU E 234 "
            pdb=" CD2 LEU E 234 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.81    0.22 2.00e-01 2.50e+01 1.21e+00
  ... (remaining 1989 not shown)

  Planarity restraints: 1962
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP E 441 "   -0.046 2.00e-02 2.50e+03   4.81e-02 5.79e+01
        pdb=" CG  TRP E 441 "    0.131 2.00e-02 2.50e+03
        pdb=" CD1 TRP E 441 "   -0.057 2.00e-02 2.50e+03
        pdb=" CD2 TRP E 441 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP E 441 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE2 TRP E 441 "    0.002 2.00e-02 2.50e+03
        pdb=" CE3 TRP E 441 "   -0.023 2.00e-02 2.50e+03
        pdb=" CZ2 TRP E 441 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ3 TRP E 441 "   -0.001 2.00e-02 2.50e+03
        pdb=" CH2 TRP E 441 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 731 "   -0.041 5.00e-02 4.00e+02   6.27e-02 6.29e+00
        pdb=" N   PRO E 732 "    0.108 5.00e-02 4.00e+02
        pdb=" CA  PRO E 732 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO E 732 "   -0.034 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL E 646 "   -0.035 5.00e-02 4.00e+02   5.25e-02 4.40e+00
        pdb=" N   PRO E 647 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO E 647 "   -0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO E 647 "   -0.029 5.00e-02 4.00e+02
  ... (remaining 1959 not shown)

  Histogram of nonbonded interaction distances:
        2.07 -     2.64: 116
        2.64 -     3.20: 10239
        3.20 -     3.77: 19918
        3.77 -     4.33: 25263
        4.33 -     4.90: 39297
  Nonbonded interactions: 94833
  Sorted by model distance:
  nonbonded pdb="MG    MG E1301 "
            pdb=" O2B ATP E1302 "
     model   vdw
     2.070 2.170
  nonbonded pdb=" ND2 ASN E 926 "
            pdb=" OD2 ASP E1128 "
     model   vdw
     2.235 3.120
  nonbonded pdb=" OD1 ASP B 193 "
            pdb=" OH  TYR B 325 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   LEU A 185 "
            pdb=" OH  TYR A 351 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OH  TYR E 530 "
            pdb=" O   PRO E 651 "
     model   vdw
     2.274 3.040
  ... (remaining 94828 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 151 through 152 or (resid 153 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 154 through 155 or (resid 156 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 157 through 164 or (resid  \ 
165 through 166 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 167 through 178 or (resid 179 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 180 through 185 or (resid 186 through 188 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 189 through 197 or (resid 198 thro \ 
ugh 199 and (name N or name CA or name C or name O or name CB )) or resid 200 th \ 
rough 262 or (resid 263 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 264 through 282 or (resid 283 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 284 through 285 or (resid 286 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 287 or (resid 288 and (name N or name  \ 
CA or name C or name O or name CB )) or resid 289 through 301 or (resid 302 and  \ 
(name N or name CA or name C or name O or name CB )) or resid 303 through 320 or \ 
 (resid 321 and (name N or name CA or name C or name O or name CB )) or resid 32 \ 
2 through 325 or (resid 326 through 327 and (name N or name CA or name C or name \ 
 O or name CB )) or resid 328 or (resid 329 through 330 and (name N or name CA o \ 
r name C or name O or name CB )) or resid 331 or (resid 332 through 334 and (nam \ 
e N or name CA or name C or name O or name CB )) or resid 335 through 340 or (re \ 
sid 341 and (name N or name CA or name C or name O or name CB )) or resid 342 th \ 
rough 351 or (resid 352 and (name N or name CA or name C or name O or name CB )) \ 
 or resid 353 through 355))
  selection = (chain 'B' and (resid 151 through 160 or (resid 161 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 162 through 221 or (resid 222 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 223 through 224 or (resid  \ 
225 through 226 and (name N or name CA or name C or name O or name CB )) or resi \ 
d 227 through 238 or (resid 239 and (name N or name CA or name C or name O or na \ 
me CB )) or resid 240 through 303 or (resid 304 and (name N or name CA or name C \ 
 or name O or name CB )) or resid 305 or (resid 313 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 314 through 332 or (resid 333 through 334  \ 
and (name N or name CA or name C or name O or name CB )) or resid 335 through 35 \ 
5))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.770
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     11.580
  Find NCS groups from input model:        0.090
  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:1.180
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.960
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5310
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   0.070  12501  Z= 0.323
  Angle     :  0.906  13.409  17314  Z= 0.557
  Chirality :  0.052   0.347   1992
  Planarity :  0.007   0.073   1962
  Dihedral  : 19.047 177.492   4701
  Min Nonbonded Distance : 2.070

Molprobity Statistics.
  All-atom Clashscore : 6.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.10 %
    Favored  : 98.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.50 (0.20), residues: 1369
  helix: -0.53 (0.17), residues: 718
  sheet: -1.05 (0.51), residues: 92
  loop : -1.47 (0.24), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG E 790 
 TYR   0.023   0.002   TYR A 229 
 PHE   0.028   0.003   PHE E1024 
 TRP   0.131   0.003   TRP E 441 
 HIS   0.012   0.002   HIS E 920 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00472 /  0.32 (12501)
  covalent geometry    : angle       0.90609 /  0.56 (17314)
  hydrogen bonds       : bond        0.13411 /  9.06 (  590)
  hydrogen bonds       : angle       6.00264 /  4.21 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  213 LEU cc_start: 0.8095 (tt) cc_final: 0.7412 (tt)
REVERT: A  276 MET cc_start: 0.3010 (mmt) cc_final: 0.2806 (mmt)
REVERT: B  253 MET cc_start: 0.7909 (tpp) cc_final: 0.7458 (tpp)
REVERT: B  258 TYR cc_start: 0.7327 (t80) cc_final: 0.6583 (t80)
REVERT: E  306 MET cc_start: 0.8139 (mmp) cc_final: 0.7832 (mmp)
REVERT: E  465 PHE cc_start: 0.6230 (t80) cc_final: 0.5888 (t80)
REVERT: E  771 GLU cc_start: 0.6965 (tt0) cc_final: 0.6738 (tt0)
REVERT: E  853 LYS cc_start: 0.7641 (tptt) cc_final: 0.7114 (tptt)
REVERT: E  892 TRP cc_start: 0.7175 (m100) cc_final: 0.6779 (m100)
REVERT: E  995 MET cc_start: 0.6181 (tmm) cc_final: 0.5849 (tmm)
REVERT: E 1009 GLN cc_start: 0.6599 (mt0) cc_final: 0.6398 (mt0)
REVERT: E 1010 ILE cc_start: 0.7779 (tp) cc_final: 0.7527 (tp)
REVERT: E 1017 LEU cc_start: 0.6607 (mp) cc_final: 0.6404 (mp)
REVERT: E 1131 HIS cc_start: 0.6615 (t70) cc_final: 0.6393 (t-90)
REVERT: E 1135 THR cc_start: 0.6702 (m) cc_final: 0.6454 (m)
REVERT: E 1163 MET cc_start: 0.7107 (ttp) cc_final: 0.6864 (ttp)
REVERT: E 1224 ARG cc_start: 0.6917 (mtm110) cc_final: 0.6638 (mtm110)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.0886
  time to fit residues: 28.3101
Evaluate side-chains
  204 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 204
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    0.0370
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    1.9990
   chunk 103 optimal weight:    1.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    0.0050
   chunk 55 optimal weight:    0.8980
   overall best weight:    0.9876

