Starting phenix.real_space_refine
on Wed Mar 12 12:41:01 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7b00_11952/03_2025/7b00_11952.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7b00_11952/03_2025/7b00_11952.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.98
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7b00_11952/03_2025/7b00_11952.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7b00_11952/03_2025/7b00_11952.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7b00_11952/03_2025/7b00_11952.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7b00_11952/03_2025/7b00_11952.cif"
  }
  resolution = 3.98
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.001
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      27      5.16       5
     C    4833      2.51       5
     N    1179      2.21       5
     O    1350      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 18 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib"
  Total number of atoms: 7389
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "A"
      Number of atoms: 3542
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 457, 3542
          Classifications: {'peptide': 457}
          Link IDs: {'PTRANS': 25, 'TRANS': 431}
    Chain: "B"
      Number of atoms: 3650
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 469, 3650
          Classifications: {'peptide': 469}
          Link IDs: {'PTRANS': 22, 'TRANS': 446}
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "D"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "E"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "F"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 85
          Unusual residues: {'AJP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 5.45, per 1000 atoms: 0.74
  Number of scatterers: 7389
  At special positions: 0
  Unit cell: (81.6, 77.35, 129.2, 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      27     16.00
     O    1350      8.00
     N    1179      7.00
     C    4833      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 154 " - pdb=" SG  CYS B 109 " 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=1, symmetry=0
  Links applied
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
      " NAG D   1 " - " NAG D   2 "
      " NAG E   1 " - " NAG E   2 "
      " NAG F   1 " - " NAG F   2 "
    NAG-ASN
      " NAG C   1 " - " ASN B 405 "
      " NAG D   1 " - " ASN B 264 "
      " NAG E   1 " - " ASN B 280 "
      " NAG F   1 " - " ASN B 323 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.21
  Conformation dependent library (CDL) restraints added in 901.3 milliseconds
  

