Starting phenix.real_space_refine
on Tue Feb 11 23:20:00 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qla_14066/02_2025/7qla_14066.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qla_14066/02_2025/7qla_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_14066/02_2025/7qla_14066.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qla_14066/02_2025/7qla_14066.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qla_14066/02_2025/7qla_14066.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qla_14066/02_2025/7qla_14066.cif"
  }
  resolution = 3.85
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/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: 4.61, per 1000 atoms: 0.67
  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: 1.66
  Conformation dependent library (CDL) restraints added in 844.8 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: 0.80
  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: 2.21

  Time building geometry restraints manager: 1.95 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:             0.470
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.240
  Check model and map are aligned:         0.040
  Set scattering table:                    0.060
  Process input model:                     19.550
  Find NCS groups from input model:        0.100
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.840
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   23.340
-------------------------------------------------------------------------------
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= 0.193
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.33 (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
 TRP   0.029   0.002   TRP A 619 
 HIS   0.016   0.001   HIS A 545 
 PHE   0.020   0.002   PHE C 114 
 TYR   0.017   0.001   TYR A 388 
 ARG   0.012   0.000   ARG A 595 

*********************** 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  : 0.821 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 LYS cc_start: 0.8445 (tptm) cc_final: 0.8219 (tptt)
REVERT: A  249 MET cc_start: 0.8077 (tpp) cc_final: 0.7598 (tpp)
REVERT: A  308 MET cc_start: 0.8469 (tpp) cc_final: 0.8136 (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: 0.6915 (mp0)
REVERT: C   95 LYS cc_start: 0.8778 (tppt) cc_final: 0.8517 (tptt)
REVERT: C  253 ASP cc_start: 0.8034 (m-30) cc_final: 0.7474 (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: 0.9100 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 167
  average time/residue: 0.1855
  time to fit residues: 41.4955
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  : 0.825 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 73 optimal weight:    4.9990
   chunk 65 optimal weight:    3.9990
   chunk 36 optimal weight:    8.9990
   chunk 22 optimal weight:    8.9990
   chunk 44 optimal weight:    0.7980
   chunk 35 optimal weight:    2.9990
   chunk 68 optimal weight:    0.8980
   chunk 26 optimal weight:    1.9990
   chunk 41 optimal weight:    5.9990
   chunk 50 optimal weight:    5.9990
   chunk 79 optimal weight:    0.4980
   overall best weight:    1.4384

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

Flipped N/Q/H residues before XYZ refinement:
A 555 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.152355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134591 restraints weight = 12375.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.138380 restraints weight = 7063.754|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3791 r_free = 0.3791 target = 0.140941 restraints weight = 4694.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7619
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   6983  Z= 0.255
  Angle     :  0.688   7.240   9467  Z= 0.350
  Chirality :  0.045   0.175   1076
  Planarity :  0.005   0.039   1200
  Dihedral  :  4.833  24.451    948
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 13.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  2.03 %
    Allowed  : 10.70 %
    Favored  : 87.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.01 (0.29), residues: 850
  helix:  0.26 (0.28), residues: 343
  sheet: -0.54 (0.44), residues: 150
  loop : -1.60 (0.32), residues: 357

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 647 
 HIS   0.007   0.001   HIS A 545 
 PHE   0.024   0.002   PHE A 258 
 TYR   0.022   0.002   TYR A 585 
 ARG   0.007   0.000   ARG C 582 

