Starting phenix.real_space_refine
on Sun May  3 00:24:36 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8zv4_60507/05_2026/8zv4_60507.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8zv4_60507/05_2026/8zv4_60507.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.93
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8zv4_60507/05_2026/8zv4_60507.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8zv4_60507/05_2026/8zv4_60507.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8zv4_60507/05_2026/8zv4_60507.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8zv4_60507/05_2026/8zv4_60507.cif"
  }
  resolution = 2.93
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.015
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       6      5.49       5
     Mg      1      5.21       5
     S      52      5.16       5
     C    5746      2.51       5
     N    1602      2.21       5
     O    1752      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 22 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9159
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 5190
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 673, 5190
          Classifications: {'peptide': 673}
          Link IDs: {'PTRANS': 24, 'TRANS': 648}
    Chain: "B"
      Number of atoms: 1906
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 247, 1906
          Classifications: {'peptide': 247}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 15, 'TRANS': 231}
    Chain: "F"
      Number of atoms: 1975
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 261, 1975
          Classifications: {'peptide': 261}
          Link IDs: {'PTRANS': 10, 'TRANS': 250}
    Chain: "A"
      Number of atoms: 36
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 36
          Unusual residues: {' MG': 1, 'ATP': 1, 'BCT': 1}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
    Chain: "F"
      Number of atoms: 52
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 52
          Unusual residues: {'1VU': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.51, per 1000 atoms: 0.27
  Number of scatterers: 9159
  At special positions: 0
  Unit cell: (98.28, 100.8, 135.24, 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      52     16.00
     P       6     15.00
     Mg      1     11.99
     O    1752      8.00
     N    1602      7.00
     C    5746      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 427.0 milliseconds
  