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1696

  Finding SS restraints...
    Secondary structure from input PDB file:
      45 helices and 4 sheets defined
      48.6% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.76
  Creating SS restraints...
    Processing helix  chain 'A' and resid 46 through 54
      removed outlier: 4.818A  pdb=" N   ASN A  52 " --> pdb=" O   ILE A  48 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 63 through 68
      removed outlier: 3.967A  pdb=" N   GLU A  67 " --> pdb=" O   LYS A  63 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ASN A  68 " --> pdb=" O   GLY A  64 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 63 through 68'
    Processing helix  chain 'A' and resid 77 through 100
      removed outlier: 4.190A  pdb=" N   GLY A  83 " --> pdb=" O   TRP A  79 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   THR A  86 " --> pdb=" O   THR A  82 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLU A  95 " --> pdb=" O   LEU A  91 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   THR A  99 " --> pdb=" O   GLU A  95 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 106 through 112
      removed outlier: 3.851A  pdb=" N   LYS A 111 " --> pdb=" O   TYR A 107 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   ASP A 112 " --> pdb=" O   SER A 108 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 126
      removed outlier: 3.643A  pdb=" N   GLY A 119 " --> pdb=" O   GLY A 115 " (cutoff:3.500A)
      removed outlier: 3.984A  pdb=" N   ARG A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
      removed outlier: 3.845A  pdb=" N   LEU A 123 " --> pdb=" O   GLY A 119 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 139 through 148
      removed outlier: 3.761A  pdb=" N   SER A 143 " --> pdb=" O   ALA A 139 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   ASN A 144 " --> pdb=" O   LEU A 140 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TYR A 145 " --> pdb=" O   THR A 141 " (cutoff:3.500A)
      removed outlier: 3.613A  pdb=" N   GLN A 148 " --> pdb=" O   ASN A 144 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 160
    Processing helix  chain 'A' and resid 161 through 178
      removed outlier: 4.500A  pdb=" N   ILE A 167 " --> pdb=" O   LEU A 163 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   CYS A 168 " --> pdb=" O   LEU A 164 " (cutoff:3.500A)
      removed outlier: 4.406A  pdb=" N   LEU A 170 " --> pdb=" O   ALA A 166 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   TRP A 174 " --> pdb=" O   LEU A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 181 through 186
      removed outlier: 3.510A  pdb=" N   ARG A 185 " --> pdb=" O   ARG A 181 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   VAL A 186 " --> pdb=" O   TRP A 182 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 181 through 186'
    Processing helix  chain 'A' and resid 187 through 190
    Processing helix  chain 'A' and resid 191 through 212
      removed outlier: 3.993A  pdb=" N   ILE A 206 " --> pdb=" O   ILE A 202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 255 through 260
      removed outlier: 4.498A  pdb=" N   VAL A 259 " --> pdb=" O   THR A 255 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 272 through 289
      removed outlier: 3.728A  pdb=" N   VAL A 279 " --> pdb=" O   LEU A 275 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   VAL A 285 " --> pdb=" O   VAL A 281 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL A 288 " --> pdb=" O   ASN A 284 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 309
      removed outlier: 3.870A  pdb=" N   THR A 305 " --> pdb=" O   ALA A 301 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 319 through 324
      removed outlier: 3.754A  pdb=" N   ALA A 323 " --> pdb=" O   PRO A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 337 through 345
      removed outlier: 3.972A  pdb=" N   ALA A 343 " --> pdb=" O   ARG A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 364 through 377
      removed outlier: 3.586A  pdb=" N   LEU A 369 " --> pdb=" O   ILE A 365 " (cutoff:3.500A)
      removed outlier: 4.305A  pdb=" N   PHE A 370 " --> pdb=" O   PRO A 366 " (cutoff:3.500A)
      removed outlier: 3.888A  pdb=" N   THR A 371 " --> pdb=" O   ALA A 367 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   LEU A 376 " --> pdb=" O   CYS A 372 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 378 through 380
      No H-bonds generated for 'chain 'A' and resid 378 through 380'
    Processing helix  chain 'A' and resid 384 through 396
      removed outlier: 3.828A  pdb=" N   ASN A 389 " --> pdb=" O   TYR A 385 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   TYR A 390 " --> pdb=" O   THR A 386 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   ILE A 394 " --> pdb=" O   TYR A 390 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 397 through 412
      removed outlier: 3.759A  pdb=" N   VAL A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   THR A 402 " --> pdb=" O   PHE A 398 " (cutoff:3.500A)
      removed outlier: 4.217A  pdb=" N   VAL A 403 " --> pdb=" O   TYR A 399 " (cutoff:3.500A)
      removed outlier: 4.294A  pdb=" N   GLN A 406 " --> pdb=" O   THR A 402 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ILE A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 434
      removed outlier: 3.808A  pdb=" N   ILE A 429 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   TYR A 430 " --> pdb=" O   PHE A 426 " (cutoff:3.500A)
      removed outlier: 3.953A  pdb=" N   LEU A 431 " --> pdb=" O   PRO A 427 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 439
      removed outlier: 3.699A  pdb=" N   LEU A 438 " --> pdb=" O   TRP A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 439 through 444
      removed outlier: 3.738A  pdb=" N   TRP A 443 " --> pdb=" O   VAL A 439 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   SER A 444 " --> pdb=" O   PHE A 440 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 439 through 444'
    Processing helix  chain 'A' and resid 451 through 456
      removed outlier: 4.288A  pdb=" N   MET A 456 " --> pdb=" O   GLY A 452 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 458 through 463
    Processing helix  chain 'A' and resid 476 through 491
      removed outlier: 3.688A  pdb=" N   ILE A 480 " --> pdb=" O   PHE A 476 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   THR A 484 " --> pdb=" O   ILE A 480 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   LEU A 485 " --> pdb=" O   GLU A 481 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 65 through 73
      removed outlier: 3.687A  pdb=" N   VAL B  71 " --> pdb=" O   GLU B  67 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   ALA B  72 " --> pdb=" O   LEU B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 74 through 106
      removed outlier: 3.535A  pdb=" N   VAL B  78 " --> pdb=" O   SER B  74 " (cutoff:3.500A)
      removed outlier: 3.868A  pdb=" N   ARG B  79 " --> pdb=" O   PRO B  75 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   THR B  80 " --> pdb=" O   GLY B  76 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   PHE B  88 " --> pdb=" O   LEU B  84 " (cutoff:3.500A)
      removed outlier: 3.995A  pdb=" N   TRP B  89 " --> pdb=" O   LEU B  85 " (cutoff:3.500A)
      removed outlier: 3.574A  pdb=" N   MET B  95 " --> pdb=" O   GLY B  91 " (cutoff:3.500A)
      removed outlier: 4.080A  pdb=" N   GLY B  98 " --> pdb=" O   GLY B  94 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   ALA B  99 " --> pdb=" O   MET B  95 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE B 102 " --> pdb=" O   GLY B  98 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   VAL B 104 " --> pdb=" O   VAL B 100 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 116 through 120
      removed outlier: 3.534A  pdb=" N   HIS B 119 " --> pdb=" O   LYS B 116 " (cutoff:3.500A)
      removed outlier: 3.949A  pdb=" N   THR B 120 " --> pdb=" O   TRP B 117 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 116 through 120'
    Processing helix  chain 'B' and resid 128 through 134
      removed outlier: 3.729A  pdb=" N   GLN B 133 " --> pdb=" O   LEU B 129 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 139 through 145
      removed outlier: 3.898A  pdb=" N   LYS B 144 " --> pdb=" O   ALA B 141 " (cutoff:3.500A)
      removed outlier: 3.680A  pdb=" N   GLY B 145 " --> pdb=" O   GLY B 142 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 146 through 151
    Processing helix  chain 'B' and resid 185 through 197
      removed outlier: 3.570A  pdb=" N   SER B 191 " --> pdb=" O   GLU B 187 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   SER B 195 " --> pdb=" O   SER B 191 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   LYS B 197 " --> pdb=" O   LEU B 193 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 223 through 228
      removed outlier: 3.503A  pdb=" N   THR B 227 " --> pdb=" O   ASP B 223 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   LYS B 228 " --> pdb=" O   THR B 224 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 223 through 228'
    Processing helix  chain 'B' and resid 228 through 239
      removed outlier: 3.701A  pdb=" N   GLU B 234 " --> pdb=" O   LYS B 230 " (cutoff:3.500A)
      removed outlier: 4.528A  pdb=" N   LEU B 237 " --> pdb=" O   LEU B 233 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ALA B 239 " --> pdb=" O   PHE B 235 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 249 through 252
      removed outlier: 3.580A  pdb=" N   LEU B 252 " --> pdb=" O   ILE B 249 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 249 through 252'
    Processing helix  chain 'B' and resid 254 through 270
      removed outlier: 3.502A  pdb=" N   TRP B 262 " --> pdb=" O   PHE B 258 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   ILE B 265 " --> pdb=" O   GLU B 261 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   SER B 270 " --> pdb=" O   THR B 266 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 283 through 291
      removed outlier: 3.716A  pdb=" N   ILE B 287 " --> pdb=" O   ASP B 283 " (cutoff:3.500A)
      removed outlier: 3.573A  pdb=" N   LEU B 288 " --> pdb=" O   LEU B 284 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 310 through 326
      removed outlier: 3.993A  pdb=" N   THR B 314 " --> pdb=" O   THR B 310 " (cutoff:3.500A)
      removed outlier: 3.561A  pdb=" N   THR B 325 " --> pdb=" O   TYR B 321 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 345 through 347
      No H-bonds generated for 'chain 'B' and resid 345 through 347'
    Processing helix  chain 'B' and resid 348 through 357
      removed outlier: 3.520A  pdb=" N   GLN B 353 " --> pdb=" O   LEU B 349 " (cutoff:3.500A)
      removed outlier: 4.654A  pdb=" N   LEU B 354 " --> pdb=" O   ARG B 350 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 403 through 406
      removed outlier: 3.565A  pdb=" N   MET B 406 " --> pdb=" O   SER B 403 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 403 through 406'
    Processing helix  chain 'B' and resid 407 through 412
    Processing helix  chain 'B' and resid 418 through 427
      removed outlier: 3.918A  pdb=" N   ASP B 427 " --> pdb=" O   ARG B 423 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 433 through 438
      removed outlier: 3.596A  pdb=" N   HIS B 437 " --> pdb=" O   ARG B 433 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'B' and resid 123 through 125
    Processing sheet with id=AA2, first strand: chain 'B' and resid 159 through 160
      removed outlier: 6.277A  pdb=" N   LEU B 205 " --> pdb=" O   GLN B 245 " (cutoff:3.500A)
      removed outlier: 8.018A  pdb=" N   ARG B 247 " --> pdb=" O   LEU B 205 " (cutoff:3.500A)
      removed outlier: 6.545A  pdb=" N   LEU B 275 " --> pdb=" O   LEU B 298 " (cutoff:3.500A)
      removed outlier: 7.243A  pdb=" N   THR B 300 " --> pdb=" O   LEU B 275 " (cutoff:3.500A)
      removed outlier: 6.055A  pdb=" N   ALA B 277 " --> pdb=" O   THR B 300 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 165 through 166
      removed outlier: 3.542A  pdb=" N   LYS B 165 " --> pdb=" O   ASP B 175 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 439 through 442
      removed outlier: 3.632A  pdb=" N   VAL B 465 " --> pdb=" O   LEU B 521 " (cutoff:3.500A)
      removed outlier: 3.900A  pdb=" N   GLU B 519 " --> pdb=" O   ASN B 467 " (cutoff:3.500A)
      removed outlier: 6.823A  pdb=" N   GLY B 520 " --> pdb=" O   SER B 497 " (cutoff:3.500A)
      removed outlier: 4.697A  pdb=" N   SER B 497 " --> pdb=" O   GLY B 520 " (cutoff:3.500A)
      removed outlier: 6.830A  pdb=" N   LEU B 522 " --> pdb=" O   LEU B 495 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ASP B 493 " --> pdb=" O   ARG B 524 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   LEU B 508 " --> pdb=" O   ALA B 492 " (cutoff:3.500A)

