Starting phenix.real_space_refine
on Thu Sep 18 06:49:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9cgi_45580/09_2025/9cgi_45580.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9cgi_45580/09_2025/9cgi_45580.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.92
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9cgi_45580/09_2025/9cgi_45580.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9cgi_45580/09_2025/9cgi_45580.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9cgi_45580/09_2025/9cgi_45580.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9cgi_45580/09_2025/9cgi_45580.map"
  }
  resolution = 2.92
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.012
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      96      5.16       5
     C    9355      2.51       5
     N    2513      2.21       5
     O    2787      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 32 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 14751
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "A"
      Number of atoms: 10576
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1314, 10576
          Classifications: {'peptide': 1314}
          Link IDs: {'PCIS': 1, 'PTRANS': 50, 'TRANS': 1262}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 806
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 101, 806
          Classifications: {'peptide': 101}
          Link IDs: {'PTRANS': 4, 'TRANS': 96}
    Chain: "C"
      Number of atoms: 1606
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1606
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 7, 'TRANS': 193}
          Chain breaks: 2
    Chain: "D"
      Number of atoms: 927
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 117, 927
          Classifications: {'peptide': 117}
          Link IDs: {'PTRANS': 5, 'TRANS': 111}
    Chain: "E"
      Number of atoms: 836
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 836
          Classifications: {'peptide': 106}
          Link IDs: {'PTRANS': 4, 'TRANS': 101}
  Time building chain proxies: 3.70, per 1000 atoms: 0.25
  Number of scatterers: 14751
  At special positions: 0
  Unit cell: (102.699, 110.667, 197.429, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      96     16.00
     O    2787      8.00
     N    2513      7.00
     C    9355      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A1191 " - pdb=" SG  CYS A1429 " 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: 1.33
  Conformation dependent library (CDL) restraints added in 655.1 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3512

