Starting phenix.real_space_refine
on Tue Mar  3 15:53:55 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qla_14066/03_2026/7qla_14066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qla_14066/03_2026/7qla_14066.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.85
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qla_14066/03_2026/7qla_14066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qla_14066/03_2026/7qla_14066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qla_14066/03_2026/7qla_14066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qla_14066/03_2026/7qla_14066.cif"
  }
  resolution = 3.85
  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=  -0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      21      5.16       5
     C    4372      2.51       5
     N    1187      2.21       5
     O    1257      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6837
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3377
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 433, 3377
          Classifications: {'peptide': 433}
          Link IDs: {'PTRANS': 21, 'TRANS': 411}
          Chain breaks: 2
    Chain: "C"
      Number of atoms: 3460
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 441, 3460
          Classifications: {'peptide': 441}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 24, 'TRANS': 416}
          Chain breaks: 8
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 2
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.70, per 1000 atoms: 0.25
  Number of scatterers: 6837
  At special positions: 0
  Unit cell: (81.75, 103.55, 110.09, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      21     16.00
     O    1257      8.00
     N    1187      7.00
     C    4372      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: 0.76
  Conformation dependent library (CDL) restraints added in 274.5 milliseconds
  

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1602

  Finding SS restraints...
    Secondary structure from input PDB file:
      29 helices and 9 sheets defined
      43.6% alpha, 16.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.21
  Creating SS restraints...
    Processing helix  chain 'A' and resid 197 through 202
      removed outlier: 3.621A  pdb=" N   LEU A 202 " --> pdb=" O   PHE A 198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 220
      removed outlier: 3.501A  pdb=" N   ALA A 216 " --> pdb=" O   ASP A 212 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 262
      removed outlier: 4.147A  pdb=" N   SER A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   THR A 248 " --> pdb=" O   LEU A 244 " (cutoff:3.500A)
      removed outlier: 5.076A  pdb=" N   VAL A 251 " --> pdb=" O   SER A 247 " (cutoff:3.500A)
      removed outlier: 4.849A  pdb=" N   VAL A 252 " --> pdb=" O   THR A 248 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 295 through 314
    Processing helix  chain 'A' and resid 315 through 323
      removed outlier: 3.760A  pdb=" N   ASN A 321 " --> pdb=" O   PRO A 317 " (cutoff:3.500A)
      removed outlier: 3.997A  pdb=" N   PHE A 323 " --> pdb=" O   LEU A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 352
    Processing helix  chain 'A' and resid 353 through 359
      removed outlier: 3.515A  pdb=" N   LEU A 358 " --> pdb=" O   PRO A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 367 through 381
      removed outlier: 3.959A  pdb=" N   SER A 381 " --> pdb=" O   ILE A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 409 through 421
      removed outlier: 3.562A  pdb=" N   LEU A 413 " --> pdb=" O   HIS A 409 " (cutoff:3.500A)
      removed outlier: 3.776A  pdb=" N   GLN A 414 " --> pdb=" O   PRO A 410 " (cutoff:3.500A)
      removed outlier: 4.021A  pdb=" N   LEU A 415 " --> pdb=" O   SER A 411 " (cutoff:3.500A)
      removed outlier: 3.714A  pdb=" N   ILE A 416 " --> pdb=" O   ASP A 412 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 429
    Processing helix  chain 'A' and resid 496 through 498
      No H-bonds generated for 'chain 'A' and resid 496 through 498'
    Processing helix  chain 'A' and resid 499 through 518
      removed outlier: 3.573A  pdb=" N   SER A 512 " --> pdb=" O   THR A 508 " (cutoff:3.500A)
      removed outlier: 3.520A  pdb=" N   GLN A 513 " --> pdb=" O   ARG A 509 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 518 through 529
      removed outlier: 3.670A  pdb=" N   SER A 525 " --> pdb=" O   SER A 521 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 533 through 538
    Processing helix  chain 'A' and resid 570 through 593
      removed outlier: 3.764A  pdb=" N   THR A 574 " --> pdb=" O   THR A 570 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   GLU A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   LEU A 588 " --> pdb=" O   VAL A 584 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   ALA A 590 " --> pdb=" O   GLU A 586 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 653
      removed outlier: 5.417A  pdb=" N   GLU A 642 " --> pdb=" O   GLY A 638 " (cutoff:3.500A)
      removed outlier: 3.895A  pdb=" N   ASN A 644 " --> pdb=" O   ALA A 640 " (cutoff:3.500A)
      removed outlier: 5.450A  pdb=" N   ARG A 645 " --> pdb=" O   ARG A 641 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   GLN A 648 " --> pdb=" O   ASN A 644 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 30 through 35
      removed outlier: 3.793A  pdb=" N   GLU C  35 " --> pdb=" O   ASP C  31 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 43 through 52
      removed outlier: 3.987A  pdb=" N   GLN C  49 " --> pdb=" O   SER C  45 " (cutoff:3.500A)
      removed outlier: 3.969A  pdb=" N   ALA C  50 " --> pdb=" O   THR C  46 " (cutoff:3.500A)
      removed outlier: 3.506A  pdb=" N   ARG C  52 " --> pdb=" O   SER C  48 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 95 through 120
      removed outlier: 3.722A  pdb=" N   ILE C 105 " --> pdb=" O   ARG C 101 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   GLY C 106 " --> pdb=" O   LEU C 102 " (cutoff:3.500A)
      removed outlier: 3.781A  pdb=" N   LEU C 107 " --> pdb=" O   ARG C 103 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   ALA C 108 " --> pdb=" O   GLN C 104 " (cutoff:3.500A)
      removed outlier: 3.924A  pdb=" N   SER C 117 " --> pdb=" O   GLU C 113 " (cutoff:3.500A)
      removed outlier: 4.168A  pdb=" N   PHE C 118 " --> pdb=" O   PHE C 114 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   SER C 119 " --> pdb=" O   ALA C 115 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 192 through 209
      removed outlier: 3.842A  pdb=" N   LEU C 196 " --> pdb=" O   PRO C 192 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   ARG C 197 " --> pdb=" O   PRO C 193 " (cutoff:3.500A)