*********************** 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: 15
    poor density    : 140
  time to evaluate  : 0.739 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  341 LEU cc_start: 0.8733 (tt) cc_final: 0.8473 (tt)
REVERT: A  404 ARG cc_start: 0.6801 (mmp-170) cc_final: 0.6514 (mmp-170)
REVERT: A  524 ARG cc_start: 0.8305 (mpp80) cc_final: 0.7425 (mpt-90)
REVERT: A  559 SER cc_start: 0.8962 (p) cc_final: 0.8732 (p)
REVERT: A  586 GLU cc_start: 0.6564 (pt0) cc_final: 0.6283 (pt0)
REVERT: A  587 GLU cc_start: 0.7421 (mp0) cc_final: 0.6948 (mp0)
REVERT: A  619 TRP cc_start: 0.6880 (t60) cc_final: 0.6344 (t60)
REVERT: C   40 TYR cc_start: 0.8533 (t80) cc_final: 0.8181 (t80)
REVERT: C  253 ASP cc_start: 0.8018 (m-30) cc_final: 0.7499 (m-30)
  outliers start: 15
  outliers final: 12
  residues processed: 146
  average time/residue: 0.2029
  time to fit residues: 39.2934
Evaluate side-chains
  136 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 124
  time to evaluate  : 0.767 
-------------------------------------------------------------------------------
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  387 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  628 CYS
Chi-restraints excluded: chain C residue  214 SER
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 41 optimal weight:    0.7980
   chunk 33 optimal weight:    5.9990
   chunk 28 optimal weight:    4.9990
   chunk 30 optimal weight:    7.9990
   chunk 70 optimal weight:    0.9990
   chunk 50 optimal weight:    0.4980
   chunk 12 optimal weight:    0.8980
   chunk 76 optimal weight:    6.9990
   chunk 26 optimal weight:    2.9990
   chunk 39 optimal weight:    0.7980
   chunk 21 optimal weight:    0.7980
   overall best weight:    0.7580

-------------------------------------------------------------------------------
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 = 0.3938 r_free = 0.3938 target = 0.151902 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.134245 restraints weight = 12529.472|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3762 r_free = 0.3762 target = 0.138113 restraints weight = 7059.120|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3797 r_free = 0.3797 target = 0.140708 restraints weight = 4643.002|
|-----------------------------------------------------------------------------|
r_work (final): 0.3796
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.2131

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6983  Z= 0.198
  Angle     :  0.646   8.236   9467  Z= 0.323
  Chirality :  0.044   0.175   1076
  Planarity :  0.004   0.043   1200
  Dihedral  :  4.789  24.353    948
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.29 %
    Favored  : 94.71 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 14.23 %
    Favored  : 82.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.97 (0.29), residues: 850
  helix:  0.33 (0.28), residues: 347
  sheet: -0.49 (0.43), residues: 151
  loop : -1.66 (0.32), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP C 647 
 HIS   0.008   0.001   HIS A 545 
 PHE   0.022   0.002   PHE C 234 
 TYR   0.024   0.002   TYR A 585 
 ARG   0.006   0.000   ARG C 197 

*********************** 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
  148 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 126
  time to evaluate  : 0.716 
Fit side-chains
   revert: symmetry clash
REVERT: A  227 ILE cc_start: 0.8021 (mm) cc_final: 0.7718 (mt)
REVERT: A  404 ARG cc_start: 0.6744 (mmp-170) cc_final: 0.6389 (mmp-170)
REVERT: A  437 LEU cc_start: 0.9231 (OUTLIER) cc_final: 0.8987 (tp)
REVERT: A  559 SER cc_start: 0.8998 (p) cc_final: 0.8739 (p)
REVERT: A  587 GLU cc_start: 0.7355 (mp0) cc_final: 0.7002 (mp0)
REVERT: A  619 TRP cc_start: 0.6950 (OUTLIER) cc_final: 0.6642 (t60)
REVERT: C   40 TYR cc_start: 0.8444 (t80) cc_final: 0.8067 (t80)
REVERT: C  253 ASP cc_start: 0.8018 (m-30) cc_final: 0.7479 (m-30)
  outliers start: 22
  outliers final: 16
  residues processed: 134
  average time/residue: 0.1846
  time to fit residues: 33.4015
Evaluate side-chains
  137 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.724 
-------------------------------------------------------------------------------
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  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  124 VAL
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  329 VAL
Chi-restraints excluded: chain C residue  350 GLU
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 76 optimal weight:    0.9990
   chunk 22 optimal weight:    5.9990
   chunk 9 optimal weight:    8.9990
   chunk 0 optimal weight:    8.9990
   chunk 39 optimal weight:    3.9990
   chunk 66 optimal weight:    0.4980
   chunk 6 optimal weight:    0.9990
   chunk 24 optimal weight:    6.9990
   chunk 10 optimal weight:    0.9980
   chunk 79 optimal weight:    2.9990
   chunk 1 optimal weight:    9.9990
   overall best weight:    1.2986

