Starting phenix.real_space_refine
on Thu Jul 31 05:32:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7sfl_25092/07_2025/7sfl_25092.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7sfl_25092/07_2025/7sfl_25092.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.87
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7sfl_25092/07_2025/7sfl_25092.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7sfl_25092/07_2025/7sfl_25092.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7sfl_25092/07_2025/7sfl_25092.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7sfl_25092/07_2025/7sfl_25092.cif"
  }
  resolution = 3.87
  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=  -0.001 sd=   0.044
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
     S      82      5.16       5
     Cl      2      4.86       5
     C    8491      2.51       5
     N    2137      2.21       5
     O    2302      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 13014
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 6479
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 829, 6479
          Classifications: {'peptide': 829}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 799}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "B"
      Number of atoms: 6493
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 830, 6493
          Classifications: {'peptide': 830}
          Incomplete info: {'backbone_only': 1}
          Link IDs: {'PTRANS': 29, 'TRANS': 800}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'FUN': 1}
          Classifications: {'undetermined': 1}
    Chain: "B"
      Number of atoms: 21
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 21
          Unusual residues: {'FUN': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 9.08, per 1000 atoms: 0.70
  Number of scatterers: 13014
  At special positions: 0
  Unit cell: (81.32, 156.22, 113.42, 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)
     Cl      2     17.00
     S      82     16.00
     O    2302      8.00
     N    2137      7.00
     C    8491      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=3, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 563 " - pdb=" SG  CYS A 568 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 577 " - pdb=" SG  CYS A 582 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 563 " - pdb=" SG  CYS B 568 " distance=2.03

  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: 3.26
  Conformation dependent library (CDL) restraints added in 1.7 seconds
  

