Starting phenix.real_space_refine
on Wed Mar  4 03:19:42 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6ram_4780/03_2026/6ram_4780.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6ram_4780/03_2026/6ram_4780.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6ram_4780/03_2026/6ram_4780.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6ram_4780/03_2026/6ram_4780.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6ram_4780/03_2026/6ram_4780.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6ram_4780/03_2026/6ram_4780.map"
  }
  resolution = 3.8
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 6
    Type Number    sf(0)   Gaussians
     P       5      5.49       5
     Mg      2      5.21       5
     S      25      5.16       5
     C    6569      2.51       5
     N    1797      2.21       5
     O    1788      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 34 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10186
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4710
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 588, 4710
          Classifications: {'peptide': 588}
          Link IDs: {'PTRANS': 24, 'TRANS': 563}
    Chain: "B"
      Number of atoms: 4519
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 572, 4519
          Classifications: {'peptide': 572}
          Link IDs: {'PTRANS': 18, 'TRANS': 553}
    Chain: "C"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 121, 897
          Classifications: {'peptide': 121}
          Link IDs: {'PTRANS': 6, 'TRANS': 114}
    Chain: "A"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {' MG': 1, 'ADP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "B"
      Number of atoms: 32
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 32
          Unusual residues: {' MG': 1, 'ATP': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
  Time building chain proxies: 2.39, per 1000 atoms: 0.23
  Number of scatterers: 10186
  At special positions: 0
  Unit cell: (102.315, 87.237, 154.011, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     S      25     16.00
     P       5     15.00
     Mg      2     11.99
     O    1788      8.00
     N    1797      7.00
     C    6569      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=2, symmetry=0
    Simple disulfide: pdb=" SG  CYS C  22 " - pdb=" SG  CYS C  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  50 " - pdb=" SG  CYS C 108 " distance=2.06

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.84
  Conformation dependent library (CDL) restraints added in 514.9 milliseconds
  

