Starting phenix.real_space_refine
on Sat Aug 23 22:33:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8spr_40682/08_2025/8spr_40682.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8spr_40682/08_2025/8spr_40682.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8spr_40682/08_2025/8spr_40682.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8spr_40682/08_2025/8spr_40682.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8spr_40682/08_2025/8spr_40682.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8spr_40682/08_2025/8spr_40682.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.004 sd=   0.064
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: 4
    Type Number    sf(0)   Gaussians
     S      40      5.16       5
     C    9458      2.51       5
     N    2575      2.21       5
     O    2959      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 69 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15032
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 6226
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 787, 6226
          Classifications: {'peptide': 787}
          Link IDs: {'CIS': 1, 'PTRANS': 29, 'TRANS': 756}
    Chain: "B"
      Number of atoms: 2795
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 371, 2795
          Classifications: {'peptide': 371}
          Link IDs: {'CIS': 2, 'PTRANS': 11, 'TRANS': 357}
    Chain: "C"
      Number of atoms: 1231
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 161, 1231
          Classifications: {'peptide': 161}
          Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 149}
    Chain: "D"
      Number of atoms: 1761
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 218, 1761
          Classifications: {'peptide': 218}
          Link IDs: {'PTRANS': 12, 'TRANS': 205}
    Chain: "E"
      Number of atoms: 721
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 93, 721
          Classifications: {'peptide': 93}
          Link IDs: {'PTRANS': 5, 'TRANS': 87}
    Chain: "F"
      Number of atoms: 2298
      Number of conformers: 2
      Conformer: "A"
        Number of residues, atoms: 302, 2286
          Classifications: {'peptide': 302}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 299}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 19
      Conformer: "B"
        Number of residues, atoms: 302, 2286
          Classifications: {'peptide': 302}
          Incomplete info: {'backbone_only': 3, 'truncation_to_alanine': 5}
          Link IDs: {'PTRANS': 2, 'TRANS': 299}
          Unresolved non-hydrogen bonds: 47
          Unresolved non-hydrogen angles: 55
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 3
          Planarities with less than four sites: {'GLU:plan': 2, 'GLN:plan1': 2, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 19
          bond proxies already assigned to first conformer: 2322
  Residues with excluded nonbonded symmetry interactions: 1
    residue:
      pdb=" N  ATYR F1150 " occ=0.50
      ... (22 atoms not shown)
      pdb=" OH BTYR F1150 " occ=0.50
  Time building chain proxies: 4.29, per 1000 atoms: 0.29
  Number of scatterers: 15032
  At special positions: 0
  Unit cell: (138.24, 140.4, 137.16, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      40     16.00
     O    2959      8.00
     N    2575      7.00
     C    9458      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 806 " - pdb=" SG  CYS F1041 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.32
  Conformation dependent library (CDL) restraints added in 795.7 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3508