    215 hydrogen bonds defined for protein.
    627 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: 1.73

  Time building geometry restraints manager: 2.54 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2204
        1.34 -     1.46: 1444
        1.46 -     1.57: 3894
        1.57 -     1.69: 0
        1.69 -     1.81: 41
  Bond restraints: 7583
  Sorted by residual:
  bond pdb=" C56 AJP A 601 "
       pdb=" C57 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.522  1.558 -0.036 2.00e-02 2.50e+03 3.24e+00
  bond pdb=" C65 AJP A 601 "
       pdb=" O64 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.373  1.408 -0.035 2.00e-02 2.50e+03 3.05e+00
  bond pdb=" C57 AJP A 601 "
       pdb=" O64 AJP A 601 "
    ideal  model  delta    sigma   weight residual
    1.414  1.443 -0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" C3  NAG F   1 "
       pdb=" O3  NAG F   1 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.16e+00
  bond pdb=" C3  NAG D   2 "
       pdb=" O3  NAG D   2 "
    ideal  model  delta    sigma   weight residual
    1.403  1.432 -0.029 2.00e-02 2.50e+03 2.08e+00
  ... (remaining 7578 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.20: 9953
        2.20 -     4.41: 321
        4.41 -     6.61: 50
        6.61 -     8.81: 23
        8.81 -    11.01: 3
  Bond angle restraints: 10350
  Sorted by residual:
  angle pdb=" N   ARG B 433 "
        pdb=" CA  ARG B 433 "
        pdb=" C   ARG B 433 "
      ideal   model   delta    sigma   weight residual
     114.56  108.83    5.73 1.27e+00 6.20e-01 2.04e+01
  angle pdb=" C   PRO A 364 "
        pdb=" N   ILE A 365 "
        pdb=" CA  ILE A 365 "
      ideal   model   delta    sigma   weight residual
     120.33  123.54   -3.21 8.00e-01 1.56e+00 1.61e+01
  angle pdb=" CA  ILE A 365 "
        pdb=" C   ILE A 365 "
        pdb=" N   PRO A 366 "
      ideal   model   delta    sigma   weight residual
     120.83  123.17   -2.34 6.10e-01 2.69e+00 1.47e+01
  angle pdb=" C   ASP A 230 "
        pdb=" N   ILE A 231 "
        pdb=" CA  ILE A 231 "
      ideal   model   delta    sigma   weight residual
     121.97  128.74   -6.77 1.80e+00 3.09e-01 1.41e+01
  angle pdb=" C   SER A 444 "
        pdb=" N   GLU A 445 "
        pdb=" CA  GLU A 445 "
      ideal   model   delta    sigma   weight residual
     121.80  130.57   -8.77 2.44e+00 1.68e-01 1.29e+01
  ... (remaining 10345 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.70: 4376
       24.70 -    49.39: 281
       49.39 -    74.09: 21
       74.09 -    98.79: 3
       98.79 -   123.48: 17
  Dihedral angle restraints: 4698
    sinusoidal: 2050
      harmonic: 2648
  Sorted by residual:
  dihedral pdb=" CB  CYS A 154 "
           pdb=" SG  CYS A 154 "
           pdb=" SG  CYS B 109 "
           pdb=" CB  CYS B 109 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -39.60  -46.40     1      1.00e+01 1.00e-02 2.98e+01
  dihedral pdb=" CA  LEU A 350 "
           pdb=" C   LEU A 350 "
           pdb=" N   PRO A 351 "
           pdb=" CA  PRO A 351 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.71  -23.29     0      5.00e+00 4.00e-02 2.17e+01
  dihedral pdb=" CA  THR A 133 "
           pdb=" C   THR A 133 "
           pdb=" N   ASN A 134 "
           pdb=" CA  ASN A 134 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.55   22.45     0      5.00e+00 4.00e-02 2.02e+01
  ... (remaining 4695 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.331: 1231
       0.331 -    0.662: 2
       0.662 -    0.992: 0
       0.992 -    1.323: 0
       1.323 -    1.654: 1
  Chirality restraints: 1234
  Sorted by residual:
  chirality pdb=" C1  NAG F   1 "
            pdb=" ND2 ASN B 323 "
            pdb=" C2  NAG F   1 "
            pdb=" O5  NAG F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -0.75   -1.65 2.00e-01 2.50e+01 6.84e+01
  chirality pdb=" C1  NAG D   2 "
            pdb=" O4  NAG D   1 "
            pdb=" C2  NAG D   2 "
            pdb=" O5  NAG D   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 4.04e+01
  chirality pdb=" C1  NAG C   2 "
            pdb=" O4  NAG C   1 "
            pdb=" C2  NAG C   2 "
            pdb=" O5  NAG C   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.28   -0.12 2.00e-02 2.50e+03 3.41e+01
  ... (remaining 1231 not shown)