      removed outlier: 4.377A  pdb=" N   ALA C 198 " --> pdb=" O   SER C 194 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 214 through 240
      removed outlier: 3.627A  pdb=" N   ALA C 220 " --> pdb=" O   SER C 216 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   ARG C 224 " --> pdb=" O   ALA C 220 " (cutoff:3.500A)
      removed outlier: 8.821A  pdb=" N   ALA C 225 " --> pdb=" O   SER C 221 " (cutoff:3.500A)
      removed outlier: 4.134A  pdb=" N   GLN C 226 " --> pdb=" O   GLN C 222 " (cutoff:3.500A)
      removed outlier: 3.635A  pdb=" N   VAL C 228 " --> pdb=" O   ARG C 224 " (cutoff:3.500A)
      removed outlier: 3.783A  pdb=" N   ALA C 229 " --> pdb=" O   ALA C 225 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   HIS C 237 " --> pdb=" O   ARG C 233 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 249 through 255
      removed outlier: 4.214A  pdb=" N   PHE C 255 " --> pdb=" O   ALA C 251 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 278 through 290
      removed outlier: 3.807A  pdb=" N   VAL C 282 " --> pdb=" O   GLY C 278 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   LEU C 283 " --> pdb=" O   GLU C 279 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLU C 288 " --> pdb=" O   GLU C 284 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 337 through 354
      removed outlier: 4.217A  pdb=" N   GLY C 343 " --> pdb=" O   LYS C 339 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   VAL C 344 " --> pdb=" O   SER C 340 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   VAL C 345 " --> pdb=" O   LEU C 341 " (cutoff:3.500A)
      removed outlier: 3.575A  pdb=" N   VAL C 351 " --> pdb=" O   TRP C 347 " (cutoff:3.500A)
      removed outlier: 4.025A  pdb=" N   TYR C 352 " --> pdb=" O   MET C 348 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 553 through 555
      No H-bonds generated for 'chain 'C' and resid 553 through 555'
    Processing helix  chain 'C' and resid 556 through 568
      removed outlier: 3.520A  pdb=" N   LEU C 560 " --> pdb=" O   THR C 556 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 569 through 571
      No H-bonds generated for 'chain 'C' and resid 569 through 571'
    Processing helix  chain 'C' and resid 572 through 580
      removed outlier: 3.541A  pdb=" N   HIS C 577 " --> pdb=" O   LYS C 573 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 648 through 667
      removed outlier: 3.597A  pdb=" N   ALA C 652 " --> pdb=" O   THR C 648 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   LEU C 653 " --> pdb=" O   ARG C 649 " (cutoff:3.500A)
      removed outlier: 4.170A  pdb=" N   GLN C 654 " --> pdb=" O   VAL C 650 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   LEU C 660 " --> pdb=" O   HIS C 656 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   LEU C 663 " --> pdb=" O   ILE C 659 " (cutoff:3.500A)
      removed outlier: 3.549A  pdb=" N   SER C 664 " --> pdb=" O   LEU C 660 " (cutoff:3.500A)
      removed outlier: 3.664A  pdb=" N   SER C 665 " --> pdb=" O   ALA C 661 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 234 through 237
      removed outlier: 6.385A  pdb=" N   ILE A 227 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 4.787A  pdb=" N   SER A 237 " --> pdb=" O   TYR A 225 " (cutoff:3.500A)
      removed outlier: 7.443A  pdb=" N   TYR A 225 " --> pdb=" O   SER A 237 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   LYS A 281 " --> pdb=" O   LEU A 284 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 396 through 401
      removed outlier: 6.706A  pdb=" N   LEU A 391 " --> pdb=" O   VAL A 398 " (cutoff:3.500A)
      removed outlier: 4.844A  pdb=" N   VAL A 400 " --> pdb=" O   GLY A 389 " (cutoff:3.500A)
      removed outlier: 7.012A  pdb=" N   GLY A 389 " --> pdb=" O   VAL A 400 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 555 through 558
      removed outlier: 3.985A  pdb=" N   GLN A 555 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   SER A 550 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   HIS A 545 " --> pdb=" O   VAL A 629 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL A 629 " --> pdb=" O   HIS A 545 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ALA A 615 " --> pdb=" O   ALA A 630 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 555 through 558
      removed outlier: 3.985A  pdb=" N   GLN A 555 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 3.952A  pdb=" N   SER A 550 " --> pdb=" O   GLN A 555 " (cutoff:3.500A)
      removed outlier: 3.926A  pdb=" N   HIS A 545 " --> pdb=" O   VAL A 629 " (cutoff:3.500A)
      removed outlier: 3.815A  pdb=" N   VAL A 629 " --> pdb=" O   HIS A 545 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   VAL A 626 " --> pdb=" O   TRP A 619 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 41
      removed outlier: 6.504A  pdb=" N   ILE C  22 " --> pdb=" O   VAL C  39 " (cutoff:3.500A)
      removed outlier: 4.301A  pdb=" N   TYR C  41 " --> pdb=" O   LEU C  20 " (cutoff:3.500A)
      removed outlier: 6.513A  pdb=" N   LEU C  20 " --> pdb=" O   TYR C  41 " (cutoff:3.500A)
      removed outlier: 5.533A  pdb=" N   LEU C  17 " --> pdb=" O   ASP C 150 " (cutoff:3.500A)
      removed outlier: 5.486A  pdb=" N   ASP C 150 " --> pdb=" O   LEU C  17 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   PHE C  19 " --> pdb=" O   SER C 148 " (cutoff:3.500A)
      removed outlier: 6.900A  pdb=" N   TRP C 143 " --> pdb=" O   VAL C 139 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 152 through 154
      removed outlier: 3.557A  pdb=" N   SER C 186 " --> pdb=" O   THR C 152 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 258 through 260
      removed outlier: 5.439A  pdb=" N   ILE C 258 " --> pdb=" O   LEU C 614 " (cutoff:3.500A)
      removed outlier: 6.446A  pdb=" N   SER C 616 " --> pdb=" O   ILE C 258 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   LEU C 260 " --> pdb=" O   SER C 616 " (cutoff:3.500A)
      removed outlier: 3.950A  pdb=" N   THR C 613 " --> pdb=" O   ASP C 608 " (cutoff:3.500A)
      removed outlier: 3.650A  pdb=" N   LEU C 605 " --> pdb=" O   HIS C 732 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 328 through 329
      removed outlier: 4.017A  pdb=" N   ASP C 295 " --> pdb=" O   LEU C 546 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   VAL C 297 " --> pdb=" O   ILE C 544 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLY C 299 " --> pdb=" O   ILE C 542 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'C' and resid 601 through 603
      removed outlier: 3.915A  pdb=" N   GLN C 601 " --> pdb=" O   VAL C 736 " (cutoff:3.500A)

    295 hydrogen bonds defined for protein.
    849 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: 1.20