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 26 sheets defined
      20.5% alpha, 16.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.67
  Creating SS restraints...
    Processing helix  chain 'A' and resid 38 through 45
    Processing helix  chain 'A' and resid 55 through 70
    Processing helix  chain 'A' and resid 106 through 116
    Processing helix  chain 'A' and resid 126 through 128
      No H-bonds generated for 'chain 'A' and resid 126 through 128'
    Processing helix  chain 'A' and resid 129 through 144
    Processing helix  chain 'A' and resid 189 through 197
      removed outlier: 3.666A  pdb=" N   LEU A 193 " --> pdb=" O   THR A 189 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 215 through 232
    Processing helix  chain 'A' and resid 280 through 286
    Processing helix  chain 'A' and resid 297 through 313
    Processing helix  chain 'A' and resid 361 through 367
      removed outlier: 4.023A  pdb=" N   LEU A 365 " --> pdb=" O   LYS A 361 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 393
      removed outlier: 4.300A  pdb=" N   GLY A 393 " --> pdb=" O   LEU A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 3.563A  pdb=" N   GLY A 451 " --> pdb=" O   ASN A 448 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   THR A 452 " --> pdb=" O   TRP A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 448 through 452'
    Processing helix  chain 'A' and resid 543 through 552
    Processing helix  chain 'A' and resid 647 through 651
    Processing helix  chain 'A' and resid 726 through 731
    Processing helix  chain 'B' and resid 22 through 27
      removed outlier: 3.989A  pdb=" N   GLU B  26 " --> pdb=" O   PHE B  23 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLU B  27 " --> pdb=" O   ASN B  24 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 59 through 63
      removed outlier: 3.955A  pdb=" N   SER C  62 " --> pdb=" O   PRO C  59 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 76 through 80
    Processing helix  chain 'C' and resid 115 through 127
      removed outlier: 3.862A  pdb=" N   GLN C 119 " --> pdb=" O   THR C 115 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 31 through 45
    Processing helix  chain 'D' and resid 47 through 61
    Processing helix  chain 'D' and resid 67 through 82
    Processing helix  chain 'D' and resid 84 through 99
      removed outlier: 4.012A  pdb=" N   ALA D  88 " --> pdb=" O   ASP D  84 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 104 through 121
      removed outlier: 4.002A  pdb=" N   VAL D 108 " --> pdb=" O   ASN D 104 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ASP D 121 " --> pdb=" O   MET D 117 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 123 through 129
    Processing helix  chain 'D' and resid 138 through 154
    Processing helix  chain 'D' and resid 160 through 189
    Processing helix  chain 'D' and resid 190 through 202
      removed outlier: 3.599A  pdb=" N   VAL D 194 " --> pdb=" O   ALA D 190 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 208 through 224
      removed outlier: 4.164A  pdb=" N   ARG D 212 " --> pdb=" O   THR D 208 " (cutoff:3.500A)
      Proline residue:  D 216  - end of helix
    Processing helix  chain 'D' and resid 227 through 241
      removed outlier: 3.559A  pdb=" N   ALA D 231 " --> pdb=" O   MET D 227 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   ASN D 241 " --> pdb=" O   ILE D 237 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 51 through 60
    Processing helix  chain 'F' and resid 1002 through 1021
    Processing helix  chain 'F' and resid 1111 through 1115
    Processing sheet with id=AA1, first strand: chain 'A' and resid 77 through 80
    Processing sheet with id=AA2, first strand: chain 'A' and resid 94 through 99
      removed outlier: 4.372A  pdb=" N   ILE A  94 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 6.754A  pdb=" N   LEU A 165 " --> pdb=" O   ILE A  94 " (cutoff:3.500A)
      removed outlier: 6.012A  pdb=" N   SER A  96 " --> pdb=" O   LEU A 165 " (cutoff:3.500A)
      removed outlier: 7.799A  pdb=" N   LEU A 167 " --> pdb=" O   SER A  96 " (cutoff:3.500A)
      removed outlier: 7.087A  pdb=" N   THR A  98 " --> pdb=" O   LEU A 167 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 149 through 150
    Processing sheet with id=AA4, first strand: chain 'A' and resid 176 through 180
      removed outlier: 7.688A  pdb=" N   VAL A 256 " --> pdb=" O   GLN A 178 " (cutoff:3.500A)
      removed outlier: 4.429A  pdb=" N   ILE A 180 " --> pdb=" O   VAL A 256 " (cutoff:3.500A)
      removed outlier: 7.053A  pdb=" N   VAL A 258 " --> pdb=" O   ILE A 180 " (cutoff:3.500A)
      removed outlier: 6.525A  pdb=" N   GLY A 253 " --> pdb=" O   LEU A 247 " (cutoff:3.500A)
      removed outlier: 4.621A  pdb=" N   LEU A 247 " --> pdb=" O   GLY A 253 " (cutoff:3.500A)
      removed outlier: 6.156A  pdb=" N   TYR A 255 " --> pdb=" O   VAL A 245 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL A 245 " --> pdb=" O   TYR A 255 " (cutoff:3.500A)
      removed outlier: 7.001A  pdb=" N   THR A 257 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
      removed outlier: 4.918A  pdb=" N   THR A 243 " --> pdb=" O   THR A 257 " (cutoff:3.500A)
      removed outlier: 6.940A  pdb=" N   ASN A 259 " --> pdb=" O   ASP A 241 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   THR A 261 " --> pdb=" O   ASN A 239 " (cutoff:3.500A)
      removed outlier: 3.917A  pdb=" N   ASN A 239 " --> pdb=" O   THR A 261 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 267 through 275
      removed outlier: 6.396A  pdb=" N   LYS A 267 " --> pdb=" O   VAL A 335 " (cutoff:3.500A)
      removed outlier: 8.147A  pdb=" N   LEU A 337 " --> pdb=" O   LYS A 267 " (cutoff:3.500A)
      removed outlier: 8.472A  pdb=" N   SER A 269 " --> pdb=" O   LEU A 337 " (cutoff:3.500A)
      removed outlier: 12.833A  pdb=" N   VAL A 339 " --> pdb=" O   SER A 269 " (cutoff:3.500A)
      removed outlier: 10.088A  pdb=" N   VAL A 271 " --> pdb=" O   VAL A 339 " (cutoff:3.500A)
      removed outlier: 12.679A  pdb=" N   VAL A 341 " --> pdb=" O   VAL A 271 " (cutoff:3.500A)
      removed outlier: 10.481A  pdb=" N   VAL A 273 " --> pdb=" O   VAL A 341 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ARG A 338 " --> pdb=" O   MET A 325 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 353 through 355
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 353 through 355
    current: chain 'A' and resid 412 through 420
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 442 through 445
      removed outlier: 3.724A  pdb=" N   GLY A 457 " --> pdb=" O   SER A 472 " (cutoff:3.500A)
      removed outlier: 3.910A  pdb=" N   LEU A 489 " --> pdb=" O   LEU A 471 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   VAL A 473 " --> pdb=" O   GLY A 487 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   ARG A 488 " --> pdb=" O   ASP A 512 " (cutoff:3.500A)
      removed outlier: 3.901A  pdb=" N   ASP A 512 " --> pdb=" O   ARG A 488 " (cutoff:3.500A)
      removed outlier: 3.653A  pdb=" N   TYR A 531 " --> pdb=" O   THR A 511 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 530 through 531
    current: chain 'A' and resid 564 through 567
    Processing sheet with id=AA8, first strand: chain 'A' and resid 523 through 524
      removed outlier: 3.923A  pdb=" N   SER A 524 " --> pdb=" O   THR A 577 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   LYS A 580 " --> pdb=" O   SER A 591 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   GLY A 590 " --> pdb=" O   TYR A 618 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   TYR A 618 " --> pdb=" O   GLY A 590 " (cutoff:3.500A)
      removed outlier: 4.112A  pdb=" N   ARG A 592 " --> pdb=" O   ALA A 616 " (cutoff:3.500A)
      removed outlier: 4.129A  pdb=" N   ASN A 594 " --> pdb=" O   ASP A 614 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   ASP A 614 " --> pdb=" O   ASN A 594 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   THR A 596 " --> pdb=" O   THR A 612 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 628 through 629
    current: chain 'A' and resid 714 through 720
      removed outlier: 3.690A  pdb=" N   THR A 735 " --> pdb=" O   THR A 720 " (cutoff:3.500A)
      removed outlier: 3.947A  pdb=" N   GLY A 771 " --> pdb=" O   PHE A 738 " (cutoff:3.500A)
      removed outlier: 3.820A  pdb=" N   TRP A 776 " --> pdb=" O   LEU A 783 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 673 through 674
      removed outlier: 3.777A  pdb=" N   CYS A 700 " --> pdb=" O   TYR A 674 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 45 through 46
    Processing sheet with id=AB2, first strand: chain 'B' and resid 66 through 68
      removed outlier: 3.954A  pdb=" N   ALA B  66 " --> pdb=" O   TYR B  73 " (cutoff:3.500A)
      removed outlier: 3.580A  pdb=" N   TYR B  73 " --> pdb=" O   ALA B  66 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   VAL B  81 " --> pdb=" O   SER B  94 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   SER B  94 " --> pdb=" O   VAL B  81 " (cutoff:3.500A)
      removed outlier: 6.706A  pdb=" N   ALA B  83 " --> pdb=" O   ILE B  92 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 123 through 125
      removed outlier: 3.879A  pdb=" N   ILE B 124 " --> pdb=" O   TYR B 132 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   TYR B 132 " --> pdb=" O   ILE B 124 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   VAL B 131 " --> pdb=" O   THR B 145 " (cutoff:3.500A)
      removed outlier: 3.730A  pdb=" N   THR B 145 " --> pdb=" O   VAL B 131 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB3
    Processing sheet with id=AB4, first strand: chain 'B' and resid 156 through 158
    Processing sheet with id=AB5, first strand: chain 'B' and resid 200 through 203
      removed outlier: 3.673A  pdb=" N   VAL B 209 " --> pdb=" O   SER B 217 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'B' and resid 252 through 253
      removed outlier: 4.294A  pdb=" N   LEU B 267 " --> pdb=" O   ARG B 281 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   ALA B 269 " --> pdb=" O   TRP B 279 " (cutoff:3.500A)
      removed outlier: 4.148A  pdb=" N   TRP B 279 " --> pdb=" O   ALA B 269 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 290 through 292
      removed outlier: 3.606A  pdb=" N   TYR B 297 " --> pdb=" O   ILE B 290 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ASP B 292 " --> pdb=" O   ARG B 295 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   LEU B 308 " --> pdb=" O   ILE B 296 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   LEU B 298 " --> pdb=" O   MET B 306 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   MET B 306 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   VAL B 314 " --> pdb=" O   THR B 309 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 331 through 333
    Processing sheet with id=AB9, first strand: chain 'B' and resid 372 through 374
      removed outlier: 3.914A  pdb=" N   LEU B 379 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'C' and resid 95 through 96
      removed outlier: 4.098A  pdb=" N   LEU C 107 " --> pdb=" O   ARG C  96 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'C' and resid 133 through 134
      removed outlier: 3.639A  pdb=" N   GLN C 133 " --> pdb=" O   THR C 142 " (cutoff:3.500A)
      removed outlier: 3.586A  pdb=" N   THR C 142 " --> pdb=" O   GLN C 133 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AC2
    Processing sheet with id=AC3, first strand: chain 'C' and resid 145 through 148
      removed outlier: 3.703A  pdb=" N   TYR C 157 " --> pdb=" O   TRP C 148 " (cutoff:3.500A)
    Processing sheet with id=AC4, first strand: chain 'C' and resid 182 through 183
    Processing sheet with id=AC5, first strand: chain 'E' and resid 32 through 34
      removed outlier: 3.587A  pdb=" N   ARG E  78 " --> pdb=" O   GLN E  34 " (cutoff:3.500A)
      removed outlier: 3.584A  pdb=" N   ASN E 103 " --> pdb=" O   THR E  94 " (cutoff:3.500A)
    Processing sheet with id=AC6, first strand: chain 'F' and resid 1044 through 1046
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1044 through 1046
    current: chain 'F' and resid 1208 through 1213
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1221 through 1223
    current: chain 'F' and resid 1259 through 1261
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1259 through 1261
    current: chain 'F' and resid 1288 through 1295
    Processing sheet with id=AC7, first strand: chain 'F' and resid 1062 through 1065
      removed outlier: 3.809A  pdb=" N   VAL F1063 " --> pdb=" O   HIS F1086 " (cutoff:3.500A)
  WARNING: can't find start of bonding for strands!
    previous: chain 'F' and resid 1084 through 1087
    current: chain 'F' and resid 1097 through 1105
      removed outlier: 4.301A  pdb=" N   LYS F1101 " --> pdb=" O   ASP F1129 " (cutoff:3.500A)
      removed outlier: 3.823A  pdb=" N   ASP F1129 " --> pdb=" O   LYS F1101 " (cutoff:3.500A)
      removed outlier: 4.069A  pdb=" N   VAL F1103 " --> pdb=" O   HIS F1127 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   HIS F1127 " --> pdb=" O   VAL F1103 " (cutoff:3.500A)
    Processing sheet with id=AC8, first strand: chain 'F' and resid 1182 through 1185

    403 hydrogen bonds defined for protein.
    1080 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 2.79