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 196 GLN
A 335 GLN
B 271 HIS
E 250 HIS
E 429 HIS
E 799 ASN
E 916 HIS
E 926 ASN
E1115 GLN
E1117 ASN
E1125 HIS
E1196 GLN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4324 r_free = 0.4324 target = 0.188562 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.153500 restraints weight = 18861.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.158148 restraints weight = 9745.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.4013 r_free = 0.4013 target = 0.161503 restraints weight = 5927.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.163642 restraints weight = 4118.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.164610 restraints weight = 3199.220|
|-----------------------------------------------------------------------------|
r_work (final): 0.4034
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6544
moved from start:          0.1057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  12501  Z= 0.171
  Angle     :  0.661   8.404  17314  Z= 0.355
  Chirality :  0.044   0.341   1992
  Planarity :  0.005   0.054   1962
  Dihedral  : 21.037 179.207   2306
  Min Nonbonded Distance : 1.973

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.80 %
    Favored  : 96.20 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  :  9.16 %
    Favored  : 89.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.57 (0.22), residues: 1369
  helix:  0.46 (0.19), residues: 722
  sheet: -1.35 (0.46), residues: 103
  loop : -1.23 (0.25), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG E 518 
 TYR   0.017   0.002   TYR E1140 
 PHE   0.028   0.002   PHE A 150 
 TRP   0.039   0.002   TRP E 441 
 HIS   0.010   0.001   HIS E 624 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.17 (12501)
  covalent geometry    : angle       0.66061 /  0.36 (17314)
  hydrogen bonds       : bond        0.04737 /  3.19 (  590)
  hydrogen bonds       : angle       4.86707 /  3.44 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 211
  time to evaluate  : 0.256 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  253 MET cc_start: 0.7945 (tpp) cc_final: 0.7221 (tpp)
REVERT: B  258 TYR cc_start: 0.7331 (t80) cc_final: 0.6518 (t80)
REVERT: E  456 LEU cc_start: 0.8296 (mm) cc_final: 0.8045 (mt)
REVERT: E  701 GLN cc_start: 0.7533 (tt0) cc_final: 0.7305 (tt0)
REVERT: E  995 MET cc_start: 0.7502 (tmm) cc_final: 0.6692 (tmm)
REVERT: E 1010 ILE cc_start: 0.8551 (tp) cc_final: 0.8224 (tp)
  outliers start: 15
  outliers final: 9
  residues processed: 214
  average time/residue: 0.0893
  time to fit residues: 27.7222
Evaluate side-chains
  214 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 205
  time to evaluate  : 0.236 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain E residue  406 MET
Chi-restraints excluded: chain E residue  523 VAL
Chi-restraints excluded: chain E residue  589 MET
Chi-restraints excluded: chain E residue  800 MET
Chi-restraints excluded: chain E residue  849 THR
Chi-restraints excluded: chain E residue 1071 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 59 optimal weight:    2.9990
   chunk 99 optimal weight:    0.9980
   chunk 56 optimal weight:    0.1980
   chunk 17 optimal weight:    4.9990
   chunk 25 optimal weight:    2.9990
   chunk 69 optimal weight:    2.9990
   chunk 4 optimal weight:    0.7980
   chunk 101 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 95 optimal weight:    0.9980
   chunk 103 optimal weight:    0.9980
   overall best weight:    0.7180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 945 ASN
E1009 GLN
E1117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.188645 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.153473 restraints weight = 19138.624|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.158213 restraints weight = 9902.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.161164 restraints weight = 6050.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.4038 r_free = 0.4038 target = 0.163669 restraints weight = 4217.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4049 r_free = 0.4049 target = 0.164721 restraints weight = 3276.175|
|-----------------------------------------------------------------------------|
r_work (final): 0.4036
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6541
moved from start:          0.1361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12501  Z= 0.142
  Angle     :  0.615   6.758  17314  Z= 0.330
  Chirality :  0.043   0.333   1992
  Planarity :  0.005   0.050   1962
  Dihedral  : 20.931 177.245   2306
  Min Nonbonded Distance : 1.983

Molprobity Statistics.
  All-atom Clashscore : 9.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.43 %
    Favored  : 96.57 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 12.55 %
    Favored  : 85.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.22), residues: 1369
  helix:  0.95 (0.19), residues: 714
  sheet: -1.51 (0.46), residues: 103
  loop : -1.19 (0.25), residues: 552

