Starting phenix.real_space_refine
on Fri Jun 13 05:08:53 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9bdq_44465/06_2025/9bdq_44465.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9bdq_44465/06_2025/9bdq_44465.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.26
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9bdq_44465/06_2025/9bdq_44465.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9bdq_44465/06_2025/9bdq_44465.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9bdq_44465/06_2025/9bdq_44465.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9bdq_44465/06_2025/9bdq_44465.cif"
  }
  resolution = 2.26
  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=   0.013
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: 5
    Type Number    sf(0)   Gaussians
     Zn      2      6.06       5
     S      96      5.16       5
     C    9304      2.51       5
     N    2491      2.21       5
     O    2774      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 14667
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 10474
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1301, 10474
          Classifications: {'peptide': 1301}
          Link IDs: {'PCIS': 1, 'PTRANS': 49, 'TRANS': 1250}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 932
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 932
          Classifications: {'peptide': 118}
          Link IDs: {'PTRANS': 6, 'TRANS': 111}
    Chain: "D"
      Number of atoms: 826
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 103, 826
          Classifications: {'peptide': 103}
          Link IDs: {'PTRANS': 4, 'TRANS': 98}
    Chain: "C"
      Number of atoms: 1597
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 200, 1597
          Classifications: {'peptide': 200}
          Link IDs: {'PTRANS': 8, 'TRANS': 191}
          Chain breaks: 2
    Chain: "E"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 836
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   8994  SG  CYS A1236      53.627  87.905  21.073  1.00 77.76           S
  ATOM   9017  SG  CYS A1239      51.028  90.349  22.532  1.00 99.78           S
  ATOM   8644  SG  CYS A1191      36.108  75.094  19.724  1.00 90.89           S
  ATOM  10201  SG  CYS A1428      39.702  77.368  18.397  1.00110.76           S
  ATOM  10207  SG  CYS A1429      37.991  75.626  20.917  1.00 91.34           S

  Time building chain proxies: 9.95, per 1000 atoms: 0.68
  Number of scatterers: 14667
  At special positions: 0
  Unit cell: (107.9, 143.59, 178.45, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Zn      2     29.99
     S      96     16.00
     O    2774      8.00
     N    2491      7.00
     C    9304      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: 3.77
  Conformation dependent library (CDL) restraints added in 2.3 seconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A2301 "
        pdb="ZN    ZN A2301 " - pdb=" NE2 HIS A1423 "
        pdb="ZN    ZN A2301 " - pdb=" ND1 HIS A1421 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A1236 "
        pdb="ZN    ZN A2301 " - pdb=" SG  CYS A1239 "
      pdb="  ZN A2302 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A1429 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A1428 "
        pdb="ZN    ZN A2302 " - pdb=" SG  CYS A1191 "
      Number of angles added : 1


  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3496

  Finding SS restraints...
    Secondary structure from input PDB file:
      89 helices and 11 sheets defined
      64.4% alpha, 5.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.60
  Creating SS restraints...
    Processing helix  chain 'A' and resid 6 through 11
    Processing helix  chain 'A' and resid 23 through 33
      removed outlier: 3.521A  pdb=" N   ALA A  33 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 56
      removed outlier: 3.907A  pdb=" N   SER A  47 " --> pdb=" O   ASP A  43 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 60 through 77
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 91 through 96
    Processing helix  chain 'A' and resid 105 through 137
      removed outlier: 3.789A  pdb=" N   ILE A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 5.010A  pdb=" N   LYS A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
      removed outlier: 5.752A  pdb=" N   LYS A 124 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 156
      removed outlier: 3.650A  pdb=" N   ASP A 156 " --> pdb=" O   ARG A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 156 through 163
    Processing helix  chain 'A' and resid 166 through 189
      removed outlier: 3.665A  pdb=" N   LYS A 189 " --> pdb=" O   LYS A 185 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 190 through 193
      removed outlier: 3.728A  pdb=" N   ARG A 193 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 190 through 193'
    Processing helix  chain 'A' and resid 231 through 255
    Processing helix  chain 'A' and resid 256 through 259
    Processing helix  chain 'A' and resid 260 through 273
      removed outlier: 3.962A  pdb=" N   ARG A 264 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      removed outlier: 3.911A  pdb=" N   ASN A 266 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 282 through 289
      removed outlier: 4.024A  pdb=" N   ILE A 286 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
    Processing helix  chain 'A' and resid 304 through 308
    Processing helix  chain 'A' and resid 309 through 326
      removed outlier: 3.822A  pdb=" N   HIS A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 346
    Processing helix  chain 'A' and resid 349 through 355
    Processing helix  chain 'A' and resid 356 through 359
    Processing helix  chain 'A' and resid 369 through 382
      removed outlier: 3.516A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
      removed outlier: 3.958A  pdb=" N   HIS A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 409
    Processing helix  chain 'A' and resid 425 through 435
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 447 through 451
    Processing helix  chain 'A' and resid 482 through 486
      removed outlier: 4.207A  pdb=" N   VAL A 486 " --> pdb=" O   TRP A 483 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
    Processing helix  chain 'A' and resid 504 through 512
    Processing helix  chain 'A' and resid 516 through 526
      removed outlier: 3.704A  pdb=" N   VAL A 524 " --> pdb=" O   MET A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 527 through 532
      removed outlier: 3.693A  pdb=" N   GLU A 531 " --> pdb=" O   GLY A 527 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 573
    Processing helix  chain 'A' and resid 574 through 580
    Processing helix  chain 'A' and resid 588 through 601
      removed outlier: 3.516A  pdb=" N   PHE A 596 " --> pdb=" O   LEU A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 725 through 730
    Processing helix  chain 'A' and resid 731 through 747
      removed outlier: 4.673A  pdb=" N   ILE A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 5.560A  pdb=" N   PHE A 738 " --> pdb=" O   SER A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 754 through 760
    Processing helix  chain 'A' and resid 780 through 784
      removed outlier: 3.632A  pdb=" N   THR A 784 " --> pdb=" O   LEU A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 822
      Proline residue:  A 812  - end of helix
    Processing helix  chain 'A' and resid 847 through 873
    Processing helix  chain 'A' and resid 904 through 910
      removed outlier: 3.918A  pdb=" N   SER A 908 " --> pdb=" O   GLN A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 940
    Processing helix  chain 'A' and resid 943 through 964
    Processing helix  chain 'A' and resid 972 through 982
      Proline residue:  A 978  - end of helix
      removed outlier: 3.534A  pdb=" N   ASN A 982 " --> pdb=" O   PRO A 978 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 982 through 992
    Processing helix  chain 'A' and resid 993 through 997
    Processing helix  chain 'A' and resid 1003 through 1009
      removed outlier: 3.651A  pdb=" N   ILE A1007 " --> pdb=" O   ASN A1003 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   PHE A1008 " --> pdb=" O   LEU A1004 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1014 through 1029
    Processing helix  chain 'A' and resid 1033 through 1042
      removed outlier: 4.121A  pdb=" N   LEU A1037 " --> pdb=" O   THR A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1056
    Processing helix  chain 'A' and resid 1067 through 1083
    Processing helix  chain 'A' and resid 1096 through 1110
    Processing helix  chain 'A' and resid 1115 through 1124
    Processing helix  chain 'A' and resid 1126 through 1137
    Processing helix  chain 'A' and resid 1141 through 1147
    Processing helix  chain 'A' and resid 1155 through 1179
      removed outlier: 5.171A  pdb=" N   ASP A1166 " --> pdb=" O   LEU A1162 " (cutoff:3.500A)
      removed outlier: 5.524A  pdb=" N   TYR A1167 " --> pdb=" O   SER A1163 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1191 through 1204
    Processing helix  chain 'A' and resid 1204 through 1209
    Processing helix  chain 'A' and resid 1220 through 1224
    Processing helix  chain 'A' and resid 1236 through 1241
    Processing helix  chain 'A' and resid 1291 through 1308
    Processing helix  chain 'A' and resid 1311 through 1323
    Processing helix  chain 'A' and resid 1329 through 1337
    Processing helix  chain 'A' and resid 1374 through 1378
      removed outlier: 3.982A  pdb=" N   ASP A1378 " --> pdb=" O   ASP A1375 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1391 through 1407
    Processing helix  chain 'B' and resid 480 through 484
      removed outlier: 4.196A  pdb=" N   PHE B 484 " --> pdb=" O   PRO B 480 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 480 through 484'
    Processing helix  chain 'B' and resid 489 through 502
    Processing helix  chain 'B' and resid 507 through 533
      removed outlier: 3.565A  pdb=" N   LEU B 511 " --> pdb=" O   ASP B 507 " (cutoff:3.500A)
      removed outlier: 4.082A  pdb=" N   CYS B 512 " --> pdb=" O   LEU B 508 " (cutoff:3.500A)
      removed outlier: 5.202A  pdb=" N   GLU B 513 " --> pdb=" O   GLU B 509 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 533 through 543
      removed outlier: 3.555A  pdb=" N   VAL B 540 " --> pdb=" O   ILE B 536 " (cutoff:3.500A)
      removed outlier: 4.284A  pdb=" N   LYS B 541 " --> pdb=" O   GLU B 537 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   GLU B 542 " --> pdb=" O   GLU B 538 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 544 through 578
      removed outlier: 4.425A  pdb=" N   ASN B 548 " --> pdb=" O   PRO B 544 " (cutoff:3.500A)
      removed outlier: 3.593A  pdb=" N   LYS B 549 " --> pdb=" O   LYS B 545 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 480 through 485
      removed outlier: 4.024A  pdb=" N   PHE D 484 " --> pdb=" O   PRO D 480 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 486 through 488
      No H-bonds generated for 'chain 'D' and resid 486 through 488'
    Processing helix  chain 'D' and resid 489 through 502
    Processing helix  chain 'D' and resid 511 through 539
      removed outlier: 3.963A  pdb=" N   GLN D 539 " --> pdb=" O   HIS D 535 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 542 through 574
      removed outlier: 3.531A  pdb=" N   MET D 574 " --> pdb=" O   HIS D 570 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 489 through 501
      removed outlier: 3.743A  pdb=" N   ASP C 501 " --> pdb=" O   ASN C 497 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 543
    Processing helix  chain 'C' and resid 545 through 574
    Processing helix  chain 'C' and resid 604 through 609
    Processing helix  chain 'C' and resid 634 through 638
    Processing helix  chain 'C' and resid 657 through 672
      removed outlier: 3.511A  pdb=" N   HIS C 671 " --> pdb=" O   LEU C 667 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 674 through 688
    Processing helix  chain 'C' and resid 690 through 707
      removed outlier: 3.853A  pdb=" N   ILE C 694 " --> pdb=" O   ASN C 690 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 480 through 485
      removed outlier: 4.454A  pdb=" N   PHE E 484 " --> pdb=" O   PRO E 480 " (cutoff:3.500A)
      removed outlier: 4.126A  pdb=" N   SER E 485 " --> pdb=" O   SER E 481 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 480 through 485'
    Processing helix  chain 'E' and resid 489 through 497
      removed outlier: 4.206A  pdb=" N   THR E 493 " --> pdb=" O   PHE E 489 " (cutoff:3.500A)
      removed outlier: 4.731A  pdb=" N   ARG E 495 " --> pdb=" O   HIS E 491 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 498 through 501
      removed outlier: 3.850A  pdb=" N   ASP E 501 " --> pdb=" O   TYR E 498 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 498 through 501'
    Processing helix  chain 'E' and resid 510 through 541
      removed outlier: 3.639A  pdb=" N   GLU E 514 " --> pdb=" O   THR E 510 " (cutoff:3.500A)
      removed outlier: 3.838A  pdb=" N   GLN E 539 " --> pdb=" O   HIS E 535 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   LYS E 541 " --> pdb=" O   GLU E 537 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 542 through 573
      removed outlier: 3.506A  pdb=" N   SER E 573 " --> pdb=" O   GLY E 569 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22
      removed outlier: 6.713A  pdb=" N   ILE A  21 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388
      removed outlier: 8.487A  pdb=" N   MET E 575 " --> pdb=" O   LEU C 594 " (cutoff:3.500A)
      removed outlier: 7.205A  pdb=" N   MET E 577 " --> pdb=" O   PRO C 596 " (cutoff:3.500A)
      removed outlier: 6.509A  pdb=" N   ILE C 598 " --> pdb=" O   MET E 577 " (cutoff:3.500A)
      removed outlier: 3.956A  pdb=" N   GLU C 593 " --> pdb=" O   ILE C 578 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 419
    Processing sheet with id=AA5, first strand: chain 'A' and resid 554 through 556
      removed outlier: 5.283A  pdb=" N   VAL A 537 " --> pdb=" O   VAL A 763 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   TYR A 765 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 713 through 716
    Processing sheet with id=AA7, first strand: chain 'A' and resid 827 through 828
      removed outlier: 3.601A  pdb=" N   SER A 835 " --> pdb=" O   ILE A 828 " (cutoff:3.500A)
      removed outlier: 4.350A  pdb=" N   GLU A 834 " --> pdb=" O   THR A 721 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 890 through 891
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1113 through 1114
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1225 through 1231
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1379 through 1381
      removed outlier: 4.423A  pdb=" N   PHE A1379 " --> pdb=" O   VAL A1386 " (cutoff:3.500A)