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 5042
        1.34 -     1.46: 3743
        1.46 -     1.59: 6499
        1.59 -     1.71: 0
        1.71 -     1.84: 76
  Bond restraints: 15360
  Sorted by residual:
  bond pdb=" CA  ILE B 380 "
       pdb=" CB  ILE B 380 "
    ideal  model  delta    sigma   weight residual
    1.553  1.533  0.020 7.40e-03 1.83e+04 7.19e+00
  bond pdb=" CB  PHE A 347 "
       pdb=" CG  PHE A 347 "
    ideal  model  delta    sigma   weight residual
    1.502  1.444  0.058 2.30e-02 1.89e+03 6.42e+00
  bond pdb=" C   PRO D 206 "
       pdb=" N   ASP D 207 "
    ideal  model  delta    sigma   weight residual
    1.332  1.298  0.035 1.40e-02 5.10e+03 6.18e+00
  bond pdb=" CA  SER C  62 "
       pdb=" C   SER C  62 "
    ideal  model  delta    sigma   weight residual
    1.524  1.476  0.048 2.25e-02 1.98e+03 4.49e+00
  bond pdb=" CA  THR A 747 "
       pdb=" C   THR A 747 "
    ideal  model  delta    sigma   weight residual
    1.522  1.487  0.035 1.72e-02 3.38e+03 4.12e+00
  ... (remaining 15355 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.01: 20049
        2.01 -     4.01: 700
        4.01 -     6.02: 96
        6.02 -     8.02: 17
        8.02 -    10.03: 4
  Bond angle restraints: 20866
  Sorted by residual:
  angle pdb=" C   PRO A 159 "
        pdb=" N   ARG A 160 "
        pdb=" CA  ARG A 160 "
      ideal   model   delta    sigma   weight residual
     121.54  129.63   -8.09 1.91e+00 2.74e-01 1.79e+01
  angle pdb=" N   HIS D 102 "
        pdb=" CA  HIS D 102 "
        pdb=" C   HIS D 102 "
      ideal   model   delta    sigma   weight residual
     108.13  111.71   -3.58 9.00e-01 1.23e+00 1.58e+01
  angle pdb=" C   THR C  61 "
        pdb=" N   SER C  62 "
        pdb=" CA  SER C  62 "
      ideal   model   delta    sigma   weight residual
     122.55  114.86    7.69 2.03e+00 2.43e-01 1.43e+01
  angle pdb=" C   TYR D 185 "
        pdb=" N   THR D 186 "
        pdb=" CA  THR D 186 "
      ideal   model   delta    sigma   weight residual
     120.72  114.54    6.18 1.67e+00 3.59e-01 1.37e+01
  angle pdb=" N   ALA A 730 "
        pdb=" CA  ALA A 730 "
        pdb=" C   ALA A 730 "
      ideal   model   delta    sigma   weight residual
     113.19  108.84    4.35 1.19e+00 7.06e-01 1.33e+01
  ... (remaining 20861 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 7983
       17.91 -    35.83: 867
       35.83 -    53.74: 131
       53.74 -    71.66: 27
       71.66 -    89.57: 17
  Dihedral angle restraints: 9025
    sinusoidal: 3491
      harmonic: 5534
  Sorted by residual:
  dihedral pdb=" CB  CYS A 806 "
           pdb=" SG  CYS A 806 "
           pdb=" SG  CYS F1041 "
           pdb=" CB  CYS F1041 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.03   68.03     1      1.00e+01 1.00e-02 6.01e+01
  dihedral pdb=" CA  ARG A  91 "
           pdb=" C   ARG A  91 "
           pdb=" N   PRO A  92 "
           pdb=" CA  PRO A  92 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  141.65   38.35     0      5.00e+00 4.00e-02 5.88e+01
  dihedral pdb=" CA  THR A 434 "
           pdb=" C   THR A 434 "
           pdb=" N   GLU A 435 "
           pdb=" CA  GLU A 435 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  143.20   36.80     0      5.00e+00 4.00e-02 5.42e+01
  ... (remaining 9022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.037: 1322
       0.037 -    0.073: 612
       0.073 -    0.110: 244
       0.110 -    0.146: 68
       0.146 -    0.183: 15
  Chirality restraints: 2261
  Sorted by residual:
  chirality pdb=" CA  VAL A 593 "
            pdb=" N   VAL A 593 "
            pdb=" C   VAL A 593 "
            pdb=" CB  VAL A 593 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.34e-01
  chirality pdb=" CA  VAL A 744 "
            pdb=" N   VAL A 744 "
            pdb=" C   VAL A 744 "
            pdb=" CB  VAL A 744 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.62   -0.18 2.00e-01 2.50e+01 8.20e-01
  chirality pdb=" CA  ILE F1045 "
            pdb=" N   ILE F1045 "
            pdb=" C   ILE F1045 "
            pdb=" CB  ILE F1045 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.60   -0.17 2.00e-01 2.50e+01 7.27e-01
  ... (remaining 2258 not shown)

  Planarity restraints: 2753
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG A  91 "    0.058 5.00e-02 4.00e+02   8.87e-02 1.26e+01
        pdb=" N   PRO A  92 "   -0.153 5.00e-02 4.00e+02
        pdb=" CA  PRO A  92 "    0.046 5.00e-02 4.00e+02
        pdb=" CD  PRO A  92 "    0.049 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU F1168 "   -0.043 5.00e-02 4.00e+02   6.58e-02 6.92e+00
        pdb=" N   PRO F1169 "    0.114 5.00e-02 4.00e+02
        pdb=" CA  PRO F1169 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO F1169 "   -0.036 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN A 789 "    0.038 5.00e-02 4.00e+02   5.79e-02 5.37e+00
        pdb=" N   PRO A 790 "   -0.100 5.00e-02 4.00e+02
        pdb=" CA  PRO A 790 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO A 790 "    0.032 5.00e-02 4.00e+02
  ... (remaining 2750 not shown)

  Histogram of nonbonded interaction distances:
        2.03 -     2.61: 328
        2.61 -     3.18: 14620
        3.18 -     3.75: 22171
        3.75 -     4.33: 30110
        4.33 -     4.90: 48518
  Nonbonded interactions: 115747
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 521 "
            pdb=" OH  TYR E  28 "
     model   vdw
     2.032 3.040
  nonbonded pdb=" O   ASN E  33 "
            pdb=" NE2 GLN E  34 "
     model   vdw
     2.105 3.120
  nonbonded pdb=" OG  SER F1051 "
            pdb=" O   ASN F1287 "
     model   vdw
     2.125 3.040
  nonbonded pdb=" O   VAL F1095 "
            pdb=" OG1 THR F1135 "
     model   vdw
     2.134 3.040
  nonbonded pdb=" OH  TYR A 674 "
            pdb=" OD2 ASP A 704 "
     model   vdw
     2.145 3.040
  ... (remaining 115742 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
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 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:             1.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     16.120
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.200
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8108
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      :  0.007   0.062  15361  Z= 0.347
  Angle     :  0.876  10.030  20868  Z= 0.493
  Chirality :  0.050   0.183   2261
  Planarity :  0.005   0.089   2753
  Dihedral  : 15.123  89.569   5514
  Min Nonbonded Distance : 2.032

Molprobity Statistics.
  All-atom Clashscore : 21.51
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  : 17.60 %
    Favored  : 82.19 %
  Rotamer:
    Outliers :  0.32 %
    Allowed  : 10.53 %
    Favored  : 89.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.16 %

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 aren not related in a simple way.
  whole: -5.91 (0.14), residues: 1923
  helix: -2.12 (0.22), residues: 364
  sheet: -4.02 (0.17), residues: 565
  loop : -4.68 (0.13), residues: 994