  Planarity restraints: 1269
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   1 "   -0.343 2.00e-02 2.50e+03   2.97e-01 1.10e+03
        pdb=" C7  NAG F   1 "    0.079 2.00e-02 2.50e+03
        pdb=" C8  NAG F   1 "   -0.069 2.00e-02 2.50e+03
        pdb=" N2  NAG F   1 "    0.524 2.00e-02 2.50e+03
        pdb=" O7  NAG F   1 "   -0.192 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG F   2 "   -0.272 2.00e-02 2.50e+03   2.27e-01 6.46e+02
        pdb=" C7  NAG F   2 "    0.072 2.00e-02 2.50e+03
        pdb=" C8  NAG F   2 "   -0.181 2.00e-02 2.50e+03
        pdb=" N2  NAG F   2 "    0.383 2.00e-02 2.50e+03
        pdb=" O7  NAG F   2 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG D   2 "   -0.224 2.00e-02 2.50e+03   1.91e-01 4.55e+02
        pdb=" C7  NAG D   2 "    0.048 2.00e-02 2.50e+03
        pdb=" C8  NAG D   2 "    0.037 2.00e-02 2.50e+03
        pdb=" N2  NAG D   2 "    0.313 2.00e-02 2.50e+03
        pdb=" O7  NAG D   2 "   -0.173 2.00e-02 2.50e+03
  ... (remaining 1266 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 32
        2.45 -     3.06: 4159
        3.06 -     3.68: 11042
        3.68 -     4.29: 15290
        4.29 -     4.90: 24995
  Nonbonded interactions: 55518
  Sorted by model distance:
  nonbonded pdb=" O3  NAG D   1 "
            pdb=" O6  NAG D   1 "
     model   vdw
     1.838 3.040
  nonbonded pdb=" O   ILE A 138 "
            pdb=" OG1 THR A 326 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   GLY A 332 "
            pdb=" OG1 THR A 336 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" O   SER B 305 "
            pdb=" OG  SER B 305 "
     model   vdw
     2.286 3.040
  nonbonded pdb=" O   SER B 302 "
            pdb=" OG  SER B 302 "
     model   vdw
     2.298 3.040
  ... (remaining 55513 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'C'
  selection = chain 'D'
  selection = chain 'E'
  selection = chain 'F'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.030
  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:          0.310
  Check model and map are aligned:         0.060
  Set scattering table:                    0.070
  Process input model:                     21.190
  Find NCS groups from input model:        0.110
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.790
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7780
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      :  0.006   0.067   7583  Z= 0.370
  Angle     :  0.968  11.014  10350  Z= 0.494
  Chirality :  0.076   1.654   1234
  Planarity :  0.014   0.297   1265
  Dihedral  : 17.032 123.481   2999
  Min Nonbonded Distance : 1.838