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E1113 
 TYR   0.012   0.001   TYR E1140 
 PHE   0.024   0.002   PHE A 150 
 TRP   0.014   0.001   TRP E 441 
 HIS   0.008   0.001   HIS E 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.14 (12501)
  covalent geometry    : angle       0.61510 /  0.33 (17314)
  hydrogen bonds       : bond        0.04275 /  2.91 (  590)
  hydrogen bonds       : angle       4.57276 /  3.22 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 209
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 MET cc_start: 0.7108 (tpp) cc_final: 0.6838 (tpp)
REVERT: B  253 MET cc_start: 0.7922 (tpp) cc_final: 0.7408 (tpp)
REVERT: B  258 TYR cc_start: 0.7406 (t80) cc_final: 0.6532 (t80)
REVERT: B  346 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6782 (pp30)
REVERT: E  230 PHE cc_start: 0.8196 (m-80) cc_final: 0.7859 (m-80)
REVERT: E  263 MET cc_start: 0.7185 (mtt) cc_final: 0.6849 (mtt)
REVERT: E  306 MET cc_start: 0.7363 (mmp) cc_final: 0.7154 (mmp)
REVERT: E  407 GLU cc_start: 0.7599 (tp30) cc_final: 0.7307 (tp30)
REVERT: E  426 GLU cc_start: 0.7897 (mm-30) cc_final: 0.7688 (tp30)
REVERT: E  485 GLN cc_start: 0.6941 (tm-30) cc_final: 0.6629 (tm-30)
REVERT: E  701 GLN cc_start: 0.7597 (tt0) cc_final: 0.7364 (tt0)
REVERT: E  800 MET cc_start: 0.5566 (tpp) cc_final: 0.5201 (mmm)
REVERT: E  831 ARG cc_start: 0.8034 (tpp-160) cc_final: 0.7764 (mmt-90)
REVERT: E  892 TRP cc_start: 0.7833 (m100) cc_final: 0.7469 (m100)
REVERT: E  995 MET cc_start: 0.7484 (tmm) cc_final: 0.6655 (tmm)
REVERT: E 1043 MET cc_start: 0.1866 (OUTLIER) cc_final: 0.0481 (pmm)
REVERT: E 1227 TYR cc_start: 0.6437 (m-10) cc_final: 0.5928 (m-10)
  outliers start: 17
  outliers final: 11
  residues processed: 213
  average time/residue: 0.0881
  time to fit residues: 27.1794
Evaluate side-chains
  224 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 211
  time to evaluate  : 0.394 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  160 GLU
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain E residue  589 MET
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  702 LEU
Chi-restraints excluded: chain E residue  825 LEU
Chi-restraints excluded: chain E residue  849 THR
Chi-restraints excluded: chain E residue 1043 MET
Chi-restraints excluded: chain E residue 1071 VAL
Chi-restraints excluded: chain E residue 1208 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 103 optimal weight:    0.7980
   chunk 51 optimal weight:    8.9990
   chunk 113 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0980
   chunk 125 optimal weight:    4.9990
   chunk 75 optimal weight:    1.9990
   chunk 124 optimal weight:    3.9990
   chunk 41 optimal weight:    0.2980
   chunk 89 optimal weight:    0.0270
   chunk 63 optimal weight:    0.8980
   chunk 34 optimal weight:   20.0000
   overall best weight:    0.4238

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 629 GLN
** E 920 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E1009 GLN
E1117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4323 r_free = 0.4323 target = 0.188610 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.152718 restraints weight = 19504.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3957 r_free = 0.3957 target = 0.157536 restraints weight = 10159.045|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3997 r_free = 0.3997 target = 0.160782 restraints weight = 6235.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.162604 restraints weight = 4370.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4039 r_free = 0.4039 target = 0.164235 restraints weight = 3465.720|
|-----------------------------------------------------------------------------|
r_work (final): 0.4041
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6531
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  12501  Z= 0.122
  Angle     :  0.582   8.112  17314  Z= 0.311
  Chirality :  0.042   0.337   1992
  Planarity :  0.005   0.048   1962
  Dihedral  : 20.836 177.248   2306
  Min Nonbonded Distance : 2.010

Molprobity Statistics.
  All-atom Clashscore : 9.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.14 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.83 %
    Allowed  : 14.93 %
    Favored  : 83.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.22), residues: 1369
  helix:  1.20 (0.19), residues: 720
  sheet: -1.47 (0.46), residues: 103
  loop : -1.11 (0.25), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 822 
 TYR   0.009   0.001   TYR A 229 
 PHE   0.026   0.001   PHE E 465 
 TRP   0.013   0.001   TRP E 885 
 HIS   0.007   0.001   HIS E 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00237 /  0.12 (12501)
  covalent geometry    : angle       0.58196 /  0.31 (17314)
  hydrogen bonds       : bond        0.03792 /  2.58 (  590)
  hydrogen bonds       : angle       4.35503 /  3.07 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 211
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 MET cc_start: 0.7130 (tpp) cc_final: 0.6750 (tpp)
REVERT: A  288 MET cc_start: 0.5913 (OUTLIER) cc_final: 0.5559 (mtm)
REVERT: B  234 THR cc_start: 0.8711 (m) cc_final: 0.8484 (t)
REVERT: B  253 MET cc_start: 0.7908 (tpp) cc_final: 0.7395 (tpp)
REVERT: B  258 TYR cc_start: 0.7451 (t80) cc_final: 0.6552 (t80)
REVERT: B  346 GLN cc_start: 0.7081 (OUTLIER) cc_final: 0.6543 (pp30)
REVERT: E  230 PHE cc_start: 0.8208 (m-80) cc_final: 0.7909 (m-80)
REVERT: E  263 MET cc_start: 0.7165 (mtt) cc_final: 0.6765 (mtt)
REVERT: E  295 ASP cc_start: 0.8566 (t0) cc_final: 0.8287 (t0)
REVERT: E  407 GLU cc_start: 0.7588 (tp30) cc_final: 0.7313 (tp30)
REVERT: E  485 GLN cc_start: 0.6934 (tm-30) cc_final: 0.6654 (tm-30)
REVERT: E  629 GLN cc_start: 0.7097 (OUTLIER) cc_final: 0.6750 (pp30)
REVERT: E  701 GLN cc_start: 0.7591 (tt0) cc_final: 0.7390 (tt0)
REVERT: E  800 MET cc_start: 0.5506 (OUTLIER) cc_final: 0.5281 (mmm)
REVERT: E  831 ARG cc_start: 0.8020 (tpp-160) cc_final: 0.7746 (mmt-90)
REVERT: E  892 TRP cc_start: 0.7822 (m100) cc_final: 0.7521 (m100)
REVERT: E 1043 MET cc_start: 0.1893 (OUTLIER) cc_final: 0.0570 (pmm)
REVERT: E 1132 MET cc_start: 0.7430 (tmm) cc_final: 0.7220 (tmm)
  outliers start: 20
  outliers final: 8
  residues processed: 219
  average time/residue: 0.1060
  time to fit residues: 33.5458
Evaluate side-chains
  221 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 208
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain E residue  405 HIS
Chi-restraints excluded: chain E residue  589 MET
Chi-restraints excluded: chain E residue  629 GLN
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  800 MET
Chi-restraints excluded: chain E residue 1043 MET
Chi-restraints excluded: chain E residue 1071 VAL
Chi-restraints excluded: chain E residue 1208 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 62 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 130 optimal weight:    0.7980
   chunk 42 optimal weight:    1.9990
   chunk 138 optimal weight:   20.0000
   chunk 104 optimal weight:    0.0970
   chunk 51 optimal weight:    8.9990
   chunk 22 optimal weight:    9.9990
   chunk 128 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 629 GLN
E 704 ASN
E1009 GLN
E1117 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4308 r_free = 0.4308 target = 0.187265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.151151 restraints weight = 19417.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.156027 restraints weight = 10189.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.159241 restraints weight = 6245.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4002 r_free = 0.4002 target = 0.161211 restraints weight = 4377.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4018 r_free = 0.4018 target = 0.162615 restraints weight = 3444.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.4028
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6561
moved from start:          0.1724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  12501  Z= 0.140
  Angle     :  0.591   8.092  17314  Z= 0.316
  Chirality :  0.042   0.335   1992
  Planarity :  0.005   0.050   1962
  Dihedral  : 20.783 177.315   2306
  Min Nonbonded Distance : 1.993

