Starting phenix.real_space_refine
on Fri Feb 14 16:29:08 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6rag_4774/02_2025/6rag_4774.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6rag_4774/02_2025/6rag_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6rag_4774/02_2025/6rag_4774.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6rag_4774/02_2025/6rag_4774.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6rag_4774/02_2025/6rag_4774.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6rag_4774/02_2025/6rag_4774.cif"
  }
  resolution = 4.2
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.003 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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 6.24, per 1000 atoms: 0.61
  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: 2.32
  Conformation dependent library (CDL) restraints added in 1.2 seconds
  

  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: 1.06
  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: 3.37

  Time building geometry restraints manager: 2.72 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:             1.520
  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:          0.330
  Check model and map are aligned:         0.060
  Set scattering table:                    0.100
  Process input model:                     24.900
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.910
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   29.990
-------------------------------------------------------------------------------
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  10400  Z= 0.622
  Angle     :  1.420  19.938  14111  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.67 (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
 TRP   0.038   0.003   TRP A 193 
 HIS   0.012   0.002   HIS B 100 
 PHE   0.025   0.003   PHE A 147 
 TYR   0.029   0.003   TYR A 588 
 ARG   0.011   0.001   ARG A 235 

*********************** 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  : 1.323 
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: 0.7289 (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: 0.7972 (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: 0.8137 (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: 0.8679 (m)
REVERT: A  560 ARG cc_start: 0.8851 (mmm-85) cc_final: 0.8472 (tpp80)
REVERT: B   25 LEU cc_start: 0.8800 (tp) cc_final: 0.8360 (tt)
REVERT: B   32 LEU cc_start: 0.8447 (mt) cc_final: 0.8210 (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: 0.7895 (tm-30)
REVERT: B  228 ASN cc_start: 0.9239 (t0) cc_final: 0.8898 (t0)
REVERT: B  253 MET cc_start: 0.8825 (mmt) cc_final: 0.8625 (mmp)
REVERT: B  347 LYS cc_start: 0.7606 (tptt) cc_final: 0.7003 (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: 0.8469 (mp)
REVERT: B  558 SER cc_start: 0.9095 (m) cc_final: 0.8819 (t)
REVERT: B  559 LEU cc_start: 0.9062 (mt) cc_final: 0.8849 (mt)
REVERT: B  569 MET cc_start: 0.6915 (ttm) cc_final: 0.6457 (ttm)
REVERT: C   37 PHE cc_start: 0.8313 (m-80) cc_final: 0.8092 (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: 0.8630 (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: 0.2705
  time to fit residues: 100.9110
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  : 1.101 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 107 optimal weight:    2.9990
   chunk 96 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 64 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 99 optimal weight:    3.9990
   chunk 38 optimal weight:    9.9990
   chunk 60 optimal weight:    0.8980
   chunk 74 optimal weight:    2.9990
   chunk 115 optimal weight:    5.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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  53 GLN
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: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.116052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.088515 restraints weight = 25883.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.090729 restraints weight = 16771.518|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.092324 restraints weight = 12556.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.3399
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7945
moved from start:          0.2692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  10400  Z= 0.212
  Angle     :  0.682   6.637  14111  Z= 0.350
  Chirality :  0.043   0.167   1609
  Planarity :  0.005   0.062   1785
  Dihedral  :  7.095 117.513   1483
  Min Nonbonded Distance : 1.773

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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.40 (0.21), residues: 1276
  helix: -0.42 (0.17), residues: 777
  sheet: -0.71 (0.40), residues: 137
  loop : -1.87 (0.30), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 193 
 HIS   0.011   0.001   HIS B 111 
 PHE   0.021   0.001   PHE A 160 
 TYR   0.025   0.001   TYR A 588 
 ARG   0.006   0.000   ARG B  23 