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2180

  Finding SS restraints...
    Secondary structure from input PDB file:
      46 helices and 14 sheets defined
      40.3% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.38
  Creating SS restraints...
    Processing helix  chain 'A' and resid 72 through 86
      removed outlier: 3.510A  pdb=" N   CYS A  76 " --> pdb=" O   GLY A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 4.434A  pdb=" N   SER A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 100 through 106
      removed outlier: 3.504A  pdb=" N   LYS A 104 " --> pdb=" O   SER A 100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 116 through 121
    Processing helix  chain 'A' and resid 123 through 135
    Processing helix  chain 'A' and resid 149 through 160
    Processing helix  chain 'A' and resid 167 through 176
      removed outlier: 4.137A  pdb=" N   ASP A 176 " --> pdb=" O   GLN A 172 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 176 through 187
    Processing helix  chain 'A' and resid 201 through 213
    Processing helix  chain 'A' and resid 234 through 253
      removed outlier: 4.164A  pdb=" N   ALA A 250 " --> pdb=" O   SER A 246 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   SER A 251 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 328
    Processing helix  chain 'A' and resid 357 through 366
      removed outlier: 4.473A  pdb=" N   THR A 361 " --> pdb=" O   GLU A 357 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   ILE A 364 " --> pdb=" O   VAL A 360 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 368 through 379
    Processing helix  chain 'A' and resid 458 through 472
    Processing helix  chain 'A' and resid 481 through 490
    Processing helix  chain 'A' and resid 491 through 497
    Processing helix  chain 'A' and resid 502 through 508
    Processing helix  chain 'A' and resid 518 through 540
    Processing helix  chain 'A' and resid 641 through 648
    Processing helix  chain 'B' and resid 299 through 303
    Processing helix  chain 'B' and resid 315 through 324
      removed outlier: 3.954A  pdb=" N   ILE B 319 " --> pdb=" O   ASN B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 325 through 328
    Processing helix  chain 'B' and resid 361 through 365
    Processing helix  chain 'B' and resid 367 through 384
      removed outlier: 3.764A  pdb=" N   ARG B 376 " --> pdb=" O   VAL B 372 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE B 377 " --> pdb=" O   LYS B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 400 through 407
    Processing helix  chain 'B' and resid 407 through 421
    Processing helix  chain 'B' and resid 436 through 442
      removed outlier: 3.811A  pdb=" N   ASP B 440 " --> pdb=" O   GLY B 436 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 444 through 448
      removed outlier: 3.507A  pdb=" N   CYS B 448 " --> pdb=" O   LYS B 445 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 464 through 473
    Processing helix  chain 'B' and resid 481 through 488
    Processing helix  chain 'B' and resid 493 through 499
      removed outlier: 3.766A  pdb=" N   ARG B 499 " --> pdb=" O   PRO B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 509
      No H-bonds generated for 'chain 'B' and resid 507 through 509'
    Processing helix  chain 'B' and resid 510 through 522
    Processing helix  chain 'B' and resid 523 through 525
      No H-bonds generated for 'chain 'B' and resid 523 through 525'
    Processing helix  chain 'F' and resid 33 through 48
      removed outlier: 4.378A  pdb=" N   GLU F  37 " --> pdb=" O   THR F  33 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 51 through 61
    Processing helix  chain 'F' and resid 65 through 74
    Processing helix  chain 'F' and resid 97 through 101
    Processing helix  chain 'F' and resid 128 through 132
    Processing helix  chain 'F' and resid 134 through 152
    Processing helix  chain 'F' and resid 169 through 187
      removed outlier: 3.811A  pdb=" N   LEU F 173 " --> pdb=" O   GLY F 169 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 205 through 211
    Processing helix  chain 'F' and resid 227 through 235
    Processing helix  chain 'F' and resid 240 through 246
    Processing helix  chain 'F' and resid 246 through 253
    Processing helix  chain 'F' and resid 263 through 276
    Processing sheet with id=AA1, first strand: chain 'A' and resid 108 through 111
      removed outlier: 3.689A  pdb=" N   GLU A 108 " --> pdb=" O   THR A  89 " (cutoff:3.500A)
      removed outlier: 6.299A  pdb=" N   ILE A  66 " --> pdb=" O   VAL A  90 " (cutoff:3.500A)
      removed outlier: 7.836A  pdb=" N   ILE A  92 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 7.261A  pdb=" N   VAL A  68 " --> pdb=" O   ILE A  92 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   LYS A  65 " --> pdb=" O   ALA A 138 " (cutoff:3.500A)
      removed outlier: 7.789A  pdb=" N   HIS A 140 " --> pdb=" O   LYS A  65 " (cutoff:3.500A)
      removed outlier: 6.459A  pdb=" N   LEU A  67 " --> pdb=" O   HIS A 140 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   VAL A 139 " --> pdb=" O   VAL A 162 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 229 through 232
    Processing sheet with id=AA3, first strand: chain 'A' and resid 282 through 284
    Processing sheet with id=AA4, first strand: chain 'A' and resid 282 through 284
      removed outlier: 6.396A  pdb=" N   THR A 334 " --> pdb=" O   MET A 350 " (cutoff:3.500A)
      removed outlier: 4.763A  pdb=" N   MET A 350 " --> pdb=" O   THR A 334 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   GLU A 336 " --> pdb=" O   LEU A 348 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 293 through 294
    Processing sheet with id=AA6, first strand: chain 'A' and resid 300 through 302
    Processing sheet with id=AA7, first strand: chain 'A' and resid 415 through 416
    Processing sheet with id=AA8, first strand: chain 'A' and resid 419 through 421
    Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 565
      removed outlier: 6.514A  pdb=" N   SER A 626 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 4.479A  pdb=" N   ARG A 619 " --> pdb=" O   ASN A 624 " (cutoff:3.500A)
      removed outlier: 7.003A  pdb=" N   ASN A 624 " --> pdb=" O   ARG A 619 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   ASN A 637 " --> pdb=" O   LYS A 564 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 661 through 663
      removed outlier: 7.505A  pdb=" N   LEU A 662 " --> pdb=" O   LEU A 724 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 695 through 700
      removed outlier: 8.101A  pdb=" N   ILE A 687 " --> pdb=" O   VAL A 673 " (cutoff:3.500A)
      removed outlier: 5.236A  pdb=" N   VAL A 673 " --> pdb=" O   ILE A 687 " (cutoff:3.500A)
      removed outlier: 6.694A  pdb=" N   VAL A 689 " --> pdb=" O   VAL A 671 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.528A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   ASP B 393 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 6.621A  pdb=" N   GLU B 459 " --> pdb=" O   ILE B 430 " (cutoff:3.500A)
      removed outlier: 6.778A  pdb=" N   ARG B 432 " --> pdb=" O   GLU B 459 " (cutoff:3.500A)
      removed outlier: 7.505A  pdb=" N   ALA B 461 " --> pdb=" O   ARG B 432 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   ALA B 434 " --> pdb=" O   ALA B 461 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 330 through 332
      removed outlier: 4.528A  pdb=" N   VAL B 342 " --> pdb=" O   ILE B 332 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   ASP B 393 " --> pdb=" O   ASN B 357 " (cutoff:3.500A)
      removed outlier: 8.740A  pdb=" N   VAL B 394 " --> pdb=" O   THR B 431 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   LYS B 433 " --> pdb=" O   VAL B 394 " (cutoff:3.500A)
      removed outlier: 6.723A  pdb=" N   LYS B 426 " --> pdb=" O   THR B 451 " (cutoff:3.500A)
      removed outlier: 8.329A  pdb=" N   TYR B 453 " --> pdb=" O   LYS B 426 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   THR B 428 " --> pdb=" O   TYR B 453 " (cutoff:3.500A)
      removed outlier: 3.877A  pdb=" N   ASP B 504 " --> pdb=" O   ASN B 452 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 80 through 82
      removed outlier: 4.433A  pdb=" N   THR F 109 " --> pdb=" O   SER F  82 " (cutoff:3.500A)
      removed outlier: 8.549A  pdb=" N   ILE F 156 " --> pdb=" O   LEU F 118 " (cutoff:3.500A)
      removed outlier: 6.434A  pdb=" N   TYR F 120 " --> pdb=" O   ILE F 156 " (cutoff:3.500A)
      removed outlier: 8.008A  pdb=" N   LEU F 158 " --> pdb=" O   TYR F 120 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   PHE F 122 " --> pdb=" O   LEU F 158 " (cutoff:3.500A)
      removed outlier: 6.337A  pdb=" N   VAL F 155 " --> pdb=" O   ILE F 193 " (cutoff:3.500A)
      removed outlier: 7.956A  pdb=" N   LEU F 195 " --> pdb=" O   VAL F 155 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   GLY F 157 " --> pdb=" O   LEU F 195 " (cutoff:3.500A)
      removed outlier: 6.999A  pdb=" N   THR F 214 " --> pdb=" O   ARG F 259 " (cutoff:3.500A)
      removed outlier: 8.568A  pdb=" N   PHE F 261 " --> pdb=" O   THR F 214 " (cutoff:3.500A)
      removed outlier: 6.792A  pdb=" N   MET F 216 " --> pdb=" O   PHE F 261 " (cutoff:3.500A)

    442 hydrogen bonds defined for protein.
    1227 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.78