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.150391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.132492 restraints weight = 12619.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.136387 restraints weight = 7131.481|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3773 r_free = 0.3773 target = 0.139023 restraints weight = 4704.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3780
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7628
moved from start:          0.2453

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6983  Z= 0.232
  Angle     :  0.653   8.697   9467  Z= 0.326
  Chirality :  0.044   0.157   1076
  Planarity :  0.004   0.044   1200
  Dihedral  :  4.754  24.221    948
  Min Nonbonded Distance : 2.590

Molprobity Statistics.
  All-atom Clashscore : 12.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.53 %
    Favored  : 94.47 %
  Rotamer:
    Outliers :  4.34 %
    Allowed  : 15.45 %
    Favored  : 80.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.88 (0.29), residues: 850
  helix:  0.42 (0.28), residues: 347
  sheet: -0.52 (0.41), residues: 163
  loop : -1.61 (0.33), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C 647 
 HIS   0.011   0.001   HIS A 545 
 PHE   0.019   0.002   PHE C 234 
 TYR   0.028   0.002   TYR A 585 
 ARG   0.004   0.000   ARG A 524 

*********************** 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
  162 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 130
  time to evaluate  : 0.937 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  227 ILE cc_start: 0.8101 (mm) cc_final: 0.7837 (mt)
REVERT: A  249 MET cc_start: 0.8165 (tpp) cc_final: 0.7817 (tpp)
REVERT: A  299 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8258 (mm)
REVERT: A  404 ARG cc_start: 0.6814 (mmp-170) cc_final: 0.6495 (mmp-170)
REVERT: A  545 HIS cc_start: 0.7885 (m170) cc_final: 0.7681 (m170)
REVERT: A  559 SER cc_start: 0.9056 (p) cc_final: 0.8818 (p)
REVERT: A  587 GLU cc_start: 0.7463 (mp0) cc_final: 0.7168 (mp0)
REVERT: A  619 TRP cc_start: 0.7005 (OUTLIER) cc_final: 0.6624 (t60)
REVERT: C   40 TYR cc_start: 0.8482 (t80) cc_final: 0.8121 (t80)
REVERT: C  253 ASP cc_start: 0.8037 (m-30) cc_final: 0.7505 (m-30)
  outliers start: 32
  outliers final: 20
  residues processed: 146
  average time/residue: 0.1827
  time to fit residues: 36.0322
Evaluate side-chains
  142 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 120
  time to evaluate  : 0.814 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  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  124 VAL
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 57 optimal weight:    0.9980
   chunk 53 optimal weight:    7.9990
   chunk 40 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 84 optimal weight:   10.0000
   chunk 38 optimal weight:    0.1980
   chunk 24 optimal weight:    0.9990
   chunk 55 optimal weight:    0.7980
   chunk 73 optimal weight:    0.0060
   chunk 75 optimal weight:    0.8980
   overall best weight:    0.5796

-------------------------------------------------------------------------------
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 = 0.3947 r_free = 0.3947 target = 0.152545 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3714 r_free = 0.3714 target = 0.134683 restraints weight = 12450.477|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.138626 restraints weight = 6987.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3803 r_free = 0.3803 target = 0.141256 restraints weight = 4598.556|
|-----------------------------------------------------------------------------|
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7574
moved from start:          0.2681

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6983  Z= 0.179
  Angle     :  0.661   9.109   9467  Z= 0.321
  Chirality :  0.044   0.184   1076
  Planarity :  0.004   0.043   1200
  Dihedral  :  4.666  23.867    948
  Min Nonbonded Distance : 2.585

Molprobity Statistics.
  All-atom Clashscore : 10.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 17.62 %
    Favored  : 78.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.29), residues: 850
  helix:  0.56 (0.28), residues: 347
  sheet: -0.47 (0.41), residues: 164
  loop : -1.55 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C 647 
 HIS   0.008   0.001   HIS A 545 
 PHE   0.018   0.002   PHE A 258 
 TYR   0.034   0.002   TYR A 585 
 ARG   0.004   0.000   ARG A 595 