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG E  78 
 TYR   0.035   0.002   TYR A 432 
 PHE   0.026   0.002   PHE B 289 
 TRP   0.018   0.002   TRP A 449 
 HIS   0.007   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00745 (15360)
  covalent geometry    : angle       0.87515 (20866)
  SS BOND              : bond        0.00033 (    1)
  SS BOND              : angle       4.39441 (    2)
  hydrogen bonds       : bond        0.21329 (  403)
  hydrogen bonds       : angle       8.58147 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  214 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 209
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 TYR cc_start: 0.7448 (m-10) cc_final: 0.7215 (m-10)
REVERT: A  545 MET cc_start: 0.8532 (mtt) cc_final: 0.8031 (mtt)
REVERT: A  677 HIS cc_start: 0.6398 (t-170) cc_final: 0.5945 (t70)
REVERT: A  768 MET cc_start: 0.8504 (mtm) cc_final: 0.8292 (mtp)
REVERT: B  278 MET cc_start: 0.7788 (mmt) cc_final: 0.7474 (mmt)
REVERT: B  306 MET cc_start: 0.8158 (ppp) cc_final: 0.7334 (ppp)
REVERT: C   56 MET cc_start: 0.8076 (mpp) cc_final: 0.7627 (mpp)
REVERT: C   81 ASP cc_start: 0.8571 (p0) cc_final: 0.8319 (p0)
REVERT: D  205 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.8538 (m-80)
REVERT: E   53 GLN cc_start: 0.8663 (tp40) cc_final: 0.8399 (tp40)
REVERT: F 1124 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8715 (ttmm)
REVERT: F 1127 HIS cc_start: 0.8773 (p90) cc_final: 0.8268 (p90)
REVERT: F 1166 TRP cc_start: 0.8752 (m-10) cc_final: 0.8465 (m100)
REVERT: F 1230 GLN cc_start: 0.8616 (tt0) cc_final: 0.8362 (tt0)
REVERT: F 1256 SER cc_start: 0.7853 (p) cc_final: 0.7427 (p)
  outliers start: 5
  outliers final: 1
  residues processed: 212
  average time/residue: 0.1399
  time to fit residues: 43.9124
Evaluate side-chains
  167 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 165
  time to evaluate  : 0.604 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain D residue  205 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 98 optimal weight:    6.9990
   chunk 107 optimal weight:    8.9990
   chunk 10 optimal weight:   30.0000
   chunk 66 optimal weight:    0.0370
   chunk 130 optimal weight:   30.0000
   chunk 124 optimal weight:    8.9990
   chunk 103 optimal weight:    4.9990
   chunk 77 optimal weight:    1.9990
   chunk 122 optimal weight:    3.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    0.8980
   overall best weight:    1.9864

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 287 ASN
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  87 GLN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  72 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4152 r_free = 0.4152 target = 0.153106 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.115901 restraints weight = 31348.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.112244 restraints weight = 22347.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.113713 restraints weight = 20738.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.114354 restraints weight = 15294.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.114473 restraints weight = 14414.688|
|-----------------------------------------------------------------------------|
r_work (final): 0.3588
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.112         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7885
moved from start:          0.1432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  15361  Z= 0.186
  Angle     :  0.734  10.079  20868  Z= 0.389
  Chirality :  0.047   0.167   2261
  Planarity :  0.005   0.089   2753
  Dihedral  :  6.445  36.532   2122
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 13.36
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 12.86 %
    Favored  : 86.98 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.26 %
    Favored  : 82.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -4.84 (0.16), residues: 1923
  helix: -0.53 (0.25), residues: 367
  sheet: -3.49 (0.19), residues: 562
  loop : -4.22 (0.15), residues: 994

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG F1205 
 TYR   0.037   0.002   TYR A 432 
 PHE   0.031   0.002   PHE F1082 
 TRP   0.021   0.001   TRP A 546 
 HIS   0.004   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00407 (15360)
  covalent geometry    : angle       0.73198 (20866)
  SS BOND              : bond        0.00083 (    1)
  SS BOND              : angle       6.20793 (    2)
  hydrogen bonds       : bond        0.05338 (  403)
  hydrogen bonds       : angle       6.26341 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 193
  time to evaluate  : 0.619 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 TYR cc_start: 0.7362 (m-10) cc_final: 0.7105 (m-10)
REVERT: A  545 MET cc_start: 0.8225 (mtt) cc_final: 0.7843 (mtt)
REVERT: A  677 HIS cc_start: 0.6488 (t-170) cc_final: 0.6105 (t70)
REVERT: B  174 LEU cc_start: 0.9239 (mm) cc_final: 0.9024 (mp)
REVERT: B  221 MET cc_start: 0.7626 (ttm) cc_final: 0.7366 (mtp)
REVERT: B  263 TYR cc_start: 0.5769 (t80) cc_final: 0.5128 (t80)
REVERT: C   49 GLU cc_start: 0.8489 (tm-30) cc_final: 0.8284 (tm-30)
REVERT: C   56 MET cc_start: 0.7902 (mpp) cc_final: 0.7545 (mpp)
REVERT: C   81 ASP cc_start: 0.8442 (p0) cc_final: 0.8239 (p0)
REVERT: C   83 ARG cc_start: 0.7554 (ptt-90) cc_final: 0.7155 (ttp-110)
REVERT: D   56 GLU cc_start: 0.8590 (tp30) cc_final: 0.8187 (tp30)
REVERT: E   53 GLN cc_start: 0.8547 (tp40) cc_final: 0.8232 (tp40)
REVERT: F 1034 ASP cc_start: 0.7400 (t0) cc_final: 0.7137 (t0)
REVERT: F 1046 MET cc_start: 0.7719 (OUTLIER) cc_final: 0.7288 (ttp)
REVERT: F 1112 MET cc_start: 0.7675 (ptp) cc_final: 0.7373 (ptp)
REVERT: F 1212 LYS cc_start: 0.7182 (mttm) cc_final: 0.6914 (ptmm)
  outliers start: 32
  outliers final: 17
  residues processed: 214
  average time/residue: 0.1208
  time to fit residues: 39.2403
Evaluate side-chains
  191 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 173
  time to evaluate  : 0.609 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain C residue   42 LEU
Chi-restraints excluded: chain D residue   49 ARG
Chi-restraints excluded: chain D residue   72 GLN
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1046 MET
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 143 optimal weight:    0.8980
   chunk 162 optimal weight:   10.0000
   chunk 165 optimal weight:   10.0000
   chunk 18 optimal weight:    0.7980
   chunk 154 optimal weight:    0.4980
   chunk 101 optimal weight:    7.9990
   chunk 148 optimal weight:    0.9980
   chunk 107 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 93 optimal weight:    9.9990
   chunk 135 optimal weight:    1.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 347 HIS
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 139 GLN
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  54 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.157607 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.118183 restraints weight = 30519.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.116031 restraints weight = 19270.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.116926 restraints weight = 18538.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.117251 restraints weight = 14986.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.117736 restraints weight = 12680.580|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3624
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3624 r_free = 0.3624    target_work(ls_wunit_k1) = 0.115         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3624
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15361  Z= 0.125
  Angle     :  0.660   9.275  20868  Z= 0.347
  Chirality :  0.045   0.165   2261
  Planarity :  0.004   0.084   2753
  Dihedral  :  5.827  36.644   2122
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.68 %
    Favored  : 89.22 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 18.03 %
    Favored  : 79.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -4.07 (0.17), residues: 1923
  helix:  0.40 (0.27), residues: 366
  sheet: -3.12 (0.20), residues: 536
  loop : -3.79 (0.15), residues: 1021

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 233 
 TYR   0.037   0.001   TYR A 432 
 PHE   0.013   0.001   PHE C  99 
 TRP   0.019   0.001   TRP A 546 
 HIS   0.006   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 (15360)
  covalent geometry    : angle       0.65957 (20866)
  SS BOND              : bond        0.00245 (    1)
  SS BOND              : angle       3.59022 (    2)
  hydrogen bonds       : bond        0.04449 (  403)
  hydrogen bonds       : angle       5.58425 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  238 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 194
  time to evaluate  : 0.620 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 TYR cc_start: 0.7368 (m-10) cc_final: 0.7093 (m-10)
REVERT: A  539 MET cc_start: 0.7754 (ptt) cc_final: 0.7189 (ptt)
REVERT: A  677 HIS cc_start: 0.6286 (t-170) cc_final: 0.5999 (t70)
REVERT: A  769 SER cc_start: 0.9394 (t) cc_final: 0.8864 (m)
REVERT: B  263 TYR cc_start: 0.5686 (t80) cc_final: 0.5257 (t80)
REVERT: B  278 MET cc_start: 0.8753 (mtp) cc_final: 0.8399 (mtm)
REVERT: B  306 MET cc_start: 0.8420 (ppp) cc_final: 0.7960 (ppp)
REVERT: C   49 GLU cc_start: 0.8411 (tm-30) cc_final: 0.8098 (tm-30)
REVERT: C   56 MET cc_start: 0.8037 (mpp) cc_final: 0.7662 (mpp)
REVERT: C   83 ARG cc_start: 0.7554 (ptt-90) cc_final: 0.7151 (ttp-110)
REVERT: D   53 THR cc_start: 0.8684 (m) cc_final: 0.8218 (p)
REVERT: E   53 GLN cc_start: 0.8600 (tp40) cc_final: 0.8345 (tp40)
REVERT: F 1034 ASP cc_start: 0.7298 (t0) cc_final: 0.7038 (t0)
REVERT: F 1046 MET cc_start: 0.7480 (OUTLIER) cc_final: 0.7205 (ttp)
REVERT: F 1112 MET cc_start: 0.7712 (ptp) cc_final: 0.7447 (ptp)
REVERT: F 1168 GLU cc_start: 0.8416 (pp20) cc_final: 0.8164 (tm-30)
REVERT: F 1212 LYS cc_start: 0.7075 (mttm) cc_final: 0.6850 (ptmm)
  outliers start: 44
  outliers final: 28
  residues processed: 222
  average time/residue: 0.1113
  time to fit residues: 38.5427
Evaluate side-chains
  206 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 177
  time to evaluate  : 0.582 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  347 HIS
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1046 MET
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 107 optimal weight:    0.3980
   chunk 75 optimal weight:    6.9990
   chunk 142 optimal weight:    3.9990
   chunk 123 optimal weight:    0.6980
   chunk 152 optimal weight:    3.9990
   chunk 89 optimal weight:    0.9990
   chunk 40 optimal weight:    1.9990
   chunk 148 optimal weight:    0.9990
   chunk 147 optimal weight:    0.6980
   chunk 112 optimal weight:    9.9990
   chunk 77 optimal weight:    7.9990
   overall best weight:    0.7584