  Finding SS restraints...
    Secondary structure from input PDB file:
      87 helices and 11 sheets defined
      64.4% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.66
  Creating SS restraints...
    Processing helix  chain 'A' and resid 23 through 33
      removed outlier: 3.697A  pdb=" N   ALA A  33 " --> pdb=" O   ALA A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 43 through 56
    Processing helix  chain 'A' and resid 60 through 77
    Processing helix  chain 'A' and resid 79 through 83
    Processing helix  chain 'A' and resid 91 through 96
    Processing helix  chain 'A' and resid 104 through 137
      removed outlier: 3.779A  pdb=" N   ILE A 120 " --> pdb=" O   LYS A 116 " (cutoff:3.500A)
      removed outlier: 4.090A  pdb=" N   ILE A 121 " --> pdb=" O   ALA A 117 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   LYS A 123 " --> pdb=" O   ASN A 119 " (cutoff:3.500A)
      removed outlier: 5.525A  pdb=" N   LYS A 124 " --> pdb=" O   ILE A 120 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 140 through 155
    Processing helix  chain 'A' and resid 156 through 163
    Processing helix  chain 'A' and resid 166 through 188
      removed outlier: 3.612A  pdb=" N   PHE A 170 " --> pdb=" O   TRP A 166 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 189 through 193
      removed outlier: 3.966A  pdb=" N   ARG A 193 " --> pdb=" O   PRO A 190 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 255
    Processing helix  chain 'A' and resid 260 through 273
      removed outlier: 3.951A  pdb=" N   ARG A 264 " --> pdb=" O   PRO A 260 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   SER A 265 " --> pdb=" O   LEU A 261 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   ASN A 266 " --> pdb=" O   ILE A 262 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   ILE A 272 " --> pdb=" O   LEU A 268 " (cutoff:3.500A)
      removed outlier: 3.777A  pdb=" N   ASP A 273 " --> pdb=" O   TRP A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 280
    Processing helix  chain 'A' and resid 282 through 288
      removed outlier: 3.832A  pdb=" N   ILE A 286 " --> pdb=" O   ARG A 282 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 289 through 300
      removed outlier: 3.621A  pdb=" N   VAL A 294 " --> pdb=" O   ILE A 290 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   LEU A 295 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 309 through 327
      removed outlier: 4.028A  pdb=" N   HIS A 314 " --> pdb=" O   ALA A 310 " (cutoff:3.500A)
      removed outlier: 3.563A  pdb=" N   CYS A 326 " --> pdb=" O   GLU A 322 " (cutoff:3.500A)
      removed outlier: 3.516A  pdb=" N   GLY A 327 " --> pdb=" O   LEU A 323 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 330 through 346
      removed outlier: 3.531A  pdb=" N   ARG A 334 " --> pdb=" O   ASP A 330 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 349 through 354
    Processing helix  chain 'A' and resid 355 through 360
      removed outlier: 3.678A  pdb=" N   PHE A 359 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 4.149A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 382
      removed outlier: 3.730A  pdb=" N   ALA A 373 " --> pdb=" O   GLU A 369 " (cutoff:3.500A)
      removed outlier: 4.179A  pdb=" N   HIS A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 411
    Processing helix  chain 'A' and resid 425 through 435
    Processing helix  chain 'A' and resid 439 through 446
    Processing helix  chain 'A' and resid 447 through 451
    Processing helix  chain 'A' and resid 479 through 487
      removed outlier: 3.933A  pdb=" N   TRP A 483 " --> pdb=" O   LYS A 480 " (cutoff:3.500A)
      removed outlier: 5.856A  pdb=" N   ASP A 484 " --> pdb=" O   ASP A 481 " (cutoff:3.500A)
      removed outlier: 4.354A  pdb=" N   VAL A 486 " --> pdb=" O   TRP A 483 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   TYR A 487 " --> pdb=" O   ASP A 484 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 488 through 492
      removed outlier: 3.513A  pdb=" N   VAL A 491 " --> pdb=" O   PRO A 488 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 512
    Processing helix  chain 'A' and resid 516 through 526
      removed outlier: 3.676A  pdb=" N   VAL A 524 " --> pdb=" O   MET A 520 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 557 through 574
    Processing helix  chain 'A' and resid 577 through 581
      removed outlier: 3.619A  pdb=" N   LYS A 580 " --> pdb=" O   LYS A 577 " (cutoff:3.500A)
      removed outlier: 4.130A  pdb=" N   GLU A 581 " --> pdb=" O   TYR A 578 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 577 through 581'
    Processing helix  chain 'A' and resid 587 through 598
    Processing helix  chain 'A' and resid 725 through 729
    Processing helix  chain 'A' and resid 731 through 747
      removed outlier: 4.985A  pdb=" N   ILE A 737 " --> pdb=" O   GLU A 733 " (cutoff:3.500A)
      removed outlier: 5.418A  pdb=" N   PHE A 738 " --> pdb=" O   SER A 734 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 753 through 760
      removed outlier: 4.091A  pdb=" N   LYS A 757 " --> pdb=" O   ASN A 753 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 780 through 784
      removed outlier: 3.679A  pdb=" N   THR A 784 " --> pdb=" O   LEU A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 821
      Proline residue:  A 812  - end of helix
    Processing helix  chain 'A' and resid 847 through 874
    Processing helix  chain 'A' and resid 904 through 910
      removed outlier: 3.854A  pdb=" N   SER A 908 " --> pdb=" O   GLN A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 922 through 940
      removed outlier: 3.730A  pdb=" N   ALA A 926 " --> pdb=" O   GLU A 922 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 943 through 964
    Processing helix  chain 'A' and resid 972 through 981
      Proline residue:  A 978  - end of helix
    Processing helix  chain 'A' and resid 982 through 992
    Processing helix  chain 'A' and resid 993 through 997
    Processing helix  chain 'A' and resid 1014 through 1029
    Processing helix  chain 'A' and resid 1033 through 1041
      removed outlier: 3.937A  pdb=" N   LEU A1037 " --> pdb=" O   THR A1033 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1049 through 1056
    Processing helix  chain 'A' and resid 1067 through 1083
      removed outlier: 3.957A  pdb=" N   ASN A1083 " --> pdb=" O   THR A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1096 through 1110
      removed outlier: 3.683A  pdb=" N   GLU A1100 " --> pdb=" O   LYS A1096 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   PHE A1107 " --> pdb=" O   GLU A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1115 through 1126
    Processing helix  chain 'A' and resid 1126 through 1138
      removed outlier: 3.851A  pdb=" N   LEU A1138 " --> pdb=" O   ILE A1134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1141 through 1153
    Processing helix  chain 'A' and resid 1156 through 1164
      removed outlier: 4.025A  pdb=" N   LEU A1162 " --> pdb=" O   LEU A1158 " (cutoff:3.500A)
      removed outlier: 3.556A  pdb=" N   HIS A1164 " --> pdb=" O   SER A1160 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1164 through 1178
    Processing helix  chain 'A' and resid 1191 through 1204
    Processing helix  chain 'A' and resid 1204 through 1209
    Processing helix  chain 'A' and resid 1220 through 1224
      removed outlier: 3.594A  pdb=" N   ALA A1224 " --> pdb=" O   ASP A1220 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 1220 through 1224'
    Processing helix  chain 'A' and resid 1236 through 1241
    Processing helix  chain 'A' and resid 1291 through 1309
      removed outlier: 3.501A  pdb=" N   GLY A1309 " --> pdb=" O   THR A1305 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1311 through 1323
    Processing helix  chain 'A' and resid 1329 through 1337
    Processing helix  chain 'A' and resid 1391 through 1407
      removed outlier: 3.881A  pdb=" N   ALA A1395 " --> pdb=" O   ILE A1391 " (cutoff:3.500A)
      removed outlier: 3.525A  pdb=" N   MET A1396 " --> pdb=" O   TYR A1392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 480 through 484
    Processing helix  chain 'B' and resid 489 through 501
      removed outlier: 3.855A  pdb=" N   HIS B 499 " --> pdb=" O   ARG B 495 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 502 through 506
      removed outlier: 3.729A  pdb=" N   TYR B 506 " --> pdb=" O   LEU B 503 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 507 through 541
      removed outlier: 3.563A  pdb=" N   LEU B 526 " --> pdb=" O   ASN B 522 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE B 527 " --> pdb=" O   SER B 523 " (cutoff:3.500A)
      removed outlier: 3.618A  pdb=" N   ASN B 528 " --> pdb=" O   ILE B 524 " (cutoff:3.500A)
      removed outlier: 3.918A  pdb=" N   HIS B 535 " --> pdb=" O   MET B 531 " (cutoff:3.500A)
      removed outlier: 3.681A  pdb=" N   ILE B 536 " --> pdb=" O   ARG B 532 " (cutoff:3.500A)
      removed outlier: 3.682A  pdb=" N   GLU B 537 " --> pdb=" O   LEU B 533 " (cutoff:3.500A)
      removed outlier: 4.138A  pdb=" N   GLU B 538 " --> pdb=" O   ASN B 534 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   GLN B 539 " --> pdb=" O   HIS B 535 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 542 through 574
      removed outlier: 3.790A  pdb=" N   MET B 574 " --> pdb=" O   HIS B 570 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 480 through 485
    Processing helix  chain 'C' and resid 489 through 501
      removed outlier: 3.713A  pdb=" N   ARG C 495 " --> pdb=" O   HIS C 491 " (cutoff:3.500A)
      removed outlier: 3.683A  pdb=" N   HIS C 499 " --> pdb=" O   ARG C 495 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 502 through 506
      removed outlier: 3.783A  pdb=" N   TYR C 506 " --> pdb=" O   LEU C 503 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 507 through 533
    Processing helix  chain 'C' and resid 533 through 541
      removed outlier: 3.843A  pdb=" N   LYS C 541 " --> pdb=" O   GLU C 537 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 542 through 574
    Processing helix  chain 'C' and resid 602 through 608
    Processing helix  chain 'C' and resid 634 through 638
      removed outlier: 3.697A  pdb=" N   LEU C 637 " --> pdb=" O   ARG C 634 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 657 through 672
      removed outlier: 3.649A  pdb=" N   ARG C 661 " --> pdb=" O   ASP C 657 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 674 through 688
    Processing helix  chain 'C' and resid 690 through 708
      removed outlier: 3.681A  pdb=" N   ILE C 694 " --> pdb=" O   ASN C 690 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   ASN C 708 " --> pdb=" O   ILE C 704 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 480 through 484
    Processing helix  chain 'D' and resid 489 through 501
      removed outlier: 3.792A  pdb=" N   HIS D 499 " --> pdb=" O   ARG D 495 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 502 through 506
      removed outlier: 3.595A  pdb=" N   TYR D 506 " --> pdb=" O   LEU D 503 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 507 through 541
      removed outlier: 3.743A  pdb=" N   HIS D 535 " --> pdb=" O   MET D 531 " (cutoff:3.500A)
      removed outlier: 4.054A  pdb=" N   LYS D 541 " --> pdb=" O   GLU D 537 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 542 through 578
      removed outlier: 3.555A  pdb=" N   ILE D 546 " --> pdb=" O   GLU D 542 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ILE D 578 " --> pdb=" O   MET D 574 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 480 through 484
    Processing helix  chain 'E' and resid 489 through 501
      removed outlier: 3.728A  pdb=" N   HIS E 499 " --> pdb=" O   ARG E 495 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 502 through 506
      removed outlier: 3.754A  pdb=" N   ASP E 505 " --> pdb=" O   HIS E 502 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   TYR E 506 " --> pdb=" O   LEU E 503 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'E' and resid 502 through 506'
    Processing helix  chain 'E' and resid 507 through 541
      removed outlier: 4.046A  pdb=" N   ASP E 530 " --> pdb=" O   LEU E 526 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   MET E 531 " --> pdb=" O   ILE E 527 " (cutoff:3.500A)
      removed outlier: 4.234A  pdb=" N   ARG E 532 " --> pdb=" O   ASN E 528 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   GLU E 537 " --> pdb=" O   LEU E 533 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   GLN E 539 " --> pdb=" O   HIS E 535 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 542 through 573
      removed outlier: 4.049A  pdb=" N   ILE E 546 " --> pdb=" O   GLU E 542 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   ILE E 547 " --> pdb=" O   ILE E 543 " (cutoff:3.500A)
      removed outlier: 4.018A  pdb=" N   SER E 573 " --> pdb=" O   GLY E 569 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 21 through 22
      removed outlier: 7.045A  pdb=" N   ILE A  21 " --> pdb=" O   LEU A 368 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 84 through 85
      removed outlier: 6.199A  pdb=" N   MET A  84 " --> pdb=" O   CYS A 227 " (cutoff:3.500A)
      removed outlier: 8.184A  pdb=" N   TYR A 229 " --> pdb=" O   MET A  84 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 385 through 388
    Processing sheet with id=AA4, first strand: chain 'A' and resid 418 through 419
    Processing sheet with id=AA5, first strand: chain 'A' and resid 475 through 476
      removed outlier: 4.859A  pdb=" N   ARG A 503 " --> pdb=" O   LEU A 476 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 551 through 556
      removed outlier: 3.988A  pdb=" N   ARG A 551 " --> pdb=" O   LYS A 542 " (cutoff:3.500A)
      removed outlier: 4.852A  pdb=" N   VAL A 537 " --> pdb=" O   VAL A 763 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   TYR A 765 " --> pdb=" O   VAL A 537 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 824 through 830
      removed outlier: 4.119A  pdb=" N   ARG A 824 " --> pdb=" O   THR A 839 " (cutoff:3.500A)
      removed outlier: 3.536A  pdb=" N   THR A 839 " --> pdb=" O   ARG A 824 " (cutoff:3.500A)
      removed outlier: 4.272A  pdb=" N   GLU A 834 " --> pdb=" O   THR A 721 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 888 through 891
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1113 through 1114
    Processing sheet with id=AB1, first strand: chain 'A' and resid 1225 through 1231
    Processing sheet with id=AB2, first strand: chain 'A' and resid 1380 through 1381