*********************** 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
  248 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 245
  time to evaluate  : 1.219 
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   99 GLN cc_start: 0.8741 (mm110) cc_final: 0.8470 (mm110)
REVERT: A  445 LEU cc_start: 0.8103 (mm) cc_final: 0.7682 (tp)
REVERT: A  455 ARG cc_start: 0.8181 (ptt180) cc_final: 0.7872 (ptt-90)
REVERT: A  502 LYS cc_start: 0.8440 (mtmt) cc_final: 0.8189 (mtmt)
REVERT: B   25 LEU cc_start: 0.8714 (tp) cc_final: 0.8436 (tt)
REVERT: B   32 LEU cc_start: 0.8352 (mt) cc_final: 0.8088 (mp)
REVERT: B  108 ASP cc_start: 0.7623 (t70) cc_final: 0.6871 (t0)
REVERT: B  154 MET cc_start: 0.8755 (ttt) cc_final: 0.8008 (ttt)
REVERT: B  253 MET cc_start: 0.8719 (mmt) cc_final: 0.8393 (mmp)
REVERT: B  347 LYS cc_start: 0.7344 (tptt) cc_final: 0.6737 (tppt)
REVERT: B  365 MET cc_start: 0.7951 (tmm) cc_final: 0.7439 (tmm)
REVERT: B  367 LEU cc_start: 0.9633 (tp) cc_final: 0.9337 (tt)
REVERT: B  380 LEU cc_start: 0.8768 (tp) cc_final: 0.8544 (tp)
REVERT: B  423 LEU cc_start: 0.8882 (mt) cc_final: 0.8518 (pp)
REVERT: B  436 LEU cc_start: 0.8882 (tp) cc_final: 0.8674 (tp)
REVERT: B  521 LEU cc_start: 0.8683 (tp) cc_final: 0.8217 (mp)
REVERT: B  559 LEU cc_start: 0.9309 (mt) cc_final: 0.9104 (mt)
REVERT: B  569 MET cc_start: 0.6918 (ttm) cc_final: 0.6364 (ttm)
REVERT: B  573 GLN cc_start: 0.8416 (tp-100) cc_final: 0.8181 (tp-100)
REVERT: C    3 GLN cc_start: 0.5462 (pt0) cc_final: 0.3906 (pt0)
REVERT: C   57 ASN cc_start: 0.7478 (m-40) cc_final: 0.6975 (t0)
REVERT: C   65 LYS cc_start: 0.8747 (ptmt) cc_final: 0.8328 (mttt)
REVERT: C   93 VAL cc_start: 0.8555 (m) cc_final: 0.8175 (p)
  outliers start: 3
  outliers final: 0
  residues processed: 247
  average time/residue: 0.2488
  time to fit residues: 84.0301
Evaluate side-chains
  171 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 171
  time to evaluate  : 1.107 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 58 optimal weight:    0.6980
   chunk 38 optimal weight:    8.9990
   chunk 1 optimal weight:    0.0470
   chunk 98 optimal weight:    0.8980
   chunk 49 optimal weight:    2.9990
   chunk 72 optimal weight:    0.7980
   chunk 90 optimal weight:    4.9990
   chunk 2 optimal weight:    0.7980
   chunk 15 optimal weight:    0.8980
   chunk 111 optimal weight:    0.7980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.6278

-------------------------------------------------------------------------------
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  39 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.116375 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.088169 restraints weight = 26120.174|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.090559 restraints weight = 16448.122|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.092165 restraints weight = 12029.898|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7929
moved from start:          0.3388

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10400  Z= 0.176
  Angle     :  0.641   8.390  14111  Z= 0.325
  Chirality :  0.042   0.196   1609
  Planarity :  0.005   0.056   1785
  Dihedral  :  6.446 104.725   1483
  Min Nonbonded Distance : 1.851

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  0.19 %
    Allowed  :  4.10 %
    Favored  : 95.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.32 (0.23), residues: 1276
  helix:  0.55 (0.18), residues: 774
  sheet: -0.85 (0.39), residues: 137
  loop : -1.45 (0.31), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.022   0.002   TRP A 193 
 HIS   0.004   0.001   HIS B 100 
 PHE   0.019   0.001   PHE A 478 
 TYR   0.018   0.001   TYR A 588 
 ARG   0.015   0.000   ARG C  19 