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 677 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 693 GLN
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D  54 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.158957 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3673 r_free = 0.3673 target = 0.119290 restraints weight = 31063.902|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.117354 restraints weight = 18191.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.118778 restraints weight = 18635.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.119109 restraints weight = 13258.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3646 r_free = 0.3646 target = 0.120084 restraints weight = 11697.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3674
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3671
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3671 r_free = 0.3671    target_work(ls_wunit_k1) = 0.118         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3671
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7783
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15361  Z= 0.120
  Angle     :  0.637   9.075  20868  Z= 0.334
  Chirality :  0.044   0.162   2261
  Planarity :  0.004   0.083   2753
  Dihedral  :  5.531  36.765   2120
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  :  9.90 %
    Favored  : 89.95 %
  Rotamer:
    Outliers :  2.77 %
    Allowed  : 19.04 %
    Favored  : 78.18 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -3.63 (0.17), residues: 1923
  helix:  0.71 (0.27), residues: 368
  sheet: -2.76 (0.20), residues: 528
  loop : -3.54 (0.16), residues: 1027

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 233 
 TYR   0.037   0.001   TYR A 432 
 PHE   0.013   0.001   PHE A 648 
 TRP   0.018   0.001   TRP A 546 
 HIS   0.005   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 (15360)
  covalent geometry    : angle       0.63650 (20866)
  SS BOND              : bond        0.00014 (    1)
  SS BOND              : angle       3.56440 (    2)
  hydrogen bonds       : bond        0.04150 (  403)
  hydrogen bonds       : angle       5.25543 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  233 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 189
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  369 MET cc_start: 0.8684 (mmp) cc_final: 0.8137 (mmm)
REVERT: A  449 TRP cc_start: 0.8695 (t60) cc_final: 0.8404 (t-100)
REVERT: A  465 TYR cc_start: 0.7309 (m-10) cc_final: 0.7042 (m-10)
REVERT: A  619 VAL cc_start: 0.9381 (t) cc_final: 0.8951 (m)
REVERT: A  769 SER cc_start: 0.9274 (t) cc_final: 0.8830 (m)
REVERT: B  221 MET cc_start: 0.8074 (mtp) cc_final: 0.7633 (mtp)
REVERT: B  263 TYR cc_start: 0.5596 (t80) cc_final: 0.5299 (t80)
REVERT: B  278 MET cc_start: 0.8763 (mtp) cc_final: 0.8407 (mtm)
REVERT: B  306 MET cc_start: 0.8427 (ppp) cc_final: 0.7941 (ppp)
REVERT: C   56 MET cc_start: 0.7977 (mpp) cc_final: 0.7645 (mpp)
REVERT: C   81 ASP cc_start: 0.8195 (p0) cc_final: 0.7979 (p0)
REVERT: C   83 ARG cc_start: 0.7504 (ptt-90) cc_final: 0.7067 (ttp-110)
REVERT: D   26 GLU cc_start: 0.7195 (tp30) cc_final: 0.6503 (tt0)
REVERT: E   53 GLN cc_start: 0.8466 (tp40) cc_final: 0.8249 (tp40)
REVERT: E  113 ASN cc_start: 0.6946 (m-40) cc_final: 0.6560 (t0)
REVERT: F 1034 ASP cc_start: 0.7287 (t0) cc_final: 0.7060 (t0)
REVERT: F 1112 MET cc_start: 0.7564 (ptp) cc_final: 0.7355 (ptp)
REVERT: F 1212 LYS cc_start: 0.6968 (mttm) cc_final: 0.6726 (ptmm)
  outliers start: 44
  outliers final: 30
  residues processed: 222
  average time/residue: 0.1133
  time to fit residues: 39.4108
Evaluate side-chains
  205 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 175
  time to evaluate  : 0.512 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  109 MET
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 70 optimal weight:    5.9990
   chunk 94 optimal weight:    9.9990
   chunk 58 optimal weight:    5.9990
   chunk 6 optimal weight:    1.9990
   chunk 163 optimal weight:    2.9990
   chunk 2 optimal weight:   10.0000
   chunk 42 optimal weight:    2.9990
   chunk 105 optimal weight:    0.9980
   chunk 52 optimal weight:    0.5980
   chunk 48 optimal weight:    7.9990
   chunk 117 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A  35 GLN
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4160 r_free = 0.4160 target = 0.157830 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.109689 restraints weight = 31758.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.111733 restraints weight = 19873.739|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.111869 restraints weight = 13461.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.112510 restraints weight = 13292.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.112749 restraints weight = 11991.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3545
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3545 r_free = 0.3545    target_work(ls_wunit_k1) = 0.109         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3545
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7924
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15361  Z= 0.151
  Angle     :  0.637   8.954  20868  Z= 0.333
  Chirality :  0.044   0.159   2261
  Planarity :  0.004   0.083   2753
  Dihedral  :  5.487  36.623   2120
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 10.88
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 11.30 %
    Favored  : 88.54 %
  Rotamer:
    Outliers :  3.28 %
    Allowed  : 19.67 %
    Favored  : 77.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -3.42 (0.18), residues: 1923
  helix:  0.81 (0.27), residues: 362
  sheet: -2.55 (0.21), residues: 522
  loop : -3.40 (0.16), residues: 1039

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F1044 
 TYR   0.038   0.002   TYR A 432 
 PHE   0.015   0.001   PHE F1018 
 TRP   0.016   0.001   TRP A 546 
 HIS   0.004   0.001   HIS A 533 

Details of bonding type rmsd
  covalent geometry    : bond        0.00334 (15360)
  covalent geometry    : angle       0.63618 (20866)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       3.56056 (    2)
  hydrogen bonds       : bond        0.04325 (  403)
  hydrogen bonds       : angle       5.20240 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 174
  time to evaluate  : 0.582 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LYS cc_start: 0.8230 (mtpt) cc_final: 0.7968 (mmtm)
REVERT: A  465 TYR cc_start: 0.7205 (m-10) cc_final: 0.6878 (m-10)
REVERT: A  738 PHE cc_start: 0.9078 (p90) cc_final: 0.8872 (p90)
REVERT: A  769 SER cc_start: 0.9455 (t) cc_final: 0.8876 (m)
REVERT: B  263 TYR cc_start: 0.5953 (t80) cc_final: 0.5457 (t80)
REVERT: B  278 MET cc_start: 0.8843 (mtp) cc_final: 0.8393 (mtm)
REVERT: C   56 MET cc_start: 0.8205 (mpp) cc_final: 0.7720 (mpp)
REVERT: C   83 ARG cc_start: 0.7444 (ptt-90) cc_final: 0.7137 (ttp-110)
REVERT: E   53 GLN cc_start: 0.8670 (tp40) cc_final: 0.8399 (tp40)
REVERT: E  113 ASN cc_start: 0.7031 (m-40) cc_final: 0.6726 (t0)
REVERT: F 1034 ASP cc_start: 0.7328 (t0) cc_final: 0.7069 (t0)
REVERT: F 1112 MET cc_start: 0.7868 (ptp) cc_final: 0.7607 (ptp)
REVERT: F 1212 LYS cc_start: 0.7019 (mttm) cc_final: 0.6690 (ptmm)
  outliers start: 52
  outliers final: 41
  residues processed: 215
  average time/residue: 0.1147
  time to fit residues: 38.5399
Evaluate side-chains
  208 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 167
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 46 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 59 optimal weight:    2.9990
   chunk 106 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 83 optimal weight:    9.9990
   chunk 185 optimal weight:    2.9990
   chunk 12 optimal weight:    5.9990
   chunk 89 optimal weight:    9.9990
   chunk 41 optimal weight:    6.9990
   chunk 120 optimal weight:    5.9990
   overall best weight:    2.3990