    843 hydrogen bonds defined for protein.
    2421 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: 3.17

  Time building geometry restraints manager: 1.76 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3519
        1.33 -     1.45: 2918
        1.45 -     1.58: 8431
        1.58 -     1.70: 0
        1.70 -     1.82: 160
  Bond restraints: 15028
  Sorted by residual:
  bond pdb=" CA  ALA A  87 "
       pdb=" C   ALA A  87 "
    ideal  model  delta    sigma   weight residual
    1.528  1.458  0.070 1.33e-02 5.65e+03 2.74e+01
  bond pdb=" CA  GLU A  90 "
       pdb=" C   GLU A  90 "
    ideal  model  delta    sigma   weight residual
    1.522  1.464  0.059 1.37e-02 5.33e+03 1.83e+01
  bond pdb=" N   LEU A 214 "
       pdb=" CA  LEU A 214 "
    ideal  model  delta    sigma   weight residual
    1.454  1.508 -0.054 1.27e-02 6.20e+03 1.81e+01
  bond pdb=" CA  HIS A1264 "
       pdb=" C   HIS A1264 "
    ideal  model  delta    sigma   weight residual
    1.524  1.498  0.026 7.00e-03 2.04e+04 1.42e+01
  bond pdb=" CA  ALA A  87 "
       pdb=" CB  ALA A  87 "
    ideal  model  delta    sigma   weight residual
    1.527  1.479  0.048 1.44e-02 4.82e+03 1.13e+01
  ... (remaining 15023 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.05: 20015
        3.05 -     6.10: 252
        6.10 -     9.14: 31
        9.14 -    12.19: 7
       12.19 -    15.24: 1
  Bond angle restraints: 20306
  Sorted by residual:
  angle pdb=" N   ASN A 211 "
        pdb=" CA  ASN A 211 "
        pdb=" C   ASN A 211 "
      ideal   model   delta    sigma   weight residual
     109.06   97.34   11.72 1.78e+00 3.16e-01 4.34e+01
  angle pdb=" N   HIS A1264 "
        pdb=" CA  HIS A1264 "
        pdb=" C   HIS A1264 "
      ideal   model   delta    sigma   weight residual
     111.02  102.97    8.05 1.52e+00 4.33e-01 2.81e+01
  angle pdb=" CB  MET B 479 "
        pdb=" CG  MET B 479 "
        pdb=" SD  MET B 479 "
      ideal   model   delta    sigma   weight residual
     112.70  127.94  -15.24 3.00e+00 1.11e-01 2.58e+01
  angle pdb=" C   TYR A  88 "
        pdb=" N   PRO A  89 "
        pdb=" CD  PRO A  89 "
      ideal   model   delta    sigma   weight residual
     120.60  109.56   11.04 2.20e+00 2.07e-01 2.52e+01
  angle pdb=" N   ILE A1267 "
        pdb=" CA  ILE A1267 "
        pdb=" C   ILE A1267 "
      ideal   model   delta    sigma   weight residual
     107.88  114.75   -6.87 1.38e+00 5.25e-01 2.48e+01
  ... (remaining 20301 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.95: 8420
       17.95 -    35.91: 667
       35.91 -    53.86: 104
       53.86 -    71.81: 14
       71.81 -    89.77: 5
  Dihedral angle restraints: 9210
    sinusoidal: 3808
      harmonic: 5402
  Sorted by residual:
  dihedral pdb=" C   THR A1140 "
           pdb=" N   THR A1140 "
           pdb=" CA  THR A1140 "
           pdb=" CB  THR A1140 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.54   12.54     0      2.50e+00 1.60e-01 2.51e+01
  dihedral pdb=" N   THR A1140 "
           pdb=" C   THR A1140 "
           pdb=" CA  THR A1140 "
           pdb=" CB  THR A1140 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.84  -12.44     0      2.50e+00 1.60e-01 2.47e+01
  dihedral pdb=" CA  THR A 104 "
           pdb=" C   THR A 104 "
           pdb=" N   SER A 105 "
           pdb=" CA  SER A 105 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -155.81  -24.19     0      5.00e+00 4.00e-02 2.34e+01
  ... (remaining 9207 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.099: 2157
       0.099 -    0.198: 136
       0.198 -    0.297: 9
       0.297 -    0.396: 2
       0.396 -    0.495: 1
  Chirality restraints: 2305
  Sorted by residual:
  chirality pdb=" CA  THR A1140 "
            pdb=" N   THR A1140 "
            pdb=" C   THR A1140 "
            pdb=" CB  THR A1140 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.03    0.50 2.00e-01 2.50e+01 6.13e+00
  chirality pdb=" CA  ASP A1139 "
            pdb=" N   ASP A1139 "
            pdb=" C   ASP A1139 "
            pdb=" CB  ASP A1139 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.15    0.36 2.00e-01 2.50e+01 3.17e+00
  chirality pdb=" CA  GLU A  90 "
            pdb=" N   GLU A  90 "
            pdb=" C   GLU A  90 "
            pdb=" CB  GLU A  90 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.55e+00
  ... (remaining 2302 not shown)