*********************** 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
  232 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 230
  time to evaluate  : 1.186 
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  256 TRP cc_start: 0.7686 (m100) cc_final: 0.7263 (m100)
REVERT: A  376 LEU cc_start: 0.5980 (mt) cc_final: 0.5720 (mt)
REVERT: A  445 LEU cc_start: 0.8048 (mm) cc_final: 0.7669 (tp)
REVERT: A  502 LYS cc_start: 0.8373 (mtmt) cc_final: 0.8139 (mtmt)
REVERT: B   25 LEU cc_start: 0.8657 (tp) cc_final: 0.8396 (tt)
REVERT: B   32 LEU cc_start: 0.8253 (mt) cc_final: 0.7717 (mt)
REVERT: B  108 ASP cc_start: 0.7655 (t70) cc_final: 0.6880 (t0)
REVERT: B  154 MET cc_start: 0.8742 (ttt) cc_final: 0.7832 (ttt)
REVERT: B  199 THR cc_start: 0.9062 (m) cc_final: 0.8671 (m)
REVERT: B  347 LYS cc_start: 0.7440 (tptt) cc_final: 0.6768 (tppt)
REVERT: B  365 MET cc_start: 0.8047 (tmm) cc_final: 0.7771 (tmm)
REVERT: B  423 LEU cc_start: 0.8895 (mt) cc_final: 0.8663 (pp)
REVERT: B  436 LEU cc_start: 0.8860 (tp) cc_final: 0.8646 (tp)
REVERT: B  559 LEU cc_start: 0.9389 (mt) cc_final: 0.9186 (mt)
REVERT: B  569 MET cc_start: 0.6851 (ttm) cc_final: 0.6276 (ttm)
REVERT: C   57 ASN cc_start: 0.7223 (m-40) cc_final: 0.6817 (t0)
REVERT: C   65 LYS cc_start: 0.8910 (ptmt) cc_final: 0.8514 (mttt)
REVERT: C   93 VAL cc_start: 0.8770 (m) cc_final: 0.8374 (p)
REVERT: C   94 TYR cc_start: 0.5815 (m-10) cc_final: 0.5319 (m-80)
  outliers start: 2
  outliers final: 0
  residues processed: 232
  average time/residue: 0.2247
  time to fit residues: 73.6019
Evaluate side-chains
  157 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 157
  time to evaluate  : 1.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 101 optimal weight:    4.9990
   chunk 35 optimal weight:    5.9990
   chunk 50 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 120 optimal weight:    4.9990
   chunk 10 optimal weight:    0.4980
   chunk 57 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 79 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 596 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 531 HIS
C   3 GLN
C  80 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3782 r_free = 0.3782 target = 0.116025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.088350 restraints weight = 26188.498|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3382 r_free = 0.3382 target = 0.090635 restraints weight = 16681.815|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.092207 restraints weight = 12364.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3404
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.3799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10400  Z= 0.198
  Angle     :  0.629   8.161  14111  Z= 0.317
  Chirality :  0.041   0.166   1609
  Planarity :  0.004   0.050   1785
  Dihedral  :  6.028 101.118   1483
  Min Nonbonded Distance : 1.903

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.91 %
    Favored  : 96.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.12 (0.23), residues: 1276
  helix:  0.92 (0.18), residues: 784
  sheet: -0.77 (0.37), residues: 143
  loop : -1.34 (0.31), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 100 
 PHE   0.019   0.001   PHE A 478 
 TYR   0.040   0.001   TYR B 187 
 ARG   0.004   0.000   ARG A 127 

*********************** 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
  217 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 216
  time to evaluate  : 1.065 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  376 LEU cc_start: 0.6077 (mt) cc_final: 0.5751 (mt)
REVERT: A  444 PHE cc_start: 0.6872 (t80) cc_final: 0.6567 (t80)
REVERT: A  445 LEU cc_start: 0.8237 (mm) cc_final: 0.7768 (tp)
REVERT: B   25 LEU cc_start: 0.8617 (tp) cc_final: 0.8405 (tt)
REVERT: B   32 LEU cc_start: 0.8265 (mt) cc_final: 0.7694 (mt)
REVERT: B   79 MET cc_start: 0.8898 (tmm) cc_final: 0.8661 (tmm)
REVERT: B  108 ASP cc_start: 0.7564 (t70) cc_final: 0.6764 (t0)
REVERT: B  154 MET cc_start: 0.8742 (ttt) cc_final: 0.7979 (ttt)
REVERT: B  199 THR cc_start: 0.9000 (m) cc_final: 0.8608 (m)
REVERT: B  347 LYS cc_start: 0.7311 (tptt) cc_final: 0.6743 (tppt)
REVERT: B  365 MET cc_start: 0.8094 (tmm) cc_final: 0.7740 (tmm)
REVERT: B  423 LEU cc_start: 0.8898 (mt) cc_final: 0.8653 (pp)
REVERT: B  431 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7694 (t0)
REVERT: B  436 LEU cc_start: 0.8942 (tp) cc_final: 0.8701 (tp)
REVERT: B  559 LEU cc_start: 0.9423 (mt) cc_final: 0.9179 (mt)
REVERT: B  569 MET cc_start: 0.6929 (ttm) cc_final: 0.6349 (ttm)
REVERT: C   65 LYS cc_start: 0.8939 (ptmt) cc_final: 0.8529 (mttt)
REVERT: C   70 ILE cc_start: 0.8420 (tt) cc_final: 0.8164 (mt)
REVERT: C   93 VAL cc_start: 0.8771 (m) cc_final: 0.8370 (p)
REVERT: C   94 TYR cc_start: 0.5404 (m-10) cc_final: 0.4907 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 217
  average time/residue: 0.2193
  time to fit residues: 68.1764
Evaluate side-chains
  155 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 154
  time to evaluate  : 1.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 15 optimal weight:    0.4980
   chunk 105 optimal weight:    5.9990
   chunk 14 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 64 optimal weight:    0.9990
   chunk 115 optimal weight:    8.9990
   chunk 21 optimal weight:    0.6980
   chunk 32 optimal weight:    8.9990
   chunk 35 optimal weight:    0.0970
   chunk 107 optimal weight:    0.0010
   chunk 69 optimal weight:    1.9990
   overall best weight:    0.4184