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

Flipped N/Q/H residues before XYZ refinement:
** A 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 350 ASN
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4149 r_free = 0.4149 target = 0.154656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.117117 restraints weight = 30292.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.114830 restraints weight = 18508.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.115769 restraints weight = 20906.504|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.116164 restraints weight = 14186.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.117070 restraints weight = 12246.346|
|-----------------------------------------------------------------------------|
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3614
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3614 r_free = 0.3614    target_work(ls_wunit_k1) = 0.114         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3614
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7812
moved from start:          0.2642

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  15361  Z= 0.194
  Angle     :  0.676  14.871  20868  Z= 0.351
  Chirality :  0.045   0.163   2261
  Planarity :  0.004   0.082   2753
  Dihedral  :  5.569  35.778   2120
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 11.86
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 12.66 %
    Favored  : 87.19 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 19.92 %
    Favored  : 76.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -3.35 (0.18), residues: 1923
  helix:  0.81 (0.27), residues: 362
  sheet: -2.50 (0.21), residues: 550
  loop : -3.33 (0.17), residues: 1011

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F1044 
 TYR   0.057   0.002   TYR A 432 
 PHE   0.018   0.002   PHE B 289 
 TRP   0.024   0.001   TRP A 546 
 HIS   0.004   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00430 (15360)
  covalent geometry    : angle       0.67474 (20866)
  SS BOND              : bond        0.00431 (    1)
  SS BOND              : angle       4.64533 (    2)
  hydrogen bonds       : bond        0.04503 (  403)
  hydrogen bonds       : angle       5.22791 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 168
  time to evaluate  : 0.610 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  251 LYS cc_start: 0.8182 (mtpt) cc_final: 0.7943 (mmtm)
REVERT: A  465 TYR cc_start: 0.7228 (m-10) cc_final: 0.6934 (m-10)
REVERT: A  545 MET cc_start: 0.8098 (mtm) cc_final: 0.7308 (mtm)
REVERT: B  263 TYR cc_start: 0.6072 (t80) cc_final: 0.5499 (t80)
REVERT: B  278 MET cc_start: 0.8760 (mtp) cc_final: 0.8470 (mtm)
REVERT: C   56 MET cc_start: 0.8221 (mpp) cc_final: 0.7722 (mpp)
REVERT: C   80 LEU cc_start: 0.9060 (tp) cc_final: 0.8691 (tt)
REVERT: C   83 ARG cc_start: 0.7571 (ptt-90) cc_final: 0.7365 (ttp-110)
REVERT: D  205 TYR cc_start: 0.8987 (OUTLIER) cc_final: 0.8778 (m-80)
REVERT: E   53 GLN cc_start: 0.8593 (tp40) cc_final: 0.8342 (tp40)
REVERT: E  113 ASN cc_start: 0.6891 (m-40) cc_final: 0.6689 (t0)
REVERT: F 1034 ASP cc_start: 0.7251 (t0) cc_final: 0.7013 (t0)
REVERT: F 1046 MET cc_start: 0.7689 (ttp) cc_final: 0.7357 (tmm)
REVERT: F 1112 MET cc_start: 0.7631 (ptp) cc_final: 0.7383 (ptp)
REVERT: F 1212 LYS cc_start: 0.7057 (mttm) cc_final: 0.6744 (ptmm)
  outliers start: 54
  outliers final: 45
  residues processed: 212
  average time/residue: 0.1111
  time to fit residues: 37.0050
Evaluate side-chains
  212 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 166
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   46 ILE
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 127 optimal weight:    4.9990
   chunk 82 optimal weight:    5.9990
   chunk 176 optimal weight:    5.9990
   chunk 111 optimal weight:    7.9990
   chunk 154 optimal weight:    0.4980
   chunk 134 optimal weight:    2.9990
   chunk 11 optimal weight:   10.0000
   chunk 103 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 67 optimal weight:    4.9990
   chunk 128 optimal weight:   40.0000
   overall best weight:    2.4586

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.152668 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.115649 restraints weight = 30791.626|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.112657 restraints weight = 22472.071|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.114099 restraints weight = 22845.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.114325 restraints weight = 15415.289|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3583 r_free = 0.3583 target = 0.114568 restraints weight = 13596.041|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3589
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3589 r_free = 0.3589    target_work(ls_wunit_k1) = 0.113         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3589
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7876
moved from start:          0.2742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  15361  Z= 0.194
  Angle     :  0.669  12.071  20868  Z= 0.350
  Chirality :  0.045   0.176   2261
  Planarity :  0.004   0.082   2753
  Dihedral  :  5.602  36.583   2120
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 12.03
  Ramachandran Plot:
    Outliers :  0.16 %
    Allowed  : 12.40 %
    Favored  : 87.45 %
  Rotamer:
    Outliers :  3.53 %
    Allowed  : 20.24 %
    Favored  : 76.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -3.30 (0.18), residues: 1923
  helix:  0.80 (0.27), residues: 363
  sheet: -2.48 (0.21), residues: 566
  loop : -3.28 (0.17), residues: 994

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F1044 
 TYR   0.045   0.002   TYR A 432 
 PHE   0.018   0.002   PHE B 289 
 TRP   0.014   0.001   TRP A 546 
 HIS   0.004   0.001   HIS B  64 

Details of bonding type rmsd
  covalent geometry    : bond        0.00432 (15360)
  covalent geometry    : angle       0.66775 (20866)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       4.41753 (    2)
  hydrogen bonds       : bond        0.04527 (  403)
  hydrogen bonds       : angle       5.19317 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  221 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 165
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  465 TYR cc_start: 0.7199 (m-10) cc_final: 0.6924 (m-10)
REVERT: B  263 TYR cc_start: 0.6152 (t80) cc_final: 0.5704 (t80)
REVERT: B  278 MET cc_start: 0.8737 (mtp) cc_final: 0.8458 (mtm)
REVERT: B  306 MET cc_start: 0.8373 (ppp) cc_final: 0.7669 (ppp)
REVERT: C   56 MET cc_start: 0.8157 (mpp) cc_final: 0.7745 (mpp)
REVERT: C   80 LEU cc_start: 0.8991 (tp) cc_final: 0.8658 (tt)
REVERT: C   83 ARG cc_start: 0.7432 (ptt-90) cc_final: 0.7213 (ptp90)
REVERT: D   79 TYR cc_start: 0.8435 (m-10) cc_final: 0.8033 (m-10)
REVERT: D  205 TYR cc_start: 0.9001 (OUTLIER) cc_final: 0.8801 (m-80)
REVERT: E   53 GLN cc_start: 0.8475 (tp40) cc_final: 0.8263 (tp40)
REVERT: F 1034 ASP cc_start: 0.7208 (t0) cc_final: 0.6961 (t0)
REVERT: F 1046 MET cc_start: 0.7654 (ttp) cc_final: 0.7367 (tmm)
REVERT: F 1112 MET cc_start: 0.7621 (ptp) cc_final: 0.7366 (ptp)
REVERT: F 1212 LYS cc_start: 0.7093 (mttm) cc_final: 0.6779 (ptmm)
REVERT: F 1295 ASN cc_start: 0.8192 (p0) cc_final: 0.7759 (p0)
  outliers start: 56
  outliers final: 48
  residues processed: 212
  average time/residue: 0.1052
  time to fit residues: 35.4295
Evaluate side-chains
  211 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 162
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  611 VAL
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue   89 LEU
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain D residue  205 TYR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 123 optimal weight:    0.0970
   chunk 173 optimal weight:   10.0000
   chunk 88 optimal weight:    1.9990
   chunk 137 optimal weight:    1.9990
   chunk 175 optimal weight:    9.9990
   chunk 26 optimal weight:    2.9990
   chunk 181 optimal weight:   10.0000
   chunk 105 optimal weight:    3.9990
   chunk 70 optimal weight:    1.9990
   chunk 177 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   overall best weight:    1.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4162 r_free = 0.4162 target = 0.154848 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.117841 restraints weight = 31080.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.115039 restraints weight = 22627.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.116436 restraints weight = 22065.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.116642 restraints weight = 15047.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.117942 restraints weight = 13420.449|
|-----------------------------------------------------------------------------|
r_work (final): 0.3616
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3615
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3615 r_free = 0.3615    target_work(ls_wunit_k1) = 0.117         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3615
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7792
moved from start:          0.2959