  Time building geometry restraints manager: 0.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2227
        1.34 -     1.46: 986
        1.46 -     1.57: 3738
        1.57 -     1.69: 0
        1.69 -     1.81: 32
  Bond restraints: 6983
  Sorted by residual:
  bond pdb=" N   ASN A 444 "
       pdb=" CA  ASN A 444 "
    ideal  model  delta    sigma   weight residual
    1.457  1.475 -0.018 1.29e-02 6.01e+03 1.90e+00
  bond pdb=" CB  GLN C 314 "
       pdb=" CG  GLN C 314 "
    ideal  model  delta    sigma   weight residual
    1.520  1.547 -0.027 3.00e-02 1.11e+03 8.32e-01
  bond pdb=" CB  LYS C  95 "
       pdb=" CG  LYS C  95 "
    ideal  model  delta    sigma   weight residual
    1.520  1.546 -0.026 3.00e-02 1.11e+03 7.77e-01
  bond pdb=" C   PRO A 566 "
       pdb=" N   PRO A 567 "
    ideal  model  delta    sigma   weight residual
    1.335  1.345 -0.011 1.28e-02 6.10e+03 6.91e-01
  bond pdb=" CA  ASN A 444 "
       pdb=" CB  ASN A 444 "
    ideal  model  delta    sigma   weight residual
    1.530  1.544 -0.014 1.69e-02 3.50e+03 6.78e-01
  ... (remaining 6978 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.37: 9088
        1.37 -     2.73: 290
        2.73 -     4.10: 66
        4.10 -     5.47: 16
        5.47 -     6.84: 7
  Bond angle restraints: 9467
  Sorted by residual:
  angle pdb=" C   ASN A 443 "
        pdb=" N   ASN A 444 "
        pdb=" CA  ASN A 444 "
      ideal   model   delta    sigma   weight residual
     121.54  127.48   -5.94 1.91e+00 2.74e-01 9.68e+00
  angle pdb=" CB  LYS C  95 "
        pdb=" CG  LYS C  95 "
        pdb=" CD  LYS C  95 "
      ideal   model   delta    sigma   weight residual
     111.30  117.23   -5.93 2.30e+00 1.89e-01 6.66e+00
  angle pdb=" CB  ARG A 595 "
        pdb=" CG  ARG A 595 "
        pdb=" CD  ARG A 595 "
      ideal   model   delta    sigma   weight residual
     111.30  116.82   -5.52 2.30e+00 1.89e-01 5.76e+00
  angle pdb=" CA  ASN A 444 "
        pdb=" CB  ASN A 444 "
        pdb=" CG  ASN A 444 "
      ideal   model   delta    sigma   weight residual
     112.60  114.96   -2.36 1.00e+00 1.00e+00 5.56e+00
  angle pdb=" CG1 ILE A 426 "
        pdb=" CB  ILE A 426 "
        pdb=" CG2 ILE A 426 "
      ideal   model   delta    sigma   weight residual
     110.70  103.86    6.84 3.00e+00 1.11e-01 5.19e+00
  ... (remaining 9462 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.33: 3736
       17.33 -    34.65: 347
       34.65 -    51.98: 63
       51.98 -    69.31: 9
       69.31 -    86.63: 6
  Dihedral angle restraints: 4161
    sinusoidal: 1671
      harmonic: 2490
  Sorted by residual:
  dihedral pdb=" CA  LEU A 387 "
           pdb=" C   LEU A 387 "
           pdb=" N   TYR A 388 "
           pdb=" CA  TYR A 388 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  155.63   24.37     0      5.00e+00 4.00e-02 2.38e+01
  dihedral pdb=" CA  VAL C 537 "
           pdb=" C   VAL C 537 "
           pdb=" N   SER C 538 "
           pdb=" CA  SER C 538 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.58   23.42     0      5.00e+00 4.00e-02 2.19e+01
  dihedral pdb=" CA  GLN C 539 "
           pdb=" C   GLN C 539 "
           pdb=" N   PRO C 540 "
           pdb=" CA  PRO C 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.27   22.73     0      5.00e+00 4.00e-02 2.07e+01
  ... (remaining 4158 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.039: 771
       0.039 -    0.078: 214
       0.078 -    0.116: 75
       0.116 -    0.155: 13
       0.155 -    0.194: 3
  Chirality restraints: 1076
  Sorted by residual:
  chirality pdb=" CB  ILE A 426 "
            pdb=" CA  ILE A 426 "
            pdb=" CG1 ILE A 426 "
            pdb=" CG2 ILE A 426 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.84   -0.19 2.00e-01 2.50e+01 9.40e-01
  chirality pdb=" CA  THR C 551 "
            pdb=" N   THR C 551 "
            pdb=" C   THR C 551 "
            pdb=" CB  THR C 551 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.17 2.00e-01 2.50e+01 7.06e-01
  chirality pdb=" CA  ASN A 444 "
            pdb=" N   ASN A 444 "
            pdb=" C   ASN A 444 "
            pdb=" CB  ASN A 444 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.94e-01
  ... (remaining 1073 not shown)

  Planarity restraints: 1200
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASN A 443 "    0.009 2.00e-02 2.50e+03   1.75e-02 3.06e+00
        pdb=" C   ASN A 443 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   ASN A 443 "    0.012 2.00e-02 2.50e+03
        pdb=" N   ASN A 444 "    0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 619 "    0.011 2.00e-02 2.50e+03   1.06e-02 2.82e+00
        pdb=" CG  TRP A 619 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 619 "    0.013 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 619 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 619 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 619 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 619 "    0.000 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 619 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 619 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 619 "   -0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A 565 "    0.026 5.00e-02 4.00e+02   3.99e-02 2.55e+00
        pdb=" N   PRO A 566 "   -0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 566 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 566 "    0.022 5.00e-02 4.00e+02
  ... (remaining 1197 not shown)

  Histogram of nonbonded interaction distances:
        2.12 -     2.67: 124
        2.67 -     3.23: 6740
        3.23 -     3.79: 10424
        3.79 -     4.34: 13660
        4.34 -     4.90: 22403
  Nonbonded interactions: 53351
  Sorted by model distance:
  nonbonded pdb=" OH  TYR C 183 "
            pdb=" OH  TYR C 185 "
     model   vdw
     2.117 3.040
  nonbonded pdb=" OG1 THR C 129 "
            pdb=" O   ALA C 132 "
     model   vdw
     2.239 3.040
  nonbonded pdb=" O   ALA C 566 "
            pdb=" OG  SER C 569 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OE2 GLU C 651 "
            pdb=" OG1 THR C 655 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OH  TYR A 225 "
            pdb=" OE1 GLN A 302 "
     model   vdw
     2.282 3.040
  ... (remaining 53346 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:             0.510
  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:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.810
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.230
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
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      :  0.003   0.031   6983  Z= 0.130
  Angle     :  0.616   6.837   9467  Z= 0.304
  Chirality :  0.042   0.194   1076
  Planarity :  0.004   0.048   1200
  Dihedral  : 13.830  86.631   2559
  Min Nonbonded Distance : 2.117