  Time building geometry restraints manager: 1.09 seconds

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

  Histogram of bond lengths:
        1.14 -     1.28: 1559
        1.28 -     1.42: 2255
        1.42 -     1.56: 5410
        1.56 -     1.70: 16
        1.70 -     1.84: 85
  Bond restraints: 9325
  Sorted by residual:
  bond pdb=" O10 1VU F5601 "
       pdb=" P1  1VU F5601 "
    ideal  model  delta    sigma   weight residual
    2.250  1.643  0.607 2.00e-02 2.50e+03 9.20e+02
  bond pdb=" O14 1VU F5601 "
       pdb=" P2  1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.682  1.468  0.214 2.00e-02 2.50e+03 1.14e+02
  bond pdb=" C16 1VU F5601 "
       pdb=" C22 1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.560  1.359  0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" C16 1VU F5601 "
       pdb=" O11 1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.425  1.593 -0.168 2.00e-02 2.50e+03 7.06e+01
  bond pdb=" C15 1VU F5601 "
       pdb=" O11 1VU F5601 "
    ideal  model  delta    sigma   weight residual
    1.459  1.307  0.152 2.00e-02 2.50e+03 5.74e+01
  ... (remaining 9320 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    11.13: 12618
       11.13 -    22.27: 6
       22.27 -    33.40: 3
       33.40 -    44.54: 0
       44.54 -    55.67: 1
  Bond angle restraints: 12628
  Sorted by residual:
  angle pdb=" O14 1VU F5601 "
        pdb=" P2  1VU F5601 "
        pdb=" O15 1VU F5601 "
      ideal   model   delta    sigma   weight residual
      53.72  109.39  -55.67 3.00e+00 1.11e-01 3.44e+02
  angle pdb=" O10 1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O9  1VU F5601 "
      ideal   model   delta    sigma   weight residual
      78.74  109.23  -30.49 3.00e+00 1.11e-01 1.03e+02
  angle pdb=" O8  1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O9  1VU F5601 "
      ideal   model   delta    sigma   weight residual
     140.21  109.92   30.29 3.00e+00 1.11e-01 1.02e+02
  angle pdb=" O10 1VU F5601 "
        pdb=" P1  1VU F5601 "
        pdb=" O7  1VU F5601 "
      ideal   model   delta    sigma   weight residual
      85.76  109.06  -23.30 3.00e+00 1.11e-01 6.03e+01
  angle pdb=" P   1VU F5601 "
        pdb=" O7  1VU F5601 "
        pdb=" P1  1VU F5601 "
      ideal   model   delta    sigma   weight residual
     143.93  124.00   19.93 3.00e+00 1.11e-01 4.41e+01
  ... (remaining 12623 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    34.17: 5602
       34.17 -    68.34: 89
       68.34 -   102.51: 6
      102.51 -   136.68: 0
      136.68 -   170.85: 5
  Dihedral angle restraints: 5702
    sinusoidal: 2315
      harmonic: 3387
  Sorted by residual:
  dihedral pdb=" CA  ASP A 160 "
           pdb=" C   ASP A 160 "
           pdb=" N   VAL A 161 "
           pdb=" CA  VAL A 161 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.03  -24.97     0      5.00e+00 4.00e-02 2.49e+01
  dihedral pdb=" O6  1VU F5601 "
           pdb=" O7  1VU F5601 "
           pdb=" P   1VU F5601 "
           pdb=" P1  1VU F5601 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -98.95   71.90 -170.85     1      3.00e+01 1.11e-03 2.12e+01
  dihedral pdb=" C   1VU F5601 "
           pdb=" C1  1VU F5601 "
           pdb=" C2  1VU F5601 "
           pdb=" O   1VU F5601 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -123.88   41.62 -165.50     1      3.00e+01 1.11e-03 2.10e+01
  ... (remaining 5699 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 1395
       0.113 -    0.226: 30
       0.226 -    0.338: 1
       0.338 -    0.451: 0
       0.451 -    0.564: 1
  Chirality restraints: 1427
  Sorted by residual:
  chirality pdb=" C22 1VU F5601 "
            pdb=" C16 1VU F5601 "
            pdb=" C23 1VU F5601 "
            pdb=" O12 1VU F5601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.99   -2.42   -0.56 2.00e-01 2.50e+01 7.95e+00
  chirality pdb=" C16 1VU F5601 "
            pdb=" C22 1VU F5601 "
            pdb=" N2  1VU F5601 "
            pdb=" O11 1VU F5601 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.69    2.46    0.24 2.00e-01 2.50e+01 1.41e+00
  chirality pdb=" CA  LYS A 694 "
            pdb=" N   LYS A 694 "
            pdb=" C   LYS A 694 "
            pdb=" CB  LYS A 694 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.35    0.16 2.00e-01 2.50e+01 6.25e-01
  ... (remaining 1424 not shown)

  Planarity restraints: 1639
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP F 178 "   -0.008 2.00e-02 2.50e+03   1.51e-02 2.27e+00
        pdb=" C   ASP F 178 "    0.026 2.00e-02 2.50e+03
        pdb=" O   ASP F 178 "   -0.010 2.00e-02 2.50e+03
        pdb=" N   ILE F 179 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE B 537 "   -0.025 5.00e-02 4.00e+02   3.71e-02 2.21e+00
        pdb=" N   PRO B 538 "    0.064 5.00e-02 4.00e+02
        pdb=" CA  PRO B 538 "   -0.019 5.00e-02 4.00e+02
        pdb=" CD  PRO B 538 "   -0.021 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR F 176 "    0.007 2.00e-02 2.50e+03   1.47e-02 2.17e+00
        pdb=" C   TYR F 176 "   -0.025 2.00e-02 2.50e+03
        pdb=" O   TYR F 176 "    0.010 2.00e-02 2.50e+03
        pdb=" N   ALA F 177 "    0.009 2.00e-02 2.50e+03
  ... (remaining 1636 not shown)