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3076

  Finding SS restraints...
    Secondary structure from input PDB file:
      68 helices and 5 sheets defined
      64.0% alpha, 4.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 286 through 300
    Processing helix  chain 'A' and resid 301 through 305
      removed outlier: 3.866A  pdb=" N   LEU A 304 " --> pdb=" O   GLY A 301 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   PHE A 305 " --> pdb=" O   VAL A 302 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 301 through 305'
    Processing helix  chain 'A' and resid 307 through 315
      removed outlier: 3.521A  pdb=" N   ALA A 315 " --> pdb=" O   ILE A 311 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 316 through 343
    Processing helix  chain 'A' and resid 351 through 360
    Processing helix  chain 'A' and resid 361 through 399
      removed outlier: 4.459A  pdb=" N   ALA A 367 " --> pdb=" O   GLU A 363 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   VAL A 380 " --> pdb=" O   ASN A 376 " (cutoff:3.500A)
      removed outlier: 4.319A  pdb=" N   ALA A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   MET A 382 " --> pdb=" O   VAL A 378 " (cutoff:3.500A)
      removed outlier: 4.067A  pdb=" N   GLU A 397 " --> pdb=" O   GLU A 393 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   HIS A 398 " --> pdb=" O   LEU A 394 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 426
      removed outlier: 3.626A  pdb=" N   ILE A 409 " --> pdb=" O   GLU A 405 " (cutoff:3.500A)
      removed outlier: 4.401A  pdb=" N   ARG A 410 " --> pdb=" O   ILE A 406 " (cutoff:3.500A)
      removed outlier: 3.578A  pdb=" N   ILE A 415 " --> pdb=" O   ILE A 411 " (cutoff:3.500A)
      removed outlier: 3.970A  pdb=" N   GLY A 422 " --> pdb=" O   VAL A 418 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 455
      removed outlier: 4.810A  pdb=" N   ILE A 436 " --> pdb=" O   ALA A 432 " (cutoff:3.500A)
      removed outlier: 4.536A  pdb=" N   VAL A 437 " --> pdb=" O   LYS A 433 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   ILE A 441 " --> pdb=" O   VAL A 437 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   LEU A 442 " --> pdb=" O   LEU A 438 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   PHE A 454 " --> pdb=" O   VAL A 450 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   ILE A 455 " --> pdb=" O   ILE A 451 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 477
    Processing helix  chain 'A' and resid 486 through 495
    Processing helix  chain 'A' and resid 496 through 499
      removed outlier: 3.641A  pdb=" N   THR A 499 " --> pdb=" O   PRO A 496 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 496 through 499'
    Processing helix  chain 'A' and resid 500 through 507
    Processing helix  chain 'A' and resid 516 through 544
      removed outlier: 4.574A  pdb=" N   LYS A 520 " --> pdb=" O   SER A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 591 through 597
      removed outlier: 3.736A  pdb=" N   MET A 595 " --> pdb=" O   GLN A 591 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 632
      removed outlier: 4.002A  pdb=" N   ILE A 603 " --> pdb=" O   PHE A 599 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   SER A 604 " --> pdb=" O   THR A 600 " (cutoff:3.500A)
      removed outlier: 3.740A  pdb=" N   ALA A 605 " --> pdb=" O   PRO A 601 " (cutoff:3.500A)
      Proline residue:  A 623  - end of helix
    Processing helix  chain 'A' and resid 635 through 642
      removed outlier: 4.966A  pdb=" N   MET A 640 " --> pdb=" O   ALA A 637 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 667
    Processing helix  chain 'A' and resid 670 through 699
      Proline residue:  A 676  - end of helix
    Processing helix  chain 'A' and resid 712 through 730
      removed outlier: 3.508A  pdb=" N   ILE A 730 " --> pdb=" O   VAL A 726 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 731 through 752
    Processing helix  chain 'A' and resid 762 through 779
      removed outlier: 4.200A  pdb=" N   THR A 766 " --> pdb=" O   THR A 762 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 801 through 812
      removed outlier: 3.627A  pdb=" N   PHE A 811 " --> pdb=" O   LEU A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 849
      removed outlier: 3.600A  pdb=" N   GLU A 834 " --> pdb=" O   GLN A 830 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 862 through 874
    Processing helix  chain 'A' and resid 896 through 913
      removed outlier: 3.502A  pdb=" N   ILE A 913 " --> pdb=" O   ASP A 909 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1034 through 1045
      Proline residue:  A1040  - end of helix
      removed outlier: 3.568A  pdb=" N   THR A1045 " --> pdb=" O   TYR A1041 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1064 through 1079
      removed outlier: 3.627A  pdb=" N   LEU A1075 " --> pdb=" O   ALA A1071 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1097 through 1109
      removed outlier: 3.652A  pdb=" N   ILE A1101 " --> pdb=" O   LYS A1097 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1110 through 1112
      No H-bonds generated for 'chain 'A' and resid 1110 through 1112'
    Processing helix  chain 'A' and resid 1119 through 1130
    Processing helix  chain 'A' and resid 1135 through 1142
      removed outlier: 3.551A  pdb=" N   LEU A1139 " --> pdb=" O   THR A1135 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1142 through 1160
    Processing helix  chain 'A' and resid 1161 through 1163
      No H-bonds generated for 'chain 'A' and resid 1161 through 1163'
    Processing helix  chain 'A' and resid 1179 through 1191
    Processing helix  chain 'B' and resid 288 through 300
      removed outlier: 3.885A  pdb=" N   VAL B 293 " --> pdb=" O   LYS B 289 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   ARG B 294 " --> pdb=" O   GLY B 290 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 306 through 315
      removed outlier: 4.066A  pdb=" N   TRP B 310 " --> pdb=" O   ILE B 306 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 316 through 344
    Processing helix  chain 'B' and resid 351 through 360
    Processing helix  chain 'B' and resid 361 through 398
      removed outlier: 3.696A  pdb=" N   GLY B 365 " --> pdb=" O   GLY B 361 " (cutoff:3.500A)
      removed outlier: 3.675A  pdb=" N   ALA B 381 " --> pdb=" O   ALA B 377 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 425
    Processing helix  chain 'B' and resid 430 through 455
      removed outlier: 4.351A  pdb=" N   ILE B 436 " --> pdb=" O   ALA B 432 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   VAL B 437 " --> pdb=" O   LYS B 433 " (cutoff:3.500A)
      removed outlier: 3.787A  pdb=" N   PHE B 454 " --> pdb=" O   VAL B 450 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 469 through 478
      removed outlier: 3.516A  pdb=" N   PHE B 473 " --> pdb=" O   LYS B 469 " (cutoff:3.500A)
      removed outlier: 4.213A  pdb=" N   GLY B 478 " --> pdb=" O   ASN B 474 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 486 through 495
    Processing helix  chain 'B' and resid 496 through 499
    Processing helix  chain 'B' and resid 500 through 501
      No H-bonds generated for 'chain 'B' and resid 500 through 501'
    Processing helix  chain 'B' and resid 502 through 507
    Processing helix  chain 'B' and resid 513 through 542
      removed outlier: 3.566A  pdb=" N   ILE B 518 " --> pdb=" O   PRO B 514 " (cutoff:3.500A)
      Proline residue:  B 519  - end of helix
      removed outlier: 3.884A  pdb=" N   LEU B 524 " --> pdb=" O   LYS B 520 " (cutoff:3.500A)
      removed outlier: 4.439A  pdb=" N   SER B 539 " --> pdb=" O   GLY B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 566 through 570
    Processing helix  chain 'B' and resid 591 through 597
      removed outlier: 3.723A  pdb=" N   SER B 597 " --> pdb=" O   MET B 593 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 600 through 633
      Proline residue:  B 623  - end of helix
      removed outlier: 3.707A  pdb=" N   ASN B 633 " --> pdb=" O   LEU B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 642
      removed outlier: 5.172A  pdb=" N   MET B 640 " --> pdb=" O   ALA B 637 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   ALA B 642 " --> pdb=" O   GLN B 639 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 651 through 666
    Processing helix  chain 'B' and resid 670 through 699
      Proline residue:  B 676  - end of helix
    Processing helix  chain 'B' and resid 712 through 730
    Processing helix  chain 'B' and resid 731 through 751
      removed outlier: 4.193A  pdb=" N   TYR B 751 " --> pdb=" O   ILE B 747 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 751 through 758
      removed outlier: 4.167A  pdb=" N   VAL B 756 " --> pdb=" O   LYS B 752 " (cutoff:3.500A)
      removed outlier: 3.912A  pdb=" N   TRP B 758 " --> pdb=" O   PRO B 754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 763 through 780
      removed outlier: 4.258A  pdb=" N   ASN B 769 " --> pdb=" O   LEU B 765 " (cutoff:3.500A)
      removed outlier: 3.780A  pdb=" N   VAL B 780 " --> pdb=" O   ARG B 776 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 801 through 811
      removed outlier: 3.845A  pdb=" N   LEU B 805 " --> pdb=" O   ARG B 801 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   PHE B 811 " --> pdb=" O   LEU B 807 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 830 through 849
      removed outlier: 3.583A  pdb=" N   GLU B 834 " --> pdb=" O   GLN B 830 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 862 through 874
    Processing helix  chain 'B' and resid 896 through 913
      removed outlier: 3.621A  pdb=" N   VAL B 900 " --> pdb=" O   ASP B 896 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   PHE B 907 " --> pdb=" O   TYR B 903 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1034 through 1045
      Proline residue:  B1040  - end of helix
    Processing helix  chain 'B' and resid 1064 through 1080
      removed outlier: 4.234A  pdb=" N   ASP B1068 " --> pdb=" O   ARG B1064 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1097 through 1108
    Processing helix  chain 'B' and resid 1119 through 1128
    Processing helix  chain 'B' and resid 1136 through 1142
    Processing helix  chain 'B' and resid 1142 through 1160
      removed outlier: 4.019A  pdb=" N   ASN B1153 " --> pdb=" O   GLN B1149 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1179 through 1191
    Processing sheet with id=AA1, first strand: chain 'A' and resid 853 through 859
      removed outlier: 7.594A  pdb=" N   MET A 818 " --> pdb=" O   PHE A 854 " (cutoff:3.500A)
      removed outlier: 8.186A  pdb=" N   ALA A 856 " --> pdb=" O   MET A 818 " (cutoff:3.500A)
      removed outlier: 6.592A  pdb=" N   CYS A 820 " --> pdb=" O   ALA A 856 " (cutoff:3.500A)
      removed outlier: 7.878A  pdb=" N   VAL A 858 " --> pdb=" O   CYS A 820 " (cutoff:3.500A)
      removed outlier: 6.902A  pdb=" N   HIS A 822 " --> pdb=" O   VAL A 858 " (cutoff:3.500A)
      removed outlier: 6.502A  pdb=" N   CYS A 791 " --> pdb=" O   ILE A 819 " (cutoff:3.500A)
      removed outlier: 6.783A  pdb=" N   GLY A 821 " --> pdb=" O   CYS A 791 " (cutoff:3.500A)
      removed outlier: 6.102A  pdb=" N   VAL A 793 " --> pdb=" O   GLY A 821 " (cutoff:3.500A)
      removed outlier: 7.703A  pdb=" N   VAL A 823 " --> pdb=" O   VAL A 793 " (cutoff:3.500A)
      removed outlier: 6.092A  pdb=" N   LEU A 884 " --> pdb=" O   VAL A 918 " (cutoff:3.500A)
      removed outlier: 7.609A  pdb=" N   ILE A 920 " --> pdb=" O   LEU A 884 " (cutoff:3.500A)
      removed outlier: 6.651A  pdb=" N   LEU A 886 " --> pdb=" O   ILE A 920 " (cutoff:3.500A)
      removed outlier: 6.742A  pdb=" N   ILE A1166 " --> pdb=" O   LEU A1198 " (cutoff:3.500A)
      removed outlier: 7.631A  pdb=" N   VAL A1200 " --> pdb=" O   ILE A1166 " (cutoff:3.500A)
      removed outlier: 6.176A  pdb=" N   MET A1168 " --> pdb=" O   VAL A1200 " (cutoff:3.500A)
      removed outlier: 3.986A  pdb=" N   SER A1169 " --> pdb=" O   TRP A1027 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 791 through 793
      removed outlier: 3.522A  pdb=" N   ILE B 920 " --> pdb=" O   LEU B 886 " (cutoff:3.500A)
      removed outlier: 6.256A  pdb=" N   ILE B1166 " --> pdb=" O   LEU B1198 " (cutoff:3.500A)
      removed outlier: 7.249A  pdb=" N   VAL B1200 " --> pdb=" O   ILE B1166 " (cutoff:3.500A)
      removed outlier: 6.271A  pdb=" N   MET B1168 " --> pdb=" O   VAL B1200 " (cutoff:3.500A)
      removed outlier: 3.659A  pdb=" N   SER B1169 " --> pdb=" O   TRP B1027 " (cutoff:3.500A)
      removed outlier: 5.926A  pdb=" N   ILE B1024 " --> pdb=" O   ARG B1055 " (cutoff:3.500A)
      removed outlier: 6.973A  pdb=" N   PHE B1057 " --> pdb=" O   ILE B1024 " (cutoff:3.500A)
      removed outlier: 6.054A  pdb=" N   VAL B1026 " --> pdb=" O   PHE B1057 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   GLY B1059 " --> pdb=" O   VAL B1026 " (cutoff:3.500A)
      removed outlier: 6.967A  pdb=" N   ILE B1054 " --> pdb=" O   ASP B1085 " (cutoff:3.500A)
      removed outlier: 8.238A  pdb=" N   MET B1087 " --> pdb=" O   ILE B1054 " (cutoff:3.500A)
      removed outlier: 6.095A  pdb=" N   VAL B1056 " --> pdb=" O   MET B1087 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   LEU B1089 " --> pdb=" O   VAL B1056 " (cutoff:3.500A)
      removed outlier: 6.570A  pdb=" N   ILE B1058 " --> pdb=" O   LEU B1089 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'B' and resid 818 through 819
      removed outlier: 6.471A  pdb=" N   MET B 818 " --> pdb=" O   PHE B 854 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'B' and resid 822 through 824
      removed outlier: 6.025A  pdb=" N   HIS B 822 " --> pdb=" O   VAL B 858 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA4
    Processing sheet with id=AA5, first strand: chain 'B' and resid 1112 through 1113