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2344

  Finding SS restraints...
    Secondary structure from input PDB file:
      57 helices and 8 sheets defined
      64.3% alpha, 11.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 20
      removed outlier: 3.966A  pdb=" N   ILE A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   LEU A  19 " --> pdb=" O   PHE A  15 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 21 through 28
      Proline residue:  A  24  - end of helix
      removed outlier: 4.927A  pdb=" N   LEU A  27 " --> pdb=" O   PRO A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 29 through 45
      removed outlier: 3.654A  pdb=" N   VAL A  38 " --> pdb=" O   LEU A  34 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 64 through 70
    Processing helix  chain 'A' and resid 72 through 120
      removed outlier: 3.705A  pdb=" N   ILE A  76 " --> pdb=" O   LEU A  72 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   LEU A  97 " --> pdb=" O   GLY A  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 138
      removed outlier: 3.526A  pdb=" N   LEU A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ARG A 136 " --> pdb=" O   ARG A 132 " (cutoff:3.500A)
      removed outlier: 3.837A  pdb=" N   VAL A 137 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 138 through 155
      removed outlier: 3.529A  pdb=" N   THR A 149 " --> pdb=" O   ASN A 145 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   LEU A 152 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      removed outlier: 7.301A  pdb=" N   VAL A 153 " --> pdb=" O   THR A 149 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   GLY A 154 " --> pdb=" O   GLY A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 157 through 171
      removed outlier: 3.905A  pdb=" N   THR A 161 " --> pdb=" O   ALA A 157 " (cutoff:3.500A)
      removed outlier: 3.869A  pdb=" N   VAL A 163 " --> pdb=" O   LEU A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 182
      removed outlier: 3.871A  pdb=" N   VAL A 179 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 196
      removed outlier: 3.529A  pdb=" N   LEU A 187 " --> pdb=" O   VAL A 183 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   THR A 192 " --> pdb=" O   LEU A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 198 through 221
      removed outlier: 4.457A  pdb=" N   GLU A 204 " --> pdb=" O   SER A 200 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 222 through 228
    Processing helix  chain 'A' and resid 233 through 285
      removed outlier: 3.577A  pdb=" N   GLU A 237 " --> pdb=" O   ARG A 233 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   LEU A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      removed outlier: 3.736A  pdb=" N   TRP A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A 259 " --> pdb=" O   ARG A 255 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   PHE A 260 " --> pdb=" O   TRP A 256 " (cutoff:3.500A)
      removed outlier: 4.053A  pdb=" N   PHE A 261 " --> pdb=" O   PHE A 257 " (cutoff:3.500A)
      Proline residue:  A 262  - end of helix
      removed outlier: 3.619A  pdb=" N   ASP A 269 " --> pdb=" O   GLY A 265 " (cutoff:3.500A)
      removed outlier: 4.493A  pdb=" N   GLY A 281 " --> pdb=" O   TYR A 277 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   ARG A 285 " --> pdb=" O   GLY A 281 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 304
    Processing helix  chain 'A' and resid 304 through 313
    Processing helix  chain 'A' and resid 313 through 332
      removed outlier: 3.822A  pdb=" N   ARG A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 398 through 408
      removed outlier: 3.704A  pdb=" N   VAL A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
      removed outlier: 3.836A  pdb=" N   VAL A 403 " --> pdb=" O   LYS A 399 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   LEU A 405 " --> pdb=" O   SER A 401 " (cutoff:3.500A)
      removed outlier: 4.187A  pdb=" N   ILE A 406 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A 407 " --> pdb=" O   VAL A 403 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 425 through 427
      No H-bonds generated for 'chain 'A' and resid 425 through 427'
    Processing helix  chain 'A' and resid 428 through 435
    Processing helix  chain 'A' and resid 450 through 455
      removed outlier: 3.673A  pdb=" N   ARG A 455 " --> pdb=" O   LEU A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 3.874A  pdb=" N   VAL A 466 " --> pdb=" O   PRO A 462 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 480
    Processing helix  chain 'A' and resid 484 through 487
      removed outlier: 3.656A  pdb=" N   GLN A 487 " --> pdb=" O   LYS A 484 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 484 through 487'
    Processing helix  chain 'A' and resid 491 through 495
      removed outlier: 3.690A  pdb=" N   GLY A 494 " --> pdb=" O   GLY A 491 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 498 through 512
      removed outlier: 3.744A  pdb=" N   LEU A 507 " --> pdb=" O   GLN A 503 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   VAL A 508 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A 510 " --> pdb=" O   ALA A 506 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 544
      removed outlier: 3.928A  pdb=" N   ALA A 539 " --> pdb=" O   ARG A 535 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 561
      removed outlier: 3.914A  pdb=" N   ILE A 559 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   HIS A 561 " --> pdb=" O   SER A 557 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 586
    Processing helix  chain 'A' and resid 587 through 598
      removed outlier: 3.758A  pdb=" N   ALA A 591 " --> pdb=" O   GLY A 587 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   GLN A 596 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 6 through 14
    Processing helix  chain 'B' and resid 15 through 17
      No H-bonds generated for 'chain 'B' and resid 15 through 17'
    Processing helix  chain 'B' and resid 20 through 37
      removed outlier: 3.684A  pdb=" N   TRP B  26 " --> pdb=" O   TRP B  22 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 40 through 52
      removed outlier: 3.651A  pdb=" N   PHE B  44 " --> pdb=" O   LEU B  40 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 58 through 103
      removed outlier: 3.565A  pdb=" N   VAL B  66 " --> pdb=" O   ALA B  62 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   TYR B  77 " --> pdb=" O   GLY B  73 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   LEU B  82 " --> pdb=" O   ALA B  78 " (cutoff:3.500A)
      removed outlier: 3.807A  pdb=" N   VAL B  85 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
      removed outlier: 3.858A  pdb=" N   LEU B  99 " --> pdb=" O   ARG B  95 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 113
      removed outlier: 4.225A  pdb=" N   TYR B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   HIS B 111 " --> pdb=" O   ARG B 107 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 114 through 133
      removed outlier: 3.552A  pdb=" N   LEU B 118 " --> pdb=" O   ARG B 114 " (cutoff:3.500A)
      removed outlier: 4.115A  pdb=" N   ASN B 120 " --> pdb=" O   GLY B 116 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 134 through 156
      removed outlier: 3.811A  pdb=" N   SER B 144 " --> pdb=" O   GLY B 140 " (cutoff:3.500A)
      removed outlier: 3.503A  pdb=" N   PHE B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   PHE B 151 " --> pdb=" O   VAL B 147 " (cutoff:3.500A)
      removed outlier: 3.542A  pdb=" N   SER B 153 " --> pdb=" O   LEU B 149 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   TYR B 155 " --> pdb=" O   PHE B 151 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   ALA B 156 " --> pdb=" O   LEU B 152 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 158 through 166
      removed outlier: 3.983A  pdb=" N   ALA B 162 " --> pdb=" O   ASN B 158 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 167 through 207
      removed outlier: 4.188A  pdb=" N   GLY B 171 " --> pdb=" O   LEU B 167 " (cutoff:3.500A)
      removed outlier: 4.006A  pdb=" N   ALA B 175 " --> pdb=" O   GLY B 171 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   LEU B 182 " --> pdb=" O   PHE B 178 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   GLU B 189 " --> pdb=" O   ARG B 185 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   ALA B 190 " --> pdb=" O   ARG B 186 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 214
    Processing helix  chain 'B' and resid 217 through 270
      removed outlier: 3.881A  pdb=" N   LEU B 227 " --> pdb=" O   TRP B 223 " (cutoff:3.500A)
      removed outlier: 3.562A  pdb=" N   GLU B 233 " --> pdb=" O   ARG B 229 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
      Proline residue:  B 244  - end of helix
      removed outlier: 3.704A  pdb=" N   ALA B 247 " --> pdb=" O   GLY B 243 " (cutoff:3.500A)
      removed outlier: 3.804A  pdb=" N   MET B 253 " --> pdb=" O   LEU B 249 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL B 268 " --> pdb=" O   GLY B 264 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 317
      removed outlier: 4.209A  pdb=" N   LEU B 285 " --> pdb=" O   PHE B 281 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   LEU B 288 " --> pdb=" O   TYR B 284 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   TRP B 290 " --> pdb=" O   ALA B 286 " (cutoff:3.500A)
      Proline residue:  B 291  - end of helix
      removed outlier: 4.378A  pdb=" N   GLY B 296 " --> pdb=" O   ILE B 292 " (cutoff:3.500A)
      removed outlier: 4.630A  pdb=" N   TRP B 297 " --> pdb=" O   LEU B 293 " (cutoff:3.500A)
      removed outlier: 4.107A  pdb=" N   LEU B 315 " --> pdb=" O   ARG B 311 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ASP B 317 " --> pdb=" O   PHE B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 331 through 335
      removed outlier: 3.797A  pdb=" N   LEU B 335 " --> pdb=" O   LEU B 332 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 376 through 383
      removed outlier: 3.602A  pdb=" N   LEU B 380 " --> pdb=" O   GLY B 376 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 401 through 405
      removed outlier: 3.568A  pdb=" N   ARG B 404 " --> pdb=" O   GLU B 401 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 411
    Processing helix  chain 'B' and resid 427 through 433
    Processing helix  chain 'B' and resid 440 through 451
      removed outlier: 3.882A  pdb=" N   GLU B 445 " --> pdb=" O   ARG B 441 " (cutoff:3.500A)
      removed outlier: 3.801A  pdb=" N   ARG B 449 " --> pdb=" O   GLU B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 460
    Processing helix  chain 'B' and resid 462 through 466
      removed outlier: 3.731A  pdb=" N   GLU B 465 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 491
      removed outlier: 4.276A  pdb=" N   LYS B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 520
    Processing helix  chain 'B' and resid 532 through 538
      removed outlier: 3.788A  pdb=" N   LEU B 536 " --> pdb=" O   ARG B 532 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   HIS B 538 " --> pdb=" O   ALA B 534 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 558 through 562
      removed outlier: 3.511A  pdb=" N   GLN B 561 " --> pdb=" O   SER B 558 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 564 through 575
      removed outlier: 3.751A  pdb=" N   LEU B 572 " --> pdb=" O   GLU B 568 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 87 through 91
      removed outlier: 3.924A  pdb=" N   THR C  91 " --> pdb=" O   PRO C  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 376 through 379
      removed outlier: 6.144A  pdb=" N   LYS A 377 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   LEU A 360 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   VAL A 353 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 376 through 379
      removed outlier: 6.144A  pdb=" N   LYS A 377 " --> pdb=" O   LEU A 360 " (cutoff:3.500A)
      removed outlier: 7.992A  pdb=" N   LEU A 360 " --> pdb=" O   LYS A 377 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   CYS A 416 " --> pdb=" O   ARG A 356 " (cutoff:3.500A)
      removed outlier: 4.838A  pdb=" N   VAL A 358 " --> pdb=" O   ARG A 414 " (cutoff:3.500A)
      removed outlier: 7.209A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 436 through 439
      removed outlier: 6.308A  pdb=" N   LEU A 519 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 8.236A  pdb=" N   LEU A 566 " --> pdb=" O   LYS A 388 " (cutoff:3.500A)
      removed outlier: 5.988A  pdb=" N   ALA A 390 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 7.324A  pdb=" N   PHE A 568 " --> pdb=" O   ALA A 390 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   GLY A 577 " --> pdb=" O   ILE A 565 " (cutoff:3.500A)
      removed outlier: 4.505A  pdb=" N   GLU A 575 " --> pdb=" O   VAL A 567 " (cutoff:3.500A)
      removed outlier: 6.676A  pdb=" N   ARG A 569 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 5.381A  pdb=" N   LEU A 573 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 448 through 449
      removed outlier: 3.532A  pdb=" N   GLY A 448 " --> pdb=" O   LEU A 490 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 351 through 361
      removed outlier: 6.434A  pdb=" N   LEU B 353 " --> pdb=" O   LYS B 347 " (cutoff:3.500A)
      removed outlier: 7.583A  pdb=" N   LYS B 347 " --> pdb=" O   LEU B 353 " (cutoff:3.500A)
      removed outlier: 6.420A  pdb=" N   ARG B 355 " --> pdb=" O   GLY B 345 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   GLY B 345 " --> pdb=" O   ARG B 355 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU B 357 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   GLY B 343 " --> pdb=" O   LEU B 357 " (cutoff:3.500A)
      removed outlier: 4.290A  pdb=" N   VAL B 344 " --> pdb=" O   GLU B 392 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   GLU B 392 " --> pdb=" O   VAL B 344 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 414 through 417
      removed outlier: 6.496A  pdb=" N   GLY B 415 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 7.223A  pdb=" N   ASP B 499 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 6.333A  pdb=" N   ALA B 417 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   TRP B 541 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLU B 552 " --> pdb=" O   VAL B 544 " (cutoff:3.500A)
      removed outlier: 6.378A  pdb=" N   ASP B 546 " --> pdb=" O   ILE B 550 " (cutoff:3.500A)
      removed outlier: 5.172A  pdb=" N   ILE B 550 " --> pdb=" O   ASP B 546 " (cutoff:3.500A)
      removed outlier: 4.066A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.659A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.529A  pdb=" N   ALA C  92 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 5.701A  pdb=" N   ARG C  38 " --> pdb=" O   GLY C  47 " (cutoff:3.500A)
      removed outlier: 5.366A  pdb=" N   GLY C  47 " --> pdb=" O   ARG C  38 " (cutoff:3.500A)

    577 hydrogen bonds defined for protein.
    1692 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: 1.54

