Starting phenix.real_space_refine
on Wed Mar  4 03:16:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rag_4774/03_2026/6rag_4774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rag_4774/03_2026/6rag_4774.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rag_4774/03_2026/6rag_4774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rag_4774/03_2026/6rag_4774.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rag_4774/03_2026/6rag_4774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rag_4774/03_2026/6rag_4774.map"
  }
  resolution = 4.2
  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=   0.048
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    6568      2.51       5
     N    1797      2.21       5
     O    1791      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 37 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: 10188
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 4690
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 586, 4690
          Classifications: {'peptide': 586}
          Link IDs: {'PTRANS': 24, 'TRANS': 561}
    Chain: "B"
      Number of atoms: 4541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 575, 4541
          Classifications: {'peptide': 575}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 18, 'TRANS': 556}
    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: 1.97, per 1000 atoms: 0.19
  Number of scatterers: 10188
  At special positions: 0
  Unit cell: (102.315, 92.622, 155.088, 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    1791      8.00
     N    1797      7.00
     C    6568      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: 0.90
  Conformation dependent library (CDL) restraints added in 438.0 milliseconds
  

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2346

  Finding SS restraints...
    Secondary structure from input PDB file:
      53 helices and 6 sheets defined
      65.2% alpha, 10.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.29
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 23
      removed outlier: 4.261A  pdb=" N   ILE A  18 " --> pdb=" O   LEU A  14 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 25 through 45
    Processing helix  chain 'A' and resid 46 through 56
      removed outlier: 4.178A  pdb=" N   PHE A  50 " --> pdb=" O   THR A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 64 through 76
      removed outlier: 5.012A  pdb=" N   LEU A  73 " --> pdb=" O   ARG A  69 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LEU A  74 " --> pdb=" O   PHE A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 119
    Processing helix  chain 'A' and resid 123 through 128
      removed outlier: 3.610A  pdb=" N   ARG A 127 " --> pdb=" O   GLY A 123 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 129 through 173
      removed outlier: 4.341A  pdb=" N   LEU A 133 " --> pdb=" O   PRO A 129 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   THR A 138 " --> pdb=" O   MET A 134 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   ASP A 140 " --> pdb=" O   ARG A 136 " (cutoff:3.500A)
      removed outlier: 5.571A  pdb=" N   VAL A 141 " --> pdb=" O   VAL A 137 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ASP A 142 " --> pdb=" O   THR A 138 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   LEU A 152 " --> pdb=" O   ILE A 148 " (cutoff:3.500A)
      removed outlier: 3.944A  pdb=" N   SER A 173 " --> pdb=" O   MET A 169 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 173 through 181
      removed outlier: 4.461A  pdb=" N   VAL A 179 " --> pdb=" O   LYS A 175 " (cutoff:3.500A)
      removed outlier: 4.344A  pdb=" N   VAL A 180 " --> pdb=" O   LEU A 176 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 183 through 222
    Processing helix  chain 'A' and resid 222 through 229
    Processing helix  chain 'A' and resid 231 through 258
      removed outlier: 3.742A  pdb=" N   LEU A 242 " --> pdb=" O   LYS A 238 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   TRP A 256 " --> pdb=" O   GLU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 259 through 286
    Processing helix  chain 'A' and resid 289 through 304
      removed outlier: 3.657A  pdb=" N   VAL A 297 " --> pdb=" O   LEU A 293 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE A 304 " --> pdb=" O   THR A 300 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 305 through 307
      No H-bonds generated for 'chain 'A' and resid 305 through 307'
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.771A  pdb=" N   ASP A 312 " --> pdb=" O   GLN A 308 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 332
      removed outlier: 3.645A  pdb=" N   GLY A 319 " --> pdb=" O   ASN A 315 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   ARG A 326 " --> pdb=" O   ALA A 322 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 374
    Processing helix  chain 'A' and resid 398 through 407
    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
      removed outlier: 3.771A  pdb=" N   HIS A 435 " --> pdb=" O   GLU A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 449 through 455
    Processing helix  chain 'A' and resid 462 through 473
      removed outlier: 3.861A  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 498 through 514
      removed outlier: 3.774A  pdb=" N   VAL A 508 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   SER A 514 " --> pdb=" O   ALA A 510 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 529 through 544
    Processing helix  chain 'A' and resid 555 through 562
    Processing helix  chain 'A' and resid 579 through 586
    Processing helix  chain 'A' and resid 587 through 594
    Processing helix  chain 'B' and resid 5 through 18
      removed outlier: 4.006A  pdb=" N   LEU B   9 " --> pdb=" O   SER B   5 " (cutoff:3.500A)
      Proline residue:  B  15  - end of helix
    Processing helix  chain 'B' and resid 20 through 54
      Proline residue:  B  42  - end of helix
      removed outlier: 4.006A  pdb=" N   ALA B  54 " --> pdb=" O   ASP B  50 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 57 through 105
      removed outlier: 4.111A  pdb=" N   TYR B  61 " --> pdb=" O   GLY B  57 " (cutoff:3.500A)
      removed outlier: 3.701A  pdb=" N   SER B  72 " --> pdb=" O   SER B  68 " (cutoff:3.500A)
      removed outlier: 4.214A  pdb=" N   VAL B  85 " --> pdb=" O   ARG B  81 " (cutoff:3.500A)
      removed outlier: 4.093A  pdb=" N   THR B 104 " --> pdb=" O   HIS B 100 " (cutoff:3.500A)
      removed outlier: 4.125A  pdb=" N   LEU B 105 " --> pdb=" O   HIS B 101 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 106 through 113
      removed outlier: 3.774A  pdb=" N   TYR B 110 " --> pdb=" O   ASP B 106 " (cutoff:3.500A)
      removed outlier: 4.140A  pdb=" N   LYS B 112 " --> pdb=" O   ASP B 108 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   HIS B 113 " --> pdb=" O   PHE B 109 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 115 through 133
    Processing helix  chain 'B' and resid 134 through 158
      removed outlier: 3.534A  pdb=" N   PHE B 145 " --> pdb=" O   SER B 141 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   LEU B 148 " --> pdb=" O   SER B 144 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 159 through 207
      removed outlier: 3.658A  pdb=" N   TYR B 164 " --> pdb=" O   ARG B 160 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   ILE B 168 " --> pdb=" O   TYR B 164 " (cutoff:3.500A)
      Proline residue:  B 170  - end of helix
      removed outlier: 3.563A  pdb=" N   PHE B 178 " --> pdb=" O   LEU B 174 " (cutoff:3.500A)
      removed outlier: 3.641A  pdb=" N   ARG B 185 " --> pdb=" O   ARG B 181 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLY B 207 " --> pdb=" O   GLU B 203 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 207 through 214
    Processing helix  chain 'B' and resid 216 through 243
      removed outlier: 3.763A  pdb=" N   ALA B 222 " --> pdb=" O   ARG B 218 " (cutoff:3.500A)
      removed outlier: 4.259A  pdb=" N   VAL B 241 " --> pdb=" O   ALA B 237 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 243 through 271
      removed outlier: 4.564A  pdb=" N   ALA B 247 " --> pdb=" O   GLY B 243 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ALA B 256 " --> pdb=" O   LEU B 252 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 274 through 288
      removed outlier: 3.631A  pdb=" N   LEU B 278 " --> pdb=" O   SER B 274 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   LEU B 285 " --> pdb=" O   PHE B 281 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 290 through 316
    Processing helix  chain 'B' and resid 376 through 384
      removed outlier: 4.146A  pdb=" N   VAL B 384 " --> pdb=" O   LEU B 380 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 406 through 412
    Processing helix  chain 'B' and resid 427 through 433
      removed outlier: 3.804A  pdb=" N   ALA B 433 " --> pdb=" O   LEU B 429 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 434 through 436
      No H-bonds generated for 'chain 'B' and resid 434 through 436'
    Processing helix  chain 'B' and resid 440 through 451
      removed outlier: 3.659A  pdb=" N   VAL B 444 " --> pdb=" O   ASP B 440 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 453 through 458
    Processing helix  chain 'B' and resid 462 through 466
      removed outlier: 4.270A  pdb=" N   GLU B 465 " --> pdb=" O   LYS B 462 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 476 through 491
      removed outlier: 3.615A  pdb=" N   LYS B 491 " --> pdb=" O   ARG B 487 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 506 through 519
    Processing helix  chain 'B' and resid 532 through 539
      removed outlier: 3.568A  pdb=" N   ALA B 535 " --> pdb=" O   ARG B 532 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   HIS B 538 " --> pdb=" O   ALA B 535 " (cutoff:3.500A)
      removed outlier: 3.860A  pdb=" N   ALA B 539 " --> pdb=" O   LEU B 536 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 555 through 560
    Processing helix  chain 'B' and resid 564 through 578
      removed outlier: 3.681A  pdb=" N   GLU B 568 " --> pdb=" O   GLY B 564 " (cutoff:3.500A)
      removed outlier: 3.774A  pdb=" N   ALA B 578 " --> pdb=" O   LYS B 574 " (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 379 through 383
      removed outlier: 4.979A  pdb=" N   VAL A 379 " --> pdb=" O   ASP A 357 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   VAL A 353 " --> pdb=" O   VAL A 383 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   VAL A 358 " --> pdb=" O   ARG A 414 " (cutoff:3.500A)
      removed outlier: 6.327A  pdb=" N   ARG A 414 " --> pdb=" O   VAL A 358 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 436 through 439
      removed outlier: 5.774A  pdb=" N   LEU A 519 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 7.588A  pdb=" N   ILE A 552 " --> pdb=" O   LEU A 519 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   LEU A 521 " --> pdb=" O   ILE A 552 " (cutoff:3.500A)
      removed outlier: 6.288A  pdb=" N   VAL A 389 " --> pdb=" O   ILE A 551 " (cutoff:3.500A)
      removed outlier: 6.451A  pdb=" N   ARG A 569 " --> pdb=" O   LEU A 573 " (cutoff:3.500A)
      removed outlier: 5.294A  pdb=" N   LEU A 573 " --> pdb=" O   ARG A 569 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 354 through 361
      removed outlier: 4.474A  pdb=" N   LEU B 354 " --> pdb=" O   LEU B 346 " (cutoff:3.500A)
      removed outlier: 5.100A  pdb=" N   VAL B 344 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   THR B 358 " --> pdb=" O   GLU B 342 " (cutoff:3.500A)
      removed outlier: 7.010A  pdb=" N   GLU B 342 " --> pdb=" O   THR B 358 " (cutoff:3.500A)
      removed outlier: 6.580A  pdb=" N   THR B 360 " --> pdb=" O   ARG B 340 " (cutoff:3.500A)
      removed outlier: 6.884A  pdb=" N   ARG B 340 " --> pdb=" O   THR B 360 " (cutoff:3.500A)
      removed outlier: 5.170A  pdb=" N   PHE B 341 " --> pdb=" O   TYR B 396 " (cutoff:3.500A)
      removed outlier: 6.976A  pdb=" N   TYR B 396 " --> pdb=" O   PHE B 341 " (cutoff:3.500A)
      removed outlier: 4.978A  pdb=" N   GLY B 343 " --> pdb=" O   ARG B 394 " (cutoff:3.500A)
      removed outlier: 4.877A  pdb=" N   ARG B 394 " --> pdb=" O   GLY B 343 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 414 through 417
      removed outlier: 6.091A  pdb=" N   GLY B 415 " --> pdb=" O   ILE B 497 " (cutoff:3.500A)
      removed outlier: 7.460A  pdb=" N   ASP B 499 " --> pdb=" O   GLY B 415 " (cutoff:3.500A)
      removed outlier: 6.454A  pdb=" N   ALA B 417 " --> pdb=" O   ASP B 499 " (cutoff:3.500A)
      removed outlier: 6.685A  pdb=" N   LEU B 496 " --> pdb=" O   LEU B 527 " (cutoff:3.500A)
      removed outlier: 7.741A  pdb=" N   ILE B 529 " --> pdb=" O   LEU B 496 " (cutoff:3.500A)
      removed outlier: 6.361A  pdb=" N   LEU B 498 " --> pdb=" O   ILE B 529 " (cutoff:3.500A)
      removed outlier: 6.220A  pdb=" N   LEU B 367 " --> pdb=" O   LEU B 528 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   TRP B 541 " --> pdb=" O   THR B 366 " (cutoff:3.500A)
      removed outlier: 4.201A  pdb=" N   LEU B 545 " --> pdb=" O   THR B 370 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   ALA C 101 " --> pdb=" O   VAL C 109 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 4 through 7
      removed outlier: 3.660A  pdb=" N   THR C  78 " --> pdb=" O   ASP C  73 " (cutoff:3.500A)
    Processing sheet with id=AA6, 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: 5.702A  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)