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.085  15361  Z= 0.140
  Angle     :  0.655  14.389  20868  Z= 0.339
  Chirality :  0.044   0.168   2261
  Planarity :  0.004   0.080   2753
  Dihedral  :  5.445  37.043   2120
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  : 10.73 %
    Favored  : 89.17 %
  Rotamer:
    Outliers :  3.40 %
    Allowed  : 20.87 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -3.08 (0.18), residues: 1923
  helix:  0.90 (0.27), residues: 363
  sheet: -2.29 (0.22), residues: 537
  loop : -3.12 (0.17), residues: 1023

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 325 
 TYR   0.042   0.001   TYR A 432 
 PHE   0.023   0.001   PHE A 738 
 TRP   0.014   0.001   TRP A 449 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (15360)
  covalent geometry    : angle       0.65389 (20866)
  SS BOND              : bond        0.00010 (    1)
  SS BOND              : angle       4.12572 (    2)
  hydrogen bonds       : bond        0.04210 (  403)
  hydrogen bonds       : angle       5.00599 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  231 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 177
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  449 TRP cc_start: 0.8656 (t60) cc_final: 0.8420 (t-100)
REVERT: A  465 TYR cc_start: 0.7248 (m-10) cc_final: 0.6987 (m-10)
REVERT: B  263 TYR cc_start: 0.5994 (t80) cc_final: 0.5543 (t80)
REVERT: B  278 MET cc_start: 0.8757 (mtp) cc_final: 0.8464 (mtm)
REVERT: C   56 MET cc_start: 0.8131 (mpp) cc_final: 0.7692 (mpp)
REVERT: C   80 LEU cc_start: 0.9040 (tp) cc_final: 0.8705 (tt)
REVERT: C   83 ARG cc_start: 0.7507 (ptt-90) cc_final: 0.7260 (ttp-110)
REVERT: E   53 GLN cc_start: 0.8510 (tp40) cc_final: 0.8272 (tp40)
REVERT: F 1034 ASP cc_start: 0.7277 (t0) cc_final: 0.7042 (t0)
REVERT: F 1046 MET cc_start: 0.7604 (ttp) cc_final: 0.7374 (ttp)
REVERT: F 1112 MET cc_start: 0.7697 (ptp) cc_final: 0.7435 (ptp)
REVERT: F 1166 TRP cc_start: 0.8174 (m-10) cc_final: 0.7678 (m100)
REVERT: F 1212 LYS cc_start: 0.7001 (mttm) cc_final: 0.6674 (ptmm)
REVERT: F 1295 ASN cc_start: 0.8345 (p0) cc_final: 0.7906 (p0)
  outliers start: 54
  outliers final: 46
  residues processed: 221
  average time/residue: 0.0953
  time to fit residues: 33.2522
Evaluate side-chains
  215 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 169
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  322 LEU
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   86 VAL
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 131 optimal weight:    0.5980
   chunk 183 optimal weight:    6.9990
   chunk 143 optimal weight:    3.9990
   chunk 188 optimal weight:   10.0000
   chunk 124 optimal weight:    0.0570
   chunk 60 optimal weight:   10.0000
   chunk 111 optimal weight:    1.9990
   chunk 160 optimal weight:    0.3980
   chunk 180 optimal weight:    9.9990
   chunk 84 optimal weight:   10.0000
   chunk 120 optimal weight:    3.9990
   overall best weight:    1.4102

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

Flipped N/Q/H residues before XYZ refinement:
** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.162013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.108461 restraints weight = 31800.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.111591 restraints weight = 17503.490|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3566 r_free = 0.3566 target = 0.113604 restraints weight = 12278.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.114652 restraints weight = 9997.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.115387 restraints weight = 8970.859|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3560
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3560 r_free = 0.3560    target_work(ls_wunit_k1) = 0.110         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3560
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.3125

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15361  Z= 0.139
  Angle     :  0.641  11.249  20868  Z= 0.334
  Chirality :  0.044   0.160   2261
  Planarity :  0.004   0.082   2753
  Dihedral  :  5.371  36.711   2120
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 10.91
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 11.35 %
    Favored  : 88.59 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 21.44 %
    Favored  : 75.41 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -2.96 (0.18), residues: 1923
  helix:  0.97 (0.27), residues: 362
  sheet: -2.15 (0.22), residues: 519
  loop : -3.07 (0.17), residues: 1042

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG F1028 
 TYR   0.063   0.002   TYR A 432 
 PHE   0.017   0.001   PHE A 738 
 TRP   0.013   0.001   TRP A 449 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 (15360)
  covalent geometry    : angle       0.64000 (20866)
  SS BOND              : bond        0.00035 (    1)
  SS BOND              : angle       3.95000 (    2)
  hydrogen bonds       : bond        0.04179 (  403)
  hydrogen bonds       : angle       4.96743 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  224 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 50
    poor density    : 174
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  422 ASN cc_start: 0.8505 (t0) cc_final: 0.8272 (t0)
REVERT: A  449 TRP cc_start: 0.8676 (t60) cc_final: 0.8354 (t-100)
REVERT: A  465 TYR cc_start: 0.7345 (m-10) cc_final: 0.7081 (m-10)
REVERT: A  539 MET cc_start: 0.8736 (tpp) cc_final: 0.8159 (tpp)
REVERT: B  263 TYR cc_start: 0.5932 (t80) cc_final: 0.5511 (t80)
REVERT: B  278 MET cc_start: 0.8669 (mtp) cc_final: 0.8423 (mtm)
REVERT: B  356 PHE cc_start: 0.8579 (m-10) cc_final: 0.8377 (m-10)
REVERT: C   56 MET cc_start: 0.8139 (mpp) cc_final: 0.7685 (mpp)
REVERT: C   80 LEU cc_start: 0.9145 (tp) cc_final: 0.8765 (tt)
REVERT: C   83 ARG cc_start: 0.7489 (ptt-90) cc_final: 0.7260 (ptp-110)
REVERT: E   53 GLN cc_start: 0.8631 (tp40) cc_final: 0.8363 (tp40)
REVERT: F 1034 ASP cc_start: 0.7262 (t0) cc_final: 0.7023 (t0)
REVERT: F 1046 MET cc_start: 0.7608 (ttp) cc_final: 0.7113 (ttp)
REVERT: F 1112 MET cc_start: 0.7701 (ptp) cc_final: 0.7428 (ptp)
REVERT: F 1166 TRP cc_start: 0.8160 (m-10) cc_final: 0.7722 (m100)
REVERT: F 1212 LYS cc_start: 0.6936 (mttm) cc_final: 0.6621 (ptmm)
REVERT: F 1295 ASN cc_start: 0.8354 (p0) cc_final: 0.7976 (p0)
  outliers start: 50
  outliers final: 45
  residues processed: 213
  average time/residue: 0.1054
  time to fit residues: 35.0508
Evaluate side-chains
  216 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 171
  time to evaluate  : 0.641 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  325 MET
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  270 LEU
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 7 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 81 optimal weight:    8.9990
   chunk 18 optimal weight:    0.2980
   chunk 19 optimal weight:    4.9990
   chunk 168 optimal weight:    0.0670
   chunk 31 optimal weight:    6.9990
   chunk 54 optimal weight:    7.9990
   chunk 181 optimal weight:    6.9990
   chunk 122 optimal weight:    9.9990
   overall best weight:    1.4520