  Time building geometry restraints manager: 1.14 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 1611
        1.31 -     1.44: 3256
        1.44 -     1.57: 5474
        1.57 -     1.70: 13
        1.70 -     1.83: 45
  Bond restraints: 10399
  Sorted by residual:
  bond pdb=" C4  ATP B 601 "
       pdb=" C5  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.388  1.459 -0.071 1.00e-02 1.00e+04 5.01e+01
  bond pdb=" C5  ATP B 601 "
       pdb=" N7  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.387  1.327  0.060 1.00e-02 1.00e+04 3.54e+01
  bond pdb=" C4  ATP B 601 "
       pdb=" N9  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.374  1.321  0.053 1.00e-02 1.00e+04 2.84e+01
  bond pdb=" CA  GLY B 368 "
       pdb=" C   GLY B 368 "
    ideal  model  delta    sigma   weight residual
    1.519  1.484  0.035 7.00e-03 2.04e+04 2.44e+01
  bond pdb=" C5  ATP B 601 "
       pdb=" C6  ATP B 601 "
    ideal  model  delta    sigma   weight residual
    1.409  1.457 -0.048 1.00e-02 1.00e+04 2.34e+01
  ... (remaining 10394 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.78: 13684
        4.78 -     9.55: 406
        9.55 -    14.33: 16
       14.33 -    19.11: 0
       19.11 -    23.88: 2
  Bond angle restraints: 14108
  Sorted by residual:
  angle pdb=" PB  ATP B 601 "
        pdb=" O3B ATP B 601 "
        pdb=" PG  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     139.87  115.99   23.88 1.00e+00 1.00e+00 5.70e+02
  angle pdb=" PA  ATP B 601 "
        pdb=" O3A ATP B 601 "
        pdb=" PB  ATP B 601 "
      ideal   model   delta    sigma   weight residual
     136.83  114.66   22.17 1.00e+00 1.00e+00 4.92e+02
  angle pdb=" N   VAL B 241 "
        pdb=" CA  VAL B 241 "
        pdb=" C   VAL B 241 "
      ideal   model   delta    sigma   weight residual
     111.62  101.60   10.02 7.90e-01 1.60e+00 1.61e+02
  angle pdb=" N   SER B 558 "
        pdb=" CA  SER B 558 "
        pdb=" C   SER B 558 "
      ideal   model   delta    sigma   weight residual
     111.36  100.23   11.13 1.09e+00 8.42e-01 1.04e+02
  angle pdb=" N   ILE B 473 "
        pdb=" CA  ILE B 473 "
        pdb=" C   ILE B 473 "
      ideal   model   delta    sigma   weight residual
     113.53  103.64    9.89 9.80e-01 1.04e+00 1.02e+02
  ... (remaining 14103 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.89: 5905
       18.89 -    37.78: 204
       37.78 -    56.66: 50
       56.66 -    75.55: 24
       75.55 -    94.44: 6
  Dihedral angle restraints: 6189
    sinusoidal: 2527
      harmonic: 3662
  Sorted by residual:
  dihedral pdb=" N   ASP B 349 "
           pdb=" C   ASP B 349 "
           pdb=" CA  ASP B 349 "
           pdb=" CB  ASP B 349 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  135.65  -12.85     0      2.50e+00 1.60e-01 2.64e+01
  dihedral pdb=" O1B ADP A 701 "
           pdb=" O3A ADP A 701 "
           pdb=" PB  ADP A 701 "
           pdb=" PA  ADP A 701 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00 -154.44   94.44     1      2.00e+01 2.50e-03 2.59e+01
  dihedral pdb=" N   GLU B 438 "
           pdb=" C   GLU B 438 "
           pdb=" CA  GLU B 438 "
           pdb=" CB  GLU B 438 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  110.37   12.43     0      2.50e+00 1.60e-01 2.47e+01
  ... (remaining 6186 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.103: 1078
       0.103 -    0.205: 399
       0.205 -    0.308: 93
       0.308 -    0.410: 25
       0.410 -    0.513: 12
  Chirality restraints: 1607
  Sorted by residual:
  chirality pdb=" CA  ASN B 123 "
            pdb=" N   ASN B 123 "
            pdb=" C   ASN B 123 "
            pdb=" CB  ASN B 123 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.00    0.51 2.00e-01 2.50e+01 6.58e+00
  chirality pdb=" CA  GLU A 533 "
            pdb=" N   GLU A 533 "
            pdb=" C   GLU A 533 "
            pdb=" CB  GLU A 533 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.83e+00
  chirality pdb=" CA  GLN A 441 "
            pdb=" N   GLN A 441 "
            pdb=" C   GLN A 441 "
            pdb=" CB  GLN A 441 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.04    0.47 2.00e-01 2.50e+01 5.61e+00
  ... (remaining 1604 not shown)

  Planarity restraints: 1784
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 223 "    0.051 2.00e-02 2.50e+03   2.56e-02 1.64e+01
        pdb=" CG  TRP B 223 "   -0.005 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 223 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 223 "   -0.020 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 223 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 223 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 223 "   -0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 223 "    0.028 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 223 "   -0.014 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 223 "    0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A  52 "    0.053 2.00e-02 2.50e+03   2.50e-02 1.57e+01
        pdb=" CG  TRP A  52 "   -0.023 2.00e-02 2.50e+03
        pdb=" CD1 TRP A  52 "   -0.010 2.00e-02 2.50e+03
        pdb=" CD2 TRP A  52 "   -0.023 2.00e-02 2.50e+03
        pdb=" NE1 TRP A  52 "   -0.008 2.00e-02 2.50e+03
        pdb=" CE2 TRP A  52 "   -0.005 2.00e-02 2.50e+03
        pdb=" CE3 TRP A  52 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A  52 "    0.031 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A  52 "   -0.011 2.00e-02 2.50e+03
        pdb=" CH2 TRP A  52 "    0.023 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU B 216 "   -0.019 2.00e-02 2.50e+03   3.94e-02 1.56e+01
        pdb=" C   LEU B 216 "    0.068 2.00e-02 2.50e+03
        pdb=" O   LEU B 216 "   -0.027 2.00e-02 2.50e+03
        pdb=" N   GLU B 217 "   -0.023 2.00e-02 2.50e+03
  ... (remaining 1781 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 459
        2.71 -     3.26: 10007
        3.26 -     3.80: 15369
        3.80 -     4.35: 20680
        4.35 -     4.90: 33370
  Nonbonded interactions: 79885
  Sorted by model distance:
  nonbonded pdb=" O2B ADP A 701 "
            pdb="MG    MG A 702 "
     model   vdw
     2.162 2.170
  nonbonded pdb=" OG1 THR A 400 "
            pdb="MG    MG A 702 "
     model   vdw
     2.173 2.170
  nonbonded pdb=" OE1 GLN A 441 "
            pdb="MG    MG A 702 "
     model   vdw
     2.233 2.170
  nonbonded pdb=" O2B ATP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.273 2.170
  nonbonded pdb=" O1G ATP B 601 "
            pdb="MG    MG B 602 "
     model   vdw
     2.316 2.170
  ... (remaining 79880 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             1.060
  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:             0.000
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.700
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.190
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.240
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
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      :  0.016   0.071  10401  Z= 1.142
  Angle     :  1.964  23.885  14112  Z= 1.407
  Chirality :  0.119   0.513   1607
  Planarity :  0.012   0.082   1784
  Dihedral  : 11.725  94.441   3839
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 10.48
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  2.82 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  2.96 %
    Favored  : 96.95 %
  Cbeta Deviations :  0.60 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.86 (0.20), residues: 1275
  helix: -1.94 (0.16), residues: 745
  sheet: -0.77 (0.42), residues: 132
  loop : -1.78 (0.27), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 229 
 TYR   0.049   0.006   TYR A 277 
 PHE   0.044   0.007   PHE B 313 
 TRP   0.053   0.008   TRP A  52 
 HIS   0.006   0.001   HIS B 400 