    634 hydrogen bonds defined for protein.
    1863 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: 1.62

  Time building geometry restraints manager: 1.21 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: 1615
        1.31 -     1.44: 2800
        1.44 -     1.56: 5924
        1.56 -     1.69: 16
        1.69 -     1.81: 45
  Bond restraints: 10400
  Sorted by residual:
  bond pdb=" C4  ATP B 602 "
       pdb=" C5  ATP B 602 "
    ideal  model  delta    sigma   weight residual
    1.388  1.464 -0.076 1.00e-02 1.00e+04 5.79e+01
  bond pdb=" C5  ATP B 602 "
       pdb=" C6  ATP B 602 "
    ideal  model  delta    sigma   weight residual
    1.409  1.474 -0.065 1.00e-02 1.00e+04 4.21e+01
  bond pdb=" N   PRO A 515 "
       pdb=" CD  PRO A 515 "
    ideal  model  delta    sigma   weight residual
    1.473  1.556 -0.083 1.40e-02 5.10e+03 3.55e+01
  bond pdb=" CA  PHE A 296 "
       pdb=" C   PHE A 296 "
    ideal  model  delta    sigma   weight residual
    1.522  1.593 -0.071 1.39e-02 5.18e+03 2.57e+01
  bond pdb=" C4  ATP B 602 "
       pdb=" N9  ATP B 602 "
    ideal  model  delta    sigma   weight residual
    1.374  1.326  0.048 1.00e-02 1.00e+04 2.30e+01
  ... (remaining 10395 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.99: 13772
        3.99 -     7.98: 292
        7.98 -    11.96: 44
       11.96 -    15.95: 1
       15.95 -    19.94: 2
  Bond angle restraints: 14111
  Sorted by residual:
  angle pdb=" PB  ATP B 602 "
        pdb=" O3B ATP B 602 "
        pdb=" PG  ATP B 602 "
      ideal   model   delta    sigma   weight residual
     139.87  119.93   19.94 1.00e+00 1.00e+00 3.98e+02
  angle pdb=" PA  ATP B 602 "
        pdb=" O3A ATP B 602 "
        pdb=" PB  ATP B 602 "
      ideal   model   delta    sigma   weight residual
     136.83  118.46   18.37 1.00e+00 1.00e+00 3.37e+02
  angle pdb=" N   VAL B 298 "
        pdb=" CA  VAL B 298 "
        pdb=" C   VAL B 298 "
      ideal   model   delta    sigma   weight residual
     110.53   98.04   12.49 9.40e-01 1.13e+00 1.77e+02
  angle pdb=" N   GLY B 296 "
        pdb=" CA  GLY B 296 "
        pdb=" C   GLY B 296 "
      ideal   model   delta    sigma   weight residual
     112.64  123.80  -11.16 1.21e+00 6.83e-01 8.51e+01
  angle pdb=" N   LEU B 536 "
        pdb=" CA  LEU B 536 "
        pdb=" C   LEU B 536 "
      ideal   model   delta    sigma   weight residual
     112.97  103.27    9.70 1.06e+00 8.90e-01 8.37e+01
  ... (remaining 14106 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    29.84: 5955
       29.84 -    59.67: 212
       59.67 -    89.51: 22
       89.51 -   119.34: 1
      119.34 -   149.17: 2
  Dihedral angle restraints: 6192
    sinusoidal: 2527
      harmonic: 3665
  Sorted by residual:
  dihedral pdb=" O1B ADP A 702 "
           pdb=" O3A ADP A 702 "
           pdb=" PB  ADP A 702 "
           pdb=" PA  ADP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     300.00  150.82  149.17     1      2.00e+01 2.50e-03 4.46e+01
  dihedral pdb=" O2A ADP A 702 "
           pdb=" O3A ADP A 702 "
           pdb=" PA  ADP A 702 "
           pdb=" PB  ADP A 702 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -60.00   62.82 -122.82     1      2.00e+01 2.50e-03 3.70e+01
  dihedral pdb=" CA  TRP B 290 "
           pdb=" C   TRP B 290 "
           pdb=" N   PRO B 291 "
           pdb=" CA  PRO B 291 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -150.78  -29.22     0      5.00e+00 4.00e-02 3.42e+01
  ... (remaining 6189 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.096: 1335
       0.096 -    0.191: 229
       0.191 -    0.287: 29
       0.287 -    0.383: 9
       0.383 -    0.478: 7
  Chirality restraints: 1609
  Sorted by residual:
  chirality pdb=" CA  ASP B 500 "
            pdb=" N   ASP B 500 "
            pdb=" C   ASP B 500 "
            pdb=" CB  ASP B 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.72e+00
  chirality pdb=" CA  VAL C 102 "
            pdb=" N   VAL C 102 "
            pdb=" C   VAL C 102 "
            pdb=" CB  VAL C 102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.90   -0.46 2.00e-01 2.50e+01 5.37e+00
  chirality pdb=" CA  LEU C 104 "
            pdb=" N   LEU C 104 "
            pdb=" C   LEU C 104 "
            pdb=" CB  LEU C 104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.05    0.46 2.00e-01 2.50e+01 5.36e+00
  ... (remaining 1606 not shown)