Molprobity Statistics.
  All-atom Clashscore : 13.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.35 %
    Favored  : 93.65 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.33 (0.28), residues: 850
  helix:  0.15 (0.29), residues: 313
  sheet: -0.63 (0.42), residues: 153
  loop : -1.84 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.000   ARG A 595 
 TYR   0.017   0.001   TYR A 388 
 PHE   0.020   0.002   PHE C 114 
 TRP   0.029   0.002   TRP A 619 
 HIS   0.016   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 ( 6983)
  covalent geometry    : angle       0.61568 ( 9467)
  hydrogen bonds       : bond        0.28649 (  289)
  hydrogen bonds       : angle       9.56075 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 167
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 LYS cc_start: 0.8445 (tptm) cc_final: 0.8218 (tptt)
REVERT: A  249 MET cc_start: 0.8077 (tpp) cc_final: 0.7597 (tpp)
REVERT: A  308 MET cc_start: 0.8469 (tpp) cc_final: 0.8137 (mmm)
REVERT: A  559 SER cc_start: 0.8921 (p) cc_final: 0.8647 (p)
REVERT: A  587 GLU cc_start: 0.7209 (mp0) cc_final: 0.6914 (mp0)
REVERT: C   95 LYS cc_start: 0.8778 (tppt) cc_final: 0.8517 (tptt)
REVERT: C  191 LYS cc_start: 0.9138 (ttpt) cc_final: 0.8733 (mtpt)
REVERT: C  253 ASP cc_start: 0.8034 (m-30) cc_final: 0.7480 (m-30)
REVERT: C  284 GLU cc_start: 0.7930 (tt0) cc_final: 0.7546 (tt0)
REVERT: C  349 GLU cc_start: 0.7582 (mm-30) cc_final: 0.7349 (mm-30)
REVERT: C  659 ILE cc_start: 0.9393 (mt) cc_final: 0.9102 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.0858
  time to fit residues: 19.3564
Evaluate side-chains
  124 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 124
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 53 optimal weight:    7.9990
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    3.9990
   chunk 62 optimal weight:    6.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    2.9990
   chunk 45 optimal weight:    0.0470
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7680

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3975 r_free = 0.3975 target = 0.155304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.137654 restraints weight = 12569.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.141558 restraints weight = 7013.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.144196 restraints weight = 4576.684|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3854 r_free = 0.3854 target = 0.146043 restraints weight = 3302.988|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.147357 restraints weight = 2559.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.3867
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7520
moved from start:          0.1618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6983  Z= 0.148
  Angle     :  0.670   7.357   9467  Z= 0.340
  Chirality :  0.045   0.174   1076
  Planarity :  0.005   0.039   1200
  Dihedral  :  4.720  24.609    948
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.65 %
    Favored  : 94.35 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 10.98 %
    Favored  : 87.53 %
  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: -0.99 (0.29), residues: 850
  helix:  0.30 (0.28), residues: 345
  sheet: -0.47 (0.43), residues: 150
  loop : -1.66 (0.32), residues: 355

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 582 
 TYR   0.021   0.002   TYR A 585 
 PHE   0.023   0.002   PHE A 258 
 TRP   0.017   0.001   TRP C 647 
 HIS   0.006   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6983)
  covalent geometry    : angle       0.66977 ( 9467)
  hydrogen bonds       : bond        0.05669 (  289)
  hydrogen bonds       : angle       6.14943 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 144
  time to evaluate  : 0.301 
Fit side-chains
   revert: symmetry clash
REVERT: A  203 ASP cc_start: 0.7929 (m-30) cc_final: 0.7596 (m-30)
REVERT: A  341 LEU cc_start: 0.8698 (tt) cc_final: 0.8449 (tt)
REVERT: A  404 ARG cc_start: 0.6660 (mmp-170) cc_final: 0.6403 (mmp-170)
REVERT: A  524 ARG cc_start: 0.8276 (mpp80) cc_final: 0.7318 (mpt-90)
REVERT: A  559 SER cc_start: 0.8926 (p) cc_final: 0.8691 (p)
REVERT: A  586 GLU cc_start: 0.6482 (pt0) cc_final: 0.6203 (pt0)
REVERT: A  587 GLU cc_start: 0.7437 (mp0) cc_final: 0.6955 (mp0)
REVERT: A  619 TRP cc_start: 0.6870 (t60) cc_final: 0.6321 (t60)
REVERT: C   40 TYR cc_start: 0.8503 (t80) cc_final: 0.8115 (t80)
REVERT: C  191 LYS cc_start: 0.9171 (ttpt) cc_final: 0.8823 (mtpt)
REVERT: C  253 ASP cc_start: 0.7976 (m-30) cc_final: 0.7453 (m-30)
REVERT: C  301 TYR cc_start: 0.7459 (m-80) cc_final: 0.6526 (m-10)
  outliers start: 11
  outliers final: 10
  residues processed: 149
  average time/residue: 0.0882
  time to fit residues: 17.7373
Evaluate side-chains
  139 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 129
  time to evaluate  : 0.263 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  628 CYS
Chi-restraints excluded: chain C residue  293 LEU
Chi-restraints excluded: chain C residue  329 VAL
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  559 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 22 optimal weight:   10.0000
   chunk 0 optimal weight:    8.9990
   chunk 71 optimal weight:    0.0670
   chunk 74 optimal weight:    4.9990
   chunk 86 optimal weight:    5.9990
   chunk 68 optimal weight:    7.9990
   chunk 58 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 35 optimal weight:    0.7980
   chunk 23 optimal weight:    4.9990
   chunk 82 optimal weight:    2.9990
   overall best weight:    1.9122

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

Flipped N/Q/H residues before XYZ refinement:
A 409 HIS
A 555 GLN
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.149386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.131582 restraints weight = 12635.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.135325 restraints weight = 7243.638|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3751 r_free = 0.3751 target = 0.137822 restraints weight = 4840.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.139424 restraints weight = 3581.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.140724 restraints weight = 2873.145|
|-----------------------------------------------------------------------------|
r_work (final): 0.3788
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2239