Details of bonding type rmsd
  covalent geometry    : bond        0.01648 (10399)
  covalent geometry    : angle       1.96419 (14108)
  SS BOND              : bond        0.02220 (    2)
  SS BOND              : angle       2.01736 (    4)
  hydrogen bonds       : bond        0.24935 (  575)
  hydrogen bonds       : angle       8.57617 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  329 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 328
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   54 ILE cc_start: 0.9395 (mm) cc_final: 0.9152 (mm)
REVERT: A  160 PHE cc_start: 0.7924 (m-80) cc_final: 0.7686 (m-80)
REVERT: A  303 LEU cc_start: 0.9286 (tp) cc_final: 0.9056 (tp)
REVERT: A  309 ASP cc_start: 0.8721 (t0) cc_final: 0.8382 (t70)
REVERT: A  321 MET cc_start: 0.8433 (tpt) cc_final: 0.8182 (tpt)
REVERT: A  359 TRP cc_start: 0.7903 (m100) cc_final: 0.6883 (m100)
REVERT: A  372 LYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7913 (tptm)
REVERT: A  376 LEU cc_start: 0.8173 (mp) cc_final: 0.7886 (mm)
REVERT: A  391 LEU cc_start: 0.9224 (mp) cc_final: 0.8647 (tt)
REVERT: A  503 GLN cc_start: 0.8433 (mm-40) cc_final: 0.8161 (tp40)
REVERT: A  538 GLU cc_start: 0.8616 (tt0) cc_final: 0.8292 (tp30)
REVERT: A  554 HIS cc_start: 0.6726 (m90) cc_final: 0.5869 (m-70)
REVERT: B   21 ARG cc_start: 0.8232 (ttp-110) cc_final: 0.7516 (ptm160)
REVERT: B  125 ASP cc_start: 0.6470 (m-30) cc_final: 0.6154 (m-30)
REVERT: B  191 GLN cc_start: 0.8573 (tp40) cc_final: 0.8209 (tm-30)
REVERT: B  282 ASN cc_start: 0.9411 (t0) cc_final: 0.9014 (t0)
REVERT: B  299 MET cc_start: 0.8777 (mmm) cc_final: 0.8476 (mmp)
REVERT: B  359 LEU cc_start: 0.8936 (tp) cc_final: 0.8701 (tt)
REVERT: B  365 MET cc_start: 0.7840 (ttp) cc_final: 0.7448 (tmm)
REVERT: B  505 VAL cc_start: 0.9116 (t) cc_final: 0.8908 (p)
REVERT: C   90 ASP cc_start: 0.7806 (m-30) cc_final: 0.7139 (m-30)
  outliers start: 1
  outliers final: 0
  residues processed: 328
  average time/residue: 0.1374
  time to fit residues: 58.3999
Evaluate side-chains
  194 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 193
  time to evaluate  : 0.351 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    0.7980
   chunk 97 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:    0.5980
   chunk 33 optimal weight:    7.9990
   chunk 123 optimal weight:    4.9990
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.3980
   chunk 51 optimal weight:    0.8980
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
** A 243 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 101 HIS
B 120 ASN
B 123 ASN
C  13 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.099960 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.080516 restraints weight = 25748.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.083339 restraints weight = 13684.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.085261 restraints weight = 8904.557|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.086574 restraints weight = 6626.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.087493 restraints weight = 5381.215|
|-----------------------------------------------------------------------------|
r_work (final): 0.3414
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7889
moved from start:          0.3558

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10401  Z= 0.151
  Angle     :  0.712   9.528  14112  Z= 0.362
  Chirality :  0.042   0.174   1607
  Planarity :  0.006   0.074   1784
  Dihedral  :  6.678  65.334   1485
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Rotamer:
    Outliers :  3.34 %
    Allowed  : 11.34 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.21 (0.22), residues: 1275
  helix: -0.42 (0.18), residues: 770
  sheet: -0.42 (0.43), residues: 130
  loop : -1.47 (0.28), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 569 
 TYR   0.020   0.002   TYR A 589 
 PHE   0.024   0.002   PHE A  88 
 TRP   0.032   0.002   TRP B 290 
 HIS   0.005   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (10399)
  covalent geometry    : angle       0.71134 (14108)
  SS BOND              : bond        0.00946 (    2)
  SS BOND              : angle       1.42057 (    4)
  hydrogen bonds       : bond        0.05267 (  575)
  hydrogen bonds       : angle       4.76241 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  262 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 227
  time to evaluate  : 0.404 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 LEU cc_start: 0.9231 (mt) cc_final: 0.8768 (tt)
REVERT: A   40 THR cc_start: 0.9122 (m) cc_final: 0.8794 (p)
REVERT: A   94 GLU cc_start: 0.7940 (tp30) cc_final: 0.7587 (tp30)
REVERT: A  118 MET cc_start: 0.9013 (mmp) cc_final: 0.8412 (mmp)
REVERT: A  305 GLN cc_start: 0.8393 (OUTLIER) cc_final: 0.8148 (tp40)
REVERT: A  309 ASP cc_start: 0.8294 (t0) cc_final: 0.7955 (t0)
REVERT: A  359 TRP cc_start: 0.7966 (m100) cc_final: 0.7420 (m100)
REVERT: A  569 ARG cc_start: 0.7508 (mtt90) cc_final: 0.7240 (mtt90)
REVERT: B   21 ARG cc_start: 0.8046 (ttp-110) cc_final: 0.7755 (ptt90)
REVERT: B   38 PHE cc_start: 0.8714 (t80) cc_final: 0.8510 (t80)
REVERT: B  132 MET cc_start: 0.8963 (tmm) cc_final: 0.8498 (tmm)
REVERT: B  185 ARG cc_start: 0.8837 (OUTLIER) cc_final: 0.8630 (ttm110)
REVERT: B  255 PHE cc_start: 0.8742 (t80) cc_final: 0.8387 (t80)
REVERT: B  281 PHE cc_start: 0.9046 (t80) cc_final: 0.8402 (t80)
REVERT: B  282 ASN cc_start: 0.8975 (t0) cc_final: 0.8768 (t0)
REVERT: B  299 MET cc_start: 0.8753 (mmm) cc_final: 0.8442 (mmp)
REVERT: B  301 LEU cc_start: 0.8562 (tt) cc_final: 0.8305 (tp)
REVERT: B  316 LEU cc_start: 0.8700 (OUTLIER) cc_final: 0.8433 (mt)
REVERT: B  365 MET cc_start: 0.7986 (ttp) cc_final: 0.7657 (tmm)
REVERT: C   51 ILE cc_start: 0.8870 (tp) cc_final: 0.8607 (tp)
REVERT: C   83 MET cc_start: 0.8195 (mpp) cc_final: 0.7984 (mpp)
REVERT: C   84 ASN cc_start: 0.8537 (m-40) cc_final: 0.7923 (p0)
REVERT: C   86 LEU cc_start: 0.8824 (mt) cc_final: 0.8177 (mt)
  outliers start: 35
  outliers final: 13
  residues processed: 247
  average time/residue: 0.1113
  time to fit residues: 37.6655
Evaluate side-chains
  187 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 171
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  305 GLN
Chi-restraints excluded: chain A residue  332 ASP
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain B residue   66 VAL
Chi-restraints excluded: chain B residue  167 LEU
Chi-restraints excluded: chain B residue  185 ARG
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue  108 CYS
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 84 optimal weight:    0.5980
   chunk 114 optimal weight:    3.9990
   chunk 94 optimal weight:    0.9990
   chunk 99 optimal weight:    0.9980
   chunk 43 optimal weight:    0.2980
   chunk 64 optimal weight:    2.9990
   chunk 29 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 95 optimal weight:    3.9990
   chunk 31 optimal weight:    5.9990
   chunk 124 optimal weight:    7.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 219 ASN
A 243 ASN
C  13 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.097841 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.078725 restraints weight = 25525.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.081463 restraints weight = 13633.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.083382 restraints weight = 8915.510|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.084677 restraints weight = 6623.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3383 r_free = 0.3383 target = 0.085547 restraints weight = 5389.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3376
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7915
moved from start:          0.4406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10401  Z= 0.138
  Angle     :  0.666   8.997  14112  Z= 0.325
  Chirality :  0.041   0.222   1607
  Planarity :  0.004   0.037   1784
  Dihedral  :  5.873  51.887   1481
  Min Nonbonded Distance : 1.935