*********************** 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
  158 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 129
  time to evaluate  : 0.775 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  249 MET cc_start: 0.8136 (tpp) cc_final: 0.7779 (tpp)
REVERT: A  299 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8139 (mm)
REVERT: A  304 GLU cc_start: 0.8748 (tp30) cc_final: 0.8534 (tp30)
REVERT: A  404 ARG cc_start: 0.6678 (mmp-170) cc_final: 0.6421 (mmp-170)
REVERT: A  506 MET cc_start: 0.7108 (ttm) cc_final: 0.6749 (ttm)
REVERT: A  559 SER cc_start: 0.9050 (p) cc_final: 0.8811 (p)
REVERT: A  619 TRP cc_start: 0.6881 (OUTLIER) cc_final: 0.6515 (t60)
REVERT: C   40 TYR cc_start: 0.8385 (t80) cc_final: 0.7980 (t80)
REVERT: C  253 ASP cc_start: 0.7961 (m-30) cc_final: 0.7407 (m-30)
  outliers start: 29
  outliers final: 18
  residues processed: 145
  average time/residue: 0.1798
  time to fit residues: 35.0857
Evaluate side-chains
  135 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 115
  time to evaluate  : 0.697 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  522 LEU
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  621 THR
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  213 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
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 76 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0970
   chunk 47 optimal weight:    7.9990
   chunk 46 optimal weight:    0.0980
   chunk 41 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 52 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 15 optimal weight:    1.9990
   chunk 84 optimal weight:    8.9990
   chunk 42 optimal weight:    9.9990
   overall best weight:    0.9982

-------------------------------------------------------------------------------
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 = 0.3935 r_free = 0.3935 target = 0.151142 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.133600 restraints weight = 12464.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.137401 restraints weight = 7027.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.139968 restraints weight = 4619.487|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7604
moved from start:          0.2858

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6983  Z= 0.205
  Angle     :  0.656   8.384   9467  Z= 0.322
  Chirality :  0.044   0.172   1076
  Planarity :  0.004   0.054   1200
  Dihedral  :  4.604  23.313    948
  Min Nonbonded Distance : 2.593

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.71 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 18.16 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.29), residues: 850
  helix:  0.63 (0.29), residues: 349
  sheet: -0.47 (0.41), residues: 165
  loop : -1.52 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP C 647 
 HIS   0.006   0.001   HIS A 545 
 PHE   0.019   0.002   PHE C 541 
 TYR   0.031   0.002   TYR A 585 
 ARG   0.010   0.000   ARG A 238 

*********************** 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
  154 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 128
  time to evaluate  : 0.747 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  263 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7781 (tpp80)
REVERT: A  299 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8152 (mm)
REVERT: A  404 ARG cc_start: 0.6719 (mmp-170) cc_final: 0.6442 (mmp-170)
REVERT: A  559 SER cc_start: 0.9065 (p) cc_final: 0.8786 (p)
REVERT: A  619 TRP cc_start: 0.6905 (OUTLIER) cc_final: 0.6530 (t60)
REVERT: C   40 TYR cc_start: 0.8404 (t80) cc_final: 0.7989 (t80)
REVERT: C   47 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6437 (tt)
REVERT: C  253 ASP cc_start: 0.7915 (m-30) cc_final: 0.7345 (m-30)
REVERT: C  349 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6856 (mm-30)
  outliers start: 26
  outliers final: 18
  residues processed: 140
  average time/residue: 0.1894
  time to fit residues: 35.7754
Evaluate side-chains
  142 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 121
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
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  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   47 LEU
Chi-restraints excluded: chain C residue  195 LEU
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  219 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  617 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 9 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   chunk 34 optimal weight:    3.9990
   chunk 61 optimal weight:    0.9980
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 83 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 4 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 66 optimal weight:    0.0370
   overall best weight:    0.7458

-------------------------------------------------------------------------------
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 = 0.3953 r_free = 0.3953 target = 0.152838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.136016 restraints weight = 12322.299|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3783 r_free = 0.3783 target = 0.139732 restraints weight = 6962.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3816 r_free = 0.3816 target = 0.142216 restraints weight = 4548.455|
|-----------------------------------------------------------------------------|
r_work (final): 0.3809
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7580
moved from start:          0.2989