    846 hydrogen bonds defined for protein.
    2424 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: 5.90

  Time building geometry restraints manager: 4.50 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 2491
        1.31 -     1.44: 3738
        1.44 -     1.56: 8552
        1.56 -     1.69: 2
        1.69 -     1.81: 160
  Bond restraints: 14943
  Sorted by residual:
  bond pdb=" N   PRO C 544 "
       pdb=" CD  PRO C 544 "
    ideal  model  delta    sigma   weight residual
    1.473  1.655 -0.182 1.40e-02 5.10e+03 1.69e+02
  bond pdb=" N   PRO A  89 "
       pdb=" CD  PRO A  89 "
    ideal  model  delta    sigma   weight residual
    1.474  1.339  0.135 1.40e-02 5.10e+03 9.32e+01
  bond pdb=" N   PRO A 417 "
       pdb=" CD  PRO A 417 "
    ideal  model  delta    sigma   weight residual
    1.473  1.605 -0.132 1.40e-02 5.10e+03 8.93e+01
  bond pdb=" C   LYS B 541 "
       pdb=" O   LYS B 541 "
    ideal  model  delta    sigma   weight residual
    1.236  1.316 -0.079 1.22e-02 6.72e+03 4.25e+01
  bond pdb=" C   SER A 599 "
       pdb=" N   ILE A 600 "
    ideal  model  delta    sigma   weight residual
    1.335  1.264  0.071 1.20e-02 6.94e+03 3.51e+01
  ... (remaining 14938 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.52: 19718
        2.52 -     5.03: 416
        5.03 -     7.55: 46
        7.55 -    10.07: 12
       10.07 -    12.59: 4
  Bond angle restraints: 20196
  Sorted by residual:
  angle pdb=" N   GLU B 542 "
        pdb=" CA  GLU B 542 "
        pdb=" C   GLU B 542 "
      ideal   model   delta    sigma   weight residual
     111.71  102.44    9.27 1.15e+00 7.56e-01 6.50e+01
  angle pdb=" CA  PRO A  89 "
        pdb=" N   PRO A  89 "
        pdb=" CD  PRO A  89 "
      ideal   model   delta    sigma   weight residual
     111.50  121.01   -9.51 1.40e+00 5.10e-01 4.61e+01
  angle pdb=" C   LYS B 545 "
        pdb=" N   ILE B 546 "
        pdb=" CA  ILE B 546 "
      ideal   model   delta    sigma   weight residual
     120.55  130.78  -10.23 1.60e+00 3.91e-01 4.09e+01
  angle pdb=" C   MET A 469 "
        pdb=" N   TYR A 470 "
        pdb=" CA  TYR A 470 "
      ideal   model   delta    sigma   weight residual
     122.31  110.76   11.55 1.81e+00 3.05e-01 4.07e+01
  angle pdb=" N   VAL D 540 "
        pdb=" CA  VAL D 540 "
        pdb=" C   VAL D 540 "
      ideal   model   delta    sigma   weight residual
     113.71  108.35    5.36 9.50e-01 1.11e+00 3.19e+01
  ... (remaining 20191 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.11: 7832
       18.11 -    36.23: 978
       36.23 -    54.34: 269
       54.34 -    72.45: 57
       72.45 -    90.56: 13
  Dihedral angle restraints: 9149
    sinusoidal: 3775
      harmonic: 5374
  Sorted by residual:
  dihedral pdb=" CA  ILE C 543 "
           pdb=" C   ILE C 543 "
           pdb=" N   PRO C 544 "
           pdb=" CA  PRO C 544 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.11  -28.89     0      5.00e+00 4.00e-02 3.34e+01
  dihedral pdb=" CA  MET B 479 "
           pdb=" C   MET B 479 "
           pdb=" N   PRO B 480 "
           pdb=" CA  PRO B 480 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -151.25  -28.75     0      5.00e+00 4.00e-02 3.31e+01
  dihedral pdb=" C   PRO D 480 "
           pdb=" N   PRO D 480 "
           pdb=" CA  PRO D 480 "
           pdb=" CB  PRO D 480 "
      ideal   model   delta  harmonic     sigma   weight residual
    -120.70 -109.24  -11.46     0      2.50e+00 1.60e-01 2.10e+01
  ... (remaining 9146 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 1566
       0.041 -    0.083: 507
       0.083 -    0.124: 164
       0.124 -    0.165: 41
       0.165 -    0.206: 17
  Chirality restraints: 2295
  Sorted by residual:
  chirality pdb=" CA  HIS E 491 "
            pdb=" N   HIS E 491 "
            pdb=" C   HIS E 491 "
            pdb=" CB  HIS E 491 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.72   -0.21 2.00e-01 2.50e+01 1.06e+00
  chirality pdb=" CA  ILE A1154 "
            pdb=" N   ILE A1154 "
            pdb=" C   ILE A1154 "
            pdb=" CB  ILE A1154 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  LEU A1092 "
            pdb=" N   LEU A1092 "
            pdb=" C   LEU A1092 "
            pdb=" CB  LEU A1092 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.20 2.00e-01 2.50e+01 1.01e+00
  ... (remaining 2292 not shown)