Molprobity Statistics.
  All-atom Clashscore : 8.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.12 %
    Favored  : 97.88 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 13.82 %
    Favored  : 83.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.48 (0.22), residues: 1275
  helix:  0.24 (0.18), residues: 773
  sheet: -0.32 (0.44), residues: 126
  loop : -1.28 (0.29), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C  67 
 TYR   0.017   0.001   TYR C 113 
 PHE   0.020   0.001   PHE A 597 
 TRP   0.025   0.002   TRP B 290 
 HIS   0.005   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (10399)
  covalent geometry    : angle       0.66550 (14108)
  SS BOND              : bond        0.00851 (    2)
  SS BOND              : angle       1.76009 (    4)
  hydrogen bonds       : bond        0.04507 (  575)
  hydrogen bonds       : angle       4.36507 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  219 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 189
  time to evaluate  : 0.346 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9171 (m) cc_final: 0.8892 (p)
REVERT: A   72 LEU cc_start: 0.7762 (mm) cc_final: 0.7462 (mm)
REVERT: A   94 GLU cc_start: 0.8009 (tp30) cc_final: 0.7760 (tp30)
REVERT: A  140 ASP cc_start: 0.6863 (m-30) cc_final: 0.6216 (m-30)
REVERT: A  145 ASN cc_start: 0.8638 (m-40) cc_final: 0.8110 (m110)
REVERT: A  305 GLN cc_start: 0.8294 (OUTLIER) cc_final: 0.8086 (tp40)
REVERT: A  359 TRP cc_start: 0.8123 (m100) cc_final: 0.7310 (m100)
REVERT: A  417 VAL cc_start: 0.8957 (OUTLIER) cc_final: 0.8723 (p)
REVERT: B   21 ARG cc_start: 0.8005 (ttp-110) cc_final: 0.7597 (ptt90)
REVERT: B   38 PHE cc_start: 0.8741 (t80) cc_final: 0.8499 (t80)
REVERT: B  130 ARG cc_start: 0.7546 (ttp-110) cc_final: 0.7342 (ttp-110)
REVERT: B  132 MET cc_start: 0.8979 (tmm) cc_final: 0.8734 (tmm)
REVERT: B  281 PHE cc_start: 0.9023 (t80) cc_final: 0.8752 (t80)
REVERT: B  282 ASN cc_start: 0.9053 (t0) cc_final: 0.8750 (t0)
REVERT: B  316 LEU cc_start: 0.8552 (OUTLIER) cc_final: 0.8350 (mt)
REVERT: B  365 MET cc_start: 0.8141 (ttp) cc_final: 0.7919 (tmm)
REVERT: B  523 LYS cc_start: 0.7982 (pttm) cc_final: 0.7719 (pttm)
REVERT: C   45 ARG cc_start: 0.8279 (mtm110) cc_final: 0.7840 (mtm110)
REVERT: C   84 ASN cc_start: 0.8472 (m-40) cc_final: 0.8263 (p0)
  outliers start: 30
  outliers final: 15
  residues processed: 207
  average time/residue: 0.1082
  time to fit residues: 30.5415
Evaluate side-chains
  179 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 161
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   71 HIS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  180 VAL
Chi-restraints excluded: chain A residue  305 GLN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  358 VAL
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   63 SER
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 75 optimal weight:    0.8980
   chunk 84 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 117 optimal weight:    0.0040
   chunk 55 optimal weight:    5.9990
   chunk 87 optimal weight:    0.7980
   chunk 71 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 42 optimal weight:    3.9990
   chunk 82 optimal weight:    0.7980
   overall best weight:    0.6792

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

Flipped N/Q/H residues before XYZ refinement:
A 243 ASN
B 287 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.097464 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3245 r_free = 0.3245 target = 0.078243 restraints weight = 25975.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.081057 restraints weight = 13810.808|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.082998 restraints weight = 9006.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 49)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.084329 restraints weight = 6682.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.085205 restraints weight = 5416.405|
|-----------------------------------------------------------------------------|
r_work (final): 0.3371
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7921
moved from start:          0.4835

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10401  Z= 0.129
  Angle     :  0.639   8.071  14112  Z= 0.311
  Chirality :  0.040   0.195   1607
  Planarity :  0.004   0.048   1784
  Dihedral  :  5.585  55.768   1481
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.62 %
    Allowed  : 15.92 %
    Favored  : 80.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.02 (0.23), residues: 1275
  helix:  0.66 (0.19), residues: 779
  sheet: -0.05 (0.47), residues: 119
  loop : -1.19 (0.29), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 569 
 TYR   0.029   0.001   TYR B  92 
 PHE   0.037   0.001   PHE A  15 
 TRP   0.020   0.001   TRP B 446 
 HIS   0.004   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 (10399)
  covalent geometry    : angle       0.63816 (14108)
  SS BOND              : bond        0.00307 (    2)
  SS BOND              : angle       1.39253 (    4)
  hydrogen bonds       : bond        0.04080 (  575)
  hydrogen bonds       : angle       4.17621 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 180
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9224 (m) cc_final: 0.8939 (p)
REVERT: A   72 LEU cc_start: 0.7747 (mm) cc_final: 0.7473 (mm)
REVERT: A   94 GLU cc_start: 0.8122 (tp30) cc_final: 0.7842 (tp30)
REVERT: A  140 ASP cc_start: 0.6779 (m-30) cc_final: 0.6271 (m-30)
REVERT: A  145 ASN cc_start: 0.8636 (m-40) cc_final: 0.8006 (m110)
REVERT: A  305 GLN cc_start: 0.8304 (mm-40) cc_final: 0.8083 (tp40)
REVERT: A  365 LYS cc_start: 0.8476 (ttmt) cc_final: 0.7988 (ttmt)
REVERT: A  391 LEU cc_start: 0.9008 (mp) cc_final: 0.8734 (mt)
REVERT: A  417 VAL cc_start: 0.8970 (OUTLIER) cc_final: 0.8697 (p)
REVERT: A  444 PHE cc_start: 0.7757 (t80) cc_final: 0.7411 (t80)
REVERT: A  508 VAL cc_start: 0.8329 (OUTLIER) cc_final: 0.7837 (p)
REVERT: A  531 GLU cc_start: 0.8447 (tm-30) cc_final: 0.8236 (tm-30)
REVERT: B  132 MET cc_start: 0.9042 (tmm) cc_final: 0.8728 (tmm)
REVERT: B  154 MET cc_start: 0.8630 (mmm) cc_final: 0.7939 (mmm)
REVERT: B  282 ASN cc_start: 0.9019 (t0) cc_final: 0.8666 (t0)
REVERT: B  523 LYS cc_start: 0.8022 (pttm) cc_final: 0.7796 (pttm)
  outliers start: 38
  outliers final: 17
  residues processed: 204
  average time/residue: 0.1009
  time to fit residues: 28.8255
Evaluate side-chains
  172 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 153
  time to evaluate  : 0.343 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   36 LEU
Chi-restraints excluded: chain A residue   71 HIS
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   94 LEU
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 35 optimal weight:    0.9980
   chunk 3 optimal weight:    0.2980
   chunk 51 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 50 optimal weight:    0.0670
   chunk 121 optimal weight:    0.7980
   chunk 28 optimal weight:    2.9990
   chunk 10 optimal weight:    0.8980
   chunk 85 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   overall best weight:    0.5918

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

Flipped N/Q/H residues before XYZ refinement:
B 123 ASN
B 280 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.097847 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.078903 restraints weight = 25809.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.081770 restraints weight = 13523.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3357 r_free = 0.3357 target = 0.083726 restraints weight = 8736.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.085034 restraints weight = 6435.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.085832 restraints weight = 5214.874|
|-----------------------------------------------------------------------------|
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.5229

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10401  Z= 0.120
  Angle     :  0.624   8.734  14112  Z= 0.301
  Chirality :  0.040   0.175   1607
  Planarity :  0.004   0.038   1784
  Dihedral  :  5.303  58.284   1481
  Min Nonbonded Distance : 1.918