  Histogram of nonbonded interaction distances:
        2.13 -     2.68: 188
        2.68 -     3.24: 8953
        3.24 -     3.79: 14257
        3.79 -     4.35: 19366
        4.35 -     4.90: 31989
  Nonbonded interactions: 74753
  Sorted by model distance:
  nonbonded pdb=" O2G ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.131 2.170
  nonbonded pdb=" O1A ATP A 801 "
            pdb="MG    MG A 802 "
     model   vdw
     2.171 2.170
  nonbonded pdb=" O   TYR B 439 "
            pdb=" OG  SER B 444 "
     model   vdw
     2.196 3.040
  nonbonded pdb=" OE2 GLU A 301 "
            pdb=" NH2 ARG A 399 "
     model   vdw
     2.251 3.120
  nonbonded pdb=" OE2 GLU A  73 "
            pdb=" OH  TYR A 143 "
     model   vdw
     2.257 3.040
  ... (remaining 74748 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 individual isotropic
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:             3.730
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     10.670
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.820
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8525
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      :  0.009   0.607   9325  Z= 0.450
  Angle     :  0.998  55.672  12628  Z= 0.432
  Chirality :  0.047   0.564   1427
  Planarity :  0.004   0.037   1639
  Dihedral  : 14.180 170.855   3522
  Min Nonbonded Distance : 2.131

Molprobity Statistics.
  All-atom Clashscore : 8.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.31 %
    Favored  : 99.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.24), residues: 1175
  helix:  0.70 (0.26), residues: 417
  sheet:  0.28 (0.33), residues: 253
  loop : -0.99 (0.26), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 243 
 TYR   0.022   0.001   TYR A 473 
 PHE   0.023   0.001   PHE A 347 
 TRP   0.008   0.001   TRP A 394 
 HIS   0.006   0.001   HIS B 446 

Details of bonding type rmsd
  covalent geometry    : bond        0.00897 ( 9325)
  covalent geometry    : angle       0.99800 (12628)
  hydrogen bonds       : bond        0.15311 (  420)
  hydrogen bonds       : angle       6.22189 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 125
  time to evaluate  : 0.358 
Fit side-chains
REVERT: A  155 CYS cc_start: 0.9198 (t) cc_final: 0.8844 (t)
REVERT: A  284 TRP cc_start: 0.8732 (p-90) cc_final: 0.8348 (p90)
REVERT: A  448 MET cc_start: 0.8062 (tpp) cc_final: 0.7832 (tpt)
REVERT: F  100 ASN cc_start: 0.9193 (m110) cc_final: 0.8894 (m110)
REVERT: F  253 MET cc_start: 0.8043 (ptp) cc_final: 0.7838 (ptm)
  outliers start: 0
  outliers final: 0
  residues processed: 125
  average time/residue: 0.6748
  time to fit residues: 89.4414
Evaluate side-chains
  87 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.349 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 108 optimal weight:    0.5980
   chunk 49 optimal weight:    2.9990
   chunk 97 optimal weight:    4.9990
   chunk 113 optimal weight:    3.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.7980
   chunk 33 optimal weight:    4.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:   40.0000
   chunk 51 optimal weight:    3.9990
   chunk 100 optimal weight:    3.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 102 HIS
A 190 ASN
A 269 HIS
A 286 ASN
A 344 ASN
A 351 ASN
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 386 GLN
** A 472 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F 147 GLN
F 183 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.135684 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3079 r_free = 0.3079 target = 0.084410 restraints weight = 16090.293|
|-----------------------------------------------------------------------------|
r_work (start): 0.3035 rms_B_bonded: 2.73
r_work: 0.2917 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2804 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2804
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8853
moved from start:          0.1352

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   9325  Z= 0.202
  Angle     :  0.633   8.890  12628  Z= 0.323
  Chirality :  0.047   0.145   1427
  Planarity :  0.004   0.040   1639
  Dihedral  : 12.537 148.446   1373
  Min Nonbonded Distance : 2.026

Molprobity Statistics.
  All-atom Clashscore : 7.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  :  8.17 %
    Favored  : 89.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.03 (0.24), residues: 1175
  helix:  0.83 (0.25), residues: 437
  sheet:  0.35 (0.33), residues: 252
  loop : -0.96 (0.27), residues: 486

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 314 
 TYR   0.034   0.002   TYR A 473 
 PHE   0.021   0.002   PHE A 347 
 TRP   0.005   0.001   TRP A 394 
 HIS   0.010   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00479 ( 9325)
  covalent geometry    : angle       0.63318 (12628)
  hydrogen bonds       : bond        0.04824 (  420)
  hydrogen bonds       : angle       4.81460 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 94
  time to evaluate  : 0.436 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  284 TRP cc_start: 0.8796 (p-90) cc_final: 0.8136 (p-90)
REVERT: A  448 MET cc_start: 0.8448 (tpp) cc_final: 0.8128 (tpt)
REVERT: F  100 ASN cc_start: 0.9223 (m110) cc_final: 0.8937 (m110)
REVERT: F  253 MET cc_start: 0.8685 (ptp) cc_final: 0.8478 (ptm)
REVERT: F  289 ARG cc_start: 0.5673 (ptp90) cc_final: 0.5386 (ptt180)
REVERT: F  290 GLU cc_start: 0.6637 (pp20) cc_final: 0.6401 (pp20)
  outliers start: 20
  outliers final: 4
  residues processed: 105
  average time/residue: 0.6870
  time to fit residues: 76.6738
Evaluate side-chains
  83 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.335 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  161 VAL
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  211 GLU
Chi-restraints excluded: chain A residue  334 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 87 optimal weight:    6.9990
   chunk 90 optimal weight:    0.0980
   chunk 24 optimal weight:    5.9990
   chunk 29 optimal weight:    7.9990
   chunk 76 optimal weight:    0.6980
   chunk 40 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9980
   chunk 105 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 6 optimal weight:    3.9990
   chunk 0 optimal weight:   10.0000
   overall best weight:    1.3584