  Planarity restraints: 2585
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR C 487 "    0.019 2.00e-02 2.50e+03   3.75e-02 1.40e+01
        pdb=" C   THR C 487 "   -0.065 2.00e-02 2.50e+03
        pdb=" O   THR C 487 "    0.024 2.00e-02 2.50e+03
        pdb=" N   PHE C 488 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR A 470 "    0.016 2.00e-02 2.50e+03   3.33e-02 1.11e+01
        pdb=" C   TYR A 470 "   -0.058 2.00e-02 2.50e+03
        pdb=" O   TYR A 470 "    0.021 2.00e-02 2.50e+03
        pdb=" N   MET A 471 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 465 "   -0.015 2.00e-02 2.50e+03   3.01e-02 9.05e+00
        pdb=" C   SER A 465 "    0.052 2.00e-02 2.50e+03
        pdb=" O   SER A 465 "   -0.019 2.00e-02 2.50e+03
        pdb=" N   ASP A 466 "   -0.018 2.00e-02 2.50e+03
  ... (remaining 2582 not shown)

  Histogram of nonbonded interaction distances:
        2.16 -     2.71: 542
        2.71 -     3.26: 15309
        3.26 -     3.80: 25180
        3.80 -     4.35: 31808
        4.35 -     4.90: 51988
  Nonbonded interactions: 124827
  Sorted by model distance:
  nonbonded pdb=" OD1 ASP A 203 "
            pdb=" N   LYS A 204 "
     model   vdw
     2.162 3.120
  nonbonded pdb=" OD1 ASN A1364 "
            pdb=" OG  SER A1367 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O   HIS B 502 "
            pdb=" ND1 HIS B 502 "
     model   vdw
     2.230 3.120
  nonbonded pdb=" OG1 THR A 721 "
            pdb=" OE1 GLU A 834 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" OG1 THR A 972 "
            pdb=" OD1 ASP A 974 "
     model   vdw
     2.232 3.040
  ... (remaining 124822 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
Found NCS groups:
ncs_group {
  reference = (chain 'B' and resid 479 through 579)
  selection = (chain 'D' and resid 479 through 579)
  selection = (chain 'E' and resid 479 through 579)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             12.560
  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:          0.690
  Check model and map are aligned:         0.090
  Set scattering table:                    0.130
  Process input model:                     40.060
  Find NCS groups from input model:        0.280
  Set up NCS constraints:                  0.060
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:13.470
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   67.360
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
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      :  0.006   0.182  14950  Z= 0.356
  Angle     :  0.814  12.587  20197  Z= 0.511
  Chirality :  0.049   0.206   2295
  Planarity :  0.005   0.072   2585
  Dihedral  : 17.378  90.563   5653
  Min Nonbonded Distance : 2.162

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.60 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 25.63 %
    Favored  : 70.69 %
  Cbeta Deviations :  0.06 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.12 (0.20), residues: 1806
  helix:  1.59 (0.16), residues: 1038
  sheet: -0.19 (0.50), residues: 101
  loop : -0.40 (0.25), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 173 
 HIS   0.008   0.001   HIS B 502 
 PHE   0.022   0.002   PHE A 399 
 TYR   0.038   0.001   TYR B 498 
 ARG   0.010   0.000   ARG A1295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14413 (  846)
  hydrogen bonds       : angle       5.32582 ( 2424)
  metal coordination   : bond        0.04001 (    7)
  metal coordination   : angle       2.21930 (    1)
  covalent geometry    : bond        0.00563 (14943)
  covalent geometry    : angle       0.81427 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  460 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 61
    poor density    : 399
  time to evaluate  : 1.783 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   19 SER cc_start: 0.8502 (m) cc_final: 0.8202 (p)
REVERT: A   44 LYS cc_start: 0.8233 (mmtt) cc_final: 0.7854 (mmpt)
REVERT: A  109 ASN cc_start: 0.8285 (m-40) cc_final: 0.7988 (m-40)
REVERT: A  112 ARG cc_start: 0.7721 (mtm110) cc_final: 0.7170 (mtt90)
REVERT: A  141 ARG cc_start: 0.7171 (ttt-90) cc_final: 0.6838 (ttp-110)
REVERT: A  150 GLU cc_start: 0.7667 (tt0) cc_final: 0.7422 (tt0)
REVERT: A  159 LYS cc_start: 0.8293 (ttpt) cc_final: 0.7954 (ttpp)
REVERT: A  179 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7991 (mp0)
REVERT: A  191 LYS cc_start: 0.7632 (ptpp) cc_final: 0.7284 (ptmm)
REVERT: A  204 LYS cc_start: 0.7965 (mttt) cc_final: 0.7633 (mttt)
REVERT: A  328 PHE cc_start: 0.8075 (m-80) cc_final: 0.7821 (m-80)
REVERT: A  332 LYS cc_start: 0.7695 (mttt) cc_final: 0.7409 (mmmm)
REVERT: A  388 GLU cc_start: 0.7695 (tt0) cc_final: 0.7453 (tm-30)
REVERT: A  419 TYR cc_start: 0.8318 (m-80) cc_final: 0.7862 (m-80)
REVERT: A  436 GLU cc_start: 0.7608 (mt-10) cc_final: 0.7183 (mt-10)
REVERT: A  481 ASP cc_start: 0.7837 (m-30) cc_final: 0.7497 (m-30)
REVERT: A  504 ARG cc_start: 0.7568 (mtp85) cc_final: 0.7219 (mtp85)
REVERT: A  511 ASN cc_start: 0.8085 (m-40) cc_final: 0.7880 (m-40)
REVERT: A  533 ASP cc_start: 0.7970 (p0) cc_final: 0.7496 (t0)
REVERT: A  534 GLN cc_start: 0.8094 (mm-40) cc_final: 0.7618 (mm110)
REVERT: A  542 LYS cc_start: 0.7690 (tttt) cc_final: 0.7479 (tttt)
REVERT: A  559 LYS cc_start: 0.8412 (mttp) cc_final: 0.8147 (mttt)
REVERT: A  568 GLU cc_start: 0.7351 (mm-30) cc_final: 0.7133 (mm-30)
REVERT: A  714 THR cc_start: 0.8330 (OUTLIER) cc_final: 0.7821 (m)
REVERT: A  725 LYS cc_start: 0.8511 (mmtp) cc_final: 0.8246 (mmtp)
REVERT: A  735 MET cc_start: 0.8543 (tpt) cc_final: 0.8340 (tpp)
REVERT: A  743 ASP cc_start: 0.7870 (m-30) cc_final: 0.7546 (m-30)
REVERT: A  782 GLU cc_start: 0.7538 (mp0) cc_final: 0.7012 (mp0)
REVERT: A  841 LYS cc_start: 0.8128 (mmtm) cc_final: 0.7614 (mmtm)
REVERT: A  853 GLU cc_start: 0.7430 (tp30) cc_final: 0.7168 (tp30)
REVERT: A  907 LYS cc_start: 0.8646 (tttt) cc_final: 0.8367 (tttp)
REVERT: A 1070 LYS cc_start: 0.7303 (ttpt) cc_final: 0.7083 (ttmm)
REVERT: A 1073 LYS cc_start: 0.7641 (mmtp) cc_final: 0.7411 (mmtp)
REVERT: A 1096 LYS cc_start: 0.7645 (mtmt) cc_final: 0.7375 (ptpp)
REVERT: A 1132 GLU cc_start: 0.7028 (tp30) cc_final: 0.6747 (tp30)
REVERT: A 1217 GLU cc_start: 0.7940 (mp0) cc_final: 0.7657 (mm-30)
REVERT: A 1220 ASP cc_start: 0.7934 (t70) cc_final: 0.7718 (t0)
REVERT: A 1259 GLN cc_start: 0.7666 (mm-40) cc_final: 0.7343 (tp40)
REVERT: A 1313 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6306 (tp30)
REVERT: A 1374 ASN cc_start: 0.7093 (m-40) cc_final: 0.6884 (m-40)
REVERT: B  491 HIS cc_start: 0.6784 (OUTLIER) cc_final: 0.6491 (p-80)
REVERT: B  494 ASP cc_start: 0.7228 (OUTLIER) cc_final: 0.7014 (t70)
REVERT: D  575 MET cc_start: 0.7446 (mmm) cc_final: 0.7226 (mmm)
REVERT: C  594 LEU cc_start: 0.7687 (mt) cc_final: 0.7179 (mt)
REVERT: E  479 MET cc_start: 0.4319 (ptt) cc_final: 0.4093 (ptt)
  outliers start: 61
  outliers final: 25
  residues processed: 447
  average time/residue: 1.3277
  time to fit residues: 649.2037
Evaluate side-chains
  393 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 365
  time to evaluate  : 1.646 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  712 PHE
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  802 SER
Chi-restraints excluded: chain A residue  975 VAL
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1040 VAL
Chi-restraints excluded: chain A residue 1079 THR
Chi-restraints excluded: chain A residue 1180 ARG
Chi-restraints excluded: chain A residue 1294 LEU
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain B residue  491 HIS
Chi-restraints excluded: chain B residue  494 ASP
Chi-restraints excluded: chain B residue  512 CYS
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  545 LYS
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain B residue  572 VAL
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  547 ILE
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  545 LYS
Chi-restraints excluded: chain C residue  573 SER
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  552 SER
Chi-restraints excluded: chain E residue  560 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 152 optimal weight:    0.9990
   chunk 137 optimal weight:    0.9980
   chunk 76 optimal weight:    0.9980
   chunk 46 optimal weight:    1.9990
   chunk 92 optimal weight:    0.1980
   chunk 73 optimal weight:    0.9980
   chunk 141 optimal weight:    0.7980
   chunk 54 optimal weight:    2.9990
   chunk 86 optimal weight:    0.8980
   chunk 105 optimal weight:    0.6980
   chunk 164 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A1169 GLN
A1179 ASN
A1183 ASN
A1324 GLN
E 499 HIS