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.35 %
    Favored  : 97.65 %
  Rotamer:
    Outliers :  2.57 %
    Allowed  : 18.40 %
    Favored  : 79.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.40 (0.23), residues: 1275
  helix:  1.01 (0.19), residues: 778
  sheet:  0.05 (0.46), residues: 124
  loop : -1.14 (0.29), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG C  45 
 TYR   0.020   0.001   TYR B  92 
 PHE   0.032   0.001   PHE A  15 
 TRP   0.008   0.001   TRP B  14 
 HIS   0.008   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (10399)
  covalent geometry    : angle       0.62370 (14108)
  SS BOND              : bond        0.00210 (    2)
  SS BOND              : angle       1.51052 (    4)
  hydrogen bonds       : bond        0.03739 (  575)
  hydrogen bonds       : angle       3.99934 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 180
  time to evaluate  : 0.397 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9226 (m) cc_final: 0.8940 (p)
REVERT: A   94 GLU cc_start: 0.8105 (tp30) cc_final: 0.7842 (tp30)
REVERT: A  140 ASP cc_start: 0.6714 (m-30) cc_final: 0.6282 (m-30)
REVERT: A  145 ASN cc_start: 0.8586 (m-40) cc_final: 0.7905 (m-40)
REVERT: A  391 LEU cc_start: 0.9001 (mp) cc_final: 0.8728 (mt)
REVERT: A  417 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8687 (p)
REVERT: A  441 GLN cc_start: 0.7982 (tt0) cc_final: 0.7592 (tp-100)
REVERT: A  444 PHE cc_start: 0.7793 (t80) cc_final: 0.7359 (t80)
REVERT: A  508 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.7871 (p)
REVERT: A  531 GLU cc_start: 0.8468 (tm-30) cc_final: 0.8253 (tm-30)
REVERT: B  112 LYS cc_start: 0.8776 (mmmt) cc_final: 0.8053 (mtmm)
REVERT: B  132 MET cc_start: 0.9119 (tmm) cc_final: 0.8708 (tmm)
REVERT: B  154 MET cc_start: 0.8564 (mmm) cc_final: 0.7886 (mmm)
REVERT: B  188 ARG cc_start: 0.9006 (mmm-85) cc_final: 0.8670 (tpp80)
REVERT: B  282 ASN cc_start: 0.9023 (t0) cc_final: 0.8582 (t0)
REVERT: B  365 MET cc_start: 0.8475 (tmm) cc_final: 0.8231 (tmm)
REVERT: B  523 LYS cc_start: 0.8035 (pttm) cc_final: 0.7722 (pptt)
REVERT: C   45 ARG cc_start: 0.8365 (mtm110) cc_final: 0.7950 (mtm110)
REVERT: C   53 LYS cc_start: 0.8013 (tppp) cc_final: 0.7438 (tppt)
REVERT: C   65 LYS cc_start: 0.8945 (pttp) cc_final: 0.8598 (pttm)
REVERT: C  107 ARG cc_start: 0.7876 (tpp80) cc_final: 0.7285 (ttt90)
  outliers start: 27
  outliers final: 17
  residues processed: 198
  average time/residue: 0.1130
  time to fit residues: 30.7026
Evaluate side-chains
  178 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 159
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   71 HIS
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  316 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 37 optimal weight:    7.9990
   chunk 119 optimal weight:    5.9990
   chunk 1 optimal weight:    0.8980
   chunk 55 optimal weight:    1.9990
   chunk 48 optimal weight:    5.9990
   chunk 98 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 40 optimal weight:    3.9990
   chunk 106 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 96 optimal weight:    1.9990
   overall best weight:    1.7788

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

Flipped N/Q/H residues before XYZ refinement:
A  87 HIS
A 128 ASN
B 419 GLN
B 538 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3526 r_free = 0.3526 target = 0.093770 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3182 r_free = 0.3182 target = 0.074696 restraints weight = 26515.365|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.077350 restraints weight = 14207.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.079183 restraints weight = 9380.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.080451 restraints weight = 7053.188|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.081309 restraints weight = 5759.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3308
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8035
moved from start:          0.5395

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  10401  Z= 0.213
  Angle     :  0.702   7.884  14112  Z= 0.345
  Chirality :  0.042   0.174   1607
  Planarity :  0.004   0.044   1784
  Dihedral  :  5.447  56.562   1481
  Min Nonbonded Distance : 1.822

Molprobity Statistics.
  All-atom Clashscore : 10.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.59 %
    Favored  : 97.41 %
  Rotamer:
    Outliers :  4.39 %
    Allowed  : 17.92 %
    Favored  : 77.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.23), residues: 1275
  helix:  0.97 (0.19), residues: 777
  sheet:  0.28 (0.47), residues: 126
  loop : -1.17 (0.30), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 229 
 TYR   0.024   0.002   TYR B  92 
 PHE   0.025   0.002   PHE A  15 
 TRP   0.010   0.001   TRP C  36 
 HIS   0.005   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00489 (10399)
  covalent geometry    : angle       0.70112 (14108)
  SS BOND              : bond        0.00420 (    2)
  SS BOND              : angle       2.19837 (    4)
  hydrogen bonds       : bond        0.04312 (  575)
  hydrogen bonds       : angle       4.29049 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  206 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 160
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9285 (m) cc_final: 0.9015 (p)
REVERT: A   94 GLU cc_start: 0.8087 (tp30) cc_final: 0.7843 (tp30)
REVERT: A  140 ASP cc_start: 0.7084 (m-30) cc_final: 0.6535 (m-30)
REVERT: A  145 ASN cc_start: 0.8636 (m-40) cc_final: 0.8052 (m-40)
REVERT: A  391 LEU cc_start: 0.9026 (mp) cc_final: 0.8726 (mt)
REVERT: A  417 VAL cc_start: 0.8895 (OUTLIER) cc_final: 0.8693 (p)
REVERT: A  531 GLU cc_start: 0.8583 (tm-30) cc_final: 0.8344 (tm-30)
REVERT: B  112 LYS cc_start: 0.8861 (mmmt) cc_final: 0.8599 (mmmt)
REVERT: B  130 ARG cc_start: 0.8259 (tmm-80) cc_final: 0.7841 (tmm-80)
REVERT: B  132 MET cc_start: 0.9148 (tmm) cc_final: 0.8429 (tmm)
REVERT: B  154 MET cc_start: 0.8732 (mmm) cc_final: 0.8189 (mmm)
REVERT: B  188 ARG cc_start: 0.9093 (mmm-85) cc_final: 0.8812 (tpp80)
REVERT: B  281 PHE cc_start: 0.8912 (t80) cc_final: 0.7547 (t80)
REVERT: B  282 ASN cc_start: 0.9085 (t0) cc_final: 0.8643 (t0)
REVERT: B  365 MET cc_start: 0.8413 (tmm) cc_final: 0.8078 (tmm)
REVERT: B  523 LYS cc_start: 0.8192 (OUTLIER) cc_final: 0.7945 (pptt)
REVERT: C   45 ARG cc_start: 0.8449 (mtm110) cc_final: 0.7982 (mtm110)
REVERT: C   53 LYS cc_start: 0.8091 (tppp) cc_final: 0.7613 (tppt)
REVERT: C   65 LYS cc_start: 0.8996 (pttp) cc_final: 0.8658 (pttm)
REVERT: C  107 ARG cc_start: 0.7947 (tpp80) cc_final: 0.7654 (ttt90)
  outliers start: 46
  outliers final: 30
  residues processed: 185
  average time/residue: 0.1095
  time to fit residues: 28.2121
Evaluate side-chains
  184 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 152
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   37 LEU
Chi-restraints excluded: chain A residue   86 VAL
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  165 LEU
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  251 VAL
Chi-restraints excluded: chain A residue  254 ILE
Chi-restraints excluded: chain A residue  305 GLN
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  417 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  576 GLU
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  260 VAL
Chi-restraints excluded: chain B residue  330 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 34 optimal weight:    2.9990
   chunk 87 optimal weight:    1.9990
   chunk 114 optimal weight:    0.9990
   chunk 104 optimal weight:    8.9990
   chunk 3 optimal weight:    4.9990
   chunk 40 optimal weight:    0.3980
   chunk 14 optimal weight:    5.9990
   chunk 124 optimal weight:    7.9990
   chunk 46 optimal weight:    0.9980
   chunk 60 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 243 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.095785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3226 r_free = 0.3226 target = 0.076852 restraints weight = 26013.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.079592 restraints weight = 13718.652|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3316 r_free = 0.3316 target = 0.081461 restraints weight = 8950.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.082762 restraints weight = 6672.170|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.083638 restraints weight = 5416.477|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.5564

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10401  Z= 0.130
  Angle     :  0.654  11.463  14112  Z= 0.314
  Chirality :  0.040   0.159   1607
  Planarity :  0.004   0.038   1784
  Dihedral  :  5.291  63.316   1481
  Min Nonbonded Distance : 1.953