Molprobity Statistics.
  All-atom Clashscore : 10.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 15.48 %
    Favored  : 82.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.22), residues: 1369
  helix:  1.37 (0.19), residues: 713
  sheet: -1.52 (0.46), residues: 103
  loop : -1.11 (0.25), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 518 
 TYR   0.009   0.001   TYR E1140 
 PHE   0.021   0.001   PHE E 465 
 TRP   0.013   0.001   TRP E 885 
 HIS   0.009   0.001   HIS E 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00285 /  0.14 (12501)
  covalent geometry    : angle       0.59063 /  0.32 (17314)
  hydrogen bonds       : bond        0.03898 /  2.67 (  590)
  hydrogen bonds       : angle       4.33641 /  3.06 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  229 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 203
  time to evaluate  : 0.433 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 MET cc_start: 0.7161 (tpp) cc_final: 0.6743 (tpp)
REVERT: A  288 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5621 (mtm)
REVERT: B  234 THR cc_start: 0.8709 (m) cc_final: 0.8464 (t)
REVERT: B  253 MET cc_start: 0.7920 (tpp) cc_final: 0.7402 (tpp)
REVERT: B  258 TYR cc_start: 0.7467 (t80) cc_final: 0.6628 (t80)
REVERT: B  346 GLN cc_start: 0.7116 (OUTLIER) cc_final: 0.6592 (pp30)
REVERT: E  295 ASP cc_start: 0.8522 (t0) cc_final: 0.8241 (t0)
REVERT: E  407 GLU cc_start: 0.7587 (tp30) cc_final: 0.7336 (tp30)
REVERT: E  485 GLN cc_start: 0.6959 (tm-30) cc_final: 0.6658 (tm-30)
REVERT: E  701 GLN cc_start: 0.7623 (tt0) cc_final: 0.7387 (tt0)
REVERT: E  800 MET cc_start: 0.5540 (OUTLIER) cc_final: 0.5318 (mmm)
REVERT: E  831 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7746 (mmt-90)
REVERT: E  995 MET cc_start: 0.7575 (tmm) cc_final: 0.7316 (tmm)
REVERT: E 1043 MET cc_start: 0.1885 (OUTLIER) cc_final: 0.0651 (pmm)
REVERT: E 1132 MET cc_start: 0.7446 (tmm) cc_final: 0.7216 (tmm)
  outliers start: 26
  outliers final: 12
  residues processed: 218
  average time/residue: 0.1155
  time to fit residues: 36.1587
Evaluate side-chains
  216 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 200
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain E residue  405 HIS
Chi-restraints excluded: chain E residue  479 VAL
Chi-restraints excluded: chain E residue  589 MET
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  704 ASN
Chi-restraints excluded: chain E residue  800 MET
Chi-restraints excluded: chain E residue  949 SER
Chi-restraints excluded: chain E residue 1043 MET
Chi-restraints excluded: chain E residue 1071 VAL
Chi-restraints excluded: chain E residue 1208 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 118 optimal weight:    0.2980
   chunk 55 optimal weight:    0.8980
   chunk 10 optimal weight:    2.9990
   chunk 95 optimal weight:    1.9990
   chunk 106 optimal weight:    0.7980
   chunk 134 optimal weight:    2.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 81 optimal weight:    0.6980
   chunk 61 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 251 HIS
** E 629 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4317 r_free = 0.4317 target = 0.188056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3901 r_free = 0.3901 target = 0.152945 restraints weight = 19070.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3961 r_free = 0.3961 target = 0.157697 restraints weight = 9845.672|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 50)----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.160828 restraints weight = 5996.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.162691 restraints weight = 4195.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.164259 restraints weight = 3314.537|
|-----------------------------------------------------------------------------|
r_work (final): 0.4021
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6561
moved from start:          0.1888

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.054  12501  Z= 0.155
  Angle     :  0.610   8.774  17314  Z= 0.323
  Chirality :  0.043   0.333   1992
  Planarity :  0.005   0.050   1962
  Dihedral  : 20.768 177.320   2306
  Min Nonbonded Distance : 1.970