Molprobity Statistics.
  All-atom Clashscore : 5.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.54 %
    Favored  : 90.46 %
  Rotamer:
    Outliers :  0.39 %
    Allowed  : 12.24 %
    Favored  : 87.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -6.20 (0.17), residues: 922
  helix: -4.76 (0.09), residues: 417
  sheet: -1.62 (0.66), residues: 52
  loop : -3.77 (0.21), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 469 
 HIS   0.007   0.001   HIS A 358 
 PHE   0.022   0.002   PHE A 226 
 TYR   0.022   0.002   TYR A  93 
 ARG   0.004   0.001   ARG A 122 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 159
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.8369 (pt) cc_final: 0.8114 (mm)
REVERT: A  184 THR cc_start: 0.8873 (t) cc_final: 0.8474 (m)
REVERT: A  211 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7677 (ttpp)
REVERT: A  264 ASN cc_start: 0.7982 (m-40) cc_final: 0.7700 (m-40)
REVERT: A  284 ASN cc_start: 0.8556 (m-40) cc_final: 0.7769 (t0)
REVERT: B  146 ARG cc_start: 0.7803 (mmt180) cc_final: 0.7238 (mmt90)
REVERT: B  187 GLU cc_start: 0.7815 (pm20) cc_final: 0.7584 (pm20)
REVERT: B  432 GLU cc_start: 0.7730 (mm-30) cc_final: 0.7429 (tp30)
  outliers start: 3
  outliers final: 1
  residues processed: 162
  average time/residue: 0.1890
  time to fit residues: 41.2878
Evaluate side-chains
  121 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 120
  time to evaluate  : 0.830 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  311 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 76 optimal weight:    2.9990
   chunk 68 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9980
   chunk 23 optimal weight:    0.4980
   chunk 46 optimal weight:    7.9990
   chunk 36 optimal weight:    0.7980
   chunk 71 optimal weight:    2.9990
   chunk 27 optimal weight:    0.9980
   chunk 43 optimal weight:    8.9990
   chunk 53 optimal weight:    4.9990
   chunk 82 optimal weight:    0.5980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** B 336 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 381 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.155741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.122316 restraints weight = 10296.781|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.121865 restraints weight = 14849.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.122836 restraints weight = 14592.265|
|-----------------------------------------------------------------------------|
r_work (final): 0.3400
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7904
moved from start:          0.1679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   7583  Z= 0.228
  Angle     :  0.735  10.830  10350  Z= 0.357
  Chirality :  0.045   0.382   1234
  Planarity :  0.005   0.048   1265
  Dihedral  : 13.186 103.068   1375
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 6.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  2.71 %
    Allowed  : 17.40 %
    Favored  : 79.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.87 (0.21), residues: 922
  helix: -3.34 (0.17), residues: 425
  sheet: -1.43 (0.68), residues: 52
  loop : -3.34 (0.24), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  82 
 HIS   0.003   0.001   HIS A 358 
 PHE   0.024   0.002   PHE A 155 
 TYR   0.014   0.001   TYR B 303 
 ARG   0.003   0.000   ARG B 338 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 125
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 ASN cc_start: 0.8544 (m-40) cc_final: 0.7986 (t0)
REVERT: A  314 MET cc_start: 0.5731 (tpt) cc_final: 0.5335 (tpt)
REVERT: B  336 GLN cc_start: 0.8311 (tm-30) cc_final: 0.7870 (pt0)
  outliers start: 21
  outliers final: 14
  residues processed: 138
  average time/residue: 0.1816
  time to fit residues: 34.4698
Evaluate side-chains
  127 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 113
  time to evaluate  : 0.678 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 48 optimal weight:    0.2980
   chunk 19 optimal weight:    0.9990
   chunk 77 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0970
   chunk 71 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   chunk 47 optimal weight:    0.6980
   chunk 10 optimal weight:    0.0370
   chunk 66 optimal weight:    0.9990
   chunk 28 optimal weight:    0.8980
   overall best weight:    0.3656

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

Flipped N/Q/H residues before XYZ refinement:
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 336 GLN
B 381 GLN
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.159243 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.124641 restraints weight = 10355.358|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.122669 restraints weight = 14344.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.124150 restraints weight = 14108.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7896
moved from start:          0.2217

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7583  Z= 0.164
  Angle     :  0.666  10.100  10350  Z= 0.316
  Chirality :  0.042   0.294   1234
  Planarity :  0.004   0.043   1265
  Dihedral  : 11.254 101.027   1375
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 5.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.35 %
    Favored  : 91.65 %
  Rotamer:
    Outliers :  4.25 %
    Allowed  : 18.56 %
    Favored  : 77.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -4.05 (0.24), residues: 922
  helix: -2.46 (0.21), residues: 424
  sheet: -1.62 (0.57), residues: 70
  loop : -3.09 (0.26), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP B 117 
 HIS   0.003   0.001   HIS B 518 
 PHE   0.025   0.002   PHE A 433 
 TYR   0.011   0.001   TYR B 303 
 ARG   0.006   0.000   ARG B 105 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 125
  time to evaluate  : 0.772 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ILE cc_start: 0.8692 (mm) cc_final: 0.8242 (mt)
REVERT: A  284 ASN cc_start: 0.8369 (m-40) cc_final: 0.7873 (t0)
REVERT: B  146 ARG cc_start: 0.7548 (mmt180) cc_final: 0.6842 (mmt90)
REVERT: B  347 GLN cc_start: 0.6939 (OUTLIER) cc_final: 0.6317 (pp30)
  outliers start: 33
  outliers final: 25
  residues processed: 148
  average time/residue: 0.1928
  time to fit residues: 40.8942
Evaluate side-chains
  138 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 112
  time to evaluate  : 1.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  456 MET
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 78 optimal weight:    8.9990
   chunk 81 optimal weight:    1.9990
   chunk 41 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 62 optimal weight:    0.6980
   chunk 50 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9990
   chunk 5 optimal weight:    0.6980
   chunk 69 optimal weight:    0.0980
   overall best weight:    0.6782

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.157371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123260 restraints weight = 10404.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121873 restraints weight = 16877.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123098 restraints weight = 16002.890|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7906
moved from start:          0.2430

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7583  Z= 0.209
  Angle     :  0.657   9.699  10350  Z= 0.314
  Chirality :  0.043   0.309   1234
  Planarity :  0.004   0.041   1265
  Dihedral  : 10.600  98.664   1375
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.24 %
    Favored  : 91.76 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 19.97 %
    Favored  : 75.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.69 (0.25), residues: 922
  helix: -2.12 (0.22), residues: 433
  sheet: -1.38 (0.61), residues: 69
  loop : -2.95 (0.27), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.001   TRP B 262 
 HIS   0.003   0.001   HIS B 455 
 PHE   0.031   0.002   PHE A 155 
 TYR   0.010   0.001   TYR A 109 
 ARG   0.004   0.000   ARG B 105 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 122
  time to evaluate  : 0.788 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ILE cc_start: 0.8788 (mm) cc_final: 0.8253 (mt)
REVERT: A  284 ASN cc_start: 0.8534 (m-40) cc_final: 0.8033 (t0)
REVERT: A  471 HIS cc_start: 0.3640 (OUTLIER) cc_final: 0.2312 (m-70)
REVERT: B  146 ARG cc_start: 0.7541 (mmt180) cc_final: 0.7339 (mmt180)
REVERT: B  262 TRP cc_start: 0.8187 (m-90) cc_final: 0.7928 (m-90)
REVERT: B  347 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6387 (pp30)
  outliers start: 37
  outliers final: 27
  residues processed: 147
  average time/residue: 0.1727
  time to fit residues: 35.6774
Evaluate side-chains
  144 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 115
  time to evaluate  : 0.831 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 62 optimal weight:    0.8980
   chunk 29 optimal weight:    0.0980
   chunk 54 optimal weight:    2.9990
   chunk 71 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 51 optimal weight:    0.7980
   chunk 32 optimal weight:    0.6980
   chunk 33 optimal weight:    0.6980
   chunk 53 optimal weight:    0.6980
   chunk 90 optimal weight:    0.0050
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.4394