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.158780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3869 r_free = 0.3869 target = 0.133541 restraints weight = 19787.813|
|-----------------------------------------------------------------------------|
r_work (start): 0.3865 rms_B_bonded: 1.59
r_work: 0.3757 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3610 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3610
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7843
moved from start:          0.1630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069  14950  Z= 0.232
  Angle     :  0.657  11.834  20197  Z= 0.338
  Chirality :  0.046   0.180   2295
  Planarity :  0.005   0.098   2585
  Dihedral  :  6.500  64.537   2023
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.86
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.21 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 25.69 %
    Favored  : 69.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.24 (0.20), residues: 1806
  helix:  1.71 (0.16), residues: 1043
  sheet: -0.29 (0.54), residues: 99
  loop : -0.38 (0.25), residues: 664

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.002   TRP A 447 
 HIS   0.007   0.001   HIS A 149 
 PHE   0.024   0.002   PHE A 399 
 TYR   0.026   0.002   TYR B 498 
 ARG   0.004   0.001   ARG A1295 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04841 (  846)
  hydrogen bonds       : angle       4.33945 ( 2424)
  metal coordination   : bond        0.01358 (    7)
  metal coordination   : angle       6.35745 (    1)
  covalent geometry    : bond        0.00563 (14943)
  covalent geometry    : angle       0.65593 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  462 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 83
    poor density    : 379
  time to evaluate  : 1.862 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 LYS cc_start: 0.8398 (mmtt) cc_final: 0.8163 (mmpt)
REVERT: A  109 ASN cc_start: 0.8264 (m-40) cc_final: 0.8044 (m-40)
REVERT: A  112 ARG cc_start: 0.7782 (mtm110) cc_final: 0.7519 (mtt90)
REVERT: A  210 LEU cc_start: 0.8651 (pp) cc_final: 0.8447 (pp)
REVERT: A  441 ASP cc_start: 0.7843 (t0) cc_final: 0.7618 (t0)
REVERT: A  714 THR cc_start: 0.8570 (OUTLIER) cc_final: 0.8258 (m)
REVERT: A  782 GLU cc_start: 0.7537 (mp0) cc_final: 0.7304 (mp0)
REVERT: A  841 LYS cc_start: 0.8561 (mmtm) cc_final: 0.8322 (mmtm)
REVERT: A  907 LYS cc_start: 0.8683 (tttt) cc_final: 0.8148 (ttpp)
REVERT: A 1073 LYS cc_start: 0.8168 (mmtp) cc_final: 0.7936 (mmtp)
REVERT: A 1078 ARG cc_start: 0.8110 (mtt180) cc_final: 0.7880 (mtt-85)
REVERT: A 1132 GLU cc_start: 0.7793 (tp30) cc_final: 0.7559 (tp30)
REVERT: A 1166 ASP cc_start: 0.7790 (OUTLIER) cc_final: 0.7574 (t70)
REVERT: A 1205 ARG cc_start: 0.7836 (OUTLIER) cc_final: 0.7581 (ttp-170)
REVERT: A 1235 GLU cc_start: 0.6824 (mp0) cc_final: 0.6615 (mp0)
REVERT: A 1259 GLN cc_start: 0.7631 (OUTLIER) cc_final: 0.7395 (tp40)
REVERT: A 1374 ASN cc_start: 0.8313 (m-40) cc_final: 0.7998 (m-40)
REVERT: B  491 HIS cc_start: 0.7026 (OUTLIER) cc_final: 0.6618 (p-80)
REVERT: D  531 MET cc_start: 0.7504 (tmm) cc_final: 0.7290 (tpt)
REVERT: D  577 MET cc_start: 0.6738 (tmt) cc_final: 0.6440 (tmt)
REVERT: C  545 LYS cc_start: 0.6998 (OUTLIER) cc_final: 0.6617 (ptmt)
REVERT: C  546 ILE cc_start: 0.7159 (mp) cc_final: 0.6880 (mt)
REVERT: C  694 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7683 (mt)
REVERT: C  695 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7310 (mm-40)
REVERT: E  479 MET cc_start: 0.4329 (ptt) cc_final: 0.4099 (ptt)
REVERT: E  518 MET cc_start: 0.4188 (OUTLIER) cc_final: 0.3690 (ppp)
  outliers start: 83
  outliers final: 25
  residues processed: 437
  average time/residue: 1.3790
  time to fit residues: 659.6070
Evaluate side-chains
  396 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 362
  time to evaluate  : 2.559 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   94 THR
Chi-restraints excluded: chain A residue  499 SER
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1084 SER
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1166 ASP
Chi-restraints excluded: chain A residue 1190 THR
Chi-restraints excluded: chain A residue 1205 ARG
Chi-restraints excluded: chain A residue 1259 GLN
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain B residue  491 HIS
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  512 CYS
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  545 LYS
Chi-restraints excluded: chain B residue  547 ILE
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  523 SER
Chi-restraints excluded: chain C residue  545 LYS
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain C residue  694 ILE
Chi-restraints excluded: chain C residue  695 GLN
Chi-restraints excluded: chain E residue  491 HIS
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Chi-restraints excluded: chain E residue  531 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 29 optimal weight:    0.9990
   chunk 75 optimal weight:    0.7980
   chunk 57 optimal weight:    0.3980
   chunk 131 optimal weight:    1.9990
   chunk 139 optimal weight:    0.7980
   chunk 87 optimal weight:    0.7980
   chunk 40 optimal weight:    0.1980
   chunk 58 optimal weight:    0.9980
   chunk 69 optimal weight:    0.8980
   chunk 148 optimal weight:    0.6980
   chunk 59 optimal weight:    6.9990
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 534 GLN
A 951 ASN
A1011 ASN
A1183 ASN
** A1256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1324 GLN
C 651 GLN
E 539 GLN
E 548 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.158950 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.133742 restraints weight = 19844.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3866 rms_B_bonded: 1.60
r_work: 0.3758 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3609 rms_B_bonded: 3.68 restraints_weight: 0.2500
r_work (final): 0.3609
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7844
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067  14950  Z= 0.201
  Angle     :  0.614  10.767  20197  Z= 0.315
  Chirality :  0.045   0.179   2295
  Planarity :  0.005   0.097   2585
  Dihedral  :  5.844  59.776   1998
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.99 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 26.06 %
    Favored  : 69.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.28 (0.20), residues: 1806
  helix:  1.81 (0.16), residues: 1043
  sheet: -0.23 (0.53), residues: 96
  loop : -0.48 (0.25), residues: 667