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.117777 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.090355 restraints weight = 26009.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.092677 restraints weight = 16610.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.094325 restraints weight = 12291.799|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7883
moved from start:          0.4127

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  10400  Z= 0.165
  Angle     :  0.623   7.575  14111  Z= 0.310
  Chirality :  0.041   0.179   1609
  Planarity :  0.004   0.050   1785
  Dihedral  :  5.616  94.106   1483
  Min Nonbonded Distance : 1.908

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.29 %
    Favored  : 97.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.55 (0.23), residues: 1276
  helix:  1.26 (0.18), residues: 773
  sheet: -0.66 (0.38), residues: 143
  loop : -1.07 (0.32), residues: 360

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP C  36 
 HIS   0.002   0.001   HIS A 476 
 PHE   0.017   0.001   PHE A 478 
 TYR   0.031   0.001   TYR B 187 
 ARG   0.005   0.000   ARG A 244 

*********************** 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  : 1.157 
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  444 PHE cc_start: 0.6880 (t80) cc_final: 0.6396 (t80)
REVERT: A  455 ARG cc_start: 0.7591 (ptt-90) cc_final: 0.7317 (ptt-90)
REVERT: B   25 LEU cc_start: 0.8595 (tp) cc_final: 0.8394 (tt)
REVERT: B   32 LEU cc_start: 0.8187 (mt) cc_final: 0.7663 (mt)
REVERT: B   79 MET cc_start: 0.8972 (tmm) cc_final: 0.8721 (tmm)
REVERT: B  154 MET cc_start: 0.8560 (ttt) cc_final: 0.8270 (ttp)
REVERT: B  199 THR cc_start: 0.8981 (m) cc_final: 0.8584 (m)
REVERT: B  253 MET cc_start: 0.8845 (mmp) cc_final: 0.8624 (mmp)
REVERT: B  319 LYS cc_start: 0.8302 (tptt) cc_final: 0.8075 (tmtt)
REVERT: B  347 LYS cc_start: 0.7343 (tptt) cc_final: 0.6710 (tppt)
REVERT: B  365 MET cc_start: 0.8184 (tmm) cc_final: 0.7874 (tmm)
REVERT: B  436 LEU cc_start: 0.8844 (tp) cc_final: 0.8611 (tp)
REVERT: B  559 LEU cc_start: 0.9370 (mt) cc_final: 0.9091 (mt)
REVERT: B  569 MET cc_start: 0.6979 (ttm) cc_final: 0.6267 (ttm)
REVERT: C   65 LYS cc_start: 0.8940 (ptmt) cc_final: 0.8471 (mttt)
REVERT: C   72 ARG cc_start: 0.7585 (tmm160) cc_final: 0.7282 (tmm-80)
REVERT: C   93 VAL cc_start: 0.8724 (m) cc_final: 0.8284 (p)
REVERT: C   94 TYR cc_start: 0.5456 (m-10) cc_final: 0.4964 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 222
  average time/residue: 0.2278
  time to fit residues: 71.2864
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  : 1.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 14 optimal weight:    6.9990
   chunk 107 optimal weight:    0.3980
   chunk 41 optimal weight:    0.6980
   chunk 81 optimal weight:    0.7980
   chunk 30 optimal weight:    7.9990
   chunk 13 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 79 optimal weight:    2.9990
   chunk 82 optimal weight:    2.9990
   chunk 112 optimal weight:    0.9990
   chunk 42 optimal weight:    0.0570
   overall best weight:    0.5900

-------------------------------------------------------------------------------
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 228 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
** B 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.118207 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.091914 restraints weight = 26604.401|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.093475 restraints weight = 17839.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.093975 restraints weight = 12732.104|
|-----------------------------------------------------------------------------|
r_work (final): 0.3423
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.4347

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10400  Z= 0.171
  Angle     :  0.618   8.626  14111  Z= 0.304
  Chirality :  0.041   0.202   1609
  Planarity :  0.004   0.050   1785
  Dihedral  :  5.194  77.932   1483
  Min Nonbonded Distance : 1.961

Molprobity Statistics.
  All-atom Clashscore : 10.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.74 %
    Favored  : 97.26 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.91 %
    Favored  : 98.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.92 (0.24), residues: 1276
  helix:  1.53 (0.19), residues: 766
  sheet: -0.36 (0.41), residues: 132
  loop : -0.89 (0.32), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP C  36 
 HIS   0.003   0.001   HIS B 101 
 PHE   0.016   0.001   PHE A 478 
 TYR   0.025   0.001   TYR B 187 
 ARG   0.003   0.000   ARG A 244 