  Planarity restraints: 2601
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR A1337 "    0.045 5.00e-02 4.00e+02   6.85e-02 7.50e+00
        pdb=" N   PRO A1338 "   -0.118 5.00e-02 4.00e+02
        pdb=" CA  PRO A1338 "    0.036 5.00e-02 4.00e+02
        pdb=" CD  PRO A1338 "    0.037 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1306 "   -0.021 2.00e-02 2.50e+03   1.70e-02 7.19e+00
        pdb=" CG  TRP A1306 "    0.046 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1306 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1306 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1306 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1306 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1306 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1306 "   -0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1306 "   -0.002 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1306 "   -0.003 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE C 489 "    0.042 5.00e-02 4.00e+02   6.46e-02 6.68e+00
        pdb=" N   PRO C 490 "   -0.112 5.00e-02 4.00e+02
        pdb=" CA  PRO C 490 "    0.034 5.00e-02 4.00e+02
        pdb=" CD  PRO C 490 "    0.036 5.00e-02 4.00e+02
  ... (remaining 2598 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 2796
        2.78 -     3.31: 13596
        3.31 -     3.84: 23650
        3.84 -     4.37: 27817
        4.37 -     4.90: 48985
  Nonbonded interactions: 116844
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A  12 "
            pdb=" OD1 ASN A 968 "
     model   vdw
     2.249 3.040
  nonbonded pdb=" O   ILE A1122 "
            pdb=" OG  SER A1126 "
     model   vdw
     2.260 3.040
  nonbonded pdb=" OH  TYR A1304 "
            pdb=" OE1 GLU A1317 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OE1 GLN A 830 "
            pdb=" OG  SER A 835 "
     model   vdw
     2.282 3.040
  nonbonded pdb=" OH  TYR A1214 "
            pdb=" O   ALA A1434 "
     model   vdw
     2.302 3.040
  ... (remaining 116839 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = chain 'B'
  selection = (chain 'D' and resid 479 through 579)
  selection = (chain 'E' and resid 479 through 579)
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.900
  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:          0.250
  Check model and map are aligned:         0.070
  Set scattering table:                    0.070
  Process input model:                     15.950
  Find NCS groups from input model:        0.120
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:7.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8541
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      :  0.005   0.070  15029  Z= 0.249
  Angle     :  0.882  15.240  20308  Z= 0.498
  Chirality :  0.054   0.495   2305
  Planarity :  0.006   0.068   2601
  Dihedral  : 12.933  89.766   5695
  Min Nonbonded Distance : 2.249

Molprobity Statistics.
  All-atom Clashscore : 3.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.25 %
    Favored  : 97.75 %
  Rotamer:
    Outliers :  0.24 %
    Allowed  :  0.36 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.11 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.05 (0.18), residues: 1819
  helix:  0.70 (0.15), residues: 1049
  sheet:  0.96 (0.48), residues: 107
  loop : -1.36 (0.21), residues: 663

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A1211 
 TYR   0.025   0.002   TYR A 539 
 PHE   0.041   0.003   PHE C 609 
 TRP   0.046   0.003   TRP A1306 
 HIS   0.010   0.001   HIS A 427 

Details of bonding type rmsd
  covalent geometry    : bond        0.00464 (15028)
  covalent geometry    : angle       0.88202 (20306)
  SS BOND              : bond        0.00011 (    1)
  SS BOND              : angle       0.64649 (    2)
  hydrogen bonds       : bond        0.14897 (  843)
  hydrogen bonds       : angle       5.33119 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  343 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 339
  time to evaluate  : 0.641 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A 1068 ILE cc_start: 0.8302 (tp) cc_final: 0.7964 (tp)
REVERT: A 1095 ASP cc_start: 0.8328 (m-30) cc_final: 0.7958 (m-30)
REVERT: A 1451 VAL cc_start: 0.8366 (t) cc_final: 0.8124 (t)
REVERT: C  479 MET cc_start: 0.5950 (tmm) cc_final: 0.5721 (tmm)
  outliers start: 4
  outliers final: 2
  residues processed: 343
  average time/residue: 0.8010
  time to fit residues: 296.0053
Evaluate side-chains
  204 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 202
  time to evaluate  : 0.632 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue  546 ILE
Chi-restraints excluded: chain D residue  547 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 98 optimal weight:    1.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    0.6980
   chunk 66 optimal weight:    0.4980
   chunk 130 optimal weight:    8.9990
   chunk 124 optimal weight:    0.0870
   chunk 103 optimal weight:    5.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    0.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    3.9990
   overall best weight:    0.6562

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

Flipped N/Q/H residues before XYZ refinement:
A  55 HIS
A 396 HIS
A 845 ASN
A 929 ASN
A1066 GLN
A1394 GLN
C 561 ASN
C 606 GLN
C 651 GLN
D 539 GLN
D 548 ASN
E 534 ASN

Total number of N/Q/H flips: 12

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.128064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.079209 restraints weight = 24422.094|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.83
r_work: 0.2919 rms_B_bonded: 3.42 restraints_weight: 0.5000
r_work (final): 0.2919
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8123
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15029  Z= 0.147
  Angle     :  0.618   9.292  20308  Z= 0.321
  Chirality :  0.043   0.210   2305
  Planarity :  0.005   0.057   2601
  Dihedral  :  4.743  43.869   1984
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  1.81 %
    Favored  : 98.13 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 10.98 %
    Favored  : 86.43 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.03 (0.20), residues: 1819
  helix:  1.66 (0.16), residues: 1076
  sheet:  0.93 (0.51), residues: 99
  loop : -1.06 (0.23), residues: 644

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 911 
 TYR   0.015   0.001   TYR A 419 
 PHE   0.030   0.001   PHE A 553 
 TRP   0.015   0.001   TRP A1306 
 HIS   0.008   0.001   HIS A  55 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 (15028)
  covalent geometry    : angle       0.61852 (20306)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.35334 (    2)
  hydrogen bonds       : bond        0.05065 (  843)
  hydrogen bonds       : angle       4.05355 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  258 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 215
  time to evaluate  : 0.634 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8371 (mp0) cc_final: 0.8151 (mp0)
REVERT: A   90 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8413 (mp0)
REVERT: A  531 GLU cc_start: 0.8334 (mp0) cc_final: 0.8108 (mp0)
REVERT: A  893 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8595 (mttp)
REVERT: A 1095 ASP cc_start: 0.8967 (m-30) cc_final: 0.8555 (m-30)
REVERT: A 1295 ARG cc_start: 0.8805 (mtt180) cc_final: 0.8550 (mmt180)
REVERT: C  531 MET cc_start: 0.9100 (tmm) cc_final: 0.8716 (ppp)
REVERT: C  577 MET cc_start: 0.8198 (tpp) cc_final: 0.7977 (tpp)
REVERT: C  651 GLN cc_start: 0.7852 (mt0) cc_final: 0.7498 (pt0)
REVERT: D  531 MET cc_start: 0.8872 (ppp) cc_final: 0.8539 (ppp)
REVERT: E  534 ASN cc_start: 0.9081 (m-40) cc_final: 0.8605 (m-40)
REVERT: E  545 LYS cc_start: 0.9211 (mtpp) cc_final: 0.8718 (mppt)
REVERT: E  548 ASN cc_start: 0.9323 (m-40) cc_final: 0.9090 (m110)
  outliers start: 43
  outliers final: 10
  residues processed: 238
  average time/residue: 0.7863
  time to fit residues: 202.5307
Evaluate side-chains
  206 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 195
  time to evaluate  : 0.615 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  892 SER
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1082 ARG
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain E residue  565 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 79 optimal weight:    0.0370
   chunk 132 optimal weight:   10.0000
   chunk 47 optimal weight:    0.6980
   chunk 71 optimal weight:    4.9990
   chunk 121 optimal weight:    5.9990
   chunk 109 optimal weight:    3.9990
   chunk 53 optimal weight:    0.9990
   chunk 126 optimal weight:    0.0570
   chunk 145 optimal weight:   20.0000
   chunk 170 optimal weight:    0.7980
   chunk 112 optimal weight:    1.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A  85 HIS
A 830 GLN
A 929 ASN
C 606 GLN
D 528 ASN
** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 591 ASN
E 535 HIS