  Planarity restraints: 1785
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 138 "    0.023 2.00e-02 2.50e+03   4.74e-02 2.25e+01
        pdb=" C   THR A 138 "   -0.082 2.00e-02 2.50e+03
        pdb=" O   THR A 138 "    0.031 2.00e-02 2.50e+03
        pdb=" N   SER A 139 "    0.028 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   TRP A  23 "   -0.052 5.00e-02 4.00e+02   7.84e-02 9.84e+00
        pdb=" N   PRO A  24 "    0.136 5.00e-02 4.00e+02
        pdb=" CA  PRO A  24 "   -0.040 5.00e-02 4.00e+02
        pdb=" CD  PRO A  24 "   -0.044 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 243 "   -0.048 5.00e-02 4.00e+02   7.16e-02 8.19e+00
        pdb=" N   PRO B 244 "    0.124 5.00e-02 4.00e+02
        pdb=" CA  PRO B 244 "   -0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO B 244 "   -0.040 5.00e-02 4.00e+02
  ... (remaining 1782 not shown)

  Histogram of nonbonded interaction distances:
        1.91 -     2.51: 32
        2.51 -     3.11: 7067
        3.11 -     3.70: 15963
        3.70 -     4.30: 21137
        4.30 -     4.90: 34422
  Nonbonded interactions: 78621
  Sorted by model distance:
  nonbonded pdb="MG    MG B 601 "
            pdb=" O1B ATP B 602 "
     model   vdw
     1.911 2.170
  nonbonded pdb="MG    MG B 601 "
            pdb=" O1G ATP B 602 "
     model   vdw
     1.923 2.170
  nonbonded pdb=" OE1 GLN B 419 "
            pdb="MG    MG B 601 "
     model   vdw
     2.024 2.170
  nonbonded pdb=" OG  SER B 378 "
            pdb="MG    MG B 601 "
     model   vdw
     2.050 2.170
  nonbonded pdb=" O   THR A 400 "
            pdb=" OG  SER A 404 "
     model   vdw
     2.252 3.040
  ... (remaining 78616 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:             1.030
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     9.640
  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:1.060
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.030
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8006
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      :  0.010   0.103  10402  Z= 0.510
  Angle     :  1.420  19.938  14115  Z= 0.926
  Chirality :  0.079   0.478   1609
  Planarity :  0.008   0.078   1785
  Dihedral  : 15.357 149.175   3840
  Min Nonbonded Distance : 1.911

Molprobity Statistics.
  All-atom Clashscore : 10.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  0.67 %
    Allowed  : 12.20 %
    Favored  : 87.13 %
  Cbeta Deviations :  0.43 %
  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: -3.67 (0.18), residues: 1276
  helix: -2.48 (0.14), residues: 768
  sheet: -0.57 (0.43), residues: 124
  loop : -2.52 (0.27), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 235 
 TYR   0.029   0.003   TYR A 588 
 PHE   0.025   0.003   PHE A 147 
 TRP   0.038   0.003   TRP A 193 
 HIS   0.012   0.002   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00968 (10400)
  covalent geometry    : angle       1.41955 (14111)
  SS BOND              : bond        0.02172 (    2)
  SS BOND              : angle       2.02293 (    4)
  hydrogen bonds       : bond        0.17221 (  634)
  hydrogen bonds       : angle       6.95447 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  280 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 273
  time to evaluate  : 0.385 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 PHE cc_start: 0.7288 (m-10) cc_final: 0.7011 (m-80)
REVERT: A  118 MET cc_start: 0.9224 (mmt) cc_final: 0.9007 (tpp)
REVERT: A  166 LEU cc_start: 0.8440 (tp) cc_final: 0.7963 (tt)
REVERT: A  205 MET cc_start: 0.8817 (tmm) cc_final: 0.8548 (tmm)
REVERT: A  218 GLU cc_start: 0.8421 (tt0) cc_final: 0.8138 (tm-30)
REVERT: A  375 VAL cc_start: 0.0141 (OUTLIER) cc_final: -0.0356 (t)
REVERT: A  430 GLU cc_start: 0.8154 (pt0) cc_final: 0.7393 (mt-10)
REVERT: A  508 VAL cc_start: 0.8884 (p) cc_final: 0.8680 (m)
REVERT: A  560 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8473 (tpp80)
REVERT: B   25 LEU cc_start: 0.8800 (tp) cc_final: 0.8360 (tt)
REVERT: B   32 LEU cc_start: 0.8446 (mt) cc_final: 0.8211 (mp)
REVERT: B  154 MET cc_start: 0.8952 (ttt) cc_final: 0.8295 (ttt)
REVERT: B  191 GLN cc_start: 0.8146 (pp30) cc_final: 0.7894 (tm-30)
REVERT: B  228 ASN cc_start: 0.9239 (t0) cc_final: 0.8896 (t0)
REVERT: B  347 LYS cc_start: 0.7606 (tptt) cc_final: 0.7004 (tppt)
REVERT: B  412 LYS cc_start: 0.9029 (ttmt) cc_final: 0.8478 (mtmm)
REVERT: B  436 LEU cc_start: 0.9108 (tp) cc_final: 0.8888 (tp)
REVERT: B  521 LEU cc_start: 0.8826 (tp) cc_final: 0.8470 (mp)
REVERT: B  558 SER cc_start: 0.9096 (m) cc_final: 0.8819 (t)
REVERT: B  559 LEU cc_start: 0.9062 (mt) cc_final: 0.8796 (mt)
REVERT: B  569 MET cc_start: 0.6915 (ttm) cc_final: 0.6458 (ttm)
REVERT: C   37 PHE cc_start: 0.8313 (m-80) cc_final: 0.8091 (m-80)
REVERT: C   53 LYS cc_start: 0.8974 (ttpp) cc_final: 0.8765 (ttmt)
REVERT: C   93 VAL cc_start: 0.8760 (m) cc_final: 0.8357 (p)
REVERT: C   98 THR cc_start: 0.8955 (m) cc_final: 0.8628 (t)
REVERT: C  109 VAL cc_start: 0.8536 (t) cc_final: 0.8227 (t)
  outliers start: 7
  outliers final: 4
  residues processed: 279
  average time/residue: 0.1146
  time to fit residues: 43.2764
Evaluate side-chains
  186 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 181
  time to evaluate  : 0.397 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 108 optimal weight:    0.8980
   chunk 49 optimal weight:    0.8980
   chunk 97 optimal weight:    0.9980
   chunk 113 optimal weight:    0.9980
   chunk 53 optimal weight:    0.4980
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.9980
   chunk 123 optimal weight:    0.8980
   chunk 65 optimal weight:    0.7980
   chunk 62 optimal weight:    0.5980
   chunk 51 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 103 GLN
A 453 ASN
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 111 HIS
** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 479 GLN
B 531 HIS
B 556 HIS
C   3 GLN
C  39 GLN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.116391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.088784 restraints weight = 26132.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.091044 restraints weight = 16802.387|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.092695 restraints weight = 12505.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 20)----------------|
| r_work = 0.3431 r_free = 0.3431 target = 0.093765 restraints weight = 10142.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.094532 restraints weight = 8846.219|
|-----------------------------------------------------------------------------|
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7898
moved from start:          0.2697