    736 hydrogen bonds defined for protein.
    2175 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: 4.39

  Time building geometry restraints manager: 3.87 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 4056
        1.34 -     1.47: 3203
        1.47 -     1.59: 5906
        1.59 -     1.71: 2
        1.71 -     1.84: 140
  Bond restraints: 13307
  Sorted by residual:
  bond pdb=" C4  FUN A1301 "
       pdb=" N2  FUN A1301 "
    ideal  model  delta    sigma   weight residual
    1.340  1.451 -0.111 2.00e-02 2.50e+03 3.08e+01
  bond pdb=" C4  FUN B1301 "
       pdb=" N2  FUN B1301 "
    ideal  model  delta    sigma   weight residual
    1.340  1.447 -0.107 2.00e-02 2.50e+03 2.87e+01
  bond pdb=" C7  FUN B1301 "
       pdb=" C8  FUN B1301 "
    ideal  model  delta    sigma   weight residual
    1.429  1.359  0.070 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" C7  FUN A1301 "
       pdb=" C8  FUN A1301 "
    ideal  model  delta    sigma   weight residual
    1.429  1.360  0.069 2.00e-02 2.50e+03 1.21e+01
  bond pdb=" N1  FUN A1301 "
       pdb=" S1  FUN A1301 "
    ideal  model  delta    sigma   weight residual
    1.647  1.708 -0.061 2.00e-02 2.50e+03 9.17e+00
  ... (remaining 13302 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.59: 17949
        3.59 -     7.18: 92
        7.18 -    10.76: 8
       10.76 -    14.35: 0
       14.35 -    17.94: 2
  Bond angle restraints: 18051
  Sorted by residual:
  angle pdb=" O1  FUN A1301 "
        pdb=" S1  FUN A1301 "
        pdb=" O2  FUN A1301 "
      ideal   model   delta    sigma   weight residual
     119.17  101.23   17.94 3.00e+00 1.11e-01 3.58e+01
  angle pdb=" O1  FUN B1301 "
        pdb=" S1  FUN B1301 "
        pdb=" O2  FUN B1301 "
      ideal   model   delta    sigma   weight residual
     119.17  101.25   17.92 3.00e+00 1.11e-01 3.57e+01
  angle pdb=" C   SER A 760 "
        pdb=" N   SER A 761 "
        pdb=" CA  SER A 761 "
      ideal   model   delta    sigma   weight residual
     121.54  128.19   -6.65 1.91e+00 2.74e-01 1.21e+01
  angle pdb=" CA  MET A 851 "
        pdb=" CB  MET A 851 "
        pdb=" CG  MET A 851 "
      ideal   model   delta    sigma   weight residual
     114.10  120.79   -6.69 2.00e+00 2.50e-01 1.12e+01
  angle pdb=" N   ILE A1081 "
        pdb=" CA  ILE A1081 "
        pdb=" C   ILE A1081 "
      ideal   model   delta    sigma   weight residual
     112.29  109.37    2.92 9.40e-01 1.13e+00 9.62e+00
  ... (remaining 18046 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.84: 7113
       17.84 -    35.67: 630
       35.67 -    53.51: 92
       53.51 -    71.35: 15
       71.35 -    89.19: 7
  Dihedral angle restraints: 7857
    sinusoidal: 3072
      harmonic: 4785
  Sorted by residual:
  dihedral pdb=" CB  CYS B 563 "
           pdb=" SG  CYS B 563 "
           pdb=" SG  CYS B 568 "
           pdb=" CB  CYS B 568 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -154.94   68.94     1      1.00e+01 1.00e-02 6.15e+01
  dihedral pdb=" CA  ASN B 571 "
           pdb=" C   ASN B 571 "
           pdb=" N   PHE B 572 "
           pdb=" CA  PHE B 572 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.16  -19.84     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  ALA A 505 "
           pdb=" C   ALA A 505 "
           pdb=" N   ASN A 506 "
           pdb=" CA  ASN A 506 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00 -160.46  -19.54     0      5.00e+00 4.00e-02 1.53e+01
  ... (remaining 7854 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 1666
       0.054 -    0.108: 366
       0.108 -    0.162: 45
       0.162 -    0.216: 3
       0.216 -    0.270: 1
  Chirality restraints: 2081
  Sorted by residual:
  chirality pdb=" CA  GLN A 914 "
            pdb=" N   GLN A 914 "
            pdb=" C   GLN A 914 "
            pdb=" CB  GLN A 914 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.24    0.27 2.00e-01 2.50e+01 1.82e+00
  chirality pdb=" CB  ILE A 747 "
            pdb=" CA  ILE A 747 "
            pdb=" CG1 ILE A 747 "
            pdb=" CG2 ILE A 747 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.48    0.17 2.00e-01 2.50e+01 6.91e-01
  chirality pdb=" CA  ASP A 755 "
            pdb=" N   ASP A 755 "
            pdb=" C   ASP A 755 "
            pdb=" CB  ASP A 755 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 6.85e-01
  ... (remaining 2078 not shown)

  Planarity restraints: 2240
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LYS B 461 "   -0.044 5.00e-02 4.00e+02   6.64e-02 7.06e+00
        pdb=" N   PRO B 462 "    0.115 5.00e-02 4.00e+02
        pdb=" CA  PRO B 462 "   -0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO B 462 "   -0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A 495 "    0.037 5.00e-02 4.00e+02   5.58e-02 4.98e+00
        pdb=" N   PRO A 496 "   -0.097 5.00e-02 4.00e+02
        pdb=" CA  PRO A 496 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 496 "    0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TYR B 655 "   -0.010 2.00e-02 2.50e+03   2.09e-02 4.37e+00
        pdb=" C   TYR B 655 "    0.036 2.00e-02 2.50e+03
        pdb=" O   TYR B 655 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   ILE B 656 "   -0.012 2.00e-02 2.50e+03
  ... (remaining 2237 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 283
        2.70 -     3.25: 14427
        3.25 -     3.80: 21393
        3.80 -     4.35: 26395
        4.35 -     4.90: 43401
  Nonbonded interactions: 105899
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 701 "
            pdb=" OD1 ASN A 769 "
     model   vdw
     2.145 3.040
  nonbonded pdb=" ND2 ASN A 298 "
            pdb=" O   GLY A 500 "
     model   vdw
     2.172 3.120
  nonbonded pdb=" NH1 ARG A1151 "
            pdb=" OE2 GLU A1154 "
     model   vdw
     2.180 3.120
  nonbonded pdb=" OD2 ASP B1032 "
            pdb=" OG1 THR B1036 "
     model   vdw
     2.191 3.040
  nonbonded pdb=" OD2 ASP B1025 "
            pdb=" OG  SER B1160 "
     model   vdw
     2.216 3.040
  ... (remaining 105894 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 'A' and (resid 287 through 1208 or resid 1301))
  selection = (chain 'B' and (resid 287 through 1208 or resid 1301))
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             6.200
  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:          0.490
  Check model and map are aligned:         0.090
  Set scattering table:                    0.100
  Process input model:                     33.320
  Find NCS groups from input model:        0.620
  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:3.040
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   43.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
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      :  0.004   0.111  13310  Z= 0.208
  Angle     :  0.733  17.940  18057  Z= 0.368
  Chirality :  0.044   0.270   2081
  Planarity :  0.005   0.066   2240
  Dihedral  : 13.509  89.187   4772
  Min Nonbonded Distance : 2.145