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.128075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3081 r_free = 0.3081 target = 0.079248 restraints weight = 24692.226|
|-----------------------------------------------------------------------------|
r_work (start): 0.3067 rms_B_bonded: 2.85
r_work: 0.2917 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2917
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8127
moved from start:          0.2517

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  15029  Z= 0.128
  Angle     :  0.583  11.251  20308  Z= 0.297
  Chirality :  0.042   0.217   2305
  Planarity :  0.004   0.050   2601
  Dihedral  :  4.321  21.534   1980
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.31
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.03 %
    Favored  : 97.86 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 12.42 %
    Favored  : 85.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.46 (0.20), residues: 1819
  helix:  2.08 (0.16), residues: 1070
  sheet:  1.01 (0.52), residues: 100
  loop : -0.98 (0.23), residues: 649

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 911 
 TYR   0.017   0.001   TYR A 419 
 PHE   0.025   0.001   PHE A 553 
 TRP   0.011   0.001   TRP A1248 
 HIS   0.004   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00285 (15028)
  covalent geometry    : angle       0.58323 (20306)
  SS BOND              : bond        0.00135 (    1)
  SS BOND              : angle       0.27716 (    2)
  hydrogen bonds       : bond        0.04485 (  843)
  hydrogen bonds       : angle       3.80963 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  243 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 205
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8490 (mp0) cc_final: 0.8197 (mp0)
REVERT: A   59 LYS cc_start: 0.8577 (mtmm) cc_final: 0.8309 (mppt)
REVERT: A   90 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8437 (mp0)
REVERT: A  419 TYR cc_start: 0.8124 (m-10) cc_final: 0.7788 (m-10)
REVERT: A  469 MET cc_start: 0.8763 (mtm) cc_final: 0.8331 (mtm)
REVERT: A  472 LYS cc_start: 0.8610 (mmtm) cc_final: 0.7895 (mtmm)
REVERT: A  473 ASP cc_start: 0.7546 (t0) cc_final: 0.7323 (t0)
REVERT: A  531 GLU cc_start: 0.8384 (mp0) cc_final: 0.8168 (mp0)
REVERT: A  719 LEU cc_start: 0.8254 (mp) cc_final: 0.7876 (tt)
REVERT: A  893 LYS cc_start: 0.8877 (mtmt) cc_final: 0.8579 (mttp)
REVERT: A 1095 ASP cc_start: 0.8990 (m-30) cc_final: 0.8590 (m-30)
REVERT: A 1132 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7902 (pp20)
REVERT: A 1158 LEU cc_start: 0.8365 (OUTLIER) cc_final: 0.7936 (tm)
REVERT: A 1160 SER cc_start: 0.8476 (t) cc_final: 0.8170 (m)
REVERT: A 1180 ARG cc_start: 0.8963 (mtt-85) cc_final: 0.8625 (ttm110)
REVERT: A 1262 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7641 (ptp-170)
REVERT: A 1447 GLU cc_start: 0.8325 (tt0) cc_final: 0.8027 (tm-30)
REVERT: B  479 MET cc_start: 0.8143 (mmm) cc_final: 0.7896 (tmm)
REVERT: B  555 ARG cc_start: 0.8691 (ptp-110) cc_final: 0.8450 (ptp90)
REVERT: B  568 GLU cc_start: 0.8351 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: C  531 MET cc_start: 0.9109 (tmm) cc_final: 0.8766 (ppp)
REVERT: C  549 LYS cc_start: 0.8025 (tttt) cc_final: 0.7784 (tttm)
REVERT: C  641 GLU cc_start: 0.8989 (mt-10) cc_final: 0.8789 (mp0)
REVERT: E  545 LYS cc_start: 0.9198 (mtpp) cc_final: 0.8823 (mppt)
  outliers start: 38
  outliers final: 8
  residues processed: 227
  average time/residue: 0.7620
  time to fit residues: 186.9502
Evaluate side-chains
  208 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 196
  time to evaluate  : 0.659 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  973 LEU
Chi-restraints excluded: chain A residue 1082 ARG
Chi-restraints excluded: chain A residue 1132 GLU
Chi-restraints excluded: chain A residue 1158 LEU
Chi-restraints excluded: chain A residue 1262 ARG
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain D residue  529 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 80 optimal weight:    4.9990
   chunk 156 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   chunk 69 optimal weight:    0.0570
   chunk 132 optimal weight:    9.9990
   chunk 157 optimal weight:    0.6980
   chunk 110 optimal weight:    0.0670
   chunk 82 optimal weight:    3.9990
   chunk 98 optimal weight:    2.9990
   chunk 11 optimal weight:    0.7980
   chunk 40 optimal weight:    4.9990
   overall best weight:    0.4436