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 472 ASN
B 446 HIS
B 483 GLN
F 147 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3884 r_free = 0.3884 target = 0.136371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 74)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.084653 restraints weight = 16141.568|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.82
r_work: 0.2929 rms_B_bonded: 3.01 restraints_weight: 0.5000
r_work: 0.2814 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2814
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8848
moved from start:          0.1562

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9325  Z= 0.157
  Angle     :  0.580   7.841  12628  Z= 0.297
  Chirality :  0.045   0.146   1427
  Planarity :  0.004   0.038   1639
  Dihedral  : 11.554 127.337   1373
  Min Nonbonded Distance : 2.056

Molprobity Statistics.
  All-atom Clashscore : 7.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 10.62 %
    Favored  : 87.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.19 (0.24), residues: 1175
  helix:  1.11 (0.25), residues: 437
  sheet:  0.47 (0.33), residues: 247
  loop : -0.92 (0.27), residues: 491

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A  77 
 TYR   0.020   0.001   TYR A 473 
 PHE   0.016   0.001   PHE A 347 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.007   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00369 ( 9325)
  covalent geometry    : angle       0.58039 (12628)
  hydrogen bonds       : bond        0.04210 (  420)
  hydrogen bonds       : angle       4.57227 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 92
  time to evaluate  : 0.419 
Fit side-chains
REVERT: A  156 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8936 (mp)
REVERT: A  257 ARG cc_start: 0.8773 (mmp80) cc_final: 0.8473 (mmp80)
REVERT: A  284 TRP cc_start: 0.8824 (p-90) cc_final: 0.8477 (p90)
REVERT: A  308 LEU cc_start: 0.8942 (tt) cc_final: 0.8720 (tt)
REVERT: A  448 MET cc_start: 0.8532 (tpp) cc_final: 0.8258 (tpt)
REVERT: B  499 ARG cc_start: 0.8663 (mpp80) cc_final: 0.8256 (tpp-160)
REVERT: F  100 ASN cc_start: 0.9231 (m110) cc_final: 0.8991 (m110)
REVERT: F  237 GLU cc_start: 0.8403 (pm20) cc_final: 0.8120 (pm20)
REVERT: F  289 ARG cc_start: 0.5654 (ptp90) cc_final: 0.5256 (ptp-170)
REVERT: F  290 GLU cc_start: 0.6603 (pp20) cc_final: 0.6395 (pp20)
  outliers start: 15
  outliers final: 4
  residues processed: 99
  average time/residue: 0.7058
  time to fit residues: 74.4638
Evaluate side-chains
  88 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 83
  time to evaluate  : 0.413 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  128 MET
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 109 optimal weight:    2.9990
   chunk 70 optimal weight:    0.0770
   chunk 53 optimal weight:    7.9990
   chunk 14 optimal weight:    5.9990
   chunk 101 optimal weight:    3.9990
   chunk 98 optimal weight:    0.1980
   chunk 26 optimal weight:    0.9990
   chunk 46 optimal weight:    2.9990
   chunk 48 optimal weight:    1.9990
   chunk 23 optimal weight:    6.9990
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.0544

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 139 GLN
F 147 GLN
F 192 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3891 r_free = 0.3891 target = 0.136869 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.085059 restraints weight = 16244.834|
|-----------------------------------------------------------------------------|
r_work (start): 0.3050 rms_B_bonded: 2.85
r_work: 0.2936 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2820 rms_B_bonded: 4.47 restraints_weight: 0.2500
r_work (final): 0.2820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8841
moved from start:          0.1725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   9325  Z= 0.134
  Angle     :  0.561   8.925  12628  Z= 0.287
  Chirality :  0.044   0.144   1427
  Planarity :  0.004   0.035   1639
  Dihedral  : 10.989 120.388   1373
  Min Nonbonded Distance : 2.054

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 12.16 %
    Favored  : 86.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.35 (0.25), residues: 1175
  helix:  1.27 (0.26), residues: 438
  sheet:  0.68 (0.34), residues: 238
  loop : -0.91 (0.27), residues: 499

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A  77 
 TYR   0.014   0.001   TYR A 473 
 PHE   0.015   0.001   PHE A 253 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.007   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 9325)
  covalent geometry    : angle       0.56118 (12628)
  hydrogen bonds       : bond        0.03871 (  420)
  hydrogen bonds       : angle       4.45301 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 88
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A  156 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8834 (tp)
REVERT: A  448 MET cc_start: 0.8588 (tpp) cc_final: 0.8355 (tpp)
REVERT: F  100 ASN cc_start: 0.9190 (m110) cc_final: 0.8930 (m110)
REVERT: F  289 ARG cc_start: 0.5576 (ptp90) cc_final: 0.5273 (ptp-170)
  outliers start: 12
  outliers final: 4
  residues processed: 95
  average time/residue: 0.6423
  time to fit residues: 65.2915
Evaluate side-chains
  85 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 80
  time to evaluate  : 0.372 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 95 optimal weight:    0.9990
   chunk 29 optimal weight:    7.9990
   chunk 96 optimal weight:    2.9990
   chunk 85 optimal weight:    0.0270
   chunk 22 optimal weight:   10.0000
   chunk 16 optimal weight:    0.0980
   chunk 0 optimal weight:   10.0000
   chunk 84 optimal weight:   10.0000
   chunk 66 optimal weight:    6.9990
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.8042