Molprobity Statistics.
  All-atom Clashscore : 15.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.24 %
    Favored  : 93.76 %
  Rotamer:
    Outliers :  0.07 %
    Allowed  :  0.36 %
    Favored  : 99.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.26 (0.20), residues: 1651
  helix:  1.11 (0.16), residues: 950
  sheet: -1.10 (0.48), residues: 122
  loop : -2.17 (0.23), residues: 579

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A1028 
 HIS   0.005   0.001   HIS B 908 
 PHE   0.023   0.002   PHE A 907 
 TYR   0.024   0.002   TYR B 751 
 ARG   0.005   0.000   ARG A 788 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.14407 (  736)
  hydrogen bonds       : angle       5.71459 ( 2175)
  SS BOND              : bond        0.00542 (    3)
  SS BOND              : angle       2.31106 (    6)
  covalent geometry    : bond        0.00441 (13307)
  covalent geometry    : angle       0.73156 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  323 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 322
  time to evaluate  : 2.386 
Fit side-chains
   revert: symmetry clash
REVERT: A  321 VAL cc_start: 0.9374 (t) cc_final: 0.9078 (p)
REVERT: A  326 MET cc_start: 0.7532 (tpp) cc_final: 0.7026 (tpp)
REVERT: A  847 ILE cc_start: 0.8664 (pt) cc_final: 0.8420 (mm)
REVERT: B  577 CYS cc_start: 0.5990 (m) cc_final: 0.5394 (m)
REVERT: B  694 PHE cc_start: 0.8948 (t80) cc_final: 0.8682 (t80)
REVERT: B  713 MET cc_start: 0.8171 (ppp) cc_final: 0.7683 (ppp)
REVERT: B  825 MET cc_start: 0.8883 (mpp) cc_final: 0.8229 (mpp)
REVERT: B 1101 ILE cc_start: 0.8138 (mt) cc_final: 0.7540 (mm)
  outliers start: 1
  outliers final: 0
  residues processed: 323
  average time/residue: 0.2093
  time to fit residues: 105.9596
Evaluate side-chains
  263 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 263
  time to evaluate  : 1.447 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 139 optimal weight:    0.1980
   chunk 125 optimal weight:    0.9990
   chunk 69 optimal weight:    4.9990
   chunk 42 optimal weight:    5.9990
   chunk 84 optimal weight:    0.5980
   chunk 66 optimal weight:    0.0020
   chunk 129 optimal weight:   10.0000
   chunk 50 optimal weight:    0.6980
   chunk 78 optimal weight:    0.3980
   chunk 96 optimal weight:    2.9990
   chunk 149 optimal weight:    0.5980
   overall best weight:    0.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 298 ASN
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 806 HIS
B 589 ASN
** B 639 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1100 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3946 r_free = 0.3946 target = 0.137089 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.113401 restraints weight = 28425.507|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.116015 restraints weight = 18865.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.117316 restraints weight = 14650.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3662
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.1315

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  13310  Z= 0.143
  Angle     :  0.654   9.420  18057  Z= 0.332
  Chirality :  0.043   0.171   2081
  Planarity :  0.004   0.063   2240
  Dihedral  :  6.138  85.856   1777
  Min Nonbonded Distance : 2.520

Molprobity Statistics.
  All-atom Clashscore : 14.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 11.03 %
    Favored  : 86.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.11 (0.20), residues: 1651
  helix:  1.17 (0.16), residues: 991
  sheet: -1.06 (0.47), residues: 124
  loop : -2.23 (0.24), residues: 536

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A1028 
 HIS   0.005   0.001   HIS B 908 
 PHE   0.031   0.002   PHE B 659 
 TYR   0.023   0.001   TYR A 739 
 ARG   0.006   0.000   ARG A1201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04632 (  736)
  hydrogen bonds       : angle       4.66406 ( 2175)
  SS BOND              : bond        0.00471 (    3)
  SS BOND              : angle       1.33817 (    6)
  covalent geometry    : bond        0.00321 (13307)
  covalent geometry    : angle       0.65375 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  321 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 292
  time to evaluate  : 1.375 
Fit side-chains
   revert: symmetry clash
REVERT: A  303 MET cc_start: 0.7790 (mtt) cc_final: 0.7145 (ttm)
REVERT: A  325 MET cc_start: 0.8226 (mtt) cc_final: 0.7979 (mtt)
REVERT: A  326 MET cc_start: 0.7573 (tpp) cc_final: 0.7260 (tpp)
REVERT: A  620 VAL cc_start: 0.8675 (t) cc_final: 0.8443 (m)
REVERT: A  878 ARG cc_start: 0.7530 (mmt180) cc_final: 0.7267 (mmt180)
REVERT: A 1041 TYR cc_start: 0.8501 (t80) cc_final: 0.8110 (t80)
REVERT: B  547 ASP cc_start: 0.8530 (m-30) cc_final: 0.8275 (m-30)
REVERT: B  694 PHE cc_start: 0.8970 (t80) cc_final: 0.8497 (t80)
REVERT: B  713 MET cc_start: 0.7599 (ppp) cc_final: 0.7066 (ppp)
REVERT: B 1101 ILE cc_start: 0.8200 (mt) cc_final: 0.7757 (mm)
  outliers start: 29
  outliers final: 16
  residues processed: 302
  average time/residue: 0.2091
  time to fit residues: 99.2587
Evaluate side-chains
  282 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 266
  time to evaluate  : 1.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  436 ILE
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  488 PHE
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  741 ILE
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1158 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 102 optimal weight:    0.6980
   chunk 75 optimal weight:    2.9990
   chunk 152 optimal weight:    2.9990
   chunk 6 optimal weight:    4.9990
   chunk 20 optimal weight:    0.8980
   chunk 113 optimal weight:    0.8980
   chunk 59 optimal weight:    0.9990
   chunk 45 optimal weight:    1.9990
   chunk 104 optimal weight:    0.3980
   chunk 53 optimal weight:    0.0570
   overall best weight:    0.5898

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

Flipped N/Q/H residues before XYZ refinement:
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 298 ASN
** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.136728 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.112182 restraints weight = 28662.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.115606 restraints weight = 18755.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.116202 restraints weight = 12956.173|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7623
moved from start:          0.1597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  13310  Z= 0.141
  Angle     :  0.643  14.337  18057  Z= 0.323
  Chirality :  0.043   0.166   2081
  Planarity :  0.004   0.063   2240
  Dihedral  :  6.087  86.478   1777
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 13.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 15.33 %
    Favored  : 82.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.06 (0.20), residues: 1651
  helix:  1.38 (0.17), residues: 956
  sheet: -1.00 (0.47), residues: 124
  loop : -2.11 (0.23), residues: 571

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A1028 
 HIS   0.004   0.001   HIS A1114 
 PHE   0.047   0.002   PHE B 659 
 TYR   0.024   0.001   TYR A 739 
 ARG   0.005   0.000   ARG A1201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04245 (  736)
  hydrogen bonds       : angle       4.50419 ( 2175)
  SS BOND              : bond        0.00265 (    3)
  SS BOND              : angle       1.13590 (    6)
  covalent geometry    : bond        0.00321 (13307)
  covalent geometry    : angle       0.64228 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 289
  time to evaluate  : 1.752 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  326 MET cc_start: 0.7563 (tpp) cc_final: 0.7040 (tpp)
REVERT: A  569 LYS cc_start: 0.6818 (tppt) cc_final: 0.6539 (tppt)
REVERT: A  878 ARG cc_start: 0.7554 (mmt180) cc_final: 0.7251 (mmt180)
REVERT: B  547 ASP cc_start: 0.8474 (m-30) cc_final: 0.8263 (m-30)
REVERT: B  694 PHE cc_start: 0.8843 (t80) cc_final: 0.8437 (t80)
REVERT: B  713 MET cc_start: 0.7599 (ppp) cc_final: 0.7052 (ppp)
REVERT: B 1040 PRO cc_start: 0.8780 (Cg_exo) cc_final: 0.8569 (Cg_endo)
  outliers start: 36
  outliers final: 23
  residues processed: 300
  average time/residue: 0.2138
  time to fit residues: 100.5329
Evaluate side-chains
  288 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 265
  time to evaluate  : 1.731 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1161 SER
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  488 PHE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue 1114 HIS
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1158 GLU
Chi-restraints excluded: chain B residue 1193 ASP
Chi-restraints excluded: chain B residue 1197 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 114 optimal weight:    0.9990
   chunk 162 optimal weight:    0.9980
   chunk 151 optimal weight:    0.9990
   chunk 63 optimal weight:    0.0010
   chunk 161 optimal weight:    1.9990
   chunk 49 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 42 optimal weight:    6.9990
   chunk 46 optimal weight:    0.9980
   chunk 9 optimal weight:    0.5980
   chunk 122 optimal weight:    2.9990
   overall best weight:    0.6986