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= 0.186
  Angle     :  0.650  10.908   9467  Z= 0.321
  Chirality :  0.044   0.185   1076
  Planarity :  0.004   0.043   1200
  Dihedral  :  4.543  23.470    948
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 12.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.82 %
    Favored  : 95.18 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 18.97 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.29), residues: 850
  helix:  0.66 (0.29), residues: 350
  sheet: -0.49 (0.41), residues: 166
  loop : -1.50 (0.34), residues: 334

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 647 
 HIS   0.007   0.001   HIS A 545 
 PHE   0.019   0.002   PHE C 541 
 TYR   0.027   0.001   TYR A 585 
 ARG   0.006   0.000   ARG A 238 

*********************** 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
  158 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 131
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: A  299 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8083 (mm)
REVERT: A  362 GLU cc_start: 0.8024 (tt0) cc_final: 0.7750 (tt0)
REVERT: A  404 ARG cc_start: 0.6642 (mmp-170) cc_final: 0.6387 (mmp-170)
REVERT: A  506 MET cc_start: 0.7062 (ttm) cc_final: 0.6807 (ttm)
REVERT: A  559 SER cc_start: 0.9047 (p) cc_final: 0.8768 (p)
REVERT: A  619 TRP cc_start: 0.6913 (OUTLIER) cc_final: 0.6538 (t60)
REVERT: C   40 TYR cc_start: 0.8355 (t80) cc_final: 0.7942 (t80)
REVERT: C   47 LEU cc_start: 0.6891 (OUTLIER) cc_final: 0.6421 (tt)
REVERT: C  253 ASP cc_start: 0.7906 (m-30) cc_final: 0.7342 (m-30)
REVERT: C  349 GLU cc_start: 0.7229 (mm-30) cc_final: 0.6857 (mm-30)
  outliers start: 27
  outliers final: 18
  residues processed: 146
  average time/residue: 0.1786
  time to fit residues: 35.3036
Evaluate side-chains
  143 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 122
  time to evaluate  : 0.810 
-------------------------------------------------------------------------------
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  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   47 LEU
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  213 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 3 optimal weight:    0.8980
   chunk 44 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 0 optimal weight:    8.9990
   chunk 72 optimal weight:    4.9990
   chunk 82 optimal weight:    0.0470
   chunk 66 optimal weight:    6.9990
   chunk 33 optimal weight:    0.8980
   chunk 78 optimal weight:    0.8980
   chunk 29 optimal weight:    0.8980
   overall best weight:    0.6878

-------------------------------------------------------------------------------
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 = 0.3958 r_free = 0.3958 target = 0.152747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.134845 restraints weight = 12428.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.138782 restraints weight = 6978.521|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.141402 restraints weight = 4564.855|
|-----------------------------------------------------------------------------|
r_work (final): 0.3815
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7578
moved from start:          0.3123

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= 0.193
  Angle     :  0.686  12.307   9467  Z= 0.335
  Chirality :  0.044   0.176   1076
  Planarity :  0.004   0.043   1200
  Dihedral  :  4.537  23.526    948
  Min Nonbonded Distance : 2.552

Molprobity Statistics.
  All-atom Clashscore : 12.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.94 %
    Favored  : 95.06 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 18.97 %
    Favored  : 76.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.29), residues: 850
  helix:  0.71 (0.29), residues: 347
  sheet: -0.41 (0.41), residues: 165
  loop : -1.49 (0.34), residues: 338

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 647 
 HIS   0.005   0.001   HIS A 545 
 PHE   0.021   0.002   PHE C 238 
 TYR   0.026   0.001   TYR A 585 
 ARG   0.007   0.000   ARG A 263 