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 806 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.024   0.002   PHE A 399 
 TYR   0.023   0.002   TYR B 498 
 ARG   0.004   0.000   ARG C 532 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04575 (  846)
  hydrogen bonds       : angle       4.23195 ( 2424)
  metal coordination   : bond        0.00865 (    7)
  metal coordination   : angle       5.52515 (    1)
  covalent geometry    : bond        0.00488 (14943)
  covalent geometry    : angle       0.61243 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 370
  time to evaluate  : 1.630 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.7892 (pt0) cc_final: 0.7647 (pt0)
REVERT: A   84 MET cc_start: 0.8244 (tpp) cc_final: 0.7752 (tpp)
REVERT: A  112 ARG cc_start: 0.7824 (mtm110) cc_final: 0.7550 (mtt90)
REVERT: A  210 LEU cc_start: 0.8660 (pp) cc_final: 0.8455 (pp)
REVERT: A  286 ILE cc_start: 0.8394 (OUTLIER) cc_final: 0.8130 (mt)
REVERT: A  385 LYS cc_start: 0.8860 (OUTLIER) cc_final: 0.8607 (mttt)
REVERT: A  460 GLU cc_start: 0.7750 (pm20) cc_final: 0.7449 (pm20)
REVERT: A  568 GLU cc_start: 0.7225 (mm-30) cc_final: 0.6992 (tp30)
REVERT: A  714 THR cc_start: 0.8583 (OUTLIER) cc_final: 0.8279 (m)
REVERT: A  782 GLU cc_start: 0.7579 (mp0) cc_final: 0.7371 (mp0)
REVERT: A  841 LYS cc_start: 0.8578 (mmtm) cc_final: 0.8335 (mmtm)
REVERT: A  878 LYS cc_start: 0.8135 (mtpp) cc_final: 0.7696 (mtpp)
REVERT: A 1078 ARG cc_start: 0.8127 (mtt180) cc_final: 0.7875 (mtt-85)
REVERT: A 1132 GLU cc_start: 0.7786 (tp30) cc_final: 0.7520 (tp30)
REVERT: A 1166 ASP cc_start: 0.7795 (OUTLIER) cc_final: 0.7593 (t0)
REVERT: A 1205 ARG cc_start: 0.7808 (OUTLIER) cc_final: 0.7552 (ttp-170)
REVERT: A 1234 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7813 (pp)
REVERT: A 1235 GLU cc_start: 0.6854 (mp0) cc_final: 0.6624 (mp0)
REVERT: C  545 LYS cc_start: 0.7274 (OUTLIER) cc_final: 0.7050 (pmmt)
REVERT: C  546 ILE cc_start: 0.7240 (mp) cc_final: 0.7039 (mt)
REVERT: E  479 MET cc_start: 0.3908 (ptt) cc_final: 0.3686 (ptt)
REVERT: E  536 ILE cc_start: 0.6776 (OUTLIER) cc_final: 0.6565 (tt)
  outliers start: 75
  outliers final: 38
  residues processed: 418
  average time/residue: 1.4122
  time to fit residues: 646.0211
Evaluate side-chains
  407 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 361
  time to evaluate  : 1.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  385 LYS
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  822 ASN
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  883 ILE
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1084 SER
Chi-restraints excluded: chain A residue 1137 LEU
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1166 ASP
Chi-restraints excluded: chain A residue 1205 ARG
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain B residue  545 LYS
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain B residue  572 VAL
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  522 ASN
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain D residue  536 ILE
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  523 SER
Chi-restraints excluded: chain C residue  540 VAL
Chi-restraints excluded: chain C residue  545 LYS
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain C residue  607 SER
Chi-restraints excluded: chain C residue  685 LEU
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain E residue  491 HIS
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Chi-restraints excluded: chain E residue  531 MET
Chi-restraints excluded: chain E residue  536 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 105 optimal weight:    0.5980
   chunk 17 optimal weight:    0.6980
   chunk 72 optimal weight:    0.9980
   chunk 21 optimal weight:    0.6980
   chunk 146 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 44 optimal weight:    0.9990
   chunk 98 optimal weight:    1.9990
   chunk 110 optimal weight:    0.9980
   chunk 131 optimal weight:    0.1980
   chunk 115 optimal weight:    1.9990
   overall best weight:    0.6380

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 534 GLN
A1011 ASN
A1182 GLN
A1183 ASN
A1241 GLN
A1256 GLN
A1324 GLN
C 648 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.158970 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3864 r_free = 0.3864 target = 0.133658 restraints weight = 19645.845|
|-----------------------------------------------------------------------------|
r_work (start): 0.3864 rms_B_bonded: 1.60
r_work: 0.3757 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3607 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3607
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7851
moved from start:          0.2294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.063  14950  Z= 0.216
  Angle     :  0.627  10.868  20197  Z= 0.319
  Chirality :  0.045   0.182   2295
  Planarity :  0.005   0.095   2585
  Dihedral  :  5.611  54.383   1993
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 8.96
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.93 %
    Favored  : 97.01 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 25.69 %
    Favored  : 69.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.25 (0.20), residues: 1806
  helix:  1.78 (0.16), residues: 1044
  sheet: -0.51 (0.54), residues: 90
  loop : -0.46 (0.25), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP A 806 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.027   0.002   PHE B 488 
 TYR   0.022   0.002   TYR B 498 
 ARG   0.004   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04573 (  846)
  hydrogen bonds       : angle       4.24330 ( 2424)
  metal coordination   : bond        0.02087 (    7)
  metal coordination   : angle      10.86823 (    1)
  covalent geometry    : bond        0.00527 (14943)
  covalent geometry    : angle       0.62272 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  445 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 75
    poor density    : 370
  time to evaluate  : 1.920 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   82 GLU cc_start: 0.7885 (pt0) cc_final: 0.7625 (pt0)
REVERT: A   84 MET cc_start: 0.8253 (tpp) cc_final: 0.7766 (tpp)
REVERT: A  385 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8620 (mttt)
REVERT: A  441 ASP cc_start: 0.7812 (t0) cc_final: 0.7313 (t0)
REVERT: A  460 GLU cc_start: 0.7788 (pm20) cc_final: 0.7489 (pm20)
REVERT: A  714 THR cc_start: 0.8588 (OUTLIER) cc_final: 0.8266 (m)
REVERT: A  782 GLU cc_start: 0.7590 (mp0) cc_final: 0.7358 (mp0)
REVERT: A  841 LYS cc_start: 0.8567 (mmtm) cc_final: 0.8317 (mmtm)
REVERT: A 1078 ARG cc_start: 0.8108 (mtt180) cc_final: 0.7829 (mtt-85)
REVERT: A 1132 GLU cc_start: 0.7772 (tp30) cc_final: 0.7479 (tp30)
REVERT: A 1166 ASP cc_start: 0.7775 (OUTLIER) cc_final: 0.7571 (t70)
REVERT: A 1205 ARG cc_start: 0.7826 (OUTLIER) cc_final: 0.7577 (ttp-110)
REVERT: A 1234 LEU cc_start: 0.8183 (OUTLIER) cc_final: 0.7863 (pp)
REVERT: A 1235 GLU cc_start: 0.6882 (mp0) cc_final: 0.6615 (mp0)
REVERT: A 1313 GLU cc_start: 0.7502 (mm-30) cc_final: 0.7219 (tm-30)
REVERT: C  546 ILE cc_start: 0.7344 (mp) cc_final: 0.7131 (mt)
REVERT: C  691 ASP cc_start: 0.7687 (m-30) cc_final: 0.7002 (m-30)
REVERT: E  479 MET cc_start: 0.3990 (ptt) cc_final: 0.3787 (ptt)
  outliers start: 75
  outliers final: 40
  residues processed: 418
  average time/residue: 1.3657
  time to fit residues: 625.7787
Evaluate side-chains
  402 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 357
  time to evaluate  : 1.569 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  385 LYS
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  822 ASN
Chi-restraints excluded: chain A residue  838 ILE
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1084 SER
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1166 ASP
Chi-restraints excluded: chain A residue 1205 ARG
Chi-restraints excluded: chain A residue 1234 LEU
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  545 LYS
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain B residue  572 VAL
Chi-restraints excluded: chain D residue  478 ILE
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  522 ASN
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain D residue  536 ILE
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  523 SER
Chi-restraints excluded: chain C residue  545 LYS
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain C residue  631 VAL
Chi-restraints excluded: chain C residue  685 LEU
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain E residue  491 HIS
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Chi-restraints excluded: chain E residue  531 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 176 optimal weight:    0.9980
   chunk 91 optimal weight:    0.8980
   chunk 82 optimal weight:    0.9990
   chunk 7 optimal weight:    0.0040
   chunk 138 optimal weight:    0.7980
   chunk 113 optimal weight:    0.0770
   chunk 104 optimal weight:    0.9990
   chunk 108 optimal weight:    0.6980
   chunk 178 optimal weight:    0.0980
   chunk 179 optimal weight:    0.2980
   chunk 110 optimal weight:    0.9990
   overall best weight:    0.2350