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

Flipped N/Q/H residues before XYZ refinement:
A 208 GLN
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3824 r_free = 0.3824 target = 0.159008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.124837 restraints weight = 10221.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.123113 restraints weight = 14576.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.124385 restraints weight = 14619.032|
|-----------------------------------------------------------------------------|
r_work (final): 0.3420
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7890
moved from start:          0.2623

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   7583  Z= 0.166
  Angle     :  0.630   9.679  10350  Z= 0.299
  Chirality :  0.042   0.300   1234
  Planarity :  0.004   0.040   1265
  Dihedral  : 10.049  93.996   1375
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 6.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 19.85 %
    Favored  : 75.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.34 (0.26), residues: 922
  helix: -1.80 (0.23), residues: 433
  sheet: -1.23 (0.63), residues: 69
  loop : -2.82 (0.28), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.001   TRP B 262 
 HIS   0.002   0.001   HIS B 518 
 PHE   0.027   0.001   PHE A 155 
 TYR   0.009   0.001   TYR A 109 
 ARG   0.003   0.000   ARG B 105 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 121
  time to evaluate  : 0.750 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 ILE cc_start: 0.8781 (mm) cc_final: 0.8260 (mt)
REVERT: A  184 THR cc_start: 0.8795 (t) cc_final: 0.8442 (m)
REVERT: A  284 ASN cc_start: 0.8513 (m-40) cc_final: 0.8007 (t0)
REVERT: A  471 HIS cc_start: 0.3719 (OUTLIER) cc_final: 0.2290 (m-70)
REVERT: B  262 TRP cc_start: 0.8270 (m-10) cc_final: 0.8001 (m-90)
REVERT: B  347 GLN cc_start: 0.7015 (OUTLIER) cc_final: 0.6475 (pp30)
  outliers start: 37
  outliers final: 28
  residues processed: 147
  average time/residue: 0.1853
  time to fit residues: 37.3795
Evaluate side-chains
  141 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 111
  time to evaluate  : 0.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  273 ILE
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  460 VAL
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  109 CYS
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 0 optimal weight:    3.9990
   chunk 64 optimal weight:    7.9990
   chunk 72 optimal weight:    2.9990
   chunk 70 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0270
   chunk 14 optimal weight:    0.8980
   chunk 33 optimal weight:    0.5980
   chunk 79 optimal weight:    7.9990
   chunk 42 optimal weight:    0.3980
   chunk 81 optimal weight:    2.9990
   chunk 6 optimal weight:    5.9990
   overall best weight:    0.9840

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156560 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.122290 restraints weight = 10433.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.120912 restraints weight = 16418.360|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.122362 restraints weight = 17541.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.2696

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   7583  Z= 0.264
  Angle     :  0.685   9.641  10350  Z= 0.325
  Chirality :  0.045   0.299   1234
  Planarity :  0.004   0.041   1265
  Dihedral  : 10.101  91.596   1375
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.79 %
    Favored  : 91.21 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 20.62 %
    Favored  : 74.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.20 (0.26), residues: 922
  helix: -1.65 (0.24), residues: 443
  sheet: -1.31 (0.62), residues: 69
  loop : -2.77 (0.29), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP B 262 
 HIS   0.004   0.001   HIS B 455 
 PHE   0.023   0.002   PHE A 155 
 TYR   0.011   0.001   TYR A 109 
 ARG   0.003   0.000   ARG B 105 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.743 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  228 GLU cc_start: 0.5486 (OUTLIER) cc_final: 0.4701 (pm20)
REVERT: A  284 ASN cc_start: 0.8521 (m-40) cc_final: 0.8173 (t0)
REVERT: A  471 HIS cc_start: 0.3773 (OUTLIER) cc_final: 0.2393 (m-70)
REVERT: B  262 TRP cc_start: 0.8225 (m-10) cc_final: 0.7978 (m-90)
REVERT: B  347 GLN cc_start: 0.6999 (OUTLIER) cc_final: 0.6459 (pp30)
  outliers start: 35
  outliers final: 29
  residues processed: 133
  average time/residue: 0.1646
  time to fit residues: 30.9227
Evaluate side-chains
  137 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 105
  time to evaluate  : 0.733 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  228 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  287 ILE
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 87 optimal weight:    3.9990
   chunk 57 optimal weight:    0.9980
   chunk 11 optimal weight:    1.9990
   chunk 68 optimal weight:    0.0030
   chunk 61 optimal weight:    0.9980
   chunk 44 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   chunk 81 optimal weight:    1.9990
   chunk 41 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 23 optimal weight:    0.6980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.157675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.122838 restraints weight = 10307.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121884 restraints weight = 16240.515|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.123101 restraints weight = 16142.262|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7583  Z= 0.205
  Angle     :  0.666   9.818  10350  Z= 0.312
  Chirality :  0.044   0.290   1234
  Planarity :  0.004   0.039   1265
  Dihedral  :  9.750  87.501   1375
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 7.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.59 %
    Favored  : 92.41 %
  Rotamer:
    Outliers :  5.15 %
    Allowed  : 21.26 %
    Favored  : 73.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.00 (0.27), residues: 922
  helix: -1.43 (0.24), residues: 440
  sheet: -1.38 (0.61), residues: 70
  loop : -2.71 (0.29), residues: 412