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   6983  Z= 0.195
  Angle     :  0.689   7.673   9467  Z= 0.348
  Chirality :  0.046   0.200   1076
  Planarity :  0.005   0.044   1200
  Dihedral  :  4.935  25.654    948
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.47 %
    Favored  : 93.53 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 14.50 %
    Favored  : 82.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.29), residues: 850
  helix:  0.34 (0.28), residues: 348
  sheet: -0.69 (0.42), residues: 155
  loop : -1.64 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 197 
 TYR   0.030   0.002   TYR A 585 
 PHE   0.025   0.002   PHE C 541 
 TRP   0.020   0.002   TRP C 647 
 HIS   0.008   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 6983)
  covalent geometry    : angle       0.68888 ( 9467)
  hydrogen bonds       : bond        0.04589 (  289)
  hydrogen bonds       : angle       5.60204 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.262 
Fit side-chains
REVERT: A  249 MET cc_start: 0.8062 (tpp) cc_final: 0.7808 (tpp)
REVERT: A  419 MET cc_start: 0.8955 (OUTLIER) cc_final: 0.8725 (ptt)
REVERT: A  437 LEU cc_start: 0.9212 (OUTLIER) cc_final: 0.8967 (tp)
REVERT: A  559 SER cc_start: 0.9072 (p) cc_final: 0.8793 (p)
REVERT: A  587 GLU cc_start: 0.7398 (mp0) cc_final: 0.7016 (mp0)
REVERT: A  619 TRP cc_start: 0.7116 (OUTLIER) cc_final: 0.6641 (t60)
REVERT: C   40 TYR cc_start: 0.8572 (t80) cc_final: 0.8282 (t80)
REVERT: C  191 LYS cc_start: 0.9192 (ttpt) cc_final: 0.8825 (mtpt)
REVERT: C  253 ASP cc_start: 0.8026 (m-30) cc_final: 0.7500 (m-30)
  outliers start: 24
  outliers final: 17
  residues processed: 137
  average time/residue: 0.0826
  time to fit residues: 15.3734
Evaluate side-chains
  145 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 125
  time to evaluate  : 0.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  619 TRP
Chi-restraints excluded: chain A residue  628 CYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  329 VAL
Chi-restraints excluded: chain C residue  470 HIS
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  559 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 38 optimal weight:    6.9990
   chunk 75 optimal weight:    2.9990
   chunk 70 optimal weight:    0.7980
   chunk 33 optimal weight:    2.9990
   chunk 81 optimal weight:    4.9990
   chunk 82 optimal weight:    0.8980
   chunk 78 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9980
   chunk 55 optimal weight:    0.9980
   chunk 62 optimal weight:    5.9990
   overall best weight:    1.3382

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

Flipped N/Q/H residues before XYZ refinement:
A 409 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.149081 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.131057 restraints weight = 12666.116|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.134885 restraints weight = 7162.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3755 r_free = 0.3755 target = 0.137535 restraints weight = 4764.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.139343 restraints weight = 3482.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.140690 restraints weight = 2736.258|
|-----------------------------------------------------------------------------|
r_work (final): 0.3798
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7603
moved from start:          0.2532

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   6983  Z= 0.157
  Angle     :  0.670   8.999   9467  Z= 0.336
  Chirality :  0.044   0.181   1076
  Planarity :  0.004   0.044   1200
  Dihedral  :  4.877  25.025    948
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 16.53 %
    Favored  : 79.40 %
  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: -0.94 (0.29), residues: 850
  helix:  0.42 (0.28), residues: 348
  sheet: -0.61 (0.41), residues: 163
  loop : -1.68 (0.33), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 524 
 TYR   0.028   0.002   TYR A 585 
 PHE   0.019   0.002   PHE C 541 
 TRP   0.013   0.001   TRP A 619 
 HIS   0.009   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00363 ( 6983)
  covalent geometry    : angle       0.66975 ( 9467)
  hydrogen bonds       : bond        0.04070 (  289)
  hydrogen bonds       : angle       5.34682 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  158 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 0.277 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.7986 (tpp) cc_final: 0.7740 (tpp)
REVERT: A  299 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8201 (mm)
REVERT: A  419 MET cc_start: 0.8958 (OUTLIER) cc_final: 0.8736 (ptt)
REVERT: A  437 LEU cc_start: 0.9226 (OUTLIER) cc_final: 0.8975 (tp)
REVERT: A  545 HIS cc_start: 0.7703 (m-70) cc_final: 0.7333 (m170)
REVERT: A  587 GLU cc_start: 0.7443 (mp0) cc_final: 0.7139 (mp0)
REVERT: A  619 TRP cc_start: 0.6984 (OUTLIER) cc_final: 0.6671 (t60)
REVERT: C   40 TYR cc_start: 0.8512 (t80) cc_final: 0.8159 (t80)
REVERT: C  191 LYS cc_start: 0.9180 (ttpt) cc_final: 0.8793 (mtpt)
REVERT: C  253 ASP cc_start: 0.8030 (m-30) cc_final: 0.7487 (m-30)
  outliers start: 30
  outliers final: 17
  residues processed: 143
  average time/residue: 0.0815
  time to fit residues: 15.9388
Evaluate side-chains
  141 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 120
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain A residue  437 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  619 TRP
Chi-restraints excluded: chain A residue  628 CYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  329 VAL
Chi-restraints excluded: chain C residue  470 HIS
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  559 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 86 optimal weight:    7.9990
   chunk 9 optimal weight:    4.9990
   chunk 69 optimal weight:    5.9990
   chunk 83 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 31 optimal weight:    0.5980
   chunk 55 optimal weight:    0.9990
   chunk 18 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 36 optimal weight:    8.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.6986

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

Flipped N/Q/H residues before XYZ refinement:
A 372 GLN
A 376 ASN
A 409 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.146764 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.128731 restraints weight = 12698.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.132492 restraints weight = 7200.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.135054 restraints weight = 4798.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.136844 restraints weight = 3529.592|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3760 r_free = 0.3760 target = 0.137993 restraints weight = 2781.183|
|-----------------------------------------------------------------------------|
r_work (final): 0.3760
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.2726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6983  Z= 0.177
  Angle     :  0.687   8.704   9467  Z= 0.343
  Chirality :  0.045   0.183   1076
  Planarity :  0.004   0.044   1200
  Dihedral  :  4.869  25.204    948
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  5.28 %
    Allowed  : 17.07 %
    Favored  : 77.64 %
  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: -0.93 (0.29), residues: 850
  helix:  0.44 (0.28), residues: 354
  sheet: -0.66 (0.41), residues: 163
  loop : -1.70 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 200 
 TYR   0.030   0.002   TYR A 585 
 PHE   0.019   0.002   PHE C 541 
 TRP   0.025   0.002   TRP C 647 
 HIS   0.006   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00412 ( 6983)
  covalent geometry    : angle       0.68735 ( 9467)
  hydrogen bonds       : bond        0.03948 (  289)
  hydrogen bonds       : angle       5.25466 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 134
  time to evaluate  : 0.257 
Fit side-chains
REVERT: A  249 MET cc_start: 0.8068 (tpp) cc_final: 0.7832 (tpp)
REVERT: A  299 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8233 (mm)
REVERT: A  404 ARG cc_start: 0.6244 (mmp-170) cc_final: 0.5965 (mmp-170)
REVERT: A  419 MET cc_start: 0.9000 (OUTLIER) cc_final: 0.8708 (ptt)
REVERT: A  586 GLU cc_start: 0.6065 (pt0) cc_final: 0.5595 (pt0)
REVERT: A  587 GLU cc_start: 0.7588 (mp0) cc_final: 0.7363 (mp0)
REVERT: A  619 TRP cc_start: 0.7164 (OUTLIER) cc_final: 0.6820 (t60)
REVERT: C   40 TYR cc_start: 0.8537 (t80) cc_final: 0.8173 (t80)
REVERT: C  191 LYS cc_start: 0.9179 (ttpt) cc_final: 0.8947 (ttpt)
REVERT: C  231 LEU cc_start: 0.8391 (OUTLIER) cc_final: 0.8146 (mp)
REVERT: C  253 ASP cc_start: 0.7924 (m-30) cc_final: 0.7396 (m-30)
  outliers start: 39
  outliers final: 22
  residues processed: 157
  average time/residue: 0.0870
  time to fit residues: 18.2988
Evaluate side-chains
  149 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 123
  time to evaluate  : 0.253 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  616 CYS
Chi-restraints excluded: chain A residue  619 TRP
Chi-restraints excluded: chain A residue  628 CYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  196 LEU
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  231 LEU
Chi-restraints excluded: chain C residue  470 HIS
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  559 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 20 optimal weight:    0.0270
   chunk 73 optimal weight:    0.2980
   chunk 31 optimal weight:    7.9990
   chunk 64 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   chunk 48 optimal weight:    6.9990
   chunk 13 optimal weight:    1.9990
   chunk 80 optimal weight:    0.9980
   chunk 58 optimal weight:    0.9990
   chunk 22 optimal weight:    9.9990
   overall best weight:    0.6640