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 139 GLN
A 534 GLN
A 896 HIS
A 940 ASN
A1011 ASN
A1182 GLN
A1183 ASN
A1324 GLN
A1374 ASN
C 648 ASN

Total number of N/Q/H flips: 11

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.160827 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3887 r_free = 0.3887 target = 0.135449 restraints weight = 19981.775|
|-----------------------------------------------------------------------------|
r_work (start): 0.3885 rms_B_bonded: 1.63
r_work: 0.3781 rms_B_bonded: 2.07 restraints_weight: 0.5000
r_work: 0.3633 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7814
moved from start:          0.2403

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062  14950  Z= 0.132
  Angle     :  0.579   9.168  20197  Z= 0.296
  Chirality :  0.042   0.155   2295
  Planarity :  0.004   0.091   2585
  Dihedral  :  5.384  56.072   1992
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 8.76
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.99 %
    Favored  : 96.95 %
  Rotamer:
    Outliers :  4.16 %
    Allowed  : 26.78 %
    Favored  : 69.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.41 (0.20), residues: 1806
  helix:  1.92 (0.16), residues: 1044
  sheet: -0.48 (0.54), residues: 90
  loop : -0.42 (0.25), residues: 672

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 806 
 HIS   0.003   0.001   HIS A1423 
 PHE   0.023   0.001   PHE A 399 
 TYR   0.019   0.001   TYR B 498 
 ARG   0.004   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03970 (  846)
  hydrogen bonds       : angle       4.11637 ( 2424)
  metal coordination   : bond        0.00859 (    7)
  metal coordination   : angle       9.13230 (    1)
  covalent geometry    : bond        0.00310 (14943)
  covalent geometry    : angle       0.57495 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  428 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 69
    poor density    : 359
  time to evaluate  : 1.990 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8237 (tpp) cc_final: 0.7731 (tpp)
REVERT: A  441 ASP cc_start: 0.7769 (t0) cc_final: 0.7547 (t0)
REVERT: A  460 GLU cc_start: 0.7773 (pm20) cc_final: 0.7482 (pm20)
REVERT: A  714 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8208 (m)
REVERT: A  782 GLU cc_start: 0.7564 (mp0) cc_final: 0.7348 (mp0)
REVERT: A  841 LYS cc_start: 0.8572 (mmtm) cc_final: 0.8331 (mmtm)
REVERT: A 1205 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7553 (ttp-170)
REVERT: A 1214 TYR cc_start: 0.8741 (t80) cc_final: 0.8460 (t80)
REVERT: D  531 MET cc_start: 0.7506 (tmm) cc_final: 0.7211 (tpt)
REVERT: E  479 MET cc_start: 0.3915 (ptt) cc_final: 0.3704 (ptt)
  outliers start: 69
  outliers final: 40
  residues processed: 399
  average time/residue: 1.5003
  time to fit residues: 651.5523
Evaluate side-chains
  395 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 353
  time to evaluate  : 1.652 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  533 ASP
Chi-restraints excluded: chain A residue  568 GLU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1084 SER
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1205 ARG
Chi-restraints excluded: chain A residue 1323 SER
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  545 LYS
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain D residue  478 ILE
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  527 ILE
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain D residue  536 ILE
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  523 SER
Chi-restraints excluded: chain C residue  607 SER
Chi-restraints excluded: chain C residue  685 LEU
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain E residue  491 HIS
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Chi-restraints excluded: chain E residue  531 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 21 optimal weight:    0.9990
   chunk 50 optimal weight:    0.9990
   chunk 168 optimal weight:    1.9990
   chunk 78 optimal weight:    0.9980
   chunk 74 optimal weight:    0.9990
   chunk 48 optimal weight:    0.0870
   chunk 136 optimal weight:    0.1980
   chunk 116 optimal weight:    0.9980
   chunk 111 optimal weight:    0.9980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.5158

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

Flipped N/Q/H residues before XYZ refinement:
A 119 ASN
A 534 GLN
A 940 ASN
A1011 ASN
A1182 GLN
A1183 ASN
A1324 GLN
C 648 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4192 r_free = 0.4192 target = 0.160059 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.134942 restraints weight = 19818.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.3874 rms_B_bonded: 1.61
r_work: 0.3767 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3619 rms_B_bonded: 3.66 restraints_weight: 0.2500
r_work (final): 0.3619
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7835
moved from start:          0.2489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  14950  Z= 0.185
  Angle     :  0.611   9.815  20197  Z= 0.311
  Chirality :  0.044   0.175   2295
  Planarity :  0.004   0.090   2585
  Dihedral  :  5.282  55.930   1988
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.10 %
    Favored  : 96.84 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 26.84 %
    Favored  : 68.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.35 (0.20), residues: 1806
  helix:  1.87 (0.16), residues: 1045
  sheet: -0.51 (0.54), residues: 90
  loop : -0.44 (0.25), residues: 671

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP A 806 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.024   0.001   PHE A 399 
 TYR   0.018   0.002   TYR B 498 
 ARG   0.006   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04261 (  846)
  hydrogen bonds       : angle       4.14754 ( 2424)
  metal coordination   : bond        0.01065 (    7)
  metal coordination   : angle       9.10994 (    1)
  covalent geometry    : bond        0.00449 (14943)
  covalent geometry    : angle       0.60733 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  448 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 78
    poor density    : 370
  time to evaluate  : 1.756 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8240 (tpp) cc_final: 0.7756 (tpp)
REVERT: A  385 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8622 (mttt)
REVERT: A  460 GLU cc_start: 0.7766 (pm20) cc_final: 0.7479 (pm20)
REVERT: A  568 GLU cc_start: 0.7095 (OUTLIER) cc_final: 0.6822 (mp0)
REVERT: A  714 THR cc_start: 0.8555 (OUTLIER) cc_final: 0.8245 (m)
REVERT: A  782 GLU cc_start: 0.7579 (mp0) cc_final: 0.7359 (mp0)
REVERT: A  799 GLU cc_start: 0.7400 (mp0) cc_final: 0.7187 (mp0)
REVERT: A  841 LYS cc_start: 0.8518 (mmtm) cc_final: 0.8272 (mmtm)
REVERT: A 1166 ASP cc_start: 0.7740 (OUTLIER) cc_final: 0.7520 (t70)
REVERT: A 1205 ARG cc_start: 0.7822 (OUTLIER) cc_final: 0.7574 (ttp-110)
REVERT: B  509 GLU cc_start: 0.5442 (OUTLIER) cc_final: 0.4521 (pm20)
REVERT: C  669 ARG cc_start: 0.7976 (mtt90) cc_final: 0.7534 (mtt180)
REVERT: C  694 ILE cc_start: 0.7954 (OUTLIER) cc_final: 0.7689 (mt)
REVERT: E  479 MET cc_start: 0.3919 (ptt) cc_final: 0.3713 (ptt)
  outliers start: 78
  outliers final: 38
  residues processed: 419
  average time/residue: 1.4892
  time to fit residues: 680.4114
Evaluate side-chains
  408 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 363
  time to evaluate  : 1.545 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 LEU
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  385 LYS
Chi-restraints excluded: chain A residue  461 LEU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  568 GLU
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1084 SER
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1166 ASP
Chi-restraints excluded: chain A residue 1205 ARG
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1323 SER
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain A residue 1436 VAL
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  533 LEU
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  542 GLU
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  527 ILE
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain D residue  536 ILE
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  520 VAL
Chi-restraints excluded: chain C residue  523 SER
Chi-restraints excluded: chain C residue  567 ILE
Chi-restraints excluded: chain C residue  685 LEU
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain C residue  694 ILE
Chi-restraints excluded: chain E residue  491 HIS
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Chi-restraints excluded: chain E residue  531 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 129 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0770
   chunk 122 optimal weight:    0.0050
   chunk 37 optimal weight:    0.9980
   chunk 128 optimal weight:    0.1980
   chunk 91 optimal weight:    0.7980
   chunk 73 optimal weight:    0.7980
   chunk 179 optimal weight:    0.3980
   chunk 80 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0870
   chunk 161 optimal weight:    0.0670
   overall best weight:    0.0868

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 119 ASN
A 427 HIS
A 534 GLN
A1011 ASN
A1183 ASN
A1324 GLN
C 648 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.162265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.137175 restraints weight = 19877.836|
|-----------------------------------------------------------------------------|
r_work (start): 0.3904 rms_B_bonded: 1.62
r_work: 0.3802 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3661 rms_B_bonded: 3.67 restraints_weight: 0.2500
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7776
moved from start:          0.2621