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10402  Z= 0.150
  Angle     :  0.679   6.557  14115  Z= 0.348
  Chirality :  0.043   0.166   1609
  Planarity :  0.005   0.063   1785
  Dihedral  :  7.086 117.699   1483
  Min Nonbonded Distance : 1.769

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  :  5.53 %
    Favored  : 94.18 %
  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: -1.40 (0.21), residues: 1276
  helix: -0.41 (0.17), residues: 778
  sheet: -0.72 (0.39), residues: 137
  loop : -1.85 (0.30), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG B  23 
 TYR   0.024   0.001   TYR A 588 
 PHE   0.020   0.001   PHE A 160 
 TRP   0.025   0.002   TRP A 193 
 HIS   0.012   0.001   HIS B 111 

Details of bonding type rmsd
  covalent geometry    : bond        0.00323 (10400)
  covalent geometry    : angle       0.67909 (14111)
  SS BOND              : bond        0.00580 (    2)
  SS BOND              : angle       0.64581 (    4)
  hydrogen bonds       : bond        0.05271 (  634)
  hydrogen bonds       : angle       4.89062 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  249 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 246
  time to evaluate  : 0.359 
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: A   99 GLN cc_start: 0.8774 (mm110) cc_final: 0.8504 (mm110)
REVERT: A  376 LEU cc_start: 0.6210 (mt) cc_final: 0.5972 (mt)
REVERT: A  445 LEU cc_start: 0.8081 (mm) cc_final: 0.7859 (tp)
REVERT: A  455 ARG cc_start: 0.8166 (ptt180) cc_final: 0.7848 (ptt-90)
REVERT: B   25 LEU cc_start: 0.8685 (tp) cc_final: 0.8410 (tt)
REVERT: B   32 LEU cc_start: 0.8326 (mt) cc_final: 0.7614 (mt)
REVERT: B  108 ASP cc_start: 0.7556 (t70) cc_final: 0.6819 (t0)
REVERT: B  154 MET cc_start: 0.8747 (ttt) cc_final: 0.8035 (ttt)
REVERT: B  347 LYS cc_start: 0.7265 (tptt) cc_final: 0.6671 (tppt)
REVERT: B  365 MET cc_start: 0.7949 (tmm) cc_final: 0.7437 (tmm)
REVERT: B  367 LEU cc_start: 0.9609 (tp) cc_final: 0.9315 (tt)
REVERT: B  380 LEU cc_start: 0.8752 (tp) cc_final: 0.8535 (tp)
REVERT: B  423 LEU cc_start: 0.8880 (mt) cc_final: 0.8536 (pp)
REVERT: B  436 LEU cc_start: 0.8882 (tp) cc_final: 0.8679 (tp)
REVERT: B  521 LEU cc_start: 0.8665 (tp) cc_final: 0.8291 (mp)
REVERT: B  559 LEU cc_start: 0.9280 (mt) cc_final: 0.9075 (mt)
REVERT: B  569 MET cc_start: 0.6886 (ttm) cc_final: 0.6324 (ttm)
REVERT: C    3 GLN cc_start: 0.5420 (pt0) cc_final: 0.3914 (pt0)
REVERT: C   57 ASN cc_start: 0.7444 (m-40) cc_final: 0.6962 (t0)
REVERT: C   65 LYS cc_start: 0.8730 (ptmt) cc_final: 0.8317 (mttt)
REVERT: C   93 VAL cc_start: 0.8543 (m) cc_final: 0.8166 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 248
  average time/residue: 0.0978
  time to fit residues: 33.6050
Evaluate side-chains
  173 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 173
  time to evaluate  : 0.410 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 99 optimal weight:    0.5980
   chunk 43 optimal weight:    0.2980
   chunk 64 optimal weight:    0.8980
   chunk 29 optimal weight:    0.7980
   chunk 71 optimal weight:    0.7980
   chunk 95 optimal weight:    0.8980
   chunk 31 optimal weight:    4.9990
   chunk 124 optimal weight:    0.9990
   chunk 62 optimal weight:    0.8980
   chunk 96 optimal weight:    2.9990
   chunk 91 optimal weight:    0.2980
   overall best weight:    0.5580

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

Flipped N/Q/H residues before XYZ refinement:
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 280 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 531 HIS
B 538 HIS
C  80 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.116525 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.088484 restraints weight = 26171.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.090954 restraints weight = 16449.797|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.092635 restraints weight = 11946.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.093650 restraints weight = 9637.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.094566 restraints weight = 8402.299|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7881
moved from start:          0.3417

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10402  Z= 0.131
  Angle     :  0.631   8.120  14115  Z= 0.318
  Chirality :  0.042   0.161   1609
  Planarity :  0.005   0.056   1785
  Dihedral  :  6.354 102.467   1483
  Min Nonbonded Distance : 1.853