Molprobity Statistics.
  All-atom Clashscore : 8.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 19.45 %
    Favored  : 77.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.58 (0.23), residues: 1275
  helix:  1.17 (0.19), residues: 783
  sheet:  0.34 (0.47), residues: 127
  loop : -1.25 (0.29), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 114 
 TYR   0.028   0.001   TYR C 113 
 PHE   0.016   0.001   PHE A 124 
 TRP   0.008   0.001   TRP B 262 
 HIS   0.005   0.001   HIS A 561 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 (10399)
  covalent geometry    : angle       0.65387 (14108)
  SS BOND              : bond        0.00249 (    2)
  SS BOND              : angle       1.39904 (    4)
  hydrogen bonds       : bond        0.03814 (  575)
  hydrogen bonds       : angle       4.06165 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  204 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 170
  time to evaluate  : 0.308 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9265 (m) cc_final: 0.8985 (p)
REVERT: A  140 ASP cc_start: 0.6994 (m-30) cc_final: 0.6498 (m-30)
REVERT: A  391 LEU cc_start: 0.9014 (mp) cc_final: 0.8722 (mt)
REVERT: A  441 GLN cc_start: 0.7974 (tt0) cc_final: 0.7657 (tp-100)
REVERT: A  508 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8032 (p)
REVERT: A  531 GLU cc_start: 0.8576 (tm-30) cc_final: 0.8308 (tm-30)
REVERT: B  112 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8134 (mttp)
REVERT: B  130 ARG cc_start: 0.8226 (tmm-80) cc_final: 0.7901 (tmm-80)
REVERT: B  131 GLU cc_start: 0.8401 (mm-30) cc_final: 0.8168 (mm-30)
REVERT: B  132 MET cc_start: 0.9166 (tmm) cc_final: 0.8470 (tmm)
REVERT: B  154 MET cc_start: 0.8689 (mmm) cc_final: 0.8130 (mmm)
REVERT: B  281 PHE cc_start: 0.8833 (t80) cc_final: 0.7535 (t80)
REVERT: B  365 MET cc_start: 0.8379 (tmm) cc_final: 0.7986 (tmm)
REVERT: B  523 LYS cc_start: 0.8180 (pttm) cc_final: 0.7959 (pptt)
REVERT: C   45 ARG cc_start: 0.8339 (mtm110) cc_final: 0.7868 (mtm110)
REVERT: C   53 LYS cc_start: 0.8008 (tppp) cc_final: 0.7598 (tppt)
REVERT: C   65 LYS cc_start: 0.8965 (pttp) cc_final: 0.8660 (pttm)
REVERT: C   87 LYS cc_start: 0.8849 (pttt) cc_final: 0.8627 (pttm)
  outliers start: 34
  outliers final: 20
  residues processed: 193
  average time/residue: 0.1072
  time to fit residues: 28.3374
Evaluate side-chains
  177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 156
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  188 LEU
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  310 LEU
Chi-restraints excluded: chain A residue  312 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain C residue   84 ASN
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 83 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 105 optimal weight:    0.6980
   chunk 42 optimal weight:    3.9990
   chunk 3 optimal weight:    0.8980
   chunk 89 optimal weight:    0.8980
   chunk 51 optimal weight:    0.8980
   chunk 72 optimal weight:    1.9990
   chunk 53 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 116 optimal weight:    6.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
** A 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 308 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 120 ASN
** C  82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3561 r_free = 0.3561 target = 0.095646 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.076576 restraints weight = 26032.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.079298 restraints weight = 13950.369|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.081171 restraints weight = 9140.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.082429 restraints weight = 6832.690|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.083272 restraints weight = 5590.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.3347
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7991
moved from start:          0.5690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  10401  Z= 0.138
  Angle     :  0.670  11.419  14112  Z= 0.319
  Chirality :  0.041   0.168   1607
  Planarity :  0.004   0.046   1784
  Dihedral  :  5.256  63.627   1481
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 9.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.76 %
    Allowed  : 20.31 %
    Favored  : 76.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.23), residues: 1275
  helix:  1.25 (0.19), residues: 781
  sheet:  0.28 (0.45), residues: 132
  loop : -1.25 (0.29), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B 188 
 TYR   0.023   0.001   TYR B  92 
 PHE   0.024   0.001   PHE A  15 
 TRP   0.010   0.001   TRP C  36 
 HIS   0.003   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10399)
  covalent geometry    : angle       0.66916 (14108)
  SS BOND              : bond        0.00717 (    2)
  SS BOND              : angle       1.55494 (    4)
  hydrogen bonds       : bond        0.03877 (  575)
  hydrogen bonds       : angle       4.05253 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 163
  time to evaluate  : 0.287 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9310 (m) cc_final: 0.9005 (p)
REVERT: A  140 ASP cc_start: 0.7022 (m-30) cc_final: 0.6478 (m-30)
REVERT: A  391 LEU cc_start: 0.9020 (mp) cc_final: 0.8731 (mt)
REVERT: A  441 GLN cc_start: 0.7973 (tt0) cc_final: 0.7660 (tp-100)
REVERT: A  508 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8048 (p)
REVERT: A  531 GLU cc_start: 0.8555 (tm-30) cc_final: 0.8288 (tm-30)
REVERT: B  112 LYS cc_start: 0.8755 (mmmt) cc_final: 0.8161 (mttp)
REVERT: B  120 ASN cc_start: 0.8191 (m-40) cc_final: 0.7966 (m110)
REVERT: B  130 ARG cc_start: 0.8291 (tmm-80) cc_final: 0.7955 (tmm-80)
REVERT: B  132 MET cc_start: 0.9164 (tmm) cc_final: 0.8559 (tmm)
REVERT: B  154 MET cc_start: 0.8662 (mmm) cc_final: 0.8106 (mmm)
REVERT: B  281 PHE cc_start: 0.8776 (t80) cc_final: 0.7589 (t80)
REVERT: B  365 MET cc_start: 0.8351 (tmm) cc_final: 0.7944 (tmm)
REVERT: B  462 LYS cc_start: 0.7701 (tptp) cc_final: 0.7446 (tptp)
REVERT: B  523 LYS cc_start: 0.8218 (OUTLIER) cc_final: 0.7963 (pptt)
REVERT: C   20 LEU cc_start: 0.8764 (tp) cc_final: 0.8465 (tp)
REVERT: C   53 LYS cc_start: 0.8027 (tppp) cc_final: 0.7666 (tppt)
REVERT: C   65 LYS cc_start: 0.8989 (pttp) cc_final: 0.8711 (pttm)
REVERT: C  107 ARG cc_start: 0.7981 (tpp80) cc_final: 0.7379 (ttt90)
  outliers start: 29
  outliers final: 20
  residues processed: 180
  average time/residue: 0.1055
  time to fit residues: 26.2004
Evaluate side-chains
  177 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 155
  time to evaluate  : 0.367 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  556 LEU
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue   71 LEU
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  133 VAL
Chi-restraints excluded: chain B residue  144 SER
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  259 THR
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  523 LYS
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 43 optimal weight:    0.0070
   chunk 62 optimal weight:    3.9990
   chunk 70 optimal weight:    0.9990
   chunk 106 optimal weight:    0.6980
   chunk 98 optimal weight:    0.7980
   chunk 29 optimal weight:    0.6980
   chunk 89 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 51 optimal weight:    4.9990
   chunk 76 optimal weight:    0.8980
   overall best weight:    0.5598

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

Flipped N/Q/H residues before XYZ refinement:
A 243 ASN
A 308 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.096719 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.077699 restraints weight = 25965.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.080445 restraints weight = 13675.554|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.082335 restraints weight = 8912.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3356 r_free = 0.3356 target = 0.083605 restraints weight = 6641.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.084504 restraints weight = 5395.997|
|-----------------------------------------------------------------------------|
r_work (final): 0.3369
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7960
moved from start:          0.5849

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10401  Z= 0.122
  Angle     :  0.675  10.358  14112  Z= 0.320
  Chirality :  0.040   0.169   1607
  Planarity :  0.004   0.053   1784
  Dihedral  :  5.163  65.060   1481
  Min Nonbonded Distance : 1.949