*********************** 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
  218 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 218
  time to evaluate  : 1.218 
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: 0.8801 (t0) cc_final: 0.8299 (t70)
REVERT: A  299 TYR cc_start: 0.8950 (m-10) cc_final: 0.8473 (m-80)
REVERT: A  376 LEU cc_start: 0.6648 (mt) cc_final: 0.6230 (mt)
REVERT: A  417 VAL cc_start: 0.5423 (t) cc_final: 0.5167 (t)
REVERT: A  444 PHE cc_start: 0.6872 (t80) cc_final: 0.6295 (t80)
REVERT: A  445 LEU cc_start: 0.8419 (mp) cc_final: 0.7815 (tp)
REVERT: B   25 LEU cc_start: 0.8656 (tp) cc_final: 0.8421 (tt)
REVERT: B   32 LEU cc_start: 0.8245 (mt) cc_final: 0.7669 (mt)
REVERT: B   79 MET cc_start: 0.8926 (tmm) cc_final: 0.8595 (tmm)
REVERT: B  108 ASP cc_start: 0.7493 (t70) cc_final: 0.6803 (t0)
REVERT: B  154 MET cc_start: 0.8596 (ttt) cc_final: 0.8186 (ttp)
REVERT: B  199 THR cc_start: 0.8957 (m) cc_final: 0.8600 (m)
REVERT: B  253 MET cc_start: 0.8928 (mmp) cc_final: 0.8725 (mmp)
REVERT: B  319 LYS cc_start: 0.8380 (tptt) cc_final: 0.8095 (tmtt)
REVERT: B  365 MET cc_start: 0.8134 (tmm) cc_final: 0.7859 (tmm)
REVERT: B  380 LEU cc_start: 0.8544 (tp) cc_final: 0.8322 (tp)
REVERT: B  436 LEU cc_start: 0.8800 (tp) cc_final: 0.8558 (tp)
REVERT: B  499 ASP cc_start: 0.5307 (t0) cc_final: 0.5107 (p0)
REVERT: B  528 LEU cc_start: 0.9107 (tp) cc_final: 0.8903 (tt)
REVERT: B  559 LEU cc_start: 0.9383 (mt) cc_final: 0.9079 (mt)
REVERT: B  569 MET cc_start: 0.7083 (ttm) cc_final: 0.6376 (ttm)
REVERT: C   65 LYS cc_start: 0.8958 (ptmt) cc_final: 0.8689 (mttt)
REVERT: C   93 VAL cc_start: 0.8768 (m) cc_final: 0.8389 (p)
REVERT: C   94 TYR cc_start: 0.5593 (m-10) cc_final: 0.5183 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 218
  average time/residue: 0.2219
  time to fit residues: 69.2665
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  : 1.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 122 optimal weight:    6.9990
   chunk 95 optimal weight:    7.9990
   chunk 63 optimal weight:    1.9990
   chunk 80 optimal weight:    0.7980
   chunk 104 optimal weight:    0.0570
   chunk 110 optimal weight:    4.9990
   chunk 7 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9990
   chunk 23 optimal weight:    0.7980
   chunk 0 optimal weight:    9.9990
   chunk 96 optimal weight:    0.5980
   overall best weight:    0.6498

-------------------------------------------------------------------------------
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 561 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C   3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  80 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.117513 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.090256 restraints weight = 26537.814|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.092613 restraints weight = 16845.634|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.094230 restraints weight = 12432.667|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.4490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10400  Z= 0.178
  Angle     :  0.633   8.029  14111  Z= 0.309
  Chirality :  0.041   0.190   1609
  Planarity :  0.004   0.047   1785
  Dihedral  :  4.929  65.142   1483
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.14 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.04 (0.24), residues: 1276
  helix:  1.64 (0.19), residues: 771
  sheet: -0.36 (0.42), residues: 133
  loop : -0.88 (0.33), residues: 372

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.051   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 101 
 PHE   0.018   0.001   PHE B 163 
 TYR   0.023   0.001   TYR B 187 
 ARG   0.003   0.000   ARG A 244 