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

Flipped N/Q/H residues before XYZ refinement:
A 370 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3917 r_free = 0.3917 target = 0.150367 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.132370 restraints weight = 12655.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.136208 restraints weight = 7188.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.138801 restraints weight = 4767.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.140592 restraints weight = 3482.929|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.141833 restraints weight = 2734.431|
|-----------------------------------------------------------------------------|
r_work (final): 0.3811
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7572
moved from start:          0.2915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   6983  Z= 0.130
  Angle     :  0.692  11.267   9467  Z= 0.339
  Chirality :  0.045   0.201   1076
  Planarity :  0.005   0.044   1200
  Dihedral  :  4.744  24.179    948
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 11.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 19.78 %
    Favored  : 75.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.29), residues: 850
  helix:  0.58 (0.28), residues: 354
  sheet: -0.54 (0.41), residues: 164
  loop : -1.71 (0.33), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 595 
 TYR   0.025   0.002   TYR A 585 
 PHE   0.018   0.002   PHE A 258 
 TRP   0.017   0.001   TRP C 647 
 HIS   0.008   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 6983)
  covalent geometry    : angle       0.69166 ( 9467)
  hydrogen bonds       : bond        0.03655 (  289)
  hydrogen bonds       : angle       5.09095 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 136
  time to evaluate  : 0.257 
Fit side-chains
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.7976 (tpp) cc_final: 0.7759 (tpp)
REVERT: A  299 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8111 (mm)
REVERT: A  419 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8669 (ptt)
REVERT: A  506 MET cc_start: 0.7065 (ttm) cc_final: 0.6743 (ttm)
REVERT: A  545 HIS cc_start: 0.7605 (m170) cc_final: 0.7367 (m170)
REVERT: A  586 GLU cc_start: 0.6054 (pt0) cc_final: 0.5647 (pt0)
REVERT: A  619 TRP cc_start: 0.6952 (OUTLIER) cc_final: 0.6620 (t60)
REVERT: C   40 TYR cc_start: 0.8392 (t80) cc_final: 0.7995 (t80)
REVERT: C   47 LEU cc_start: 0.6920 (OUTLIER) cc_final: 0.6433 (tt)
REVERT: C  191 LYS cc_start: 0.9098 (ttpt) cc_final: 0.8769 (mtpt)
REVERT: C  253 ASP cc_start: 0.7918 (m-30) cc_final: 0.7350 (m-30)
  outliers start: 32
  outliers final: 21
  residues processed: 152
  average time/residue: 0.0816
  time to fit residues: 16.9329
Evaluate side-chains
  147 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 122
  time to evaluate  : 0.271 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  619 TRP
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  628 CYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  290 VAL
Chi-restraints excluded: chain C residue  470 HIS
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  617 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 10 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 68 optimal weight:    0.9980
   chunk 61 optimal weight:    0.8980
   chunk 62 optimal weight:    3.9990
   chunk 58 optimal weight:    5.9990
   chunk 28 optimal weight:    0.9980
   chunk 51 optimal weight:    5.9990
   chunk 1 optimal weight:    0.4980
   chunk 11 optimal weight:    0.9980
   chunk 70 optimal weight:    1.9990
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3920 r_free = 0.3920 target = 0.150815 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.132766 restraints weight = 12558.023|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.136551 restraints weight = 7226.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.139129 restraints weight = 4840.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.140907 restraints weight = 3569.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.142140 restraints weight = 2818.584|
|-----------------------------------------------------------------------------|
r_work (final): 0.3812
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.3057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6983  Z= 0.135
  Angle     :  0.696  11.209   9467  Z= 0.338
  Chirality :  0.045   0.229   1076
  Planarity :  0.004   0.043   1200
  Dihedral  :  4.665  23.933    948
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.88 %
    Allowed  : 19.65 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.73 (0.29), residues: 850
  helix:  0.62 (0.28), residues: 354
  sheet: -0.50 (0.41), residues: 163
  loop : -1.64 (0.34), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 595 
 TYR   0.025   0.002   TYR A 585 
 PHE   0.016   0.002   PHE C 234 
 TRP   0.016   0.001   TRP C 647 
 HIS   0.006   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00318 ( 6983)
  covalent geometry    : angle       0.69563 ( 9467)
  hydrogen bonds       : bond        0.03586 (  289)
  hydrogen bonds       : angle       5.06694 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.278 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8064 (mm)
REVERT: A  404 ARG cc_start: 0.6677 (mmp-170) cc_final: 0.6425 (mmp-170)
REVERT: A  419 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8674 (ptt)
REVERT: A  545 HIS cc_start: 0.7807 (m170) cc_final: 0.7603 (m170)
REVERT: A  586 GLU cc_start: 0.6055 (pt0) cc_final: 0.5724 (pt0)
REVERT: A  619 TRP cc_start: 0.6949 (OUTLIER) cc_final: 0.6597 (t60)
REVERT: C   40 TYR cc_start: 0.8401 (t80) cc_final: 0.8018 (t80)
REVERT: C   47 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6453 (tt)
REVERT: C  191 LYS cc_start: 0.9089 (ttpt) cc_final: 0.8749 (mtpt)
REVERT: C  253 ASP cc_start: 0.7905 (m-30) cc_final: 0.7354 (m-30)
REVERT: C  357 ASN cc_start: 0.8860 (m-40) cc_final: 0.8649 (m-40)
  outliers start: 36
  outliers final: 22
  residues processed: 147
  average time/residue: 0.0838
  time to fit residues: 16.8903
Evaluate side-chains
  146 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 0.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  252 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  576 LEU
Chi-restraints excluded: chain A residue  619 TRP
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  329 VAL
Chi-restraints excluded: chain C residue  470 HIS
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  617 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 75 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 15 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 60 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 78 optimal weight:    0.8980
   chunk 71 optimal weight:    0.0770
   overall best weight:    0.9540