*********************** 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
  154 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 123
  time to evaluate  : 0.776 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 LYS cc_start: 0.8759 (OUTLIER) cc_final: 0.8555 (tptt)
REVERT: A  249 MET cc_start: 0.8180 (tpp) cc_final: 0.7829 (tpp)
REVERT: A  299 LEU cc_start: 0.8720 (OUTLIER) cc_final: 0.8070 (mm)
REVERT: A  362 GLU cc_start: 0.7995 (tt0) cc_final: 0.7760 (tt0)
REVERT: A  404 ARG cc_start: 0.6613 (mmp-170) cc_final: 0.6362 (mmp-170)
REVERT: A  506 MET cc_start: 0.7110 (ttm) cc_final: 0.6796 (ttm)
REVERT: A  559 SER cc_start: 0.9031 (p) cc_final: 0.8756 (p)
REVERT: A  619 TRP cc_start: 0.6924 (OUTLIER) cc_final: 0.6531 (t60)
REVERT: C  253 ASP cc_start: 0.7886 (m-30) cc_final: 0.7325 (m-30)
  outliers start: 31
  outliers final: 22
  residues processed: 141
  average time/residue: 0.1919
  time to fit residues: 36.6539
Evaluate side-chains
  143 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 118
  time to evaluate  : 0.770 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  219 LYS
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  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 A residue  628 CYS
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue  124 VAL
Chi-restraints excluded: chain C residue  213 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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 87
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 30 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 72 optimal weight:    3.9990
   chunk 76 optimal weight:    0.8980
   chunk 14 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0970
   chunk 1 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 52 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7780

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3922 r_free = 0.3922 target = 0.151368 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.132324 restraints weight = 12231.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3731 r_free = 0.3731 target = 0.136391 restraints weight = 6971.130|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.139225 restraints weight = 4592.946|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7562
moved from start:          0.3262

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6983  Z= 0.198
  Angle     :  0.688  13.930   9467  Z= 0.336
  Chirality :  0.045   0.254   1076
  Planarity :  0.004   0.043   1200
  Dihedral  :  4.545  23.526    948
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 11.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.51 %
    Favored  : 76.56 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.57 (0.29), residues: 850
  helix:  0.73 (0.29), residues: 348
  sheet: -0.47 (0.40), residues: 166
  loop : -1.47 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 236 
 HIS   0.009   0.001   HIS A 545 
 PHE   0.018   0.002   PHE C 541 
 TYR   0.025   0.002   TYR A 585 
 ARG   0.007   0.000   ARG C 233 

*********************** 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
  150 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 121
  time to evaluate  : 0.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  219 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8620 (tptt)
REVERT: A  249 MET cc_start: 0.8197 (tpp) cc_final: 0.7826 (tpp)
REVERT: A  299 LEU cc_start: 0.8653 (OUTLIER) cc_final: 0.8032 (mm)
REVERT: A  362 GLU cc_start: 0.8066 (tt0) cc_final: 0.7778 (tt0)
REVERT: A  404 ARG cc_start: 0.6630 (mmp-170) cc_final: 0.6358 (mmp-170)
REVERT: A  506 MET cc_start: 0.7240 (ttm) cc_final: 0.6910 (ttm)
REVERT: A  559 SER cc_start: 0.9034 (p) cc_final: 0.8761 (p)
REVERT: A  619 TRP cc_start: 0.6967 (OUTLIER) cc_final: 0.6531 (t60)
REVERT: C   40 TYR cc_start: 0.8105 (t80) cc_final: 0.7783 (t80)
REVERT: C  253 ASP cc_start: 0.7908 (m-30) cc_final: 0.7302 (m-30)
  outliers start: 29
  outliers final: 24
  residues processed: 137
  average time/residue: 0.1834
  time to fit residues: 33.7948
Evaluate side-chains
  144 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 117
  time to evaluate  : 0.771 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  219 LYS
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  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  124 VAL
Chi-restraints excluded: chain C residue  213 SER
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain C residue  329 VAL
Chi-restraints excluded: chain C residue  338 ARG
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
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 5 optimal weight:    0.9980
   chunk 14 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 71 optimal weight:    2.9990
   chunk 26 optimal weight:    0.6980
   chunk 53 optimal weight:    0.2980
   chunk 64 optimal weight:    3.9990
   chunk 18 optimal weight:    1.9990
   chunk 60 optimal weight:    2.9990
   chunk 36 optimal weight:    3.9990
   chunk 20 optimal weight:    2.9990
   overall best weight:    1.3984

-------------------------------------------------------------------------------
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 = 0.3889 r_free = 0.3889 target = 0.148634 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.129418 restraints weight = 12400.491|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3695 r_free = 0.3695 target = 0.133494 restraints weight = 7002.880|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.136166 restraints weight = 4609.339|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7607
moved from start:          0.3303