*********************** 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
  215 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 215
  time to evaluate  : 1.222 
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: 0.8813 (t0) cc_final: 0.8322 (t70)
REVERT: A  256 TRP cc_start: 0.7586 (m100) cc_final: 0.7062 (m100)
REVERT: A  299 TYR cc_start: 0.8927 (m-80) cc_final: 0.8548 (m-80)
REVERT: A  376 LEU cc_start: 0.6292 (mt) cc_final: 0.5931 (mt)
REVERT: A  444 PHE cc_start: 0.6894 (t80) cc_final: 0.6441 (t80)
REVERT: A  445 LEU cc_start: 0.8275 (mp) cc_final: 0.7773 (tp)
REVERT: B   25 LEU cc_start: 0.8645 (tp) cc_final: 0.8419 (tt)
REVERT: B   32 LEU cc_start: 0.8309 (mt) cc_final: 0.7715 (mt)
REVERT: B   79 MET cc_start: 0.8817 (tmm) cc_final: 0.8498 (tmm)
REVERT: B  108 ASP cc_start: 0.7317 (t70) cc_final: 0.7080 (t0)
REVERT: B  154 MET cc_start: 0.8646 (ttt) cc_final: 0.7760 (ttt)
REVERT: B  199 THR cc_start: 0.8960 (m) cc_final: 0.8585 (m)
REVERT: B  253 MET cc_start: 0.8921 (mmp) cc_final: 0.8706 (mmp)
REVERT: B  319 LYS cc_start: 0.8379 (tptt) cc_final: 0.8111 (tmtt)
REVERT: B  365 MET cc_start: 0.8131 (tmm) cc_final: 0.7844 (tmm)
REVERT: B  380 LEU cc_start: 0.8589 (tp) cc_final: 0.8379 (tp)
REVERT: B  436 LEU cc_start: 0.8808 (tp) cc_final: 0.8574 (tp)
REVERT: B  521 LEU cc_start: 0.8434 (mt) cc_final: 0.8205 (mp)
REVERT: B  528 LEU cc_start: 0.9132 (tp) cc_final: 0.8927 (tt)
REVERT: B  559 LEU cc_start: 0.9331 (mt) cc_final: 0.9117 (mt)
REVERT: B  569 MET cc_start: 0.7081 (ttm) cc_final: 0.6745 (ttm)
REVERT: C   18 LEU cc_start: 0.7304 (tp) cc_final: 0.7024 (tp)
REVERT: C   65 LYS cc_start: 0.8961 (ptmt) cc_final: 0.8593 (mttt)
REVERT: C   83 MET cc_start: 0.6948 (mmm) cc_final: 0.6260 (mmp)
REVERT: C   93 VAL cc_start: 0.8718 (m) cc_final: 0.8310 (p)
REVERT: C   94 TYR cc_start: 0.5644 (m-10) cc_final: 0.5191 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 215
  average time/residue: 0.2208
  time to fit residues: 66.8298
Evaluate side-chains
  159 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 1.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 100 optimal weight:    0.7980
   chunk 103 optimal weight:    0.0970
   chunk 104 optimal weight:    0.6980
   chunk 38 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0770
   chunk 29 optimal weight:    0.9980
   chunk 51 optimal weight:    0.0870
   chunk 119 optimal weight:    0.9980
   chunk 14 optimal weight:    0.1980
   chunk 107 optimal weight:    0.5980
   chunk 108 optimal weight:    0.2980
   overall best weight:    0.1514

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

Flipped N/Q/H residues before XYZ refinement:
A 596 GLN
B 431 ASN
** 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 = 0.3846 r_free = 0.3846 target = 0.120056 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.092692 restraints weight = 26395.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.095227 restraints weight = 16616.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.096979 restraints weight = 12051.900|
|-----------------------------------------------------------------------------|
r_work (final): 0.3489
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.4815

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  10400  Z= 0.154
  Angle     :  0.630   8.635  14111  Z= 0.306
  Chirality :  0.041   0.189   1609
  Planarity :  0.004   0.048   1785
  Dihedral  :  4.603  57.479   1483
  Min Nonbonded Distance : 2.027

Molprobity Statistics.
  All-atom Clashscore : 8.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.19 %
    Favored  : 97.81 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.24), residues: 1276
  helix:  1.79 (0.18), residues: 785
  sheet: -0.34 (0.41), residues: 148
  loop : -0.74 (0.35), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.057   0.002   TRP C  36 
 HIS   0.002   0.001   HIS C  80 
 PHE   0.017   0.001   PHE A 478 
 TYR   0.022   0.001   TYR B 187 
 ARG   0.008   0.000   ARG B 549 