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.150198 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.132396 restraints weight = 12606.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.136253 restraints weight = 7071.407|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.138815 restraints weight = 4654.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.140488 restraints weight = 3404.066|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.141871 restraints weight = 2701.194|
|-----------------------------------------------------------------------------|
r_work (final): 0.3822
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7573
moved from start:          0.3173

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6983  Z= 0.139
  Angle     :  0.729  13.028   9467  Z= 0.352
  Chirality :  0.045   0.274   1076
  Planarity :  0.005   0.044   1200
  Dihedral  :  4.667  23.957    948
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 12.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  4.47 %
    Allowed  : 19.92 %
    Favored  : 75.61 %
  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: -0.76 (0.29), residues: 850
  helix:  0.55 (0.28), residues: 354
  sheet: -0.49 (0.41), residues: 164
  loop : -1.62 (0.34), residues: 332

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 595 
 TYR   0.024   0.001   TYR A 585 
 PHE   0.018   0.002   PHE C 238 
 TRP   0.015   0.001   TRP C 647 
 HIS   0.005   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 6983)
  covalent geometry    : angle       0.72863 ( 9467)
  hydrogen bonds       : bond        0.03528 (  289)
  hydrogen bonds       : angle       5.09665 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  162 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 129
  time to evaluate  : 0.258 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 LYS cc_start: 0.8739 (tptt) cc_final: 0.8516 (tptt)
REVERT: A  299 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8057 (mm)
REVERT: A  506 MET cc_start: 0.6961 (ttm) cc_final: 0.6734 (ttm)
REVERT: A  545 HIS cc_start: 0.7637 (m170) cc_final: 0.7409 (m170)
REVERT: A  586 GLU cc_start: 0.6081 (pt0) cc_final: 0.5791 (pt0)
REVERT: A  619 TRP cc_start: 0.6902 (OUTLIER) cc_final: 0.6558 (t60)
REVERT: C   40 TYR cc_start: 0.8406 (t80) cc_final: 0.8011 (t80)
REVERT: C   47 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6439 (tt)
REVERT: C  191 LYS cc_start: 0.9078 (ttpt) cc_final: 0.8725 (mtpt)
REVERT: C  253 ASP cc_start: 0.7881 (m-30) cc_final: 0.7317 (m-30)
REVERT: C  357 ASN cc_start: 0.8876 (m-40) cc_final: 0.8667 (m-40)
REVERT: C  471 PHE cc_start: 0.8363 (OUTLIER) cc_final: 0.7012 (t80)
  outliers start: 33
  outliers final: 23
  residues processed: 147
  average time/residue: 0.0806
  time to fit residues: 16.1469
Evaluate side-chains
  151 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 124
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  619 TRP
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  246 LEU
Chi-restraints excluded: chain C residue  329 VAL
Chi-restraints excluded: chain C residue  470 HIS
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  559 THR
Chi-restraints excluded: chain C residue  617 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 58 optimal weight:    0.7980
   chunk 27 optimal weight:    5.9990
   chunk 17 optimal weight:    2.9990
   chunk 4 optimal weight:    5.9990
   chunk 7 optimal weight:    0.4980
   chunk 81 optimal weight:    1.9990
   chunk 63 optimal weight:    0.9990
   chunk 77 optimal weight:    6.9990
   chunk 16 optimal weight:    0.9980
   chunk 56 optimal weight:    1.9990
   chunk 73 optimal weight:    0.0030
   overall best weight:    0.6592

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

Flipped N/Q/H residues before XYZ refinement:
** A 545 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3949 r_free = 0.3949 target = 0.152068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.134249 restraints weight = 12503.085|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.138032 restraints weight = 7114.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.140632 restraints weight = 4736.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.142434 restraints weight = 3464.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.143431 restraints weight = 2722.662|
|-----------------------------------------------------------------------------|
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7555
moved from start:          0.3277

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6983  Z= 0.127
  Angle     :  0.705  11.403   9467  Z= 0.341
  Chirality :  0.045   0.259   1076
  Planarity :  0.005   0.043   1200
  Dihedral  :  4.569  23.342    948
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 13.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.41 %
    Favored  : 94.59 %
  Rotamer:
    Outliers :  4.07 %
    Allowed  : 20.46 %
    Favored  : 75.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.65 (0.29), residues: 850
  helix:  0.64 (0.29), residues: 350
  sheet: -0.17 (0.42), residues: 157
  loop : -1.67 (0.33), residues: 343

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 595 
 TYR   0.025   0.001   TYR A 585 
 PHE   0.019   0.002   PHE C 238 
 TRP   0.014   0.001   TRP C 647 
 HIS   0.005   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 6983)
  covalent geometry    : angle       0.70516 ( 9467)
  hydrogen bonds       : bond        0.03447 (  289)
  hydrogen bonds       : angle       5.02041 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 134
  time to evaluate  : 0.262 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 LYS cc_start: 0.8695 (tptt) cc_final: 0.8461 (tptt)
REVERT: A  299 LEU cc_start: 0.8704 (OUTLIER) cc_final: 0.8059 (mm)
REVERT: A  404 ARG cc_start: 0.5969 (mmp-170) cc_final: 0.5649 (mmp-170)
REVERT: A  506 MET cc_start: 0.7007 (ttm) cc_final: 0.6753 (ttm)
REVERT: A  586 GLU cc_start: 0.5960 (pt0) cc_final: 0.5701 (pt0)
REVERT: A  619 TRP cc_start: 0.6937 (OUTLIER) cc_final: 0.6568 (t60)
REVERT: C   40 TYR cc_start: 0.8309 (t80) cc_final: 0.7874 (t80)
REVERT: C   47 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6419 (tt)
REVERT: C  191 LYS cc_start: 0.9102 (ttpt) cc_final: 0.8745 (mtpt)
REVERT: C  253 ASP cc_start: 0.7855 (m-30) cc_final: 0.7301 (m-30)
REVERT: C  471 PHE cc_start: 0.8280 (OUTLIER) cc_final: 0.6866 (t80)
  outliers start: 30
  outliers final: 24
  residues processed: 150
  average time/residue: 0.0803
  time to fit residues: 16.4827
Evaluate side-chains
  150 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 122
  time to evaluate  : 0.259 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  419 MET
Chi-restraints excluded: chain A residue  514 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  616 CYS
Chi-restraints excluded: chain A residue  619 TRP
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  246 LEU
Chi-restraints excluded: chain C residue  329 VAL
Chi-restraints excluded: chain C residue  470 HIS
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  534 VAL
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  559 THR
Chi-restraints excluded: chain C residue  617 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 21 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 72 optimal weight:    3.9990
   chunk 79 optimal weight:    5.9990
   chunk 85 optimal weight:    4.9990
   chunk 7 optimal weight:    2.9990
   chunk 1 optimal weight:    3.9990
   chunk 80 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 84 optimal weight:    9.9990
   chunk 53 optimal weight:    7.9990
   overall best weight:    2.5588