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 139 GLN
F 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.137423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.086074 restraints weight = 16133.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.79
r_work: 0.2953 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2839 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.1864

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   9325  Z= 0.120
  Angle     :  0.573   9.378  12628  Z= 0.289
  Chirality :  0.044   0.153   1427
  Planarity :  0.003   0.034   1639
  Dihedral  : 10.339 116.885   1373
  Min Nonbonded Distance : 2.065

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 12.56 %
    Favored  : 86.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.25), residues: 1175
  helix:  1.37 (0.26), residues: 437
  sheet:  0.68 (0.33), residues: 238
  loop : -0.84 (0.27), residues: 500

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG F  53 
 TYR   0.013   0.001   TYR A 444 
 PHE   0.021   0.001   PHE A 263 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.006   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00273 ( 9325)
  covalent geometry    : angle       0.57266 (12628)
  hydrogen bonds       : bond        0.03584 (  420)
  hydrogen bonds       : angle       4.38985 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.395 
Fit side-chains
REVERT: A  156 LEU cc_start: 0.9043 (OUTLIER) cc_final: 0.8824 (tp)
REVERT: A  448 MET cc_start: 0.8608 (tpp) cc_final: 0.8384 (tpp)
REVERT: F   53 ARG cc_start: 0.8034 (mtm110) cc_final: 0.7825 (ttm-80)
REVERT: F  100 ASN cc_start: 0.9188 (m110) cc_final: 0.8947 (m110)
REVERT: F  289 ARG cc_start: 0.5535 (ptp90) cc_final: 0.5315 (ptt180)
  outliers start: 13
  outliers final: 5
  residues processed: 92
  average time/residue: 0.6368
  time to fit residues: 62.7877
Evaluate side-chains
  85 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.368 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:   30.0000
   chunk 58 optimal weight:    1.9990
   chunk 22 optimal weight:    9.9990
   chunk 16 optimal weight:   30.0000
   chunk 49 optimal weight:    0.0060
   chunk 34 optimal weight:    7.9990
   chunk 79 optimal weight:    1.9990
   chunk 86 optimal weight:    2.9990
   chunk 72 optimal weight:    0.9990
   chunk 26 optimal weight:    0.8980
   chunk 81 optimal weight:    2.9990
   overall best weight:    1.1802

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 637 ASN
F 139 GLN
F 147 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.137780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3087 r_free = 0.3087 target = 0.084745 restraints weight = 16039.638|
|-----------------------------------------------------------------------------|
r_work (start): 0.3044 rms_B_bonded: 2.86
r_work: 0.2931 rms_B_bonded: 3.04 restraints_weight: 0.5000
r_work: 0.2818 rms_B_bonded: 4.45 restraints_weight: 0.2500
r_work (final): 0.2818
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8839
moved from start:          0.1941

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   9325  Z= 0.143
  Angle     :  0.574  10.221  12628  Z= 0.291
  Chirality :  0.045   0.147   1427
  Planarity :  0.003   0.034   1639
  Dihedral  :  9.792 116.661   1373
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 6.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.74 %
    Favored  : 96.26 %
  Rotamer:
    Outliers :  1.43 %
    Allowed  : 12.87 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.49 (0.25), residues: 1175
  helix:  1.42 (0.26), residues: 436
  sheet:  0.57 (0.32), residues: 251
  loop : -0.79 (0.27), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 257 
 TYR   0.011   0.001   TYR A 473 
 PHE   0.018   0.001   PHE A 253 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.007   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 9325)
  covalent geometry    : angle       0.57357 (12628)
  hydrogen bonds       : bond        0.03796 (  420)
  hydrogen bonds       : angle       4.36508 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.398 
Fit side-chains
REVERT: A  156 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8801 (tp)
REVERT: A  257 ARG cc_start: 0.8745 (mmp80) cc_final: 0.8379 (mtp85)
REVERT: A  448 MET cc_start: 0.8622 (tpp) cc_final: 0.8342 (tpp)
REVERT: F  100 ASN cc_start: 0.9205 (m110) cc_final: 0.8978 (m110)
REVERT: F  289 ARG cc_start: 0.5457 (ptp90) cc_final: 0.5238 (ptp-170)
  outliers start: 14
  outliers final: 7
  residues processed: 94
  average time/residue: 0.6213
  time to fit residues: 62.4721
Evaluate side-chains
  87 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain F residue  144 ILE
Chi-restraints excluded: chain F residue  243 GLU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 15 optimal weight:    5.9990
   chunk 0 optimal weight:   10.0000
   chunk 45 optimal weight:    0.5980
   chunk 107 optimal weight:    0.9990
   chunk 61 optimal weight:    0.9990
   chunk 60 optimal weight:   50.0000
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    9.9990
   chunk 84 optimal weight:    7.9990
   chunk 79 optimal weight:    0.5980
   chunk 33 optimal weight:    0.9990
   overall best weight:    0.8386

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 139 GLN
F 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.138015 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.086358 restraints weight = 15951.278|
|-----------------------------------------------------------------------------|
r_work (start): 0.3074 rms_B_bonded: 2.81
r_work: 0.2960 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2844 rms_B_bonded: 4.43 restraints_weight: 0.2500
r_work (final): 0.2844
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8823
moved from start:          0.2058

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   9325  Z= 0.121
  Angle     :  0.567  10.798  12628  Z= 0.289
  Chirality :  0.044   0.141   1427
  Planarity :  0.003   0.033   1639
  Dihedral  :  9.320 115.325   1373
  Min Nonbonded Distance : 2.033