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 20.59 %
    Favored  : 76.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.23), residues: 1275
  helix:  1.36 (0.19), residues: 779
  sheet:  0.35 (0.45), residues: 132
  loop : -1.21 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG B 188 
 TYR   0.022   0.001   TYR B  92 
 PHE   0.015   0.001   PHE A 304 
 TRP   0.009   0.001   TRP B 290 
 HIS   0.003   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 (10399)
  covalent geometry    : angle       0.67517 (14108)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       1.28424 (    4)
  hydrogen bonds       : bond        0.03656 (  575)
  hydrogen bonds       : angle       3.93645 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  187 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 159
  time to evaluate  : 0.377 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9299 (m) cc_final: 0.9011 (p)
REVERT: A  140 ASP cc_start: 0.7063 (m-30) cc_final: 0.6564 (m-30)
REVERT: A  391 LEU cc_start: 0.9034 (mp) cc_final: 0.8753 (mt)
REVERT: A  441 GLN cc_start: 0.7963 (tt0) cc_final: 0.7662 (tp-100)
REVERT: A  508 VAL cc_start: 0.8465 (OUTLIER) cc_final: 0.8080 (p)
REVERT: A  531 GLU cc_start: 0.8564 (tm-30) cc_final: 0.8320 (tm-30)
REVERT: B  130 ARG cc_start: 0.8339 (tmm-80) cc_final: 0.8000 (tmm-80)
REVERT: B  132 MET cc_start: 0.9187 (tmm) cc_final: 0.8562 (tmm)
REVERT: B  154 MET cc_start: 0.8624 (mmm) cc_final: 0.8024 (mmm)
REVERT: B  281 PHE cc_start: 0.8740 (t80) cc_final: 0.7500 (t80)
REVERT: B  282 ASN cc_start: 0.8866 (t0) cc_final: 0.8511 (t0)
REVERT: B  365 MET cc_start: 0.8348 (tmm) cc_final: 0.7910 (tmm)
REVERT: B  462 LYS cc_start: 0.7732 (tptp) cc_final: 0.7510 (tptp)
REVERT: B  523 LYS cc_start: 0.8235 (pttm) cc_final: 0.8011 (pptt)
REVERT: C   53 LYS cc_start: 0.7996 (tppp) cc_final: 0.7656 (tppt)
REVERT: C   65 LYS cc_start: 0.8986 (pttp) cc_final: 0.8757 (pttm)
REVERT: C   83 MET cc_start: 0.9136 (mpp) cc_final: 0.8889 (mpp)
REVERT: C  107 ARG cc_start: 0.7977 (tpp80) cc_final: 0.7467 (ttt90)
  outliers start: 28
  outliers final: 21
  residues processed: 173
  average time/residue: 0.1024
  time to fit residues: 25.0054
Evaluate side-chains
  176 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 154
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain A residue  597 PHE
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  370 THR
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 18 optimal weight:    1.9990
   chunk 91 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 0 optimal weight:   10.0000
   chunk 115 optimal weight:    0.6980
   chunk 40 optimal weight:    4.9990
   chunk 122 optimal weight:    5.9990
   chunk 117 optimal weight:    3.9990
   chunk 108 optimal weight:    0.6980
   chunk 83 optimal weight:    0.9980
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
A 243 ASN
A 308 GLN
B 120 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3571 r_free = 0.3571 target = 0.096306 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3229 r_free = 0.3229 target = 0.077140 restraints weight = 25850.930|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.079853 restraints weight = 13777.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3320 r_free = 0.3320 target = 0.081733 restraints weight = 9032.105|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3343 r_free = 0.3343 target = 0.082960 restraints weight = 6748.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.083827 restraints weight = 5529.122|
|-----------------------------------------------------------------------------|
r_work (final): 0.3357
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7979
moved from start:          0.5889

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  10401  Z= 0.135
  Angle     :  0.688  11.383  14112  Z= 0.327
  Chirality :  0.040   0.154   1607
  Planarity :  0.004   0.051   1784
  Dihedral  :  5.146  64.054   1481
  Min Nonbonded Distance : 1.906

Molprobity Statistics.
  All-atom Clashscore : 9.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 21.93 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.23), residues: 1275
  helix:  1.36 (0.19), residues: 779
  sheet:  0.43 (0.45), residues: 132
  loop : -1.22 (0.30), residues: 364

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C  38 
 TYR   0.022   0.001   TYR B  92 
 PHE   0.026   0.001   PHE A  15 
 TRP   0.009   0.001   TRP C  36 
 HIS   0.004   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (10399)
  covalent geometry    : angle       0.68810 (14108)
  SS BOND              : bond        0.00153 (    2)
  SS BOND              : angle       1.36072 (    4)
  hydrogen bonds       : bond        0.03712 (  575)
  hydrogen bonds       : angle       3.95074 ( 1692)

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

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

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2550 Ramachandran restraints generated.
    1275 Oldfield, 0 Emsley, 1275 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 157
  time to evaluate  : 0.370 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   40 THR cc_start: 0.9313 (m) cc_final: 0.9008 (p)
REVERT: A  140 ASP cc_start: 0.7011 (m-30) cc_final: 0.6560 (m-30)
REVERT: A  391 LEU cc_start: 0.9039 (mp) cc_final: 0.8764 (mt)
REVERT: A  441 GLN cc_start: 0.7971 (tt0) cc_final: 0.7643 (tp-100)
REVERT: A  508 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8011 (p)
REVERT: A  531 GLU cc_start: 0.8575 (tm-30) cc_final: 0.8325 (tm-30)
REVERT: B  130 ARG cc_start: 0.8394 (tmm-80) cc_final: 0.8023 (tmm-80)
REVERT: B  132 MET cc_start: 0.9191 (tmm) cc_final: 0.8541 (tmm)
REVERT: B  154 MET cc_start: 0.8633 (mmm) cc_final: 0.8034 (mmm)
REVERT: B  281 PHE cc_start: 0.8754 (t80) cc_final: 0.7521 (t80)
REVERT: B  282 ASN cc_start: 0.8878 (t0) cc_final: 0.8504 (t0)
REVERT: B  365 MET cc_start: 0.8341 (tmm) cc_final: 0.7913 (tmm)
REVERT: C   53 LYS cc_start: 0.7993 (tppp) cc_final: 0.7641 (tppt)
REVERT: C   65 LYS cc_start: 0.8979 (pttp) cc_final: 0.8749 (pttm)
REVERT: C   83 MET cc_start: 0.9200 (mpp) cc_final: 0.8964 (mpp)
REVERT: C  107 ARG cc_start: 0.8009 (tpp80) cc_final: 0.7741 (ttt90)
  outliers start: 22
  outliers final: 19
  residues processed: 168
  average time/residue: 0.0985
  time to fit residues: 23.3132
Evaluate side-chains
  171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 151
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 GLU
Chi-restraints excluded: chain A residue  101 VAL
Chi-restraints excluded: chain A residue  118 MET
Chi-restraints excluded: chain A residue  245 ASP
Chi-restraints excluded: chain A residue  308 GLN
Chi-restraints excluded: chain A residue  353 VAL
Chi-restraints excluded: chain A residue  438 ILE
Chi-restraints excluded: chain A residue  508 VAL
Chi-restraints excluded: chain A residue  574 VAL
Chi-restraints excluded: chain B residue   92 TYR
Chi-restraints excluded: chain B residue  163 PHE
Chi-restraints excluded: chain B residue  173 PHE
Chi-restraints excluded: chain B residue  176 MET
Chi-restraints excluded: chain B residue  203 GLU
Chi-restraints excluded: chain B residue  258 LEU
Chi-restraints excluded: chain B residue  344 VAL
Chi-restraints excluded: chain B residue  528 LEU
Chi-restraints excluded: chain B residue  569 MET
Chi-restraints excluded: chain C residue  104 LEU
Chi-restraints excluded: chain C residue  122 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 63 optimal weight:    5.9990
   chunk 16 optimal weight:    0.4980
   chunk 7 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 37 optimal weight:    0.8980
   chunk 59 optimal weight:    0.8980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
A 308 GLN
B 120 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.096658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3234 r_free = 0.3234 target = 0.077411 restraints weight = 26062.052|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.080145 restraints weight = 13815.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.082036 restraints weight = 9039.641|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.083300 restraints weight = 6730.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.084100 restraints weight = 5486.987|
|-----------------------------------------------------------------------------|
r_work (final): 0.3360
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7971
moved from start:          0.5963

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10401  Z= 0.130
  Angle     :  0.688  11.006  14112  Z= 0.326
  Chirality :  0.040   0.152   1607
  Planarity :  0.004   0.051   1784
  Dihedral  :  5.117  64.622   1481
  Min Nonbonded Distance : 1.913

Molprobity Statistics.
  All-atom Clashscore : 8.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 22.12 %
    Favored  : 75.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.83 (0.23), residues: 1275
  helix:  1.40 (0.19), residues: 780
  sheet:  0.47 (0.45), residues: 132
  loop : -1.25 (0.30), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG C  38 
 TYR   0.022   0.001   TYR B  92 
 PHE   0.012   0.001   PHE A 124 
 TRP   0.009   0.001   TRP B 446 
 HIS   0.003   0.001   HIS C  80 

Details of bonding type rmsd
  covalent geometry    : bond        0.00297 (10399)
  covalent geometry    : angle       0.68797 (14108)
  SS BOND              : bond        0.00151 (    2)
  SS BOND              : angle       1.29215 (    4)
  hydrogen bonds       : bond        0.03718 (  575)
  hydrogen bonds       : angle       3.90964 ( 1692)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1620.18 seconds
wall clock time: 28 minutes 35.53 seconds (1715.53 seconds total)