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

Flipped N/Q/H residues before XYZ refinement:
A1011 ASN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 606 GLN
** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 548 ASN
** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.128130 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.078995 restraints weight = 24525.829|
|-----------------------------------------------------------------------------|
r_work (start): 0.3057 rms_B_bonded: 2.88
r_work: 0.2908 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2908
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8096
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15029  Z= 0.117
  Angle     :  0.552   7.550  20308  Z= 0.281
  Chirality :  0.041   0.184   2305
  Planarity :  0.004   0.049   2601
  Dihedral  :  4.139  20.984   1980
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.42 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 13.45 %
    Favored  : 84.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.77 (0.20), residues: 1819
  helix:  2.32 (0.16), residues: 1074
  sheet:  1.01 (0.52), residues: 100
  loop : -0.83 (0.23), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 361 
 TYR   0.011   0.001   TYR A 389 
 PHE   0.020   0.001   PHE A 553 
 TRP   0.014   0.001   TRP A1306 
 HIS   0.005   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 (15028)
  covalent geometry    : angle       0.55242 (20306)
  SS BOND              : bond        0.00131 (    1)
  SS BOND              : angle       0.27426 (    2)
  hydrogen bonds       : bond        0.04094 (  843)
  hydrogen bonds       : angle       3.70024 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  241 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 205
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8541 (mp0) cc_final: 0.8220 (mp0)
REVERT: A   90 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8444 (mp0)
REVERT: A  419 TYR cc_start: 0.8086 (m-10) cc_final: 0.7808 (m-10)
REVERT: A  469 MET cc_start: 0.8788 (OUTLIER) cc_final: 0.8194 (ptp)
REVERT: A  472 LYS cc_start: 0.8566 (mmtm) cc_final: 0.7962 (mtmm)
REVERT: A  531 GLU cc_start: 0.8407 (mp0) cc_final: 0.8118 (mp0)
REVERT: A  719 LEU cc_start: 0.8185 (mp) cc_final: 0.7845 (tt)
REVERT: A  893 LYS cc_start: 0.8905 (mtmt) cc_final: 0.8602 (mttp)
REVERT: A 1095 ASP cc_start: 0.8930 (m-30) cc_final: 0.8545 (m-30)
REVERT: A 1132 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7926 (pp20)
REVERT: A 1180 ARG cc_start: 0.8989 (mtt-85) cc_final: 0.8634 (ttm110)
REVERT: A 1295 ARG cc_start: 0.8901 (mmm160) cc_final: 0.8399 (mtt-85)
REVERT: A 1447 GLU cc_start: 0.8375 (tt0) cc_final: 0.8084 (tm-30)
REVERT: B  555 ARG cc_start: 0.8707 (ptp-110) cc_final: 0.8451 (ptp90)
REVERT: B  568 GLU cc_start: 0.8372 (tm-30) cc_final: 0.8037 (tm-30)
REVERT: C  535 HIS cc_start: 0.8384 (m90) cc_final: 0.8052 (m90)
REVERT: C  641 GLU cc_start: 0.9031 (mt-10) cc_final: 0.8738 (mp0)
REVERT: C  675 ARG cc_start: 0.8300 (tmm-80) cc_final: 0.8060 (ttp80)
REVERT: D  531 MET cc_start: 0.8733 (pp-130) cc_final: 0.8280 (ppp)
REVERT: D  581 LYS cc_start: 0.7662 (mtmm) cc_final: 0.7399 (mmpt)
  outliers start: 36
  outliers final: 12
  residues processed: 222
  average time/residue: 0.7651
  time to fit residues: 183.6787
Evaluate side-chains
  201 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 186
  time to evaluate  : 0.629 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  735 MET
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1082 ARG
Chi-restraints excluded: chain A residue 1132 GLU
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain E residue  575 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 161 optimal weight:   30.0000
   chunk 176 optimal weight:    7.9990
   chunk 105 optimal weight:    2.9990
   chunk 164 optimal weight:   20.0000
   chunk 0 optimal weight:    3.9990
   chunk 7 optimal weight:    0.0970
   chunk 124 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 82 optimal weight:    3.9990
   chunk 72 optimal weight:    0.0970
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
E 534 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3780 r_free = 0.3780 target = 0.126251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3044 r_free = 0.3044 target = 0.077147 restraints weight = 24613.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3025 rms_B_bonded: 2.85
r_work: 0.2873 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2873
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8144
moved from start:          0.2980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15029  Z= 0.143
  Angle     :  0.571   7.921  20308  Z= 0.291
  Chirality :  0.043   0.273   2305
  Planarity :  0.004   0.048   2601
  Dihedral  :  4.103  20.302   1980
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.58 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 13.99 %
    Favored  : 83.79 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.87 (0.20), residues: 1819
  helix:  2.39 (0.16), residues: 1074
  sheet:  0.90 (0.52), residues: 100
  loop : -0.72 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 911 
 TYR   0.013   0.001   TYR A 284 
 PHE   0.019   0.001   PHE A 553 
 TRP   0.010   0.001   TRP A1248 
 HIS   0.006   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 (15028)
  covalent geometry    : angle       0.57084 (20306)
  SS BOND              : bond        0.00143 (    1)
  SS BOND              : angle       0.29273 (    2)
  hydrogen bonds       : bond        0.04439 (  843)
  hydrogen bonds       : angle       3.72239 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 0.562 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8550 (mp0) cc_final: 0.8227 (mp0)
REVERT: A   78 LYS cc_start: 0.7917 (mptt) cc_final: 0.7602 (mmpt)
REVERT: A   90 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8510 (mp0)
REVERT: A  419 TYR cc_start: 0.8170 (m-10) cc_final: 0.7890 (m-10)
REVERT: A  469 MET cc_start: 0.8806 (OUTLIER) cc_final: 0.8275 (ptp)
REVERT: A  531 GLU cc_start: 0.8451 (mp0) cc_final: 0.8104 (mp0)
REVERT: A  893 LYS cc_start: 0.8965 (mtmt) cc_final: 0.8680 (mttp)
REVERT: A 1026 MET cc_start: 0.8385 (OUTLIER) cc_final: 0.7650 (mtp)
REVERT: A 1032 MET cc_start: 0.8714 (mtt) cc_final: 0.8113 (mtt)
REVERT: A 1095 ASP cc_start: 0.8911 (m-30) cc_final: 0.8546 (m-30)
REVERT: A 1132 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7995 (pp20)
REVERT: A 1180 ARG cc_start: 0.9017 (mtt-85) cc_final: 0.8636 (ttm110)
REVERT: A 1245 MET cc_start: 0.8021 (ttp) cc_final: 0.7440 (ttt)
REVERT: A 1295 ARG cc_start: 0.8890 (mmm160) cc_final: 0.8416 (mtt-85)
REVERT: A 1447 GLU cc_start: 0.8377 (tt0) cc_final: 0.8083 (tm-30)
REVERT: B  555 ARG cc_start: 0.8742 (ptp-110) cc_final: 0.8428 (ptp90)
REVERT: B  568 GLU cc_start: 0.8385 (tm-30) cc_final: 0.8048 (tm-30)
REVERT: C  549 LYS cc_start: 0.8140 (OUTLIER) cc_final: 0.7851 (ttmm)
REVERT: C  665 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7611 (tttp)
REVERT: D  531 MET cc_start: 0.8766 (pp-130) cc_final: 0.8360 (ppp)
REVERT: E  548 ASN cc_start: 0.9215 (m-40) cc_final: 0.8955 (m110)
  outliers start: 37
  outliers final: 14
  residues processed: 210
  average time/residue: 0.7110
  time to fit residues: 161.6703
Evaluate side-chains
  202 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 182
  time to evaluate  : 0.461 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  882 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1026 MET
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1082 ARG
Chi-restraints excluded: chain A residue 1132 GLU
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain C residue  549 LYS
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  665 LYS
Chi-restraints excluded: chain D residue  572 VAL
Chi-restraints excluded: chain E residue  575 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 156 optimal weight:    0.9980
   chunk 154 optimal weight:    4.9990
   chunk 147 optimal weight:    6.9990
   chunk 61 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0670
   chunk 81 optimal weight:    3.9990
   chunk 104 optimal weight:    4.9990
   chunk 139 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 71 optimal weight:    0.7980
   overall best weight:    0.9120

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1237 GLN
D 591 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3769 r_free = 0.3769 target = 0.125538 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3037 r_free = 0.3037 target = 0.076749 restraints weight = 24670.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.3020 rms_B_bonded: 2.78
r_work: 0.2872 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2872
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8201
moved from start:          0.3117

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  15029  Z= 0.150
  Angle     :  0.572   8.153  20308  Z= 0.292
  Chirality :  0.042   0.187   2305
  Planarity :  0.004   0.047   2601
  Dihedral  :  4.086  19.757   1980
  Min Nonbonded Distance : 2.526

Molprobity Statistics.
  All-atom Clashscore : 5.75
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.42 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 14.89 %
    Favored  : 82.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.94 (0.20), residues: 1819
  helix:  2.44 (0.16), residues: 1074
  sheet:  0.86 (0.51), residues: 100
  loop : -0.68 (0.24), residues: 645