Molprobity Statistics.
  All-atom Clashscore : 10.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.73 %
    Favored  : 96.27 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 16.39 %
    Favored  : 81.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.22), residues: 1369
  helix:  1.40 (0.19), residues: 715
  sheet: -1.47 (0.47), residues: 95
  loop : -1.12 (0.25), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 518 
 TYR   0.011   0.001   TYR E1140 
 PHE   0.035   0.002   PHE E 465 
 TRP   0.014   0.001   TRP E 885 
 HIS   0.009   0.001   HIS E 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00323 /  0.16 (12501)
  covalent geometry    : angle       0.60959 /  0.32 (17314)
  hydrogen bonds       : bond        0.03937 /  2.69 (  590)
  hydrogen bonds       : angle       4.33829 /  3.06 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 206
  time to evaluate  : 0.405 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 GLU cc_start: 0.6302 (mp0) cc_final: 0.6008 (mp0)
REVERT: A  256 MET cc_start: 0.7148 (tpp) cc_final: 0.6712 (tpp)
REVERT: B  234 THR cc_start: 0.8699 (m) cc_final: 0.8448 (t)
REVERT: B  253 MET cc_start: 0.7909 (tpp) cc_final: 0.7389 (tpp)
REVERT: B  258 TYR cc_start: 0.7424 (t80) cc_final: 0.6638 (t80)
REVERT: B  346 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6607 (pp30)
REVERT: E  295 ASP cc_start: 0.8491 (t0) cc_final: 0.8257 (t0)
REVERT: E  407 GLU cc_start: 0.7562 (tp30) cc_final: 0.7354 (tp30)
REVERT: E  485 GLN cc_start: 0.7009 (tm-30) cc_final: 0.6696 (tm-30)
REVERT: E  542 GLU cc_start: 0.7543 (mm-30) cc_final: 0.7260 (tm-30)
REVERT: E  648 MET cc_start: 0.6808 (mmp) cc_final: 0.6215 (mmt)
REVERT: E  701 GLN cc_start: 0.7677 (tt0) cc_final: 0.7376 (tt0)
REVERT: E  800 MET cc_start: 0.5589 (OUTLIER) cc_final: 0.5361 (mmm)
REVERT: E  831 ARG cc_start: 0.8028 (tpp-160) cc_final: 0.7731 (mmt-90)
REVERT: E  892 TRP cc_start: 0.7874 (m100) cc_final: 0.7562 (m100)
REVERT: E 1043 MET cc_start: 0.1871 (OUTLIER) cc_final: 0.1633 (pmm)
  outliers start: 21
  outliers final: 14
  residues processed: 214
  average time/residue: 0.1083
  time to fit residues: 33.7524
Evaluate side-chains
  221 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 204
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  251 HIS
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  402 LYS
Chi-restraints excluded: chain E residue  405 HIS
Chi-restraints excluded: chain E residue  589 MET
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  800 MET
Chi-restraints excluded: chain E residue  825 LEU
Chi-restraints excluded: chain E residue  949 SER
Chi-restraints excluded: chain E residue 1043 MET
Chi-restraints excluded: chain E residue 1071 VAL
Chi-restraints excluded: chain E residue 1208 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 92 optimal weight:    5.9990
   chunk 99 optimal weight:    1.9990
   chunk 83 optimal weight:    0.9980
   chunk 135 optimal weight:    5.9990
   chunk 133 optimal weight:    0.0370
   chunk 108 optimal weight:    0.2980
   chunk 118 optimal weight:    3.9990
   chunk 46 optimal weight:    7.9990
   chunk 114 optimal weight:    1.9990
   chunk 54 optimal weight:    2.9990
   overall best weight:    1.0662

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 267 GLN
E 704 ASN
E1009 GLN
E1117 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.185680 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.149417 restraints weight = 19449.969|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3914 r_free = 0.3914 target = 0.154048 restraints weight = 10174.708|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3956 r_free = 0.3956 target = 0.157361 restraints weight = 6299.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3980 r_free = 0.3980 target = 0.159375 restraints weight = 4445.184|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3999 r_free = 0.3999 target = 0.160869 restraints weight = 3511.401|
|-----------------------------------------------------------------------------|
r_work (final): 0.4007
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6605
moved from start:          0.2026

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040  12501  Z= 0.168
  Angle     :  0.634   9.544  17314  Z= 0.333
  Chirality :  0.043   0.332   1992
  Planarity :  0.005   0.051   1962
  Dihedral  : 20.754 177.321   2306
  Min Nonbonded Distance : 1.959

Molprobity Statistics.
  All-atom Clashscore : 11.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 16.76 %
    Favored  : 80.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.22), residues: 1369
  helix:  1.40 (0.19), residues: 710
  sheet: -1.52 (0.46), residues: 95
  loop : -1.16 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG E 518 
 TYR   0.014   0.001   TYR E1140 
 PHE   0.038   0.002   PHE E 465 
 TRP   0.013   0.001   TRP E 885 
 HIS   0.027   0.001   HIS B 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00351 /  0.17 (12501)
  covalent geometry    : angle       0.63351 /  0.33 (17314)
  hydrogen bonds       : bond        0.04058 /  2.79 (  590)
  hydrogen bonds       : angle       4.36702 /  3.08 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  227 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 200
  time to evaluate  : 0.376 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 GLU cc_start: 0.6355 (mp0) cc_final: 0.6089 (mp0)
REVERT: A  256 MET cc_start: 0.7205 (tpp) cc_final: 0.6766 (tpp)
REVERT: B  253 MET cc_start: 0.7849 (tpp) cc_final: 0.7292 (tpp)
REVERT: B  258 TYR cc_start: 0.7462 (t80) cc_final: 0.6685 (t80)
REVERT: B  346 GLN cc_start: 0.7190 (OUTLIER) cc_final: 0.6705 (pp30)
REVERT: E  295 ASP cc_start: 0.8511 (t0) cc_final: 0.8259 (t0)
REVERT: E  407 GLU cc_start: 0.7558 (tp30) cc_final: 0.7270 (tt0)
REVERT: E  478 GLU cc_start: 0.7451 (tp30) cc_final: 0.7149 (tp30)
REVERT: E  485 GLN cc_start: 0.7013 (tm-30) cc_final: 0.6716 (tm-30)
REVERT: E  542 GLU cc_start: 0.7531 (mm-30) cc_final: 0.7238 (tm-30)
REVERT: E  648 MET cc_start: 0.6851 (mmp) cc_final: 0.6330 (mmt)
REVERT: E  701 GLN cc_start: 0.7619 (tt0) cc_final: 0.7405 (tt0)
REVERT: E  800 MET cc_start: 0.5682 (OUTLIER) cc_final: 0.5432 (mmm)
REVERT: E  825 LEU cc_start: 0.7941 (OUTLIER) cc_final: 0.7692 (mt)
REVERT: E  831 ARG cc_start: 0.8024 (tpp-160) cc_final: 0.7727 (mmt-90)
REVERT: E  892 TRP cc_start: 0.7905 (m100) cc_final: 0.7557 (m100)
REVERT: E  995 MET cc_start: 0.7628 (tmm) cc_final: 0.6613 (tmm)
REVERT: E 1043 MET cc_start: 0.1860 (OUTLIER) cc_final: 0.0607 (pmm)
REVERT: E 1227 TYR cc_start: 0.6528 (m-10) cc_final: 0.6096 (m-10)
  outliers start: 27
  outliers final: 16
  residues processed: 209
  average time/residue: 0.0969
  time to fit residues: 29.3318
Evaluate side-chains
  219 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 199
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  251 HIS
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  402 LYS
Chi-restraints excluded: chain E residue  405 HIS
Chi-restraints excluded: chain E residue  589 MET
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  704 ASN
Chi-restraints excluded: chain E residue  800 MET
Chi-restraints excluded: chain E residue  825 LEU
Chi-restraints excluded: chain E residue  849 THR
Chi-restraints excluded: chain E residue  949 SER
Chi-restraints excluded: chain E residue 1043 MET
Chi-restraints excluded: chain E residue 1071 VAL
Chi-restraints excluded: chain E residue 1208 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 93 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   chunk 60 optimal weight:    4.9990
   chunk 85 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 88 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 46 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 136 optimal weight:    0.5980
   chunk 86 optimal weight:    0.6980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 251 HIS
E 773 HIS
E1117 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.186284 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.150094 restraints weight = 19315.759|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.154844 restraints weight = 10072.382|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3967 r_free = 0.3967 target = 0.158217 restraints weight = 6187.727|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.160101 restraints weight = 4326.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4007 r_free = 0.4007 target = 0.161591 restraints weight = 3427.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.4012
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6593
moved from start:          0.2105