*********************** 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
  221 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 221
  time to evaluate  : 1.144 
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: 0.8765 (t0) cc_final: 0.8317 (t70)
REVERT: A  299 TYR cc_start: 0.8899 (m-80) cc_final: 0.8480 (m-80)
REVERT: A  444 PHE cc_start: 0.6999 (t80) cc_final: 0.6693 (t80)
REVERT: A  551 ILE cc_start: 0.8943 (mp) cc_final: 0.8241 (tp)
REVERT: B   25 LEU cc_start: 0.8588 (tp) cc_final: 0.8369 (tt)
REVERT: B   32 LEU cc_start: 0.8158 (mt) cc_final: 0.7703 (mt)
REVERT: B   79 MET cc_start: 0.8777 (tmm) cc_final: 0.8532 (tmm)
REVERT: B  154 MET cc_start: 0.8509 (ttt) cc_final: 0.8021 (ttp)
REVERT: B  199 THR cc_start: 0.8946 (m) cc_final: 0.8583 (m)
REVERT: B  319 LYS cc_start: 0.8400 (tptt) cc_final: 0.8170 (tmtt)
REVERT: B  365 MET cc_start: 0.8122 (tmm) cc_final: 0.7912 (tmm)
REVERT: B  436 LEU cc_start: 0.8763 (tp) cc_final: 0.8510 (tp)
REVERT: B  499 ASP cc_start: 0.5409 (t0) cc_final: 0.5000 (p0)
REVERT: B  559 LEU cc_start: 0.9322 (mt) cc_final: 0.9061 (mt)
REVERT: B  569 MET cc_start: 0.6958 (ttm) cc_final: 0.6625 (ttm)
REVERT: C   18 LEU cc_start: 0.7252 (tp) cc_final: 0.7048 (tp)
REVERT: C   37 PHE cc_start: 0.8065 (m-80) cc_final: 0.7764 (m-80)
REVERT: C   65 LYS cc_start: 0.8952 (ptmt) cc_final: 0.8542 (mttm)
REVERT: C   83 MET cc_start: 0.6600 (mmm) cc_final: 0.6244 (mmp)
REVERT: C   93 VAL cc_start: 0.8773 (m) cc_final: 0.8411 (p)
REVERT: C   94 TYR cc_start: 0.5675 (m-10) cc_final: 0.5218 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 221
  average time/residue: 0.2122
  time to fit residues: 66.6632
Evaluate side-chains
  162 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 162
  time to evaluate  : 1.130 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 82 optimal weight:    0.8980
   chunk 94 optimal weight:    1.9990
   chunk 49 optimal weight:    8.9990
   chunk 14 optimal weight:    0.9990
   chunk 98 optimal weight:    0.9980
   chunk 86 optimal weight:    0.8980
   chunk 48 optimal weight:    5.9990
   chunk 52 optimal weight:    3.9990
   chunk 85 optimal weight:    1.9990
   chunk 59 optimal weight:    1.9990
   chunk 58 optimal weight:    3.9990
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
B 481 GLN
B 538 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 = 0.3811 r_free = 0.3811 target = 0.117508 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.090343 restraints weight = 26566.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.092785 restraints weight = 16624.140|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.094437 restraints weight = 12044.714|
|-----------------------------------------------------------------------------|
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4794

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  10400  Z= 0.217
  Angle     :  0.659   8.956  14111  Z= 0.323
  Chirality :  0.042   0.186   1609
  Planarity :  0.004   0.045   1785
  Dihedral  :  4.540  54.123   1483
  Min Nonbonded Distance : 1.960

Molprobity Statistics.
  All-atom Clashscore : 10.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.06 %
    Favored  : 96.94 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.24), residues: 1276
  helix:  1.68 (0.18), residues: 776
  sheet: -0.37 (0.42), residues: 133
  loop : -0.73 (0.33), residues: 367

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP C  36 
 HIS   0.004   0.001   HIS B 101 
 PHE   0.022   0.001   PHE B 163 
 TYR   0.020   0.001   TYR B 187 
 ARG   0.005   0.000   ARG B 188 

*********************** 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  : 1.120 
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: 0.8777 (t0) cc_final: 0.8216 (t70)
REVERT: A  299 TYR cc_start: 0.8927 (m-80) cc_final: 0.8462 (m-80)
REVERT: A  444 PHE cc_start: 0.7076 (t80) cc_final: 0.6840 (t80)
REVERT: B   25 LEU cc_start: 0.8697 (tp) cc_final: 0.8454 (tt)
REVERT: B   32 LEU cc_start: 0.8316 (mt) cc_final: 0.7554 (mt)
REVERT: B   79 MET cc_start: 0.8771 (tmm) cc_final: 0.8411 (tmm)
REVERT: B  154 MET cc_start: 0.8466 (ttt) cc_final: 0.8060 (ttt)
REVERT: B  199 THR cc_start: 0.8977 (m) cc_final: 0.8606 (m)
REVERT: B  319 LYS cc_start: 0.8435 (tptt) cc_final: 0.8204 (tmtt)
REVERT: B  365 MET cc_start: 0.8159 (tmm) cc_final: 0.7892 (tmm)
REVERT: B  426 GLU cc_start: 0.8744 (pm20) cc_final: 0.8093 (pm20)
REVERT: B  436 LEU cc_start: 0.8891 (tp) cc_final: 0.8641 (tp)
REVERT: B  481 GLN cc_start: 0.8338 (mm110) cc_final: 0.8098 (mp10)
REVERT: B  559 LEU cc_start: 0.9339 (mt) cc_final: 0.9130 (mt)
REVERT: B  569 MET cc_start: 0.7025 (ttm) cc_final: 0.6650 (ttm)
REVERT: C   65 LYS cc_start: 0.9018 (ptmt) cc_final: 0.8772 (mttt)
REVERT: C   83 MET cc_start: 0.6707 (mmm) cc_final: 0.6026 (mmp)
REVERT: C   93 VAL cc_start: 0.8612 (m) cc_final: 0.8220 (p)
REVERT: C   94 TYR cc_start: 0.5882 (m-10) cc_final: 0.5373 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 207
  average time/residue: 0.2081
  time to fit residues: 62.3647
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  : 1.092 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 78 optimal weight:    0.9990
   chunk 49 optimal weight:    3.9990
   chunk 5 optimal weight:    6.9990
   chunk 14 optimal weight:    0.8980
   chunk 116 optimal weight:    5.9990
   chunk 115 optimal weight:    0.4980
   chunk 94 optimal weight:    2.9990
   chunk 37 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9990
   chunk 24 optimal weight:    0.5980
   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 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 573 GLN
C  80 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.119004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.091333 restraints weight = 26889.068|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.093860 restraints weight = 16498.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.095599 restraints weight = 11921.626|
|-----------------------------------------------------------------------------|
r_work (final): 0.3457
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.4887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  10400  Z= 0.179
  Angle     :  0.640   8.513  14111  Z= 0.312
  Chirality :  0.041   0.178   1609
  Planarity :  0.004   0.046   1785
  Dihedral  :  4.523  52.838   1483
  Min Nonbonded Distance : 1.988