Molprobity Statistics.
  All-atom Clashscore : 9.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.81 %
    Favored  : 96.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.24 (0.23), residues: 1276
  helix:  0.61 (0.18), residues: 774
  sheet: -0.71 (0.39), residues: 135
  loop : -1.45 (0.31), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 244 
 TYR   0.017   0.001   TYR A 588 
 PHE   0.016   0.001   PHE A 478 
 TRP   0.022   0.002   TRP A 193 
 HIS   0.004   0.001   HIS B 100 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10400)
  covalent geometry    : angle       0.63041 (14111)
  SS BOND              : bond        0.00473 (    2)
  SS BOND              : angle       1.22274 (    4)
  hydrogen bonds       : bond        0.04568 (  634)
  hydrogen bonds       : angle       4.37881 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  240 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 239
  time to evaluate  : 0.356 
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: A  256 TRP cc_start: 0.7694 (m100) cc_final: 0.7262 (m100)
REVERT: A  376 LEU cc_start: 0.5864 (mt) cc_final: 0.5608 (mt)
REVERT: A  444 PHE cc_start: 0.6869 (t80) cc_final: 0.6658 (t80)
REVERT: A  445 LEU cc_start: 0.8123 (mm) cc_final: 0.7704 (tp)
REVERT: B   32 LEU cc_start: 0.8189 (mt) cc_final: 0.7673 (mt)
REVERT: B  154 MET cc_start: 0.8728 (ttt) cc_final: 0.7917 (ttt)
REVERT: B  199 THR cc_start: 0.9028 (m) cc_final: 0.8649 (m)
REVERT: B  228 ASN cc_start: 0.9053 (t0) cc_final: 0.8787 (t0)
REVERT: B  319 LYS cc_start: 0.8351 (tppt) cc_final: 0.8027 (tmtt)
REVERT: B  347 LYS cc_start: 0.7291 (tptt) cc_final: 0.6672 (tppt)
REVERT: B  365 MET cc_start: 0.7994 (tmm) cc_final: 0.7622 (tmm)
REVERT: B  431 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7574 (t0)
REVERT: B  436 LEU cc_start: 0.8856 (tp) cc_final: 0.8640 (tp)
REVERT: B  559 LEU cc_start: 0.9386 (mt) cc_final: 0.9168 (mt)
REVERT: B  569 MET cc_start: 0.6784 (ttm) cc_final: 0.6189 (ttm)
REVERT: C    3 GLN cc_start: 0.6238 (pt0) cc_final: 0.5587 (pt0)
REVERT: C   57 ASN cc_start: 0.7073 (m-40) cc_final: 0.6828 (t0)
REVERT: C   65 LYS cc_start: 0.8967 (ptmt) cc_final: 0.8550 (mttt)
REVERT: C   93 VAL cc_start: 0.8737 (m) cc_final: 0.8340 (p)
REVERT: C   94 TYR cc_start: 0.5667 (m-10) cc_final: 0.5382 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 240
  average time/residue: 0.0862
  time to fit residues: 29.6437
Evaluate side-chains
  158 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 157
  time to evaluate  : 0.299 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 117 optimal weight:    0.0050
   chunk 55 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 71 optimal weight:    0.9990
   chunk 8 optimal weight:    0.7980
   chunk 42 optimal weight:    0.2980
   chunk 82 optimal weight:    1.9990
   chunk 49 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   overall best weight:    0.5394

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

Flipped N/Q/H residues before XYZ refinement:
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 538 HIS
** B 573 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3808 r_free = 0.3808 target = 0.117579 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.090051 restraints weight = 26274.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.092457 restraints weight = 16753.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.094068 restraints weight = 12256.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.095211 restraints weight = 9977.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3474 r_free = 0.3474 target = 0.095946 restraints weight = 8641.726|
|-----------------------------------------------------------------------------|
r_work (final): 0.3466
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7854
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10402  Z= 0.125
  Angle     :  0.624   8.315  14115  Z= 0.310
  Chirality :  0.041   0.168   1609
  Planarity :  0.004   0.051   1785
  Dihedral  :  5.889  98.024   1483
  Min Nonbonded Distance : 1.912

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.90 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.81 %
    Favored  : 96.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  0.30 (0.23), residues: 1276
  helix:  1.06 (0.18), residues: 777
  sheet: -0.53 (0.39), residues: 136
  loop : -1.29 (0.32), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 480 
 TYR   0.040   0.001   TYR B 187 
 PHE   0.020   0.001   PHE A 160 
 TRP   0.026   0.001   TRP C  36 
 HIS   0.003   0.001   HIS A 476 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (10400)
  covalent geometry    : angle       0.62342 (14111)
  SS BOND              : bond        0.00395 (    2)
  SS BOND              : angle       1.05133 (    4)
  hydrogen bonds       : bond        0.04305 (  634)
  hydrogen bonds       : angle       4.13750 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 226
  time to evaluate  : 0.400 
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: A  112 ASP cc_start: 0.8842 (t0) cc_final: 0.8406 (t70)
REVERT: A  376 LEU cc_start: 0.6083 (mt) cc_final: 0.5847 (mt)
REVERT: A  444 PHE cc_start: 0.6940 (t80) cc_final: 0.6694 (t80)
REVERT: A  445 LEU cc_start: 0.8139 (mm) cc_final: 0.7714 (tp)
REVERT: A  455 ARG cc_start: 0.7688 (ptt-90) cc_final: 0.7464 (ptt-90)
REVERT: A  502 LYS cc_start: 0.8570 (mtmt) cc_final: 0.8366 (mtpt)
REVERT: B   32 LEU cc_start: 0.8158 (mt) cc_final: 0.7636 (mt)
REVERT: B  154 MET cc_start: 0.8695 (ttt) cc_final: 0.7783 (ttt)
REVERT: B  199 THR cc_start: 0.8968 (m) cc_final: 0.8571 (m)
REVERT: B  319 LYS cc_start: 0.8419 (tppt) cc_final: 0.8126 (tmtt)
REVERT: B  347 LYS cc_start: 0.7134 (tptt) cc_final: 0.6559 (tppt)
REVERT: B  365 MET cc_start: 0.7970 (tmm) cc_final: 0.7695 (tmm)
REVERT: B  436 LEU cc_start: 0.8928 (tp) cc_final: 0.8690 (tp)
REVERT: B  521 LEU cc_start: 0.8337 (mt) cc_final: 0.8083 (mp)
REVERT: B  559 LEU cc_start: 0.9433 (mt) cc_final: 0.9195 (mt)
REVERT: B  569 MET cc_start: 0.6864 (ttm) cc_final: 0.6216 (ttm)
REVERT: C    3 GLN cc_start: 0.6327 (pt0) cc_final: 0.5979 (pt0)
REVERT: C   55 THR cc_start: 0.8357 (p) cc_final: 0.8104 (p)
REVERT: C   65 LYS cc_start: 0.8927 (ptmt) cc_final: 0.8529 (mttt)
REVERT: C   93 VAL cc_start: 0.8685 (m) cc_final: 0.8306 (p)
REVERT: C   94 TYR cc_start: 0.5882 (m-10) cc_final: 0.5446 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 226
  average time/residue: 0.0860
  time to fit residues: 28.1917
Evaluate side-chains
  164 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 164
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 85 optimal weight:    2.9990
   chunk 58 optimal weight:    0.0670
   chunk 46 optimal weight:    4.9990
   chunk 11 optimal weight:    0.0980
   chunk 114 optimal weight:   10.0000
   chunk 87 optimal weight:    5.9990
   chunk 94 optimal weight:    5.9990
   chunk 80 optimal weight:    1.9990
   chunk 120 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.2324

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

Flipped N/Q/H residues before XYZ refinement:
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  53 GLN
** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
C  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.114152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.086998 restraints weight = 26117.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.088071 restraints weight = 19484.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.088766 restraints weight = 13710.872|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.091290 restraints weight = 12592.135|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.091282 restraints weight = 9931.356|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.4004

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  10402  Z= 0.157
  Angle     :  0.653   8.256  14115  Z= 0.325
  Chirality :  0.042   0.181   1609
  Planarity :  0.004   0.047   1785
  Dihedral  :  5.625  93.164   1483
  Min Nonbonded Distance : 1.885

Molprobity Statistics.
  All-atom Clashscore : 11.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.76 %
    Favored  : 97.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.23), residues: 1276
  helix:  1.19 (0.19), residues: 771
  sheet: -0.46 (0.41), residues: 124
  loop : -1.08 (0.32), residues: 381