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  12501  Z= 0.146
  Angle     :  0.627   9.411  17314  Z= 0.327
  Chirality :  0.043   0.335   1992
  Planarity :  0.005   0.053   1962
  Dihedral  : 20.735 177.010   2306
  Min Nonbonded Distance : 1.964

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.87 %
    Favored  : 96.13 %
  Rotamer:
    Outliers :  2.38 %
    Allowed  : 16.94 %
    Favored  : 80.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.28 (0.22), residues: 1369
  helix:  1.44 (0.20), residues: 710
  sheet: -1.49 (0.46), residues: 95
  loop : -1.14 (0.25), residues: 564

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 518 
 TYR   0.012   0.001   TYR E1140 
 PHE   0.038   0.002   PHE E 465 
 TRP   0.013   0.001   TRP E1154 
 HIS   0.008   0.001   HIS E 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00302 /  0.15 (12501)
  covalent geometry    : angle       0.62695 /  0.33 (17314)
  hydrogen bonds       : bond        0.03914 /  2.69 (  590)
  hydrogen bonds       : angle       4.33550 /  3.06 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 202
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 GLU cc_start: 0.6363 (mp0) cc_final: 0.6106 (mp0)
REVERT: A  256 MET cc_start: 0.7215 (tpp) cc_final: 0.6753 (tpp)
REVERT: B  234 THR cc_start: 0.8709 (m) cc_final: 0.8429 (t)
REVERT: B  253 MET cc_start: 0.7869 (tpp) cc_final: 0.7318 (tpp)
REVERT: B  258 TYR cc_start: 0.7445 (t80) cc_final: 0.6679 (t80)
REVERT: B  346 GLN cc_start: 0.7195 (OUTLIER) cc_final: 0.6696 (pp30)
REVERT: E  263 MET cc_start: 0.7010 (OUTLIER) cc_final: 0.6640 (mmp)
REVERT: E  295 ASP cc_start: 0.8478 (t0) cc_final: 0.8237 (t0)
REVERT: E  478 GLU cc_start: 0.7411 (tp30) cc_final: 0.7122 (tp30)
REVERT: E  485 GLN cc_start: 0.7003 (tm-30) cc_final: 0.6724 (tm-30)
REVERT: E  542 GLU cc_start: 0.7515 (mm-30) cc_final: 0.7188 (tm-30)
REVERT: E  648 MET cc_start: 0.6835 (mmp) cc_final: 0.6251 (mmt)
REVERT: E  669 LYS cc_start: 0.7740 (ptpt) cc_final: 0.7468 (ptpt)
REVERT: E  671 MET cc_start: 0.8347 (mtt) cc_final: 0.8078 (mtm)
REVERT: E  701 GLN cc_start: 0.7632 (tt0) cc_final: 0.7364 (tt0)
REVERT: E  825 LEU cc_start: 0.7920 (OUTLIER) cc_final: 0.7690 (mt)
REVERT: E  892 TRP cc_start: 0.7884 (m100) cc_final: 0.7572 (m100)
REVERT: E 1043 MET cc_start: 0.1482 (OUTLIER) cc_final: 0.0661 (pmm)
  outliers start: 26
  outliers final: 17
  residues processed: 211
  average time/residue: 0.1054
  time to fit residues: 32.0381
Evaluate side-chains
  218 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 197
  time to evaluate  : 0.412 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  251 HIS
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  263 MET
Chi-restraints excluded: chain E residue  286 MET
Chi-restraints excluded: chain E residue  405 HIS
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  762 LEU
Chi-restraints excluded: chain E residue  825 LEU
Chi-restraints excluded: chain E residue  849 THR
Chi-restraints excluded: chain E residue  949 SER
Chi-restraints excluded: chain E residue 1043 MET
Chi-restraints excluded: chain E residue 1071 VAL
Chi-restraints excluded: chain E residue 1150 HIS
Chi-restraints excluded: chain E residue 1208 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 13 optimal weight:    0.9990
   chunk 69 optimal weight:    2.9990
   chunk 25 optimal weight:    4.9990
   chunk 73 optimal weight:    7.9990
   chunk 118 optimal weight:    0.0470
   chunk 75 optimal weight:    0.9990
   chunk 53 optimal weight:    0.5980
   chunk 2 optimal weight:    0.5980
   chunk 32 optimal weight:    0.0370
   chunk 10 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0010
   overall best weight:    0.2562