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

Flipped N/Q/H residues before XYZ refinement:
** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.136144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.112203 restraints weight = 28474.994|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.115309 restraints weight = 18644.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.115842 restraints weight = 13608.923|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7631
moved from start:          0.1868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  13310  Z= 0.145
  Angle     :  0.648  11.057  18057  Z= 0.325
  Chirality :  0.044   0.186   2081
  Planarity :  0.004   0.062   2240
  Dihedral  :  6.021  87.444   1777
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 14.51
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.88 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 16.91 %
    Favored  : 79.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.20), residues: 1651
  helix:  1.33 (0.16), residues: 961
  sheet: -0.91 (0.47), residues: 122
  loop : -2.15 (0.23), residues: 568

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B 704 
 HIS   0.004   0.001   HIS B 809 
 PHE   0.045   0.002   PHE B 659 
 TYR   0.017   0.001   TYR A 903 
 ARG   0.004   0.000   ARG A1201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04099 (  736)
  hydrogen bonds       : angle       4.46378 ( 2175)
  SS BOND              : bond        0.00221 (    3)
  SS BOND              : angle       1.04852 (    6)
  covalent geometry    : bond        0.00336 (13307)
  covalent geometry    : angle       0.64776 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  330 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 284
  time to evaluate  : 1.590 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.8201 (mtt) cc_final: 0.7990 (mtt)
REVERT: A  326 MET cc_start: 0.7564 (tpp) cc_final: 0.7046 (tpp)
REVERT: A  569 LYS cc_start: 0.6793 (tppt) cc_final: 0.6509 (tppt)
REVERT: A  748 TYR cc_start: 0.8115 (t80) cc_final: 0.7761 (t80)
REVERT: B  577 CYS cc_start: 0.5288 (m) cc_final: 0.4674 (m)
REVERT: B  694 PHE cc_start: 0.8841 (t80) cc_final: 0.8512 (t80)
REVERT: B  713 MET cc_start: 0.7661 (ppp) cc_final: 0.7176 (ppp)
REVERT: B  772 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8363 (tm-30)
REVERT: B  825 MET cc_start: 0.8943 (mpp) cc_final: 0.8610 (mpp)
REVERT: B 1065 ILE cc_start: 0.8313 (mm) cc_final: 0.8100 (mm)
REVERT: B 1101 ILE cc_start: 0.8325 (mt) cc_final: 0.8054 (mm)
  outliers start: 46
  outliers final: 29
  residues processed: 302
  average time/residue: 0.2574
  time to fit residues: 122.1055
Evaluate side-chains
  280 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 250
  time to evaluate  : 1.529 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  568 CYS
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1038 LEU
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  488 PHE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  772 GLN
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue 1114 HIS
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1156 LEU
Chi-restraints excluded: chain B residue 1158 GLU
Chi-restraints excluded: chain B residue 1162 THR
Chi-restraints excluded: chain B residue 1193 ASP
Chi-restraints excluded: chain B residue 1197 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 106 optimal weight:    0.9990
   chunk 6 optimal weight:    4.9990
   chunk 126 optimal weight:    0.7980
   chunk 142 optimal weight:    0.6980
   chunk 144 optimal weight:    1.9990
   chunk 56 optimal weight:    2.9990
   chunk 148 optimal weight:    0.9980
   chunk 25 optimal weight:    0.0370
   chunk 17 optimal weight:    1.9990
   chunk 36 optimal weight:    0.5980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.6258

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

Flipped N/Q/H residues before XYZ refinement:
** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3942 r_free = 0.3942 target = 0.136443 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.112001 restraints weight = 28719.889|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.115779 restraints weight = 18894.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.116259 restraints weight = 12469.115|
|-----------------------------------------------------------------------------|
r_work (final): 0.3652
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7615
moved from start:          0.2027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.067  13310  Z= 0.144
  Angle     :  0.644   9.859  18057  Z= 0.325
  Chirality :  0.045   0.404   2081
  Planarity :  0.004   0.063   2240
  Dihedral  :  5.987  88.563   1777
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 14.67
  Ramachandran Plot:
    Outliers :  0.06 %
    Allowed  :  5.51 %
    Favored  : 94.43 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 17.84 %
    Favored  : 78.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.02 (0.20), residues: 1651
  helix:  1.35 (0.17), residues: 963
  sheet: -0.96 (0.47), residues: 121
  loop : -2.18 (0.23), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A1028 
 HIS   0.004   0.001   HIS B 908 
 PHE   0.065   0.002   PHE B 659 
 TYR   0.017   0.001   TYR A 903 
 ARG   0.003   0.000   ARG A1201 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04009 (  736)
  hydrogen bonds       : angle       4.43011 ( 2175)
  SS BOND              : bond        0.00182 (    3)
  SS BOND              : angle       1.00120 (    6)
  covalent geometry    : bond        0.00335 (13307)
  covalent geometry    : angle       0.64389 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  325 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 55
    poor density    : 270
  time to evaluate  : 1.295 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  569 LYS cc_start: 0.6784 (tppt) cc_final: 0.6522 (tppt)
REVERT: A  748 TYR cc_start: 0.8129 (t80) cc_final: 0.7778 (t80)
REVERT: A  878 ARG cc_start: 0.7535 (mmt180) cc_final: 0.7282 (mmt180)
REVERT: B  523 LEU cc_start: 0.8985 (mt) cc_final: 0.8733 (mt)
REVERT: B  547 ASP cc_start: 0.8548 (m-30) cc_final: 0.8192 (t0)
REVERT: B  577 CYS cc_start: 0.5581 (m) cc_final: 0.4219 (m)
REVERT: B  694 PHE cc_start: 0.8820 (t80) cc_final: 0.8530 (t80)
REVERT: B  713 MET cc_start: 0.7634 (ppp) cc_final: 0.7153 (ppp)
REVERT: B  772 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8399 (tm-30)
REVERT: B  825 MET cc_start: 0.8961 (mpp) cc_final: 0.8638 (mpp)
REVERT: B 1043 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9243 (mm)
REVERT: B 1065 ILE cc_start: 0.8314 (mm) cc_final: 0.8109 (mm)
REVERT: B 1072 MET cc_start: 0.8226 (mmm) cc_final: 0.7945 (tmm)
  outliers start: 55
  outliers final: 35
  residues processed: 299
  average time/residue: 0.2077
  time to fit residues: 96.7116
Evaluate side-chains
  293 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 256
  time to evaluate  : 1.427 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  568 CYS
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue 1038 LEU
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  385 VAL
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  488 PHE
Chi-restraints excluded: chain B residue  526 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  772 GLN
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue 1043 LEU
Chi-restraints excluded: chain B residue 1114 HIS
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1156 LEU
Chi-restraints excluded: chain B residue 1158 GLU
Chi-restraints excluded: chain B residue 1162 THR
Chi-restraints excluded: chain B residue 1193 ASP
Chi-restraints excluded: chain B residue 1197 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 164 optimal weight:    0.8980
   chunk 85 optimal weight:    0.9980
   chunk 92 optimal weight:    0.9980
   chunk 6 optimal weight:    3.9990
   chunk 13 optimal weight:    3.9990
   chunk 150 optimal weight:    8.9990
   chunk 26 optimal weight:    7.9990
   chunk 58 optimal weight:    0.6980
   chunk 44 optimal weight:    2.9990
   chunk 131 optimal weight:    3.9990
   chunk 102 optimal weight:    0.9980
   overall best weight:    0.9180