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071  14950  Z= 0.118
  Angle     :  0.576  10.466  20197  Z= 0.295
  Chirality :  0.041   0.146   2295
  Planarity :  0.004   0.087   2585
  Dihedral  :  5.051  57.660   1984
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  2.44 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 28.53 %
    Favored  : 67.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.47 (0.20), residues: 1806
  helix:  2.01 (0.16), residues: 1037
  sheet: -0.44 (0.54), residues: 90
  loop : -0.43 (0.25), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 806 
 HIS   0.006   0.001   HIS C 491 
 PHE   0.021   0.001   PHE A 399 
 TYR   0.017   0.001   TYR B 498 
 ARG   0.007   0.000   ARG A 141 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  846)
  hydrogen bonds       : angle       4.02212 ( 2424)
  metal coordination   : bond        0.00693 (    7)
  metal coordination   : angle       5.90857 (    1)
  covalent geometry    : bond        0.00265 (14943)
  covalent geometry    : angle       0.57427 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  424 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 66
    poor density    : 358
  time to evaluate  : 1.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8221 (tpp) cc_final: 0.7749 (tpp)
REVERT: A  286 ILE cc_start: 0.8283 (pt) cc_final: 0.7943 (mt)
REVERT: A  460 GLU cc_start: 0.7750 (pm20) cc_final: 0.7471 (pm20)
REVERT: A  714 THR cc_start: 0.8435 (OUTLIER) cc_final: 0.8116 (m)
REVERT: A  841 LYS cc_start: 0.8526 (mmtm) cc_final: 0.8282 (mmtm)
REVERT: A 1166 ASP cc_start: 0.7708 (OUTLIER) cc_final: 0.7486 (t70)
REVERT: A 1214 TYR cc_start: 0.8720 (t80) cc_final: 0.8457 (t80)
REVERT: D  531 MET cc_start: 0.7532 (tmm) cc_final: 0.7182 (tpt)
REVERT: C  669 ARG cc_start: 0.7953 (mtt90) cc_final: 0.7501 (mtt180)
REVERT: C  694 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7714 (mt)
REVERT: E  479 MET cc_start: 0.3673 (ptt) cc_final: 0.3447 (ptt)
  outliers start: 66
  outliers final: 32
  residues processed: 398
  average time/residue: 1.6966
  time to fit residues: 743.4893
Evaluate side-chains
  376 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 341
  time to evaluate  : 2.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  210 LEU
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  822 ASN
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue  991 LEU
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1166 ASP
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1323 SER
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain A residue 1436 VAL
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  527 ILE
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain C residue  694 ILE
Chi-restraints excluded: chain E residue  491 HIS
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Chi-restraints excluded: chain E residue  531 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 110 optimal weight:    1.9990
   chunk 135 optimal weight:    2.9990
   chunk 180 optimal weight:    0.9980
   chunk 89 optimal weight:    0.6980
   chunk 90 optimal weight:    0.6980
   chunk 35 optimal weight:    0.9990
   chunk 67 optimal weight:    0.9990
   chunk 158 optimal weight:    0.5980
   chunk 28 optimal weight:    0.4980
   chunk 58 optimal weight:    0.1980
   chunk 117 optimal weight:    0.0770
   overall best weight:    0.4138

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 119 ASN
A 427 HIS
** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 945 ASN
A1011 ASN
A1086 ASN
A1183 ASN
A1324 GLN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4205 r_free = 0.4205 target = 0.161022 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3889 r_free = 0.3889 target = 0.135672 restraints weight = 19708.582|
|-----------------------------------------------------------------------------|
r_work (start): 0.3882 rms_B_bonded: 1.62
r_work: 0.3779 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3635 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7813
moved from start:          0.2679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060  14950  Z= 0.165
  Angle     :  0.617   9.177  20197  Z= 0.315
  Chirality :  0.043   0.156   2295
  Planarity :  0.004   0.087   2585
  Dihedral  :  4.934  57.126   1981
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 9.10
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.21 %
    Favored  : 96.73 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 28.95 %
    Favored  : 67.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.44 (0.20), residues: 1806
  helix:  2.00 (0.16), residues: 1033
  sheet: -0.30 (0.53), residues: 95
  loop : -0.48 (0.25), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.002   TRP A 806 
 HIS   0.004   0.001   HIS A1120 
 PHE   0.032   0.002   PHE B 488 
 TYR   0.019   0.001   TYR B 498 
 ARG   0.009   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04044 (  846)
  hydrogen bonds       : angle       4.10823 ( 2424)
  metal coordination   : bond        0.00890 (    7)
  metal coordination   : angle       6.94320 (    1)
  covalent geometry    : bond        0.00398 (14943)
  covalent geometry    : angle       0.61482 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  409 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 357
  time to evaluate  : 2.513 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8212 (tpp) cc_final: 0.7715 (tpp)
REVERT: A  286 ILE cc_start: 0.8367 (OUTLIER) cc_final: 0.8135 (mt)
REVERT: A  460 GLU cc_start: 0.7767 (pm20) cc_final: 0.7495 (pm20)
REVERT: A  714 THR cc_start: 0.8458 (OUTLIER) cc_final: 0.8145 (m)
REVERT: A  815 PHE cc_start: 0.8495 (m-10) cc_final: 0.8156 (m-10)
REVERT: A  841 LYS cc_start: 0.8525 (mmtm) cc_final: 0.8271 (mmtm)
REVERT: A 1214 TYR cc_start: 0.8732 (t80) cc_final: 0.8460 (t80)
REVERT: B  509 GLU cc_start: 0.5339 (OUTLIER) cc_final: 0.4475 (pm20)
REVERT: D  531 MET cc_start: 0.7555 (tmm) cc_final: 0.7209 (tpt)
REVERT: C  669 ARG cc_start: 0.7963 (mtt90) cc_final: 0.7529 (mtt180)
REVERT: E  479 MET cc_start: 0.3736 (ptt) cc_final: 0.3516 (ptt)
  outliers start: 52
  outliers final: 30
  residues processed: 390
  average time/residue: 1.5239
  time to fit residues: 648.2554
Evaluate side-chains
  386 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 353
  time to evaluate  : 1.718 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  286 ILE
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  442 ASP
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain A residue 1436 VAL
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  527 ILE
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  520 VAL
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Chi-restraints excluded: chain E residue  531 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 55 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 118 optimal weight:    0.8980
   chunk 167 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   chunk 91 optimal weight:    0.8980
   chunk 79 optimal weight:    0.6980
   chunk 25 optimal weight:    0.2980
   chunk 143 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 178 optimal weight:    0.5980
   overall best weight:    0.5780

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 119 ASN
** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1011 ASN
A1182 GLN
A1183 ASN
A1324 GLN
** A1374 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 648 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4194 r_free = 0.4194 target = 0.160156 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.134776 restraints weight = 19571.729|
|-----------------------------------------------------------------------------|
r_work (start): 0.3876 rms_B_bonded: 1.62
r_work: 0.3769 rms_B_bonded: 2.06 restraints_weight: 0.5000
r_work: 0.3622 rms_B_bonded: 3.65 restraints_weight: 0.2500
r_work (final): 0.3622
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7834
moved from start:          0.2748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  14950  Z= 0.202
  Angle     :  0.652   9.457  20197  Z= 0.332
  Chirality :  0.045   0.173   2295
  Planarity :  0.004   0.085   2585
  Dihedral  :  5.049  56.537   1981
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  3.77 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  2.96 %
    Allowed  : 29.86 %
    Favored  : 67.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.32 (0.20), residues: 1806
  helix:  1.89 (0.16), residues: 1032
  sheet: -0.42 (0.52), residues: 95
  loop : -0.49 (0.24), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 806 
 HIS   0.005   0.001   HIS A1120 
 PHE   0.024   0.002   PHE A 399 
 TYR   0.018   0.002   TYR B 498 
 ARG   0.008   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04382 (  846)
  hydrogen bonds       : angle       4.20281 ( 2424)
  metal coordination   : bond        0.01020 (    7)
  metal coordination   : angle       7.81916 (    1)
  covalent geometry    : bond        0.00490 (14943)
  covalent geometry    : angle       0.64994 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  412 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 49
    poor density    : 363
  time to evaluate  : 2.292 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8246 (tpp) cc_final: 0.7770 (tpp)
REVERT: A  460 GLU cc_start: 0.7774 (pm20) cc_final: 0.7495 (pm20)
REVERT: A  472 LYS cc_start: 0.8073 (OUTLIER) cc_final: 0.7844 (mmtp)
REVERT: A  714 THR cc_start: 0.8534 (OUTLIER) cc_final: 0.8214 (m)
REVERT: A  815 PHE cc_start: 0.8549 (m-10) cc_final: 0.8195 (m-10)
REVERT: A  841 LYS cc_start: 0.8517 (mmtm) cc_final: 0.8266 (mmtm)
REVERT: A 1214 TYR cc_start: 0.8721 (t80) cc_final: 0.8464 (t80)
REVERT: B  509 GLU cc_start: 0.5319 (OUTLIER) cc_final: 0.4464 (pm20)
REVERT: C  669 ARG cc_start: 0.7966 (mtt90) cc_final: 0.7519 (mtt180)
  outliers start: 49
  outliers final: 28
  residues processed: 393
  average time/residue: 1.7835
  time to fit residues: 763.9989
Evaluate side-chains
  390 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 359
  time to evaluate  : 1.785 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  472 LYS
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain A residue 1436 VAL
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain B residue  499 HIS
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  527 ILE
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  520 VAL
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 73 optimal weight:    0.4980
   chunk 49 optimal weight:    1.9990
   chunk 117 optimal weight:    0.3980
   chunk 5 optimal weight:    0.9980
   chunk 56 optimal weight:    0.4980
   chunk 119 optimal weight:    1.9990
   chunk 82 optimal weight:    0.3980
   chunk 77 optimal weight:    0.9990
   chunk 129 optimal weight:    0.9980
   chunk 31 optimal weight:    0.5980
   chunk 8 optimal weight:    0.9990
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 119 ASN
A 331 GLN
A 427 HIS
** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1011 ASN
A1182 GLN
A1183 ASN
A1324 GLN
D 499 HIS
C 648 ASN