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 244 
 TYR   0.029   0.001   TYR B 187 
 PHE   0.022   0.001   PHE A 478 
 TRP   0.043   0.002   TRP C  36 
 HIS   0.004   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00355 (10400)
  covalent geometry    : angle       0.65229 (14111)
  SS BOND              : bond        0.00648 (    2)
  SS BOND              : angle       1.41661 (    4)
  hydrogen bonds       : bond        0.04443 (  634)
  hydrogen bonds       : angle       4.26158 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  222 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 222
  time to evaluate  : 0.399 
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  112 ASP cc_start: 0.8915 (t0) cc_final: 0.8306 (t70)
REVERT: A  127 ARG cc_start: 0.8025 (mtt-85) cc_final: 0.7817 (mmt90)
REVERT: A  405 LEU cc_start: 0.8211 (tp) cc_final: 0.7994 (tp)
REVERT: A  444 PHE cc_start: 0.6935 (t80) cc_final: 0.6707 (t80)
REVERT: A  445 LEU cc_start: 0.8349 (mm) cc_final: 0.7853 (tp)
REVERT: A  478 PHE cc_start: 0.2653 (t80) cc_final: 0.2322 (t80)
REVERT: A  502 LYS cc_start: 0.8608 (mtmt) cc_final: 0.8403 (mtpt)
REVERT: A  544 MET cc_start: 0.7434 (mtt) cc_final: 0.7172 (mtt)
REVERT: B   32 LEU cc_start: 0.8398 (mt) cc_final: 0.7743 (mt)
REVERT: B   79 MET cc_start: 0.9002 (tmm) cc_final: 0.8781 (tmm)
REVERT: B  154 MET cc_start: 0.8750 (ttt) cc_final: 0.7898 (ttt)
REVERT: B  199 THR cc_start: 0.8990 (m) cc_final: 0.8596 (m)
REVERT: B  319 LYS cc_start: 0.8412 (tppt) cc_final: 0.8150 (tmtt)
REVERT: B  365 MET cc_start: 0.8143 (tmm) cc_final: 0.7815 (tmm)
REVERT: B  436 LEU cc_start: 0.8971 (tp) cc_final: 0.8725 (tp)
REVERT: B  500 ASP cc_start: 0.7059 (m-30) cc_final: 0.6706 (m-30)
REVERT: B  559 LEU cc_start: 0.9373 (mt) cc_final: 0.9083 (mt)
REVERT: B  569 MET cc_start: 0.7051 (ttm) cc_final: 0.6357 (ttm)
REVERT: C   65 LYS cc_start: 0.8981 (ptmt) cc_final: 0.8501 (mttt)
REVERT: C   93 VAL cc_start: 0.8607 (m) cc_final: 0.8082 (p)
REVERT: C   94 TYR cc_start: 0.5889 (m-10) cc_final: 0.5467 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.1005
  time to fit residues: 31.5430
Evaluate side-chains
  158 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 158
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 78 optimal weight:    0.8980
   chunk 99 optimal weight:    5.9990
   chunk 34 optimal weight:    0.9990
   chunk 84 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9990
   chunk 119 optimal weight:    4.9990
   chunk 8 optimal weight:    0.6980
   chunk 11 optimal weight:    5.9990
   chunk 61 optimal weight:    0.5980
   chunk 82 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.7382

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

Flipped N/Q/H residues before XYZ refinement:
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 538 HIS
C  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.115796 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.089150 restraints weight = 26630.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.090420 restraints weight = 17601.770|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.091008 restraints weight = 12933.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.091211 restraints weight = 12595.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3388 r_free = 0.3388 target = 0.091393 restraints weight = 11732.004|
|-----------------------------------------------------------------------------|
r_work (final): 0.3380
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7936
moved from start:          0.4269

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  10402  Z= 0.126
  Angle     :  0.625   8.237  14115  Z= 0.307
  Chirality :  0.042   0.175   1609
  Planarity :  0.004   0.048   1785
  Dihedral  :  5.253  79.720   1483
  Min Nonbonded Distance : 1.945

Molprobity Statistics.
  All-atom Clashscore : 10.18
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.48 %
    Favored  : 97.52 %
  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:  0.81 (0.24), residues: 1276
  helix:  1.44 (0.19), residues: 771
  sheet: -0.45 (0.40), residues: 132
  loop : -0.92 (0.33), residues: 373

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 244 
 TYR   0.026   0.001   TYR B 187 
 PHE   0.019   0.001   PHE A 478 
 TRP   0.040   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10400)
  covalent geometry    : angle       0.62442 (14111)
  SS BOND              : bond        0.00582 (    2)
  SS BOND              : angle       1.36889 (    4)
  hydrogen bonds       : bond        0.04220 (  634)
  hydrogen bonds       : angle       4.10677 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  220 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 220
  time to evaluate  : 0.394 
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: A  256 TRP cc_start: 0.7685 (m100) cc_final: 0.6992 (m100)
REVERT: A  299 TYR cc_start: 0.8952 (m-10) cc_final: 0.8415 (m-80)
REVERT: A  376 LEU cc_start: 0.6574 (mt) cc_final: 0.6219 (mt)
REVERT: A  405 LEU cc_start: 0.8114 (tp) cc_final: 0.7899 (tp)
REVERT: A  444 PHE cc_start: 0.6990 (t80) cc_final: 0.6743 (t80)
REVERT: A  445 LEU cc_start: 0.8341 (mm) cc_final: 0.7813 (tp)
REVERT: A  478 PHE cc_start: 0.2880 (t80) cc_final: 0.2610 (t80)
REVERT: A  502 LYS cc_start: 0.8596 (mtmt) cc_final: 0.8376 (mtpt)
REVERT: B   32 LEU cc_start: 0.8306 (mt) cc_final: 0.7719 (mt)
REVERT: B   79 MET cc_start: 0.8898 (tmm) cc_final: 0.8667 (tmm)
REVERT: B  154 MET cc_start: 0.8716 (ttt) cc_final: 0.8187 (ttp)
REVERT: B  199 THR cc_start: 0.8972 (m) cc_final: 0.8614 (m)
REVERT: B  319 LYS cc_start: 0.8443 (tppt) cc_final: 0.8202 (tmtt)
REVERT: B  365 MET cc_start: 0.8115 (tmm) cc_final: 0.7774 (tmm)
REVERT: B  436 LEU cc_start: 0.8927 (tp) cc_final: 0.8693 (tp)
REVERT: B  499 ASP cc_start: 0.6296 (t70) cc_final: 0.5174 (t0)
REVERT: B  559 LEU cc_start: 0.9330 (mt) cc_final: 0.9036 (mt)
REVERT: B  569 MET cc_start: 0.7067 (ttm) cc_final: 0.6383 (ttm)
REVERT: C   65 LYS cc_start: 0.9039 (ptmt) cc_final: 0.8598 (mttt)
REVERT: C   83 MET cc_start: 0.6493 (mmm) cc_final: 0.5895 (mmt)
REVERT: C   93 VAL cc_start: 0.8619 (m) cc_final: 0.8164 (p)
REVERT: C   94 TYR cc_start: 0.5963 (m-10) cc_final: 0.5597 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 220
  average time/residue: 0.1031
  time to fit residues: 31.9895
Evaluate side-chains
  163 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 163
  time to evaluate  : 0.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 46 optimal weight:    4.9990
   chunk 60 optimal weight:    0.4980
   chunk 13 optimal weight:    5.9990
   chunk 21 optimal weight:    0.2980
   chunk 72 optimal weight:    0.9980
   chunk 17 optimal weight:    0.3980
   chunk 113 optimal weight:    7.9990
   chunk 96 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 118 optimal weight:    2.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    0.6382

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

Flipped N/Q/H residues before XYZ refinement:
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
C  80 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.117169 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.089474 restraints weight = 26284.096|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.091809 restraints weight = 16857.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.093418 restraints weight = 12525.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.094478 restraints weight = 10248.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.094940 restraints weight = 8973.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3453
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7880
moved from start:          0.4469

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10402  Z= 0.122
  Angle     :  0.632   7.946  14115  Z= 0.308
  Chirality :  0.042   0.195   1609
  Planarity :  0.004   0.048   1785
  Dihedral  :  4.968  67.364   1483
  Min Nonbonded Distance : 1.976