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E1009 GLN
E1117 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4314 r_free = 0.4314 target = 0.187637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.151693 restraints weight = 19192.755|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.156445 restraints weight = 10033.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3986 r_free = 0.3986 target = 0.159724 restraints weight = 6160.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.161810 restraints weight = 4340.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.163166 restraints weight = 3400.977|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6549
moved from start:          0.2164

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064  12501  Z= 0.124
  Angle     :  0.624  10.938  17314  Z= 0.322
  Chirality :  0.042   0.339   1992
  Planarity :  0.005   0.056   1962
  Dihedral  : 20.709 176.492   2306
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 10.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.29 %
    Favored  : 96.71 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 17.95 %
    Favored  : 80.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.23), residues: 1369
  helix:  1.53 (0.20), residues: 708
  sheet: -1.39 (0.46), residues: 101
  loop : -1.11 (0.25), residues: 560

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG E 803 
 TYR   0.011   0.001   TYR A 229 
 PHE   0.034   0.001   PHE E 465 
 TRP   0.015   0.001   TRP E 885 
 HIS   0.011   0.001   HIS B 251 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00252 /  0.12 (12501)
  covalent geometry    : angle       0.62404 /  0.32 (17314)
  hydrogen bonds       : bond        0.03672 /  2.52 (  590)
  hydrogen bonds       : angle       4.24137 /  2.98 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  230 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 209
  time to evaluate  : 0.299 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 GLU cc_start: 0.6310 (mp0) cc_final: 0.6088 (mp0)
REVERT: A  256 MET cc_start: 0.7222 (tpp) cc_final: 0.6746 (tpp)
REVERT: B  234 THR cc_start: 0.8690 (m) cc_final: 0.8418 (t)
REVERT: B  253 MET cc_start: 0.7985 (tpp) cc_final: 0.7433 (tpp)
REVERT: B  258 TYR cc_start: 0.7465 (t80) cc_final: 0.6699 (t80)
REVERT: B  346 GLN cc_start: 0.7175 (OUTLIER) cc_final: 0.6667 (pp30)
REVERT: E  263 MET cc_start: 0.6933 (OUTLIER) cc_final: 0.6558 (mmp)
REVERT: E  295 ASP cc_start: 0.8420 (t0) cc_final: 0.8216 (t0)
REVERT: E  478 GLU cc_start: 0.7333 (tp30) cc_final: 0.7053 (tp30)
REVERT: E  485 GLN cc_start: 0.6982 (tm-30) cc_final: 0.6705 (tm-30)
REVERT: E  542 GLU cc_start: 0.7494 (mm-30) cc_final: 0.7171 (tm-30)
REVERT: E  630 LEU cc_start: 0.7895 (tp) cc_final: 0.7642 (tt)
REVERT: E  648 MET cc_start: 0.6718 (mmp) cc_final: 0.6144 (mmt)
REVERT: E  671 MET cc_start: 0.8331 (mtt) cc_final: 0.8120 (mtm)
REVERT: E  701 GLN cc_start: 0.7560 (tt0) cc_final: 0.7317 (tt0)
REVERT: E  825 LEU cc_start: 0.7931 (OUTLIER) cc_final: 0.7702 (mt)
REVERT: E  882 ARG cc_start: 0.6862 (ttm110) cc_final: 0.6484 (ttp80)
REVERT: E  892 TRP cc_start: 0.7846 (m100) cc_final: 0.7582 (m100)
REVERT: E 1043 MET cc_start: 0.1359 (OUTLIER) cc_final: 0.0506 (pmm)
REVERT: E 1132 MET cc_start: 0.7440 (tmm) cc_final: 0.7187 (tmm)
  outliers start: 21
  outliers final: 15
  residues processed: 216
  average time/residue: 0.1079
  time to fit residues: 33.2268
Evaluate side-chains
  221 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 202
  time to evaluate  : 0.302 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  168 ASN
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  263 MET
Chi-restraints excluded: chain E residue  286 MET
Chi-restraints excluded: chain E residue  405 HIS
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  762 LEU
Chi-restraints excluded: chain E residue  825 LEU
Chi-restraints excluded: chain E residue 1043 MET
Chi-restraints excluded: chain E residue 1071 VAL
Chi-restraints excluded: chain E residue 1150 HIS
Chi-restraints excluded: chain E residue 1208 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 131 optimal weight:    2.9990
   chunk 95 optimal weight:    2.9990
   chunk 142 optimal weight:   10.0000
   chunk 138 optimal weight:   20.0000
   chunk 132 optimal weight:    3.9990
   chunk 69 optimal weight:    3.9990
   chunk 90 optimal weight:    0.0010
   chunk 82 optimal weight:    0.5980
   chunk 57 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9980
   chunk 4 optimal weight:    1.9990
   overall best weight:    1.1190

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
B 251 HIS
** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 815 HIS
E1009 GLN
E1117 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4304 r_free = 0.4304 target = 0.186415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.151500 restraints weight = 18841.553|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.156201 restraints weight = 9797.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3987 r_free = 0.3987 target = 0.159278 restraints weight = 5980.484|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.161295 restraints weight = 4190.459|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4026 r_free = 0.4026 target = 0.162599 restraints weight = 3292.825|
|-----------------------------------------------------------------------------|
r_work (final): 0.4011
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6592
moved from start:          0.2322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041  12501  Z= 0.174
  Angle     :  0.663   9.697  17314  Z= 0.342
  Chirality :  0.044   0.334   1992
  Planarity :  0.005   0.055   1962
  Dihedral  : 20.706 177.312   2306
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 12.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.09 %
    Favored  : 95.91 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 17.40 %
    Favored  : 80.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.22), residues: 1369
  helix:  1.43 (0.19), residues: 707
  sheet: -1.61 (0.45), residues: 103
  loop : -1.13 (0.25), residues: 559