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

Flipped N/Q/H residues before XYZ refinement:
** B 589 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3928 r_free = 0.3928 target = 0.135319 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.110906 restraints weight = 28880.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.114600 restraints weight = 19626.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.115140 restraints weight = 12478.308|
|-----------------------------------------------------------------------------|
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7634
moved from start:          0.2172

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13310  Z= 0.158
  Angle     :  0.654  10.443  18057  Z= 0.330
  Chirality :  0.045   0.248   2081
  Planarity :  0.004   0.064   2240
  Dihedral  :  5.964  89.850   1777
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 14.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.63 %
    Favored  : 94.37 %
  Rotamer:
    Outliers :  3.44 %
    Allowed  : 19.70 %
    Favored  : 76.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.07 (0.20), residues: 1651
  helix:  1.32 (0.17), residues: 959
  sheet: -1.03 (0.48), residues: 118
  loop : -2.27 (0.23), residues: 574

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 892 
 HIS   0.004   0.001   HIS B 908 
 PHE   0.068   0.002   PHE B 659 
 TYR   0.018   0.001   TYR A 903 
 ARG   0.004   0.000   ARG A 358 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04002 (  736)
  hydrogen bonds       : angle       4.45803 ( 2175)
  SS BOND              : bond        0.00227 (    3)
  SS BOND              : angle       1.01064 (    6)
  covalent geometry    : bond        0.00369 (13307)
  covalent geometry    : angle       0.65337 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  316 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 48
    poor density    : 268
  time to evaluate  : 1.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  435 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6468 (tm-30)
REVERT: A  569 LYS cc_start: 0.6765 (tppt) cc_final: 0.6448 (tppt)
REVERT: A  748 TYR cc_start: 0.8179 (t80) cc_final: 0.7804 (t80)
REVERT: A 1106 GLU cc_start: 0.8426 (mm-30) cc_final: 0.7985 (mm-30)
REVERT: B  523 LEU cc_start: 0.8931 (mt) cc_final: 0.8664 (mt)
REVERT: B  547 ASP cc_start: 0.8612 (m-30) cc_final: 0.8261 (t0)
REVERT: B  577 CYS cc_start: 0.5534 (m) cc_final: 0.4285 (m)
REVERT: B  694 PHE cc_start: 0.8831 (t80) cc_final: 0.8495 (t80)
REVERT: B  713 MET cc_start: 0.7702 (ppp) cc_final: 0.7153 (ppp)
REVERT: B  772 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8402 (tm-30)
REVERT: B  776 ARG cc_start: 0.8609 (mtp85) cc_final: 0.8347 (mtp85)
REVERT: B  825 MET cc_start: 0.8975 (mpp) cc_final: 0.8704 (mpp)
REVERT: B 1043 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9230 (mm)
  outliers start: 48
  outliers final: 33
  residues processed: 295
  average time/residue: 0.2462
  time to fit residues: 112.4830
Evaluate side-chains
  290 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 254
  time to evaluate  : 1.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  435 GLN
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue 1038 LEU
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  488 PHE
Chi-restraints excluded: chain B residue  526 ILE
Chi-restraints excluded: chain B residue  531 LEU
Chi-restraints excluded: chain B residue  592 VAL
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  772 GLN
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue 1043 LEU
Chi-restraints excluded: chain B residue 1114 HIS
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1156 LEU
Chi-restraints excluded: chain B residue 1158 GLU
Chi-restraints excluded: chain B residue 1162 THR
Chi-restraints excluded: chain B residue 1193 ASP
Chi-restraints excluded: chain B residue 1197 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 88 optimal weight:    6.9990
   chunk 96 optimal weight:    4.9990
   chunk 139 optimal weight:    2.9990
   chunk 23 optimal weight:    0.3980
   chunk 147 optimal weight:    3.9990
   chunk 117 optimal weight:    0.9990
   chunk 121 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 68 optimal weight:    0.7980
   chunk 83 optimal weight:    1.9990
   chunk 42 optimal weight:    2.9990
   overall best weight:    1.0184

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

Flipped N/Q/H residues before XYZ refinement:
B 843 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.134859 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.110860 restraints weight = 28792.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.114902 restraints weight = 19174.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.115195 restraints weight = 13270.252|
|-----------------------------------------------------------------------------|
r_work (final): 0.3634
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7643
moved from start:          0.2299

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048  13310  Z= 0.167
  Angle     :  0.675  10.737  18057  Z= 0.340
  Chirality :  0.045   0.234   2081
  Planarity :  0.004   0.064   2240
  Dihedral  :  5.963  88.094   1777
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 15.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.99 %
    Favored  : 76.22 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.13 (0.21), residues: 1651
  helix:  1.27 (0.17), residues: 959
  sheet: -1.13 (0.48), residues: 120
  loop : -2.27 (0.23), residues: 572

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.001   TRP A 892 
 HIS   0.004   0.001   HIS B 908 
 PHE   0.067   0.002   PHE B 659 
 TYR   0.023   0.002   TYR B 751 
 ARG   0.006   0.000   ARG A 898 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04063 (  736)
  hydrogen bonds       : angle       4.51605 ( 2175)
  SS BOND              : bond        0.00163 (    3)
  SS BOND              : angle       1.17191 (    6)
  covalent geometry    : bond        0.00392 (13307)
  covalent geometry    : angle       0.67484 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  313 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 53
    poor density    : 260
  time to evaluate  : 1.848 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  748 TYR cc_start: 0.8224 (t80) cc_final: 0.7828 (t80)
REVERT: A  903 TYR cc_start: 0.8291 (t80) cc_final: 0.7993 (t80)
REVERT: A 1106 GLU cc_start: 0.8410 (mm-30) cc_final: 0.8065 (mm-30)
REVERT: B  523 LEU cc_start: 0.8916 (mt) cc_final: 0.8653 (mt)
REVERT: B  671 LEU cc_start: 0.9016 (OUTLIER) cc_final: 0.8783 (tt)
REVERT: B  694 PHE cc_start: 0.8851 (t80) cc_final: 0.8560 (t80)
REVERT: B  713 MET cc_start: 0.7700 (ppp) cc_final: 0.7140 (ppp)
REVERT: B  772 GLN cc_start: 0.8824 (OUTLIER) cc_final: 0.8481 (tm-30)
REVERT: B  776 ARG cc_start: 0.8579 (mtp85) cc_final: 0.8267 (mtp85)
REVERT: B  825 MET cc_start: 0.8946 (mpp) cc_final: 0.8677 (mpp)
REVERT: B 1043 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9231 (mm)
REVERT: B 1053 LYS cc_start: 0.8266 (OUTLIER) cc_final: 0.7922 (ttpp)
REVERT: B 1065 ILE cc_start: 0.8371 (mm) cc_final: 0.8160 (mm)
  outliers start: 53
  outliers final: 36
  residues processed: 292
  average time/residue: 0.2186
  time to fit residues: 98.6117
Evaluate side-chains
  289 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 249
  time to evaluate  : 1.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  570 LEU
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue 1038 LEU
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  526 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  665 PHE
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  772 GLN
Chi-restraints excluded: chain B residue  792 LEU
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue  902 MET
Chi-restraints excluded: chain B residue 1043 LEU
Chi-restraints excluded: chain B residue 1053 LYS
Chi-restraints excluded: chain B residue 1114 HIS
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1156 LEU
Chi-restraints excluded: chain B residue 1158 GLU
Chi-restraints excluded: chain B residue 1162 THR
Chi-restraints excluded: chain B residue 1193 ASP
Chi-restraints excluded: chain B residue 1197 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 87 optimal weight:    2.9990
   chunk 9 optimal weight:    0.6980
   chunk 72 optimal weight:    0.5980
   chunk 109 optimal weight:    5.9990
   chunk 53 optimal weight:    3.9990
   chunk 64 optimal weight:    0.9990
   chunk 15 optimal weight:    2.9990
   chunk 149 optimal weight:    2.9990
   chunk 56 optimal weight:    0.4980
   chunk 26 optimal weight:    5.9990
   chunk 111 optimal weight:    2.9990
   overall best weight:    1.1584