Total number of N/Q/H flips: 10

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.160632 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3881 r_free = 0.3881 target = 0.135162 restraints weight = 19693.483|
|-----------------------------------------------------------------------------|
r_work (start): 0.3881 rms_B_bonded: 1.64
r_work: 0.3773 rms_B_bonded: 2.08 restraints_weight: 0.5000
r_work: 0.3625 rms_B_bonded: 3.70 restraints_weight: 0.2500
r_work (final): 0.3625
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7842
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.044  14950  Z= 0.182
  Angle     :  0.654  11.943  20197  Z= 0.331
  Chirality :  0.044   0.162   2295
  Planarity :  0.004   0.053   2585
  Dihedral  :  5.059  56.677   1981
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 8.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.53 %
    Allowed  : 30.34 %
    Favored  : 67.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.30 (0.20), residues: 1806
  helix:  1.83 (0.16), residues: 1040
  sheet: -0.32 (0.53), residues: 91
  loop : -0.47 (0.25), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 806 
 HIS   0.005   0.001   HIS D 535 
 PHE   0.024   0.002   PHE A 399 
 TYR   0.018   0.002   TYR B 498 
 ARG   0.011   0.000   ARG A1010 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04308 (  846)
  hydrogen bonds       : angle       4.20175 ( 2424)
  metal coordination   : bond        0.00895 (    7)
  metal coordination   : angle       7.77149 (    1)
  covalent geometry    : bond        0.00439 (14943)
  covalent geometry    : angle       0.65208 (20196)

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

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

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3612 Ramachandran restraints generated.
    1806 Oldfield, 0 Emsley, 1806 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  403 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 361
  time to evaluate  : 1.701 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   84 MET cc_start: 0.8247 (tpp) cc_final: 0.7820 (tpp)
REVERT: A  460 GLU cc_start: 0.7780 (pm20) cc_final: 0.7489 (pm20)
REVERT: A  568 GLU cc_start: 0.7253 (mm-30) cc_final: 0.7045 (tp30)
REVERT: A  714 THR cc_start: 0.8554 (OUTLIER) cc_final: 0.8232 (m)
REVERT: A  815 PHE cc_start: 0.8545 (m-10) cc_final: 0.8206 (m-10)
REVERT: A  841 LYS cc_start: 0.8549 (mmtm) cc_final: 0.8269 (mmtm)
REVERT: A 1214 TYR cc_start: 0.8735 (t80) cc_final: 0.8472 (t80)
REVERT: B  509 GLU cc_start: 0.5435 (OUTLIER) cc_final: 0.4555 (pm20)
REVERT: D  531 MET cc_start: 0.7593 (tmm) cc_final: 0.7123 (tpt)
REVERT: C  669 ARG cc_start: 0.7925 (mtt90) cc_final: 0.7454 (mtt180)
  outliers start: 42
  outliers final: 30
  residues processed: 385
  average time/residue: 1.6037
  time to fit residues: 675.1540
Evaluate side-chains
  386 residues out of total 1658 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 354
  time to evaluate  : 1.642 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  121 ILE
Chi-restraints excluded: chain A residue  219 LYS
Chi-restraints excluded: chain A residue  317 LYS
Chi-restraints excluded: chain A residue  319 MET
Chi-restraints excluded: chain A residue  482 GLU
Chi-restraints excluded: chain A residue  506 VAL
Chi-restraints excluded: chain A residue  714 THR
Chi-restraints excluded: chain A residue  798 ILE
Chi-restraints excluded: chain A residue  855 CYS
Chi-restraints excluded: chain A residue  919 LEU
Chi-restraints excluded: chain A residue  933 THR
Chi-restraints excluded: chain A residue 1025 ARG
Chi-restraints excluded: chain A residue 1142 LYS
Chi-restraints excluded: chain A residue 1218 VAL
Chi-restraints excluded: chain A residue 1330 LEU
Chi-restraints excluded: chain A residue 1436 VAL
Chi-restraints excluded: chain A residue 1451 VAL
Chi-restraints excluded: chain A residue 1456 LEU
Chi-restraints excluded: chain B residue  487 THR
Chi-restraints excluded: chain B residue  509 GLU
Chi-restraints excluded: chain B residue  531 MET
Chi-restraints excluded: chain B residue  541 LYS
Chi-restraints excluded: chain B residue  543 ILE
Chi-restraints excluded: chain B residue  559 LYS
Chi-restraints excluded: chain D residue  503 LEU
Chi-restraints excluded: chain D residue  527 ILE
Chi-restraints excluded: chain D residue  535 HIS
Chi-restraints excluded: chain C residue  518 MET
Chi-restraints excluded: chain C residue  520 VAL
Chi-restraints excluded: chain C residue  690 ASN
Chi-restraints excluded: chain E residue  506 TYR
Chi-restraints excluded: chain E residue  518 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 181
   random chunks:
   chunk 156 optimal weight:    0.5980
   chunk 41 optimal weight:    0.6980
   chunk 14 optimal weight:    0.9980
   chunk 51 optimal weight:    0.9990
   chunk 147 optimal weight:    0.5980
   chunk 126 optimal weight:    1.9990
   chunk 6 optimal weight:    0.9990
   chunk 135 optimal weight:    1.9990
   chunk 155 optimal weight:    0.9980
   chunk 37 optimal weight:    0.9990
   chunk 25 optimal weight:    0.4980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A  79 ASN
A 119 ASN
A 331 GLN
A 427 HIS
** A 534 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1011 ASN
A1183 ASN
C 648 ASN
C 686 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4189 r_free = 0.4189 target = 0.159689 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3872 r_free = 0.3872 target = 0.134376 restraints weight = 19680.580|
|-----------------------------------------------------------------------------|
r_work (start): 0.3873 rms_B_bonded: 1.61
r_work: 0.3766 rms_B_bonded: 2.05 restraints_weight: 0.5000
r_work: 0.3618 rms_B_bonded: 3.63 restraints_weight: 0.2500
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7845
moved from start:          0.2843

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.057  14950  Z= 0.228
  Angle     :  0.688  11.502  20197  Z= 0.346
  Chirality :  0.046   0.183   2295
  Planarity :  0.004   0.054   2585
  Dihedral  :  5.147  55.930   1981
  Min Nonbonded Distance : 2.400

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.15 %
    Favored  : 95.85 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 30.52 %
    Favored  : 67.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    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:  1.25 (0.20), residues: 1806
  helix:  1.76 (0.16), residues: 1040
  sheet: -0.35 (0.53), residues: 92
  loop : -0.43 (0.25), residues: 674

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.028   0.002   TRP A 806 
 HIS   0.006   0.001   HIS A1120 
 PHE   0.025   0.002   PHE A 399 
 TYR   0.020   0.002   TYR B 498 
 ARG   0.008   0.000   ARG A 824 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04604 (  846)
  hydrogen bonds       : angle       4.27856 ( 2424)
  metal coordination   : bond        0.01149 (    7)
  metal coordination   : angle       9.12817 (    1)
  covalent geometry    : bond        0.00558 (14943)
  covalent geometry    : angle       0.68506 (20196)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 20788.81 seconds
wall clock time: 362 minutes 51.73 seconds (21771.73 seconds total)