Molprobity Statistics.
  All-atom Clashscore : 6.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.12 %
    Allowed  : 14.10 %
    Favored  : 84.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.57 (0.25), residues: 1175
  helix:  1.41 (0.26), residues: 437
  sheet:  0.69 (0.32), residues: 245
  loop : -0.68 (0.27), residues: 493

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  53 
 TYR   0.010   0.001   TYR A 401 
 PHE   0.021   0.001   PHE A 253 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.006   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00278 ( 9325)
  covalent geometry    : angle       0.56714 (12628)
  hydrogen bonds       : bond        0.03523 (  420)
  hydrogen bonds       : angle       4.27061 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.395 
Fit side-chains
REVERT: B  309 GLU cc_start: 0.8166 (pm20) cc_final: 0.7912 (pm20)
REVERT: F  100 ASN cc_start: 0.9166 (m110) cc_final: 0.8935 (m110)
REVERT: F  289 ARG cc_start: 0.5566 (ptp90) cc_final: 0.5307 (ptp-170)
REVERT: F  290 GLU cc_start: 0.5917 (pp20) cc_final: 0.5658 (pp20)
  outliers start: 11
  outliers final: 6
  residues processed: 91
  average time/residue: 0.6414
  time to fit residues: 62.3001
Evaluate side-chains
  86 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 80
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 64 optimal weight:    9.9990
   chunk 91 optimal weight:    0.0770
   chunk 114 optimal weight:    0.9980
   chunk 50 optimal weight:    5.9990
   chunk 80 optimal weight:    0.0870
   chunk 81 optimal weight:    0.9990
   chunk 72 optimal weight:    1.9990
   chunk 26 optimal weight:    1.9990
   chunk 105 optimal weight:    2.9990
   chunk 113 optimal weight:    2.9990
   chunk 68 optimal weight:    0.0030
   overall best weight:    0.4328

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 139 GLN
F 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.139205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.087687 restraints weight = 15902.721|
|-----------------------------------------------------------------------------|
r_work (start): 0.3096 rms_B_bonded: 2.88
r_work: 0.2983 rms_B_bonded: 3.06 restraints_weight: 0.5000
r_work: 0.2867 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.2867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8789
moved from start:          0.2174

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.035   9325  Z= 0.103
  Angle     :  0.575  11.485  12628  Z= 0.290
  Chirality :  0.044   0.140   1427
  Planarity :  0.004   0.060   1639
  Dihedral  :  9.089 108.509   1373
  Min Nonbonded Distance : 2.039

Molprobity Statistics.
  All-atom Clashscore : 6.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  1.23 %
    Allowed  : 14.61 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.64 (0.25), residues: 1175
  helix:  1.43 (0.26), residues: 436
  sheet:  0.75 (0.32), residues: 243
  loop : -0.61 (0.27), residues: 496

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.000   ARG A 257 
 TYR   0.009   0.001   TYR A 401 
 PHE   0.024   0.001   PHE A 253 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.005   0.000   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 ( 9325)
  covalent geometry    : angle       0.57537 (12628)
  hydrogen bonds       : bond        0.03198 (  420)
  hydrogen bonds       : angle       4.18497 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 85
  time to evaluate  : 0.368 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.8727 (mmp80) cc_final: 0.8348 (mtp85)
REVERT: B  309 GLU cc_start: 0.8144 (pm20) cc_final: 0.7896 (pm20)
REVERT: F  100 ASN cc_start: 0.9143 (m110) cc_final: 0.8932 (m110)
REVERT: F  289 ARG cc_start: 0.5495 (ptp90) cc_final: 0.5258 (ptt180)
REVERT: F  290 GLU cc_start: 0.6023 (pp20) cc_final: 0.5749 (pp20)
  outliers start: 12
  outliers final: 4
  residues processed: 93
  average time/residue: 0.6606
  time to fit residues: 65.5026
Evaluate side-chains
  85 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  195 PHE
Chi-restraints excluded: chain B residue  446 HIS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 89 optimal weight:    0.9980
   chunk 90 optimal weight:    0.7980
   chunk 47 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 17 optimal weight:    9.9990
   chunk 10 optimal weight:    2.9990
   chunk 70 optimal weight:    1.9990
   chunk 83 optimal weight:    1.9990
   chunk 51 optimal weight:    2.9990
   chunk 64 optimal weight:    8.9990
   chunk 86 optimal weight:    0.6980
   overall best weight:    1.2984

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 139 GLN
F 147 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.137188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.085587 restraints weight = 15942.968|
|-----------------------------------------------------------------------------|
r_work (start): 0.3060 rms_B_bonded: 2.71
r_work: 0.2944 rms_B_bonded: 2.93 restraints_weight: 0.5000
r_work: 0.2828 rms_B_bonded: 4.40 restraints_weight: 0.2500
r_work (final): 0.2828
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8832
moved from start:          0.2221

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   9325  Z= 0.153
  Angle     :  0.612  12.180  12628  Z= 0.307
  Chirality :  0.045   0.144   1427
  Planarity :  0.004   0.039   1639
  Dihedral  :  9.100 107.719   1373
  Min Nonbonded Distance : 2.002

Molprobity Statistics.
  All-atom Clashscore : 6.94
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 15.02 %
    Favored  : 84.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.25), residues: 1175
  helix:  1.44 (0.26), residues: 436
  sheet:  0.70 (0.32), residues: 247
  loop : -0.62 (0.28), residues: 492