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

Flipped N/Q/H residues before XYZ refinement:
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.160646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.113447 restraints weight = 31495.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.113680 restraints weight = 19037.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.113891 restraints weight = 13654.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.114558 restraints weight = 14013.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3558 r_free = 0.3558 target = 0.114649 restraints weight = 12110.759|
|-----------------------------------------------------------------------------|
r_work (final): 0.3520
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3520
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3520 r_free = 0.3520    target_work(ls_wunit_k1) = 0.108         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3520
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3210

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  15361  Z= 0.139
  Angle     :  0.639  11.103  20868  Z= 0.333
  Chirality :  0.044   0.196   2261
  Planarity :  0.004   0.081   2753
  Dihedral  :  5.354  37.607   2120
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  : 11.15 %
    Favored  : 88.80 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 21.88 %
    Favored  : 75.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -2.87 (0.18), residues: 1923
  helix:  1.05 (0.28), residues: 362
  sheet: -2.11 (0.22), residues: 524
  loop : -3.00 (0.17), residues: 1037

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 325 
 TYR   0.058   0.002   TYR A 432 
 PHE   0.018   0.001   PHE A 738 
 TRP   0.012   0.001   TRP A 449 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 (15360)
  covalent geometry    : angle       0.63820 (20866)
  SS BOND              : bond        0.00017 (    1)
  SS BOND              : angle       3.92546 (    2)
  hydrogen bonds       : bond        0.04112 (  403)
  hydrogen bonds       : angle       4.92092 ( 1080)

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

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

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3846 Ramachandran restraints generated.
    1923 Oldfield, 0 Emsley, 1923 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 171
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  422 ASN cc_start: 0.8502 (t0) cc_final: 0.8295 (t0)
REVERT: A  449 TRP cc_start: 0.8682 (t60) cc_final: 0.8386 (t-100)
REVERT: A  465 TYR cc_start: 0.7264 (m-10) cc_final: 0.6989 (m-10)
REVERT: A  539 MET cc_start: 0.8806 (tpp) cc_final: 0.8270 (tpp)
REVERT: B  263 TYR cc_start: 0.5869 (t80) cc_final: 0.5323 (t80)
REVERT: B  278 MET cc_start: 0.8864 (mtp) cc_final: 0.8530 (mtm)
REVERT: B  356 PHE cc_start: 0.8649 (m-10) cc_final: 0.8359 (m-10)
REVERT: C   56 MET cc_start: 0.8181 (mpp) cc_final: 0.7690 (mpp)
REVERT: C   80 LEU cc_start: 0.9139 (tp) cc_final: 0.8815 (tt)
REVERT: C   83 ARG cc_start: 0.7497 (ptt-90) cc_final: 0.7252 (ptp-110)
REVERT: D   64 PHE cc_start: 0.8316 (t80) cc_final: 0.7843 (t80)
REVERT: E   53 GLN cc_start: 0.8660 (tp40) cc_final: 0.8402 (tp40)
REVERT: F 1034 ASP cc_start: 0.7309 (t0) cc_final: 0.7034 (t0)
REVERT: F 1046 MET cc_start: 0.7593 (ttp) cc_final: 0.7118 (ttp)
REVERT: F 1112 MET cc_start: 0.7780 (ptp) cc_final: 0.7510 (ptp)
REVERT: F 1166 TRP cc_start: 0.8290 (m-10) cc_final: 0.7783 (m100)
REVERT: F 1212 LYS cc_start: 0.6898 (mttm) cc_final: 0.6546 (ptmm)
REVERT: F 1295 ASN cc_start: 0.8368 (p0) cc_final: 0.7981 (p0)
  outliers start: 47
  outliers final: 45
  residues processed: 209
  average time/residue: 0.0975
  time to fit residues: 32.1558
Evaluate side-chains
  209 residues out of total 1600 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 164
  time to evaluate  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  129 THR
Chi-restraints excluded: chain A residue  139 ASP
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  230 TYR
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  405 VAL
Chi-restraints excluded: chain A residue  438 VAL
Chi-restraints excluded: chain A residue  444 VAL
Chi-restraints excluded: chain A residue  452 THR
Chi-restraints excluded: chain A residue  458 ILE
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  511 THR
Chi-restraints excluded: chain A residue  524 SER
Chi-restraints excluded: chain A residue  629 VAL
Chi-restraints excluded: chain A residue  633 THR
Chi-restraints excluded: chain A residue  720 THR
Chi-restraints excluded: chain A residue  778 SER
Chi-restraints excluded: chain B residue   63 LEU
Chi-restraints excluded: chain B residue  157 VAL
Chi-restraints excluded: chain B residue  209 VAL
Chi-restraints excluded: chain B residue  239 THR
Chi-restraints excluded: chain B residue  249 THR
Chi-restraints excluded: chain B residue  298 LEU
Chi-restraints excluded: chain B residue  300 ASP
Chi-restraints excluded: chain B residue  387 VAL
Chi-restraints excluded: chain C residue   61 THR
Chi-restraints excluded: chain C residue  108 VAL
Chi-restraints excluded: chain C residue  165 VAL
Chi-restraints excluded: chain D residue   67 TYR
Chi-restraints excluded: chain D residue   92 ILE
Chi-restraints excluded: chain D residue  181 VAL
Chi-restraints excluded: chain D residue  185 TYR
Chi-restraints excluded: chain D residue  186 THR
Chi-restraints excluded: chain E residue   31 ASP
Chi-restraints excluded: chain E residue   43 VAL
Chi-restraints excluded: chain E residue   51 THR
Chi-restraints excluded: chain E residue   94 THR
Chi-restraints excluded: chain E residue  111 SER
Chi-restraints excluded: chain F residue 1107 LEU
Chi-restraints excluded: chain F residue 1146 THR
Chi-restraints excluded: chain F residue 1174 VAL
Chi-restraints excluded: chain F residue 1256 SER
Chi-restraints excluded: chain F residue 1262 VAL
Chi-restraints excluded: chain F residue 1268 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 191
   random chunks:
   chunk 134 optimal weight:    5.9990
   chunk 144 optimal weight:    0.0470
   chunk 79 optimal weight:   10.0000
   chunk 24 optimal weight:    0.0270
   chunk 114 optimal weight:    7.9990
   chunk 14 optimal weight:   30.0000
   chunk 85 optimal weight:    0.6980
   chunk 143 optimal weight:    0.9990
   chunk 38 optimal weight:    0.0970
   chunk 158 optimal weight:    2.9990
   chunk 54 optimal weight:    7.9990
   overall best weight:    0.3736

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

Flipped N/Q/H residues before XYZ refinement:
** A 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 264 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 359 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  34 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4218 r_free = 0.4218 target = 0.159522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3734 r_free = 0.3734 target = 0.121402 restraints weight = 30761.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.119048 restraints weight = 21927.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.120567 restraints weight = 18139.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3696 r_free = 0.3696 target = 0.120968 restraints weight = 14605.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.120953 restraints weight = 13132.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3705
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3705
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3705 r_free = 0.3705    target_work(ls_wunit_k1) = 0.120         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3705
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7750
moved from start:          0.3597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  15361  Z= 0.109
  Angle     :  0.626  10.942  20868  Z= 0.324
  Chirality :  0.044   0.166   2261
  Planarity :  0.004   0.080   2753
  Dihedral  :  5.101  39.659   2120
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 10.43
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  9.17 %
    Favored  : 90.78 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 22.51 %
    Favored  : 74.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.22 %
    Twisted Proline : 1.45 %
    Twisted General : 0.11 %

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 aren not related in a simple way.
  whole: -2.66 (0.19), residues: 1923
  helix:  1.05 (0.28), residues: 362
  sheet: -1.82 (0.23), residues: 511
  loop : -2.89 (0.17), residues: 1050

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 233 
 TYR   0.058   0.001   TYR A 432 
 PHE   0.017   0.001   PHE A 738 
 TRP   0.015   0.001   TRP A 739 
 HIS   0.004   0.001   HIS B 347 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (15360)
  covalent geometry    : angle       0.62535 (20866)
  SS BOND              : bond        0.00023 (    1)
  SS BOND              : angle       3.40173 (    2)
  hydrogen bonds       : bond        0.03774 (  403)
  hydrogen bonds       : angle       4.69312 ( 1080)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2833.00 seconds
wall clock time: 49 minutes 44.80 seconds (2984.80 seconds total)