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.134148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.110358 restraints weight = 28833.274|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.112304 restraints weight = 19968.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.112955 restraints weight = 16001.506|
|-----------------------------------------------------------------------------|
r_work (final): 0.3603
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7687
moved from start:          0.2420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055  13310  Z= 0.181
  Angle     :  0.708  10.618  18057  Z= 0.355
  Chirality :  0.046   0.205   2081
  Planarity :  0.004   0.065   2240
  Dihedral  :  5.975  85.876   1777
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.00 %
    Favored  : 94.00 %
  Rotamer:
    Outliers :  3.72 %
    Allowed  : 21.85 %
    Favored  : 74.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.22 (0.20), residues: 1651
  helix:  1.17 (0.17), residues: 966
  sheet: -1.13 (0.48), residues: 118
  loop : -2.30 (0.23), residues: 567

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.001   TRP A 892 
 HIS   0.004   0.001   HIS B 908 
 PHE   0.065   0.002   PHE B 659 
 TYR   0.025   0.002   TYR B 751 
 ARG   0.006   0.000   ARG A 898 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04126 (  736)
  hydrogen bonds       : angle       4.60280 ( 2175)
  SS BOND              : bond        0.00567 (    3)
  SS BOND              : angle       1.25381 (    6)
  covalent geometry    : bond        0.00424 (13307)
  covalent geometry    : angle       0.70798 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  301 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 52
    poor density    : 249
  time to evaluate  : 1.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.8777 (mpp) cc_final: 0.8536 (mpt)
REVERT: A  713 MET cc_start: 0.7633 (pmm) cc_final: 0.7212 (ppp)
REVERT: A 1106 GLU cc_start: 0.8395 (mm-30) cc_final: 0.8091 (mm-30)
REVERT: B  523 LEU cc_start: 0.8930 (mt) cc_final: 0.8652 (mt)
REVERT: B  577 CYS cc_start: 0.6161 (m) cc_final: 0.5765 (m)
REVERT: B  595 MET cc_start: 0.8232 (tpt) cc_final: 0.7944 (tpt)
REVERT: B  671 LEU cc_start: 0.9041 (OUTLIER) cc_final: 0.8805 (tt)
REVERT: B  694 PHE cc_start: 0.8867 (t80) cc_final: 0.8612 (t80)
REVERT: B  713 MET cc_start: 0.7709 (ppp) cc_final: 0.7154 (ppp)
REVERT: B  772 GLN cc_start: 0.8848 (OUTLIER) cc_final: 0.8493 (tm-30)
REVERT: B  825 MET cc_start: 0.8943 (mpp) cc_final: 0.8605 (mpp)
REVERT: B 1043 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9240 (mm)
REVERT: B 1065 ILE cc_start: 0.8419 (mm) cc_final: 0.8209 (mm)
  outliers start: 52
  outliers final: 39
  residues processed: 281
  average time/residue: 0.2042
  time to fit residues: 89.6026
Evaluate side-chains
  286 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 244
  time to evaluate  : 1.525 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  358 ARG
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  659 PHE
Chi-restraints excluded: chain A residue  663 LEU
Chi-restraints excluded: chain A residue  701 SER
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue 1038 LEU
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  526 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  665 PHE
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  772 GLN
Chi-restraints excluded: chain B residue  792 LEU
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  805 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue  902 MET
Chi-restraints excluded: chain B residue 1043 LEU
Chi-restraints excluded: chain B residue 1114 HIS
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1156 LEU
Chi-restraints excluded: chain B residue 1158 GLU
Chi-restraints excluded: chain B residue 1162 THR
Chi-restraints excluded: chain B residue 1193 ASP
Chi-restraints excluded: chain B residue 1197 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 104 optimal weight:    0.0870
   chunk 1 optimal weight:    0.8980
   chunk 78 optimal weight:    0.9980
   chunk 146 optimal weight:    0.9980
   chunk 21 optimal weight:    0.8980
   chunk 55 optimal weight:    0.9990
   chunk 79 optimal weight:    0.4980
   chunk 82 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 107 optimal weight:    0.3980
   chunk 84 optimal weight:    0.9990
   overall best weight:    0.5558

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

Flipped N/Q/H residues before XYZ refinement:
A 757 ASN
B 591 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.136031 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.112171 restraints weight = 28559.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.115692 restraints weight = 18533.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.116012 restraints weight = 13629.944|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7618
moved from start:          0.2528

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  13310  Z= 0.142
  Angle     :  0.694  10.606  18057  Z= 0.345
  Chirality :  0.045   0.191   2081
  Planarity :  0.004   0.064   2240
  Dihedral  :  5.892  83.767   1777
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 14.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 22.28 %
    Favored  : 74.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.20), residues: 1651
  helix:  1.22 (0.17), residues: 968
  sheet: -1.34 (0.48), residues: 118
  loop : -2.21 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.001   TRP A 892 
 HIS   0.004   0.001   HIS B 908 
 PHE   0.065   0.002   PHE B 659 
 TYR   0.045   0.002   TYR A 354 
 ARG   0.006   0.000   ARG A 898 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03985 (  736)
  hydrogen bonds       : angle       4.52761 ( 2175)
  SS BOND              : bond        0.00277 (    3)
  SS BOND              : angle       0.96772 (    6)
  covalent geometry    : bond        0.00329 (13307)
  covalent geometry    : angle       0.69410 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  312 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 45
    poor density    : 267
  time to evaluate  : 1.475 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  325 MET cc_start: 0.8789 (mpp) cc_final: 0.8525 (mpt)
REVERT: A  713 MET cc_start: 0.7570 (pmm) cc_final: 0.7216 (ppp)
REVERT: A  757 ASN cc_start: 0.5671 (OUTLIER) cc_final: 0.5023 (p0)
REVERT: A 1106 GLU cc_start: 0.8365 (mm-30) cc_final: 0.8145 (mm-30)
REVERT: B  523 LEU cc_start: 0.8908 (mt) cc_final: 0.8639 (mt)
REVERT: B  524 LEU cc_start: 0.8662 (tt) cc_final: 0.8458 (tp)
REVERT: B  577 CYS cc_start: 0.5962 (m) cc_final: 0.5549 (m)
REVERT: B  694 PHE cc_start: 0.8789 (t80) cc_final: 0.8569 (t80)
REVERT: B  713 MET cc_start: 0.7511 (ppp) cc_final: 0.7009 (ppp)
REVERT: B  772 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8482 (tm-30)
REVERT: B  825 MET cc_start: 0.8923 (mpp) cc_final: 0.8648 (mpp)
REVERT: B 1043 LEU cc_start: 0.9536 (OUTLIER) cc_final: 0.9238 (mm)
REVERT: B 1065 ILE cc_start: 0.8379 (mm) cc_final: 0.8147 (mm)
  outliers start: 45
  outliers final: 34
  residues processed: 294
  average time/residue: 0.2513
  time to fit residues: 117.8138
Evaluate side-chains
  287 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 250
  time to evaluate  : 2.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  358 ARG
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  757 ASN
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue 1038 LEU
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  329 VAL
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  346 PHE
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  526 ILE
Chi-restraints excluded: chain B residue  529 THR
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  665 PHE
Chi-restraints excluded: chain B residue  772 GLN
Chi-restraints excluded: chain B residue  792 LEU
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue 1043 LEU
Chi-restraints excluded: chain B residue 1114 HIS
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1156 LEU
Chi-restraints excluded: chain B residue 1158 GLU
Chi-restraints excluded: chain B residue 1162 THR
Chi-restraints excluded: chain B residue 1193 ASP
Chi-restraints excluded: chain B residue 1197 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 17 optimal weight:    0.5980
   chunk 92 optimal weight:    0.8980
   chunk 102 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0370
   chunk 2 optimal weight:    0.9990
   chunk 111 optimal weight:    3.9990
   chunk 68 optimal weight:    0.0040
   chunk 98 optimal weight:    0.9980
   chunk 135 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0970
   overall best weight:    0.2868