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6983  Z= 0.246
  Angle     :  0.728  16.447   9467  Z= 0.355
  Chirality :  0.046   0.239   1076
  Planarity :  0.004   0.044   1200
  Dihedral  :  4.642  24.213    948
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 13.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  4.20 %
    Allowed  : 19.78 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.66 (0.29), residues: 850
  helix:  0.67 (0.29), residues: 350
  sheet: -0.52 (0.40), residues: 165
  loop : -1.53 (0.34), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP C 647 
 HIS   0.012   0.001   HIS A 545 
 PHE   0.022   0.002   PHE C 541 
 TYR   0.025   0.002   TYR A 585 
 ARG   0.008   0.000   ARG C 233 

********************** 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
  157 residues out of total 739 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.761 
Fit side-chains
   revert: symmetry clash
REVERT: A  219 LYS cc_start: 0.8850 (OUTLIER) cc_final: 0.8623 (tptt)
REVERT: A  249 MET cc_start: 0.8232 (tpp) cc_final: 0.8009 (tpp)
REVERT: A  299 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8033 (mm)
REVERT: A  404 ARG cc_start: 0.6707 (mmp-170) cc_final: 0.6407 (mmp-170)
REVERT: A  506 MET cc_start: 0.7307 (ttm) cc_final: 0.6969 (ttm)
REVERT: A  559 SER cc_start: 0.9050 (p) cc_final: 0.8798 (p)
REVERT: A  619 TRP cc_start: 0.7129 (OUTLIER) cc_final: 0.6659 (t60)
REVERT: C   40 TYR cc_start: 0.8232 (t80) cc_final: 0.7896 (t80)
REVERT: C  116 LYS cc_start: 0.8413 (ttpt) cc_final: 0.7839 (ttpt)
REVERT: C  253 ASP cc_start: 0.7969 (m-30) cc_final: 0.7360 (m-30)
  outliers start: 31
  outliers final: 23
  residues processed: 141
  average time/residue: 0.1819
  time to fit residues: 34.7924
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  : 0.732 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  209 LEU
Chi-restraints excluded: chain A residue  219 LYS
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  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  213 SER
Chi-restraints excluded: chain C residue  214 SER
Chi-restraints excluded: chain C residue  219 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
Chi-restraints excluded: chain C residue  569 SER
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 42 optimal weight:    7.9990
   chunk 55 optimal weight:    2.9990
   chunk 21 optimal weight:    0.8980
   chunk 54 optimal weight:    3.9990
   chunk 50 optimal weight:    0.9990
   chunk 69 optimal weight:    5.9990
   chunk 40 optimal weight:    0.0030
   chunk 19 optimal weight:    0.9980
   chunk 64 optimal weight:    1.9990
   chunk 70 optimal weight:    0.6980
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.7192

-------------------------------------------------------------------------------
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 = 0.3917 r_free = 0.3917 target = 0.151157 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3675 r_free = 0.3675 target = 0.132257 restraints weight = 12210.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.136359 restraints weight = 6853.555|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.139208 restraints weight = 4474.691|
|-----------------------------------------------------------------------------|
r_work (final): 0.3767
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7566
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   6983  Z= 0.197
  Angle     :  0.717  17.808   9467  Z= 0.347
  Chirality :  0.045   0.255   1076
  Planarity :  0.004   0.042   1200
  Dihedral  :  4.565  23.507    948
  Min Nonbonded Distance : 2.540

Molprobity Statistics.
  All-atom Clashscore : 12.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.06 %
    Favored  : 94.94 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 20.87 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.29), residues: 850
  helix:  0.69 (0.29), residues: 348
  sheet: -0.49 (0.40), residues: 166
  loop : -1.46 (0.34), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP C 647 
 HIS   0.012   0.001   HIS A 545 
 PHE   0.017   0.002   PHE C 541 
 TYR   0.024   0.002   TYR A 585 
 ARG   0.015   0.001   ARG A 524 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2044.02 seconds
wall clock time: 37 minutes 33.65 seconds (2253.65 seconds total)