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.53 %
    Favored  : 98.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.91 (0.24), residues: 1276
  helix:  1.51 (0.18), residues: 783
  sheet: -0.45 (0.41), residues: 133
  loop : -0.94 (0.33), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C  45 
 TYR   0.023   0.001   TYR B 187 
 PHE   0.019   0.001   PHE A 124 
 TRP   0.029   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00266 (10400)
  covalent geometry    : angle       0.63140 (14111)
  SS BOND              : bond        0.00566 (    2)
  SS BOND              : angle       1.20520 (    4)
  hydrogen bonds       : bond        0.04118 (  634)
  hydrogen bonds       : angle       4.02546 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  211 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 211
  time to evaluate  : 0.347 
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: A  112 ASP cc_start: 0.8827 (t0) cc_final: 0.8344 (t70)
REVERT: A  299 TYR cc_start: 0.8933 (m-10) cc_final: 0.8544 (m-80)
REVERT: A  376 LEU cc_start: 0.6246 (mt) cc_final: 0.5915 (mt)
REVERT: A  445 LEU cc_start: 0.8312 (mm) cc_final: 0.7853 (tp)
REVERT: B   32 LEU cc_start: 0.8253 (mt) cc_final: 0.7624 (mt)
REVERT: B   79 MET cc_start: 0.8874 (tmm) cc_final: 0.8648 (tmm)
REVERT: B  154 MET cc_start: 0.8608 (ttt) cc_final: 0.8158 (ttp)
REVERT: B  199 THR cc_start: 0.8962 (m) cc_final: 0.8593 (m)
REVERT: B  319 LYS cc_start: 0.8448 (tppt) cc_final: 0.8169 (tmtt)
REVERT: B  365 MET cc_start: 0.8071 (tmm) cc_final: 0.7722 (tmm)
REVERT: B  423 LEU cc_start: 0.8887 (mt) cc_final: 0.8612 (pp)
REVERT: B  436 LEU cc_start: 0.8870 (tp) cc_final: 0.8588 (tp)
REVERT: B  559 LEU cc_start: 0.9328 (mt) cc_final: 0.9115 (mt)
REVERT: B  569 MET cc_start: 0.7218 (ttm) cc_final: 0.6837 (ttm)
REVERT: C   65 LYS cc_start: 0.8991 (ptmt) cc_final: 0.8595 (mttm)
REVERT: C   72 ARG cc_start: 0.7614 (tmm160) cc_final: 0.7244 (tmm-80)
REVERT: C   83 MET cc_start: 0.6603 (mmm) cc_final: 0.6017 (mmp)
REVERT: C   93 VAL cc_start: 0.8438 (m) cc_final: 0.8019 (p)
REVERT: C   94 TYR cc_start: 0.5979 (m-10) cc_final: 0.5634 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 211
  average time/residue: 0.0943
  time to fit residues: 28.2079
Evaluate side-chains
  155 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.403 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 27 optimal weight:    0.0870
   chunk 34 optimal weight:    4.9990
   chunk 22 optimal weight:    0.6980
   chunk 65 optimal weight:    2.9990
   chunk 69 optimal weight:    0.7980
   chunk 60 optimal weight:    0.9990
   chunk 32 optimal weight:    0.6980
   chunk 24 optimal weight:    0.8980
   chunk 105 optimal weight:    5.9990
   chunk 39 optimal weight:    0.9990
   chunk 23 optimal weight:    0.5980
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 531 HIS
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3827 r_free = 0.3827 target = 0.118746 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.091193 restraints weight = 26721.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.093730 restraints weight = 16476.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.095485 restraints weight = 11861.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3490 r_free = 0.3490 target = 0.096660 restraints weight = 9481.489|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.097454 restraints weight = 8158.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3505
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7847
moved from start:          0.4619

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10402  Z= 0.119
  Angle     :  0.627   9.093  14115  Z= 0.305
  Chirality :  0.041   0.193   1609
  Planarity :  0.004   0.047   1785
  Dihedral  :  4.703  60.157   1483
  Min Nonbonded Distance : 1.989

Molprobity Statistics.
  All-atom Clashscore : 9.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.86 %
    Favored  : 99.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.09 (0.24), residues: 1276
  helix:  1.67 (0.19), residues: 782
  sheet: -0.53 (0.41), residues: 133
  loop : -0.83 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 244 
 TYR   0.022   0.001   TYR B 187 
 PHE   0.023   0.001   PHE A 478 
 TRP   0.047   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 (10400)
  covalent geometry    : angle       0.62624 (14111)
  SS BOND              : bond        0.00637 (    2)
  SS BOND              : angle       1.35852 (    4)
  hydrogen bonds       : bond        0.04020 (  634)
  hydrogen bonds       : angle       3.95344 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 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: 0
    poor density    : 206
  time to evaluate  : 0.359 
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: A  112 ASP cc_start: 0.8846 (t0) cc_final: 0.8365 (t70)
REVERT: A  299 TYR cc_start: 0.8887 (m-10) cc_final: 0.8472 (m-80)
REVERT: A  444 PHE cc_start: 0.7063 (t80) cc_final: 0.6722 (t80)
REVERT: A  445 LEU cc_start: 0.8404 (mm) cc_final: 0.7875 (tp)
REVERT: B   32 LEU cc_start: 0.8246 (mt) cc_final: 0.7700 (mt)
REVERT: B   79 MET cc_start: 0.8882 (tmm) cc_final: 0.8626 (tmm)
REVERT: B  154 MET cc_start: 0.8680 (ttt) cc_final: 0.8092 (ttt)
REVERT: B  199 THR cc_start: 0.8958 (m) cc_final: 0.8599 (m)
REVERT: B  319 LYS cc_start: 0.8478 (tppt) cc_final: 0.8185 (tmtt)
REVERT: B  365 MET cc_start: 0.8135 (tmm) cc_final: 0.7829 (tmm)
REVERT: B  423 LEU cc_start: 0.8786 (mt) cc_final: 0.8569 (pp)
REVERT: B  436 LEU cc_start: 0.8912 (tp) cc_final: 0.8569 (tp)
REVERT: B  569 MET cc_start: 0.7319 (ttm) cc_final: 0.6914 (ttm)
REVERT: C   72 ARG cc_start: 0.7688 (tmm160) cc_final: 0.7435 (tmm-80)
REVERT: C   83 MET cc_start: 0.6431 (mmm) cc_final: 0.5712 (mmp)
REVERT: C   93 VAL cc_start: 0.8500 (m) cc_final: 0.8035 (p)
REVERT: C   94 TYR cc_start: 0.5985 (m-10) cc_final: 0.5579 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 206
  average time/residue: 0.0937
  time to fit residues: 27.7652
Evaluate side-chains
  150 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 150
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 112 optimal weight:    0.8980
   chunk 109 optimal weight:    0.0030
   chunk 53 optimal weight:    0.8980
   chunk 124 optimal weight:    6.9990
   chunk 106 optimal weight:    0.7980
   chunk 100 optimal weight:    0.8980
   chunk 116 optimal weight:    6.9990
   chunk 69 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0030
   overall best weight:    0.5000

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
C  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3833 r_free = 0.3833 target = 0.119131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.091609 restraints weight = 26975.582|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.094126 restraints weight = 16805.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.095857 restraints weight = 12155.640|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.096925 restraints weight = 9748.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.097763 restraints weight = 8486.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3510
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7839
moved from start:          0.4774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10402  Z= 0.114
  Angle     :  0.619   8.089  14115  Z= 0.301
  Chirality :  0.041   0.188   1609
  Planarity :  0.004   0.046   1785
  Dihedral  :  4.480  55.484   1483
  Min Nonbonded Distance : 2.001

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.38 %
    Favored  : 99.62 %
  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:  1.19 (0.24), residues: 1276
  helix:  1.75 (0.18), residues: 785
  sheet: -0.50 (0.42), residues: 133
  loop : -0.80 (0.34), residues: 358