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

Flipped N/Q/H residues before XYZ refinement:
A 757 ASN
** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.136225 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.112220 restraints weight = 28562.326|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.115544 restraints weight = 18613.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.115935 restraints weight = 14166.260|
|-----------------------------------------------------------------------------|
r_work (final): 0.3647
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2597

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.251  13310  Z= 0.222
  Angle     :  0.939  59.176  18057  Z= 0.513
  Chirality :  0.047   0.503   2081
  Planarity :  0.004   0.064   2240
  Dihedral  :  5.890  83.737   1777
  Min Nonbonded Distance : 2.080

Molprobity Statistics.
  All-atom Clashscore : 16.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  3.08 %
    Allowed  : 22.64 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.20), residues: 1651
  helix:  1.22 (0.17), residues: 968
  sheet: -1.36 (0.48), residues: 118
  loop : -2.23 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 892 
 HIS   0.004   0.001   HIS B 908 
 PHE   0.065   0.002   PHE B 659 
 TYR   0.039   0.002   TYR A 354 
 ARG   0.022   0.001   ARG B1151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03992 (  736)
  hydrogen bonds       : angle       4.53261 ( 2175)
  SS BOND              : bond        0.02173 (    3)
  SS BOND              : angle       9.13557 (    6)
  covalent geometry    : bond        0.00507 (13307)
  covalent geometry    : angle       0.92400 (18051)

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

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

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3302 Ramachandran restraints generated.
    1651 Oldfield, 0 Emsley, 1651 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  296 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 253
  time to evaluate  : 2.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  288 ILE cc_start: 0.4041 (OUTLIER) cc_final: 0.3509 (mt)
REVERT: A  325 MET cc_start: 0.8787 (mpp) cc_final: 0.8532 (mpt)
REVERT: A  713 MET cc_start: 0.7572 (pmm) cc_final: 0.7212 (ppp)
REVERT: A  902 MET cc_start: 0.8553 (tpp) cc_final: 0.8248 (tpp)
REVERT: A 1106 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8140 (mm-30)
REVERT: B  523 LEU cc_start: 0.8889 (mt) cc_final: 0.8455 (mt)
REVERT: B  577 CYS cc_start: 0.5976 (m) cc_final: 0.5545 (m)
REVERT: B  694 PHE cc_start: 0.8784 (t80) cc_final: 0.8563 (t80)
REVERT: B  713 MET cc_start: 0.7505 (ppp) cc_final: 0.7002 (ppp)
REVERT: B  772 GLN cc_start: 0.8832 (OUTLIER) cc_final: 0.8478 (tm-30)
REVERT: B  825 MET cc_start: 0.8862 (mpp) cc_final: 0.8601 (mpp)
REVERT: B 1043 LEU cc_start: 0.9520 (OUTLIER) cc_final: 0.9229 (mm)
REVERT: B 1065 ILE cc_start: 0.8358 (mm) cc_final: 0.8142 (mm)
  outliers start: 43
  outliers final: 36
  residues processed: 279
  average time/residue: 0.3512
  time to fit residues: 155.7451
Evaluate side-chains
  286 residues out of total 1396 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 247
  time to evaluate  : 2.753 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  288 ILE
Chi-restraints excluded: chain A residue  323 VAL
Chi-restraints excluded: chain A residue  337 SER
Chi-restraints excluded: chain A residue  358 ARG
Chi-restraints excluded: chain A residue  415 ILE
Chi-restraints excluded: chain A residue  472 ILE
Chi-restraints excluded: chain A residue  523 LEU
Chi-restraints excluded: chain A residue  531 LEU
Chi-restraints excluded: chain A residue  568 CYS
Chi-restraints excluded: chain A residue  587 MET
Chi-restraints excluded: chain A residue  722 LEU
Chi-restraints excluded: chain A residue  756 VAL
Chi-restraints excluded: chain A residue  835 MET
Chi-restraints excluded: chain A residue  922 LEU
Chi-restraints excluded: chain A residue 1038 LEU
Chi-restraints excluded: chain A residue 1042 LEU
Chi-restraints excluded: chain A residue 1204 HIS
Chi-restraints excluded: chain B residue  304 LEU
Chi-restraints excluded: chain B residue  337 SER
Chi-restraints excluded: chain B residue  346 PHE
Chi-restraints excluded: chain B residue  420 LEU
Chi-restraints excluded: chain B residue  540 VAL
Chi-restraints excluded: chain B residue  640 MET
Chi-restraints excluded: chain B residue  657 LEU
Chi-restraints excluded: chain B residue  659 PHE
Chi-restraints excluded: chain B residue  665 PHE
Chi-restraints excluded: chain B residue  772 GLN
Chi-restraints excluded: chain B residue  792 LEU
Chi-restraints excluded: chain B residue  804 LEU
Chi-restraints excluded: chain B residue  883 THR
Chi-restraints excluded: chain B residue  902 MET
Chi-restraints excluded: chain B residue 1043 LEU
Chi-restraints excluded: chain B residue 1114 HIS
Chi-restraints excluded: chain B residue 1144 THR
Chi-restraints excluded: chain B residue 1156 LEU
Chi-restraints excluded: chain B residue 1158 GLU
Chi-restraints excluded: chain B residue 1162 THR
Chi-restraints excluded: chain B residue 1193 ASP
Chi-restraints excluded: chain B residue 1197 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 165
   random chunks:
   chunk 96 optimal weight:    1.9990
   chunk 77 optimal weight:    0.5980
   chunk 141 optimal weight:    0.8980
   chunk 129 optimal weight:   10.0000
   chunk 80 optimal weight:    0.5980
   chunk 93 optimal weight:    6.9990
   chunk 75 optimal weight:    0.6980
   chunk 27 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 99 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 757 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 591 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.136197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.112438 restraints weight = 28630.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.115367 restraints weight = 18764.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.115850 restraints weight = 14447.848|
|-----------------------------------------------------------------------------|
r_work (final): 0.3644
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7626
moved from start:          0.2584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.251  13310  Z= 0.222
  Angle     :  0.939  59.176  18057  Z= 0.513
  Chirality :  0.047   0.503   2081
  Planarity :  0.004   0.064   2240
  Dihedral  :  5.890  83.737   1777
  Min Nonbonded Distance : 1.718

Molprobity Statistics.
  All-atom Clashscore : 18.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.39 %
    Favored  : 94.61 %
  Rotamer:
    Outliers :  2.79 %
    Allowed  : 22.92 %
    Favored  : 74.28 %
  Cbeta Deviations :  0.07 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.16 (0.20), residues: 1651
  helix:  1.22 (0.17), residues: 968
  sheet: -1.36 (0.48), residues: 118
  loop : -2.23 (0.23), residues: 565

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A 892 
 HIS   0.004   0.001   HIS B 908 
 PHE   0.065   0.002   PHE B 659 
 TYR   0.039   0.002   TYR A 354 
 ARG   0.022   0.001   ARG B1151 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03992 (  736)
  hydrogen bonds       : angle       4.53262 ( 2175)
  SS BOND              : bond        0.02173 (    3)
  SS BOND              : angle       9.13557 (    6)
  covalent geometry    : bond        0.00507 (13307)
  covalent geometry    : angle       0.92400 (18051)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5032.91 seconds
wall clock time: 93 minutes 19.30 seconds (5599.30 seconds total)