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 361 
 TYR   0.013   0.001   TYR A 284 
 PHE   0.017   0.001   PHE A 553 
 TRP   0.010   0.001   TRP A1248 
 HIS   0.007   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 (15028)
  covalent geometry    : angle       0.57215 (20306)
  SS BOND              : bond        0.00136 (    1)
  SS BOND              : angle       0.32112 (    2)
  hydrogen bonds       : bond        0.04413 (  843)
  hydrogen bonds       : angle       3.73311 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  228 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 187
  time to evaluate  : 0.612 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8578 (mp0) cc_final: 0.8249 (mp0)
REVERT: A   78 LYS cc_start: 0.8033 (mptt) cc_final: 0.7697 (mmpt)
REVERT: A   90 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8582 (mp0)
REVERT: A  419 TYR cc_start: 0.8188 (m-10) cc_final: 0.7933 (m-10)
REVERT: A  426 LYS cc_start: 0.9019 (mttm) cc_final: 0.8791 (tmtt)
REVERT: A  469 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8352 (ptp)
REVERT: A  472 LYS cc_start: 0.8487 (OUTLIER) cc_final: 0.8027 (mmpt)
REVERT: A  531 GLU cc_start: 0.8462 (mp0) cc_final: 0.8140 (mp0)
REVERT: A  893 LYS cc_start: 0.9087 (mtmt) cc_final: 0.8774 (mttp)
REVERT: A 1026 MET cc_start: 0.8465 (OUTLIER) cc_final: 0.7737 (mtp)
REVERT: A 1032 MET cc_start: 0.8739 (mtt) cc_final: 0.8155 (mtt)
REVERT: A 1132 GLU cc_start: 0.8418 (OUTLIER) cc_final: 0.8058 (pp20)
REVERT: A 1180 ARG cc_start: 0.9005 (mtt-85) cc_final: 0.8639 (ttm110)
REVERT: A 1245 MET cc_start: 0.8178 (ttp) cc_final: 0.7612 (ttt)
REVERT: A 1295 ARG cc_start: 0.8892 (mmm160) cc_final: 0.8459 (mmt180)
REVERT: A 1447 GLU cc_start: 0.8392 (tt0) cc_final: 0.8114 (tm-30)
REVERT: B  555 ARG cc_start: 0.8775 (ptp-110) cc_final: 0.8453 (ptp90)
REVERT: B  568 GLU cc_start: 0.8429 (tm-30) cc_final: 0.8099 (tm-30)
REVERT: C  531 MET cc_start: 0.9005 (tmm) cc_final: 0.8703 (ppp)
REVERT: C  549 LYS cc_start: 0.8190 (OUTLIER) cc_final: 0.7723 (tttm)
REVERT: C  577 MET cc_start: 0.8298 (tpt) cc_final: 0.7929 (tpt)
REVERT: C  665 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7658 (tttp)
REVERT: D  531 MET cc_start: 0.8785 (pp-130) cc_final: 0.8389 (ppp)
REVERT: E  545 LYS cc_start: 0.9105 (mtpp) cc_final: 0.8627 (mppt)
REVERT: E  548 ASN cc_start: 0.9203 (m-40) cc_final: 0.8956 (m110)
  outliers start: 41
  outliers final: 14
  residues processed: 210
  average time/residue: 0.7669
  time to fit residues: 174.0935
Evaluate side-chains
  206 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 185
  time to evaluate  : 0.600 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  472 LYS
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  882 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1026 MET
Chi-restraints excluded: chain A residue 1075 ILE
Chi-restraints excluded: chain A residue 1132 GLU
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain A residue 1294 LEU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain C residue  549 LYS
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  665 LYS
Chi-restraints excluded: chain D residue  572 VAL
Chi-restraints excluded: chain E residue  575 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 1 optimal weight:    0.0870
   chunk 169 optimal weight:    2.9990
   chunk 62 optimal weight:    0.9980
   chunk 94 optimal weight:    1.9990
   chunk 87 optimal weight:    0.0770
   chunk 17 optimal weight:    1.9990
   chunk 72 optimal weight:    0.0370
   chunk 141 optimal weight:    0.8980
   chunk 101 optimal weight:    0.9990
   chunk 138 optimal weight:    0.8980
   overall best weight:    0.3994

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

Flipped N/Q/H residues before XYZ refinement:
A 770 ASN
A1011 ASN
A1237 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.127435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3069 r_free = 0.3069 target = 0.078513 restraints weight = 24544.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3043 rms_B_bonded: 2.81
r_work: 0.2885 rms_B_bonded: 3.46 restraints_weight: 0.5000
r_work (final): 0.2885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8206
moved from start:          0.3264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  15029  Z= 0.115
  Angle     :  0.559   9.624  20308  Z= 0.283
  Chirality :  0.041   0.202   2305
  Planarity :  0.004   0.047   2601
  Dihedral  :  3.967  20.376   1980
  Min Nonbonded Distance : 2.541

Molprobity Statistics.
  All-atom Clashscore : 5.65
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.58 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.16 %
    Allowed  : 15.61 %
    Favored  : 82.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.20), residues: 1819
  helix:  2.55 (0.16), residues: 1073
  sheet:  0.99 (0.53), residues: 100
  loop : -0.58 (0.24), residues: 646

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 911 
 TYR   0.009   0.001   TYR A 389 
 PHE   0.016   0.001   PHE A 553 
 TRP   0.012   0.001   TRP A1248 
 HIS   0.007   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 (15028)
  covalent geometry    : angle       0.55919 (20306)
  SS BOND              : bond        0.00091 (    1)
  SS BOND              : angle       0.30365 (    2)
  hydrogen bonds       : bond        0.03863 (  843)
  hydrogen bonds       : angle       3.63738 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  232 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 196
  time to evaluate  : 0.626 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8573 (mp0) cc_final: 0.8233 (mp0)
REVERT: A   78 LYS cc_start: 0.7992 (mptt) cc_final: 0.7650 (mmpt)
REVERT: A  204 LYS cc_start: 0.9323 (mtpp) cc_final: 0.8825 (mppt)
REVERT: A  419 TYR cc_start: 0.8278 (m-10) cc_final: 0.8029 (m-10)
REVERT: A  469 MET cc_start: 0.8780 (OUTLIER) cc_final: 0.8112 (ptp)
REVERT: A  472 LYS cc_start: 0.8522 (OUTLIER) cc_final: 0.7893 (mtmm)
REVERT: A  531 GLU cc_start: 0.8437 (mp0) cc_final: 0.8124 (mp0)
REVERT: A  893 LYS cc_start: 0.9060 (mtmt) cc_final: 0.8775 (mttp)
REVERT: A 1066 GLN cc_start: 0.8630 (tt0) cc_final: 0.8411 (tp40)
REVERT: A 1132 GLU cc_start: 0.8417 (OUTLIER) cc_final: 0.8061 (pp20)
REVERT: A 1180 ARG cc_start: 0.8993 (mtt-85) cc_final: 0.8636 (ttm110)
REVERT: A 1245 MET cc_start: 0.8225 (ttp) cc_final: 0.7653 (ttt)
REVERT: A 1295 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8464 (mtt-85)
REVERT: A 1314 CYS cc_start: 0.8189 (m) cc_final: 0.7798 (m)
REVERT: A 1447 GLU cc_start: 0.8381 (tt0) cc_final: 0.8099 (tm-30)
REVERT: B  555 ARG cc_start: 0.8803 (ptp-110) cc_final: 0.8490 (ptp90)
REVERT: B  568 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8174 (tm-30)
REVERT: C  531 MET cc_start: 0.8996 (tmm) cc_final: 0.8629 (ppp)
REVERT: C  549 LYS cc_start: 0.8094 (OUTLIER) cc_final: 0.7709 (ttmm)
REVERT: C  577 MET cc_start: 0.8227 (tpt) cc_final: 0.7912 (tpt)
REVERT: C  665 LYS cc_start: 0.8307 (OUTLIER) cc_final: 0.7667 (tttp)
REVERT: D  531 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8401 (ppp)
REVERT: D  581 LYS cc_start: 0.7887 (mtmm) cc_final: 0.7561 (mmpt)
REVERT: E  531 MET cc_start: 0.9282 (tmm) cc_final: 0.9082 (tmm)
REVERT: E  545 LYS cc_start: 0.9038 (mtpp) cc_final: 0.8673 (mppt)
  outliers start: 36
  outliers final: 10
  residues processed: 217
  average time/residue: 0.7721
  time to fit residues: 181.1447
Evaluate side-chains
  204 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 188
  time to evaluate  : 0.605 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  222 LYS
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  472 LYS
Chi-restraints excluded: chain A residue  882 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1132 GLU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain C residue  549 LYS
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  598 ILE
Chi-restraints excluded: chain C residue  665 LYS
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain E residue  575 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.6980
   chunk 85 optimal weight:    2.9990
   chunk 177 optimal weight:    7.9990
   chunk 12 optimal weight:    2.9990
   chunk 126 optimal weight:    1.9990
   chunk 161 optimal weight:    0.5980
   chunk 104 optimal weight:    0.9990
   chunk 139 optimal weight:    3.9990
   chunk 72 optimal weight:    2.9990
   overall best weight:    1.2586