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C  19 
 TYR   0.021   0.001   TYR B 187 
 PHE   0.022   0.001   PHE A 478 
 TRP   0.036   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 101 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (10400)
  covalent geometry    : angle       0.61920 (14111)
  SS BOND              : bond        0.00519 (    2)
  SS BOND              : angle       1.22086 (    4)
  hydrogen bonds       : bond        0.03944 (  634)
  hydrogen bonds       : angle       3.87565 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 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: 0
    poor density    : 207
  time to evaluate  : 0.411 
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: A  112 ASP cc_start: 0.8855 (t0) cc_final: 0.8352 (t70)
REVERT: A  176 LEU cc_start: 0.8803 (mp) cc_final: 0.8596 (mp)
REVERT: A  299 TYR cc_start: 0.8794 (m-10) cc_final: 0.8446 (m-80)
REVERT: A  444 PHE cc_start: 0.7085 (t80) cc_final: 0.6661 (t80)
REVERT: A  445 LEU cc_start: 0.8394 (mm) cc_final: 0.7854 (tp)
REVERT: B   79 MET cc_start: 0.8828 (tmm) cc_final: 0.8584 (tmm)
REVERT: B  154 MET cc_start: 0.8615 (ttt) cc_final: 0.7976 (ttp)
REVERT: B  199 THR cc_start: 0.8943 (m) cc_final: 0.8584 (m)
REVERT: B  319 LYS cc_start: 0.8472 (tppt) cc_final: 0.8262 (tmtt)
REVERT: B  365 MET cc_start: 0.8116 (tmm) cc_final: 0.7851 (tmm)
REVERT: B  380 LEU cc_start: 0.8544 (tp) cc_final: 0.8341 (tp)
REVERT: B  436 LEU cc_start: 0.8776 (tp) cc_final: 0.8440 (tp)
REVERT: B  559 LEU cc_start: 0.9215 (mt) cc_final: 0.9012 (mt)
REVERT: B  569 MET cc_start: 0.7126 (ttm) cc_final: 0.6794 (ttm)
REVERT: C   65 LYS cc_start: 0.8996 (ptmt) cc_final: 0.8523 (mttt)
REVERT: C   83 MET cc_start: 0.6551 (mmm) cc_final: 0.5954 (mmp)
REVERT: C   93 VAL cc_start: 0.8510 (m) cc_final: 0.8037 (p)
REVERT: C   94 TYR cc_start: 0.5943 (m-10) cc_final: 0.5555 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.0948
  time to fit residues: 28.6771
Evaluate side-chains
  155 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 155
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 64 optimal weight:    0.5980
   chunk 110 optimal weight:    5.9990
   chunk 121 optimal weight:    0.8980
   chunk 7 optimal weight:    0.7980
   chunk 56 optimal weight:    6.9990
   chunk 87 optimal weight:    0.7980
   chunk 124 optimal weight:    0.7980
   chunk 75 optimal weight:    2.9990
   chunk 25 optimal weight:    0.6980
   chunk 120 optimal weight:    0.8980
   chunk 97 optimal weight:    2.9990
   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 145 ASN
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 538 HIS
C  80 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.118415 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.090883 restraints weight = 26779.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.093348 restraints weight = 16678.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.095055 restraints weight = 12145.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3484 r_free = 0.3484 target = 0.096267 restraints weight = 9760.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.096945 restraints weight = 8390.302|
|-----------------------------------------------------------------------------|
r_work (final): 0.3497
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.4858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  10402  Z= 0.124
  Angle     :  0.627   8.296  14115  Z= 0.306
  Chirality :  0.041   0.179   1609
  Planarity :  0.004   0.046   1785
  Dihedral  :  4.380  52.467   1483
  Min Nonbonded Distance : 1.995

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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 (0.24), residues: 1276
  helix:  1.75 (0.18), residues: 782
  sheet: -0.48 (0.42), residues: 131
  loop : -0.72 (0.34), residues: 363

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C  19 
 TYR   0.017   0.001   TYR B 187 
 PHE   0.022   0.001   PHE A 478 
 TRP   0.041   0.002   TRP C  36 
 HIS   0.005   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 (10400)
  covalent geometry    : angle       0.62710 (14111)
  SS BOND              : bond        0.00635 (    2)
  SS BOND              : angle       1.23439 (    4)
  hydrogen bonds       : bond        0.03961 (  634)
  hydrogen bonds       : angle       3.92703 ( 1863)

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

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

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2552 Ramachandran restraints generated.
    1276 Oldfield, 0 Emsley, 1276 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  200 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.405 
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: A  112 ASP cc_start: 0.8872 (t0) cc_final: 0.8305 (t70)
REVERT: A  444 PHE cc_start: 0.7065 (t80) cc_final: 0.6752 (t80)
REVERT: A  445 LEU cc_start: 0.8398 (mm) cc_final: 0.7797 (tp)
REVERT: B   79 MET cc_start: 0.8833 (tmm) cc_final: 0.8604 (tmm)
REVERT: B  154 MET cc_start: 0.8662 (ttt) cc_final: 0.8388 (ttp)
REVERT: B  164 TYR cc_start: 0.7633 (m-80) cc_final: 0.7266 (m-80)
REVERT: B  319 LYS cc_start: 0.8488 (tppt) cc_final: 0.8278 (tmtt)
REVERT: B  365 MET cc_start: 0.8100 (tmm) cc_final: 0.7852 (tmm)
REVERT: B  436 LEU cc_start: 0.8816 (tp) cc_final: 0.8474 (tp)
REVERT: B  559 LEU cc_start: 0.9218 (mt) cc_final: 0.9011 (mt)
REVERT: B  569 MET cc_start: 0.7180 (ttm) cc_final: 0.6842 (ttm)
REVERT: C   65 LYS cc_start: 0.9115 (ptmt) cc_final: 0.8744 (mttt)
REVERT: C   83 MET cc_start: 0.6410 (mmm) cc_final: 0.5921 (mmp)
REVERT: C   93 VAL cc_start: 0.8538 (m) cc_final: 0.8048 (p)
REVERT: C   94 TYR cc_start: 0.6095 (m-10) cc_final: 0.5728 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 200
  average time/residue: 0.0928
  time to fit residues: 27.0839
Evaluate side-chains
  153 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 116 optimal weight:    6.9990
   chunk 60 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9980
   chunk 86 optimal weight:    0.4980
   chunk 45 optimal weight:    0.0170
   chunk 41 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0870
   chunk 15 optimal weight:    0.8980
   chunk 38 optimal weight:    6.9990
   chunk 83 optimal weight:    0.9990
   chunk 59 optimal weight:    0.9990
   overall best weight:    0.4996

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

Flipped N/Q/H residues before XYZ refinement:
A 145 ASN
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
C  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.119241 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.091998 restraints weight = 26975.123|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3457 r_free = 0.3457 target = 0.094542 restraints weight = 16645.028|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.096236 restraints weight = 11931.695|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.097455 restraints weight = 9566.982|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.098135 restraints weight = 8218.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3518
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.5012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036  10402  Z= 0.117
  Angle     :  0.635   8.383  14115  Z= 0.307
  Chirality :  0.041   0.179   1609
  Planarity :  0.004   0.046   1785
  Dihedral  :  4.331  52.992   1483
  Min Nonbonded Distance : 2.008

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.48 %
    Favored  : 99.52 %
  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:  1.23 (0.24), residues: 1276
  helix:  1.78 (0.18), residues: 778
  sheet: -0.48 (0.42), residues: 132
  loop : -0.73 (0.34), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C  19 
 TYR   0.019   0.001   TYR B 302 
 PHE   0.021   0.001   PHE B 163 
 TRP   0.051   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 454 

Details of bonding type rmsd
  covalent geometry    : bond        0.00255 (10400)
  covalent geometry    : angle       0.63192 (14111)
  SS BOND              : bond        0.00670 (    2)
  SS BOND              : angle       3.76279 (    4)
  hydrogen bonds       : bond        0.03910 (  634)
  hydrogen bonds       : angle       3.87531 ( 1863)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1619.84 seconds
wall clock time: 28 minutes 39.38 seconds (1719.38 seconds total)