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.26 (0.24), residues: 1276
  helix:  1.80 (0.18), residues: 769
  sheet: -0.28 (0.42), residues: 141
  loop : -0.73 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.053   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 101 
 PHE   0.018   0.001   PHE A 478 
 TYR   0.019   0.001   TYR B 302 
 ARG   0.002   0.000   ARG B 480 

********************** 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
  197 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 197
  time to evaluate  : 1.096 
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: 0.8739 (t0) cc_final: 0.8262 (t70)
REVERT: A  299 TYR cc_start: 0.8858 (m-80) cc_final: 0.8506 (m-80)
REVERT: B   25 LEU cc_start: 0.8656 (tp) cc_final: 0.8405 (tt)
REVERT: B   32 LEU cc_start: 0.8294 (mt) cc_final: 0.7721 (mt)
REVERT: B   79 MET cc_start: 0.8708 (tmm) cc_final: 0.8485 (tmm)
REVERT: B  199 THR cc_start: 0.8981 (m) cc_final: 0.8637 (m)
REVERT: B  319 LYS cc_start: 0.8428 (tptt) cc_final: 0.8186 (tmtt)
REVERT: B  365 MET cc_start: 0.8117 (tmm) cc_final: 0.7915 (tmm)
REVERT: B  436 LEU cc_start: 0.8888 (tp) cc_final: 0.8561 (tp)
REVERT: B  481 GLN cc_start: 0.8254 (mm110) cc_final: 0.7994 (mp10)
REVERT: B  569 MET cc_start: 0.6964 (ttm) cc_final: 0.6646 (ttm)
REVERT: C   65 LYS cc_start: 0.8955 (ptmt) cc_final: 0.8511 (mttt)
REVERT: C   83 MET cc_start: 0.6925 (mmm) cc_final: 0.6487 (mmp)
REVERT: C   93 VAL cc_start: 0.8621 (m) cc_final: 0.8229 (p)
REVERT: C   94 TYR cc_start: 0.5874 (m-10) cc_final: 0.5381 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 197
  average time/residue: 0.2068
  time to fit residues: 59.0717
Evaluate side-chains
  156 residues out of total 1049 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 156
  time to evaluate  : 1.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 127
   random chunks:
   chunk 118 optimal weight:    0.9990
   chunk 67 optimal weight:    2.9990
   chunk 119 optimal weight:    5.9990
   chunk 54 optimal weight:    0.9990
   chunk 82 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 83 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 126 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 96 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 431 ASN
B 573 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3814 r_free = 0.3814 target = 0.117838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.090460 restraints weight = 26336.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.092973 restraints weight = 16338.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3454 r_free = 0.3454 target = 0.094663 restraints weight = 11760.264|
|-----------------------------------------------------------------------------|
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7931
moved from start:          0.4942

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038  10400  Z= 0.191
  Angle     :  0.647   8.130  14111  Z= 0.316
  Chirality :  0.042   0.178   1609
  Planarity :  0.004   0.046   1785
  Dihedral  :  4.431  52.023   1483
  Min Nonbonded Distance : 1.984

Molprobity Statistics.
  All-atom Clashscore : 10.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.19 %
    Favored  : 99.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.27 (0.24), residues: 1276
  helix:  1.81 (0.18), residues: 770
  sheet: -0.37 (0.43), residues: 131
  loop : -0.68 (0.33), residues: 375

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP C  36 
 HIS   0.003   0.001   HIS B 101 
 PHE   0.024   0.001   PHE B 163 
 TYR   0.017   0.001   TYR B 187 
 ARG   0.002   0.000   ARG C  72 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3083.82 seconds
wall clock time: 56 minutes 4.89 seconds (3364.89 seconds total)