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP B 262 
 HIS   0.003   0.001   HIS B 455 
 PHE   0.022   0.002   PHE A 155 
 TYR   0.010   0.001   TYR A 109 
 ARG   0.002   0.000   ARG B 338 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  146 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 106
  time to evaluate  : 0.810 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  184 THR cc_start: 0.8863 (t) cc_final: 0.8492 (m)
REVERT: A  284 ASN cc_start: 0.8520 (m-40) cc_final: 0.8028 (t0)
REVERT: A  464 PHE cc_start: 0.5736 (OUTLIER) cc_final: 0.5499 (m-10)
REVERT: A  471 HIS cc_start: 0.3831 (OUTLIER) cc_final: 0.2465 (m-70)
REVERT: B  262 TRP cc_start: 0.8335 (m-10) cc_final: 0.8088 (m-90)
REVERT: B  299 LEU cc_start: 0.8888 (tp) cc_final: 0.8683 (mt)
REVERT: B  347 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6498 (pp30)
  outliers start: 40
  outliers final: 29
  residues processed: 134
  average time/residue: 0.1659
  time to fit residues: 31.3070
Evaluate side-chains
  136 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 104
  time to evaluate  : 0.708 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  308 GLU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 57 optimal weight:    7.9990
   chunk 43 optimal weight:    3.9990
   chunk 65 optimal weight:    0.9980
   chunk 53 optimal weight:    0.7980
   chunk 69 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0470
   chunk 86 optimal weight:    9.9990
   chunk 17 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 16 optimal weight:    0.6980
   chunk 19 optimal weight:    1.9990
   overall best weight:    0.9080

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.156475 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.121718 restraints weight = 10404.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.120823 restraints weight = 15867.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3391 r_free = 0.3391 target = 0.121986 restraints weight = 16437.050|
|-----------------------------------------------------------------------------|
r_work (final): 0.3388
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7937
moved from start:          0.2904

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   7583  Z= 0.252
  Angle     :  0.688  11.656  10350  Z= 0.325
  Chirality :  0.045   0.288   1234
  Planarity :  0.004   0.040   1265
  Dihedral  :  9.586  84.157   1375
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 8.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 22.68 %
    Favored  : 72.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.90 (0.27), residues: 922
  helix: -1.33 (0.25), residues: 444
  sheet: -1.40 (0.61), residues: 70
  loop : -2.67 (0.30), residues: 408

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 262 
 HIS   0.003   0.001   HIS B 455 
 PHE   0.035   0.002   PHE A 155 
 TYR   0.024   0.001   TYR B 303 
 ARG   0.003   0.000   ARG B 338 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 107
  time to evaluate  : 0.730 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.7393 (OUTLIER) cc_final: 0.6957 (mm)
REVERT: A  284 ASN cc_start: 0.8579 (m-40) cc_final: 0.8123 (t0)
REVERT: A  471 HIS cc_start: 0.3935 (OUTLIER) cc_final: 0.2571 (m-70)
REVERT: B  262 TRP cc_start: 0.8373 (m-10) cc_final: 0.8125 (m-90)
REVERT: B  347 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6511 (pp30)
  outliers start: 34
  outliers final: 27
  residues processed: 130
  average time/residue: 0.1703
  time to fit residues: 30.6439
Evaluate side-chains
  134 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 104
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   87 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  401 VAL
Chi-restraints excluded: chain A residue  420 ILE
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 19 optimal weight:    0.9980
   chunk 81 optimal weight:    0.0980
   chunk 56 optimal weight:    0.4980
   chunk 42 optimal weight:    0.9990
   chunk 71 optimal weight:    2.9990
   chunk 52 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 11 optimal weight:    0.8980
   chunk 72 optimal weight:    0.8980
   chunk 86 optimal weight:    7.9990
   chunk 58 optimal weight:    0.0870
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.158694 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.124443 restraints weight = 10302.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.123399 restraints weight = 17499.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.124770 restraints weight = 15116.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7891
moved from start:          0.3038

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   7583  Z= 0.194
  Angle     :  0.741  24.668  10350  Z= 0.336
  Chirality :  0.046   0.506   1234
  Planarity :  0.004   0.038   1265
  Dihedral  :  9.356  80.781   1375
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.03 %
    Favored  : 91.97 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 23.07 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.80 (0.27), residues: 922
  helix: -1.22 (0.25), residues: 445
  sheet: -1.29 (0.62), residues: 70
  loop : -2.67 (0.29), residues: 407

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 262 
 HIS   0.002   0.001   HIS A 349 
 PHE   0.035   0.002   PHE A 155 
 TYR   0.017   0.001   TYR A 109 
 ARG   0.003   0.000   ARG B 338 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 109
  time to evaluate  : 0.754 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.7260 (OUTLIER) cc_final: 0.6810 (mm)
REVERT: A  124 TRP cc_start: 0.8372 (OUTLIER) cc_final: 0.7617 (t60)
REVERT: A  184 THR cc_start: 0.8924 (t) cc_final: 0.8554 (m)
REVERT: A  284 ASN cc_start: 0.8505 (m-40) cc_final: 0.8062 (t0)
REVERT: A  471 HIS cc_start: 0.3906 (OUTLIER) cc_final: 0.2605 (m-70)
REVERT: B  258 PHE cc_start: 0.6443 (m-80) cc_final: 0.6028 (m-80)
REVERT: B  262 TRP cc_start: 0.8370 (m-10) cc_final: 0.8109 (m-90)
REVERT: B  347 GLN cc_start: 0.7017 (OUTLIER) cc_final: 0.6504 (pp30)
  outliers start: 35
  outliers final: 29
  residues processed: 134
  average time/residue: 0.1785
  time to fit residues: 33.3105
Evaluate side-chains
  134 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 101
  time to evaluate  : 0.820 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   46 CYS
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   60 VAL
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 TRP
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  168 CYS
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  231 ILE
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 6 optimal weight:    0.0570
   chunk 34 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 67 optimal weight:    0.1980
   chunk 15 optimal weight:    0.5980
   chunk 56 optimal weight:    0.0970
   chunk 19 optimal weight:    0.8980
   chunk 36 optimal weight:    0.5980
   chunk 42 optimal weight:    3.9990
   chunk 35 optimal weight:    0.7980
   chunk 4 optimal weight:    0.9980
   overall best weight:    0.3096