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG E 518 
 TYR   0.014   0.002   TYR E1140 
 PHE   0.037   0.002   PHE E 465 
 TRP   0.018   0.002   TRP E 885 
 HIS   0.008   0.001   HIS E 608 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00366 /  0.17 (12501)
  covalent geometry    : angle       0.66347 /  0.34 (17314)
  hydrogen bonds       : bond        0.04105 /  2.80 (  590)
  hydrogen bonds       : angle       4.36855 /  3.08 ( 1686)

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

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

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2738 Ramachandran restraints generated.
    1369 Oldfield, 0 Emsley, 1369 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 208
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  160 GLU cc_start: 0.6336 (mp0) cc_final: 0.6090 (mp0)
REVERT: A  256 MET cc_start: 0.7181 (tpp) cc_final: 0.6715 (tpp)
REVERT: B  234 THR cc_start: 0.8687 (m) cc_final: 0.8419 (t)
REVERT: B  253 MET cc_start: 0.7874 (tpp) cc_final: 0.7350 (tpp)
REVERT: B  258 TYR cc_start: 0.7429 (t80) cc_final: 0.6722 (t80)
REVERT: B  346 GLN cc_start: 0.7237 (OUTLIER) cc_final: 0.6709 (pp30)
REVERT: E  263 MET cc_start: 0.6959 (OUTLIER) cc_final: 0.6598 (mmp)
REVERT: E  478 GLU cc_start: 0.7458 (tp30) cc_final: 0.7182 (tp30)
REVERT: E  485 GLN cc_start: 0.7016 (tm-30) cc_final: 0.6747 (tm-30)
REVERT: E  542 GLU cc_start: 0.7513 (mm-30) cc_final: 0.7183 (tm-30)
REVERT: E  582 MET cc_start: 0.7133 (tpp) cc_final: 0.6872 (ttm)
REVERT: E  648 MET cc_start: 0.6926 (mmp) cc_final: 0.6324 (mmt)
REVERT: E  669 LYS cc_start: 0.7748 (ptpt) cc_final: 0.7478 (ptpt)
REVERT: E  671 MET cc_start: 0.8365 (mtt) cc_final: 0.8146 (mtm)
REVERT: E  701 GLN cc_start: 0.7649 (tt0) cc_final: 0.7391 (tt0)
REVERT: E  825 LEU cc_start: 0.7950 (OUTLIER) cc_final: 0.7703 (mt)
REVERT: E  882 ARG cc_start: 0.6905 (ttm110) cc_final: 0.6456 (ttp80)
REVERT: E  892 TRP cc_start: 0.7909 (m100) cc_final: 0.7611 (m100)
REVERT: E  898 CYS cc_start: 0.7231 (t) cc_final: 0.6912 (t)
REVERT: E  987 ARG cc_start: 0.8502 (mtp85) cc_final: 0.8282 (ttp80)
REVERT: E 1043 MET cc_start: 0.1560 (OUTLIER) cc_final: 0.0628 (pmm)
REVERT: E 1151 ASP cc_start: 0.5250 (t0) cc_final: 0.4852 (t0)
REVERT: E 1227 TYR cc_start: 0.6588 (m-10) cc_final: 0.6125 (m-10)
  outliers start: 25
  outliers final: 15
  residues processed: 220
  average time/residue: 0.1106
  time to fit residues: 35.2197
Evaluate side-chains
  223 residues out of total 1219 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 204
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  173 ILE
Chi-restraints excluded: chain A residue  260 LEU
Chi-restraints excluded: chain A residue  288 MET
Chi-restraints excluded: chain A residue  289 ILE
Chi-restraints excluded: chain A residue  340 LEU
Chi-restraints excluded: chain B residue  299 LEU
Chi-restraints excluded: chain B residue  346 GLN
Chi-restraints excluded: chain E residue  234 LEU
Chi-restraints excluded: chain E residue  263 MET
Chi-restraints excluded: chain E residue  286 MET
Chi-restraints excluded: chain E residue  638 THR
Chi-restraints excluded: chain E residue  762 LEU
Chi-restraints excluded: chain E residue  815 HIS
Chi-restraints excluded: chain E residue  825 LEU
Chi-restraints excluded: chain E residue  849 THR
Chi-restraints excluded: chain E residue 1043 MET
Chi-restraints excluded: chain E residue 1071 VAL
Chi-restraints excluded: chain E residue 1150 HIS
Chi-restraints excluded: chain E residue 1208 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 143
   random chunks:
   chunk 74 optimal weight:    1.9990
   chunk 70 optimal weight:    2.9990
   chunk 55 optimal weight:    0.7980
   chunk 110 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0370
   chunk 69 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 130 optimal weight:    1.9990
   overall best weight:    0.6858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 279 ASN
B 251 HIS
** B 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 815 HIS
** E 844 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E1009 GLN
E1117 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.186407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.150249 restraints weight = 19269.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3929 r_free = 0.3929 target = 0.155140 restraints weight = 10120.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.158368 restraints weight = 6203.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3995 r_free = 0.3995 target = 0.160489 restraints weight = 4359.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.162032 restraints weight = 3405.142|
|-----------------------------------------------------------------------------|
r_work (final): 0.4014
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6587
moved from start:          0.2384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  12501  Z= 0.143
  Angle     :  0.656  10.048  17314  Z= 0.336
  Chirality :  0.043   0.370   1992
  Planarity :  0.005   0.055   1962
  Dihedral  : 20.670 177.175   2306
  Min Nonbonded Distance : 1.952

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.58 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  1.92 %
    Allowed  : 18.41 %
    Favored  : 79.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.23), residues: 1369
  helix:  1.48 (0.19), residues: 707
  sheet: -1.49 (0.46), residues: 101
  loop : -1.08 (0.26), residues: 561

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG E 803 
 TYR   0.011   0.001   TYR E1140 
 PHE   0.034   0.002   PHE E 465 
 TRP   0.015   0.001   TRP E 885 
 HIS   0.013   0.001   HIS E 815 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00295 /  0.14 (12501)
  covalent geometry    : angle       0.65587 /  0.34 (17314)
  hydrogen bonds       : bond        0.03874 /  2.66 (  590)
  hydrogen bonds       : angle       4.32424 /  3.05 ( 1686)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2017.14 seconds
wall clock time: 35 minutes 28.21 seconds (2128.21 seconds total)