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

Flipped N/Q/H residues before XYZ refinement:
** A 370 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.144721 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126117 restraints weight = 12723.172|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.129892 restraints weight = 7347.106|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.132476 restraints weight = 4932.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3715 r_free = 0.3715 target = 0.134262 restraints weight = 3673.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3729 r_free = 0.3729 target = 0.135414 restraints weight = 2920.763|
|-----------------------------------------------------------------------------|
r_work (final): 0.3733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.3355

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.044   6983  Z= 0.244
  Angle     :  0.821  11.113   9467  Z= 0.407
  Chirality :  0.049   0.303   1076
  Planarity :  0.005   0.046   1200
  Dihedral  :  4.977  26.292    948
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 16.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.06 %
    Favored  : 92.94 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 21.41 %
    Favored  : 74.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.01 (0.29), residues: 850
  helix:  0.45 (0.28), residues: 349
  sheet: -0.79 (0.39), residues: 168
  loop : -1.76 (0.33), residues: 333

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 595 
 TYR   0.034   0.002   TYR A 585 
 PHE   0.028   0.003   PHE C 238 
 TRP   0.020   0.002   TRP C 647 
 HIS   0.004   0.001   HIS C  99 

Details of bonding type rmsd
  covalent geometry    : bond        0.00575 ( 6983)
  covalent geometry    : angle       0.82059 ( 9467)
  hydrogen bonds       : bond        0.04032 (  289)
  hydrogen bonds       : angle       5.34237 (  849)

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

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

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1700 Ramachandran restraints generated.
    850 Oldfield, 0 Emsley, 850 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 126
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 LYS cc_start: 0.8827 (tptt) cc_final: 0.8583 (tptt)
REVERT: A  299 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8350 (mm)
REVERT: A  506 MET cc_start: 0.7156 (ttm) cc_final: 0.6839 (ttm)
REVERT: A  619 TRP cc_start: 0.7136 (OUTLIER) cc_final: 0.6741 (t60)
REVERT: C   40 TYR cc_start: 0.8534 (t80) cc_final: 0.8279 (t80)
REVERT: C  116 LYS cc_start: 0.8604 (ttpt) cc_final: 0.8034 (ttpt)
REVERT: C  191 LYS cc_start: 0.9188 (ttpt) cc_final: 0.8910 (mtpt)
REVERT: C  253 ASP cc_start: 0.7963 (m-30) cc_final: 0.7416 (m-30)
REVERT: C  338 ARG cc_start: 0.8504 (mmt-90) cc_final: 0.8021 (mmt90)
REVERT: C  471 PHE cc_start: 0.8566 (OUTLIER) cc_final: 0.7948 (t80)
  outliers start: 29
  outliers final: 22
  residues processed: 141
  average time/residue: 0.0873
  time to fit residues: 16.5620
Evaluate side-chains
  145 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 120
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  228 LEU
Chi-restraints excluded: chain A residue  245 VAL
Chi-restraints excluded: chain A residue  254 THR
Chi-restraints excluded: chain A residue  270 THR
Chi-restraints excluded: chain A residue  299 LEU
Chi-restraints excluded: chain A residue  375 THR
Chi-restraints excluded: chain A residue  387 LEU
Chi-restraints excluded: chain A residue  522 LEU
Chi-restraints excluded: chain A residue  557 CYS
Chi-restraints excluded: chain A residue  619 TRP
Chi-restraints excluded: chain A residue  621 THR
Chi-restraints excluded: chain A residue  628 CYS
Chi-restraints excluded: chain C residue   31 ASP
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  246 LEU
Chi-restraints excluded: chain C residue  470 HIS
Chi-restraints excluded: chain C residue  471 PHE
Chi-restraints excluded: chain C residue  551 THR
Chi-restraints excluded: chain C residue  555 SER
Chi-restraints excluded: chain C residue  559 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 43 optimal weight:    0.0980
   chunk 22 optimal weight:    8.9990
   chunk 39 optimal weight:    0.9990
   chunk 21 optimal weight:    0.7980
   chunk 34 optimal weight:    0.0010
   chunk 59 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0870
   chunk 77 optimal weight:    5.9990
   chunk 75 optimal weight:    0.9990
   chunk 48 optimal weight:    3.9990
   chunk 63 optimal weight:    0.9990
   overall best weight:    0.3764

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

Flipped N/Q/H residues before XYZ refinement:
A 298 GLN
A 370 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.152206 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.134261 restraints weight = 12414.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.138010 restraints weight = 7146.563|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.140581 restraints weight = 4796.108|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.142374 restraints weight = 3539.923|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3835 r_free = 0.3835 target = 0.143370 restraints weight = 2797.217|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7570
moved from start:          0.3458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   6983  Z= 0.132
  Angle     :  0.756  10.940   9467  Z= 0.371
  Chirality :  0.046   0.202   1076
  Planarity :  0.005   0.042   1200
  Dihedral  :  4.739  24.014    948
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 13.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.59 %
    Favored  : 95.41 %
  Rotamer:
    Outliers :  3.25 %
    Allowed  : 23.04 %
    Favored  : 73.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.81 (0.29), residues: 850
  helix:  0.48 (0.28), residues: 350
  sheet: -0.30 (0.41), residues: 160
  loop : -1.71 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 595 
 TYR   0.035   0.002   TYR A 585 
 PHE   0.024   0.002   PHE C 238 
 TRP   0.015   0.001   TRP C 647 
 HIS   0.008   0.001   HIS A 545 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 6983)
  covalent geometry    : angle       0.75633 ( 9467)
  hydrogen bonds       : bond        0.03573 (  289)
  hydrogen bonds       : angle       5.04779 (  849)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1199.94 seconds
wall clock time: 21 minutes 30.45 seconds (1290.45 seconds total)