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

Flipped N/Q/H residues before XYZ refinement:
** A 488 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3838 r_free = 0.3838 target = 0.160188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.126273 restraints weight = 10312.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.123941 restraints weight = 12877.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.125753 restraints weight = 13195.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7872
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   7583  Z= 0.163
  Angle     :  0.723  21.466  10350  Z= 0.329
  Chirality :  0.046   0.501   1234
  Planarity :  0.004   0.036   1265
  Dihedral  :  9.046  76.525   1375
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 7.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  3.87 %
    Allowed  : 23.71 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.58 (0.27), residues: 922
  helix: -1.01 (0.25), residues: 440
  sheet: -1.16 (0.65), residues: 60
  loop : -2.57 (0.29), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B 262 
 HIS   0.002   0.001   HIS A 349 
 PHE   0.035   0.001   PHE A 155 
 TYR   0.026   0.001   TYR B 303 
 ARG   0.003   0.000   ARG B 338 

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

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

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1844 Ramachandran restraints generated.
    922 Oldfield, 0 Emsley, 922 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 112
  time to evaluate  : 0.843 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 ILE cc_start: 0.7307 (OUTLIER) cc_final: 0.6752 (mm)
REVERT: A   49 ILE cc_start: 0.8526 (mm) cc_final: 0.8117 (mt)
REVERT: A  124 TRP cc_start: 0.8293 (OUTLIER) cc_final: 0.7618 (t60)
REVERT: A  184 THR cc_start: 0.8852 (t) cc_final: 0.8529 (m)
REVERT: A  284 ASN cc_start: 0.8507 (m-40) cc_final: 0.8039 (t0)
REVERT: A  464 PHE cc_start: 0.5802 (OUTLIER) cc_final: 0.5447 (m-10)
REVERT: A  471 HIS cc_start: 0.3886 (OUTLIER) cc_final: 0.2712 (m-70)
REVERT: B  258 PHE cc_start: 0.6524 (m-80) cc_final: 0.6051 (m-80)
REVERT: B  262 TRP cc_start: 0.8398 (m-10) cc_final: 0.8125 (m-90)
REVERT: B  347 GLN cc_start: 0.7032 (OUTLIER) cc_final: 0.6520 (pp30)
  outliers start: 30
  outliers final: 25
  residues processed: 132
  average time/residue: 0.1698
  time to fit residues: 31.4015
Evaluate side-chains
  135 residues out of total 776 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 105
  time to evaluate  : 0.818 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ILE
Chi-restraints excluded: chain A residue   98 VAL
Chi-restraints excluded: chain A residue  124 TRP
Chi-restraints excluded: chain A residue  125 ILE
Chi-restraints excluded: chain A residue  163 LEU
Chi-restraints excluded: chain A residue  164 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  200 LEU
Chi-restraints excluded: chain A residue  311 LEU
Chi-restraints excluded: chain A residue  349 HIS
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  378 MET
Chi-restraints excluded: chain A residue  423 ASN
Chi-restraints excluded: chain A residue  431 LEU
Chi-restraints excluded: chain A residue  436 PHE
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  448 VAL
Chi-restraints excluded: chain A residue  451 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  465 LEU
Chi-restraints excluded: chain A residue  471 HIS
Chi-restraints excluded: chain B residue  123 LEU
Chi-restraints excluded: chain B residue  246 VAL
Chi-restraints excluded: chain B residue  279 THR
Chi-restraints excluded: chain B residue  347 GLN
Chi-restraints excluded: chain B residue  405 ASN
Chi-restraints excluded: chain B residue  465 VAL
Chi-restraints excluded: chain B residue  473 LEU
Chi-restraints excluded: chain B residue  482 LEU
Chi-restraints excluded: chain B residue  508 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 91
   random chunks:
   chunk 23 optimal weight:    0.9990
   chunk 42 optimal weight:    4.9990
   chunk 10 optimal weight:    0.6980
   chunk 46 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 62 optimal weight:    1.9990
   chunk 0 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 88 optimal weight:    0.0010
   chunk 35 optimal weight:    0.9980
   chunk 86 optimal weight:    9.9990
   overall best weight:    0.7388

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

Flipped N/Q/H residues before XYZ refinement:
** B 518 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.158124 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 70)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.124288 restraints weight = 10188.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3392 r_free = 0.3392 target = 0.121991 restraints weight = 16343.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.122860 restraints weight = 14539.195|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7926
moved from start:          0.3228

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   7583  Z= 0.226
  Angle     :  0.742  21.800  10350  Z= 0.340
  Chirality :  0.047   0.456   1234
  Planarity :  0.004   0.036   1265
  Dihedral  :  8.909  71.817   1375
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.46 %
    Favored  : 91.54 %
  Rotamer:
    Outliers :  4.38 %
    Allowed  : 23.84 %
    Favored  : 71.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.56 (0.27), residues: 922
  helix: -0.96 (0.25), residues: 444
  sheet: -1.20 (0.65), residues: 60
  loop : -2.61 (0.29), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 262 
 HIS   0.003   0.001   HIS A 358 
 PHE   0.033   0.002   PHE A 155 
 TYR   0.020   0.001   TYR A 109 
 ARG   0.003   0.000   ARG B 328 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2397.44 seconds
wall clock time: 43 minutes 2.60 seconds (2582.60 seconds total)