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 257 
 TYR   0.014   0.001   TYR A 444 
 PHE   0.023   0.001   PHE A 253 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.007   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 9325)
  covalent geometry    : angle       0.61168 (12628)
  hydrogen bonds       : bond        0.03820 (  420)
  hydrogen bonds       : angle       4.30288 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 79
  time to evaluate  : 0.374 
Fit side-chains
REVERT: B  309 GLU cc_start: 0.8175 (pm20) cc_final: 0.7911 (pm20)
REVERT: F  100 ASN cc_start: 0.9142 (m110) cc_final: 0.8936 (m110)
REVERT: F  289 ARG cc_start: 0.5535 (ptp90) cc_final: 0.5297 (ptp-170)
  outliers start: 8
  outliers final: 5
  residues processed: 85
  average time/residue: 0.7104
  time to fit residues: 64.0862
Evaluate side-chains
  84 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 107 optimal weight:    1.9990
   chunk 36 optimal weight:    0.3980
   chunk 7 optimal weight:    4.9990
   chunk 69 optimal weight:    0.9990
   chunk 115 optimal weight:    0.5980
   chunk 63 optimal weight:   30.0000
   chunk 65 optimal weight:    8.9990
   chunk 90 optimal weight:    2.9990
   chunk 51 optimal weight:    5.9990
   chunk 18 optimal weight:    6.9990
   chunk 98 optimal weight:    3.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3888 r_free = 0.3888 target = 0.136903 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 73)----------------|
| r_work = 0.3091 r_free = 0.3091 target = 0.085157 restraints weight = 15951.218|
|-----------------------------------------------------------------------------|
r_work (start): 0.3053 rms_B_bonded: 2.82
r_work: 0.2937 rms_B_bonded: 3.00 restraints_weight: 0.5000
r_work: 0.2822 rms_B_bonded: 4.42 restraints_weight: 0.2500
r_work (final): 0.2822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8840
moved from start:          0.2255

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   9325  Z= 0.161
  Angle     :  0.635  12.710  12628  Z= 0.317
  Chirality :  0.045   0.141   1427
  Planarity :  0.004   0.056   1639
  Dihedral  :  9.106 108.066   1373
  Min Nonbonded Distance : 1.987

Molprobity Statistics.
  All-atom Clashscore : 7.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  : 15.12 %
    Favored  : 84.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.60 (0.25), residues: 1175
  helix:  1.40 (0.26), residues: 436
  sheet:  0.61 (0.32), residues: 250
  loop : -0.59 (0.28), residues: 489

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 257 
 TYR   0.013   0.001   TYR A 444 
 PHE   0.024   0.001   PHE A 253 
 TRP   0.004   0.001   TRP A 559 
 HIS   0.007   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00386 ( 9325)
  covalent geometry    : angle       0.63542 (12628)
  hydrogen bonds       : bond        0.03890 (  420)
  hydrogen bonds       : angle       4.32826 ( 1227)

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

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

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2350 Ramachandran restraints generated.
    1175 Oldfield, 0 Emsley, 1175 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 78
  time to evaluate  : 0.364 
Fit side-chains
REVERT: A  257 ARG cc_start: 0.8717 (mmp80) cc_final: 0.8282 (mtm-85)
REVERT: B  309 GLU cc_start: 0.8172 (pm20) cc_final: 0.7890 (pm20)
REVERT: F  100 ASN cc_start: 0.9141 (m110) cc_final: 0.8926 (m110)
REVERT: F  289 ARG cc_start: 0.5494 (ptp90) cc_final: 0.5259 (ptp-170)
  outliers start: 8
  outliers final: 5
  residues processed: 85
  average time/residue: 0.7599
  time to fit residues: 68.4356
Evaluate side-chains
  81 residues out of total 979 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 VAL
Chi-restraints excluded: chain A residue  117 THR
Chi-restraints excluded: chain A residue  499 ILE
Chi-restraints excluded: chain B residue  446 HIS
Chi-restraints excluded: chain F residue  144 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 117
   random chunks:
   chunk 111 optimal weight:    0.0170
   chunk 0 optimal weight:   10.0000
   chunk 43 optimal weight:    0.9990
   chunk 103 optimal weight:    1.9990
   chunk 62 optimal weight:   50.0000
   chunk 23 optimal weight:    3.9990
   chunk 63 optimal weight:    7.9990
   chunk 73 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   chunk 64 optimal weight:    8.9990
   chunk 47 optimal weight:    0.7980
   overall best weight:    0.9624

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

Flipped N/Q/H residues before XYZ refinement:
** A 358 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
F 147 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3899 r_free = 0.3899 target = 0.137653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.086232 restraints weight = 15715.225|
|-----------------------------------------------------------------------------|
r_work (start): 0.3062 rms_B_bonded: 2.76
r_work: 0.2947 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2832 rms_B_bonded: 4.38 restraints_weight: 0.2500
r_work (final): 0.2832
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8825
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   9325  Z= 0.132
  Angle     :  0.618  12.702  12628  Z= 0.308
  Chirality :  0.045   0.141   1427
  Planarity :  0.004   0.051   1639
  Dihedral  :  9.023 108.099   1373
  Min Nonbonded Distance : 1.985

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.49 %
    Favored  : 96.51 %
  Rotamer:
    Outliers :  0.72 %
    Allowed  : 15.02 %
    Favored  : 84.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.25), residues: 1175
  helix:  1.41 (0.26), residues: 436
  sheet:  0.75 (0.33), residues: 241
  loop : -0.54 (0.28), residues: 498

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 257 
 TYR   0.012   0.001   TYR A 444 
 PHE   0.025   0.001   PHE A 253 
 TRP   0.005   0.001   TRP A 559 
 HIS   0.006   0.001   HIS B 411 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 9325)
  covalent geometry    : angle       0.61845 (12628)
  hydrogen bonds       : bond        0.03579 (  420)
  hydrogen bonds       : angle       4.28197 ( 1227)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4058.64 seconds
wall clock time: 69 minutes 50.97 seconds (4190.97 seconds total)