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 860 GLN
A1237 GLN
C 651 GLN
D 591 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3752 r_free = 0.3752 target = 0.124304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3010 r_free = 0.3010 target = 0.075313 restraints weight = 24683.540|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 2.77
r_work: 0.2854 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2854
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8220
moved from start:          0.3370

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.074  15029  Z= 0.180
  Angle     :  0.602   8.326  20308  Z= 0.305
  Chirality :  0.043   0.166   2305
  Planarity :  0.004   0.047   2601
  Dihedral  :  4.080  20.308   1980
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 6.13
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.58 %
    Favored  : 97.31 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.97 %
    Favored  : 81.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.02 (0.20), residues: 1819
  helix:  2.49 (0.16), residues: 1068
  sheet:  0.78 (0.52), residues: 101
  loop : -0.58 (0.24), residues: 650

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 361 
 TYR   0.016   0.001   TYR A 284 
 PHE   0.019   0.001   PHE A 399 
 TRP   0.018   0.001   TRP A1306 
 HIS   0.006   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00444 (15028)
  covalent geometry    : angle       0.60178 (20306)
  SS BOND              : bond        0.00154 (    1)
  SS BOND              : angle       0.42216 (    2)
  hydrogen bonds       : bond        0.04698 (  843)
  hydrogen bonds       : angle       3.81776 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  226 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 189
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8617 (mp0) cc_final: 0.8259 (mp0)
REVERT: A   78 LYS cc_start: 0.8115 (mptt) cc_final: 0.7749 (mmpt)
REVERT: A   90 GLU cc_start: 0.8803 (OUTLIER) cc_final: 0.8538 (mp0)
REVERT: A  141 ARG cc_start: 0.7951 (mtm-85) cc_final: 0.7684 (mmm-85)
REVERT: A  204 LYS cc_start: 0.9325 (mtpp) cc_final: 0.8893 (mtmt)
REVERT: A  419 TYR cc_start: 0.8282 (m-10) cc_final: 0.7989 (m-10)
REVERT: A  426 LYS cc_start: 0.9009 (mttm) cc_final: 0.8794 (tmtt)
REVERT: A  469 MET cc_start: 0.8811 (OUTLIER) cc_final: 0.8417 (ptp)
REVERT: A  472 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8119 (mmpt)
REVERT: A  531 GLU cc_start: 0.8469 (mp0) cc_final: 0.8104 (mp0)
REVERT: A  893 LYS cc_start: 0.9096 (mtmt) cc_final: 0.8776 (mttp)
REVERT: A 1132 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8128 (pp20)
REVERT: A 1160 SER cc_start: 0.8546 (t) cc_final: 0.8280 (m)
REVERT: A 1180 ARG cc_start: 0.9009 (mtt-85) cc_final: 0.8604 (ttm110)
REVERT: A 1245 MET cc_start: 0.8256 (ttp) cc_final: 0.7651 (ttt)
REVERT: A 1295 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8456 (mtt-85)
REVERT: A 1314 CYS cc_start: 0.8190 (m) cc_final: 0.7816 (m)
REVERT: A 1447 GLU cc_start: 0.8351 (tt0) cc_final: 0.8098 (tm-30)
REVERT: B  555 ARG cc_start: 0.8832 (ptp-110) cc_final: 0.8520 (ptp90)
REVERT: B  568 GLU cc_start: 0.8449 (tm-30) cc_final: 0.8078 (tm-30)
REVERT: C  531 MET cc_start: 0.8999 (tmm) cc_final: 0.8627 (ppp)
REVERT: C  549 LYS cc_start: 0.8151 (OUTLIER) cc_final: 0.7645 (tttm)
REVERT: C  665 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.7662 (tttp)
REVERT: D  531 MET cc_start: 0.8793 (OUTLIER) cc_final: 0.8397 (ppp)
REVERT: D  581 LYS cc_start: 0.7844 (mtmm) cc_final: 0.7525 (mmpt)
REVERT: E  548 ASN cc_start: 0.9188 (m-40) cc_final: 0.8937 (m110)
  outliers start: 37
  outliers final: 14
  residues processed: 208
  average time/residue: 0.7847
  time to fit residues: 176.5643
Evaluate side-chains
  207 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 186
  time to evaluate  : 0.570 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   90 GLU
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  472 LYS
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1072 ILE
Chi-restraints excluded: chain A residue 1082 ARG
Chi-restraints excluded: chain A residue 1132 GLU
Chi-restraints excluded: chain A residue 1185 LEU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain C residue  549 LYS
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  665 LYS
Chi-restraints excluded: chain D residue  529 LEU
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain D residue  577 MET
Chi-restraints excluded: chain E residue  575 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 131 optimal weight:    9.9990
   chunk 149 optimal weight:    2.9990
   chunk 2 optimal weight:    0.5980
   chunk 159 optimal weight:    3.9990
   chunk 150 optimal weight:    0.7980
   chunk 112 optimal weight:    0.4980
   chunk 110 optimal weight:    0.7980
   chunk 143 optimal weight:   20.0000
   chunk 119 optimal weight:    7.9990
   chunk 181 optimal weight:    0.9990
   chunk 111 optimal weight:    0.6980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A1237 GLN
D 522 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.125828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3036 r_free = 0.3036 target = 0.076663 restraints weight = 24681.459|
|-----------------------------------------------------------------------------|
r_work (start): 0.3022 rms_B_bonded: 2.85
r_work: 0.2870 rms_B_bonded: 3.45 restraints_weight: 0.5000
r_work (final): 0.2870
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8157
moved from start:          0.3463

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15029  Z= 0.134
  Angle     :  0.626  23.057  20308  Z= 0.313
  Chirality :  0.043   0.399   2305
  Planarity :  0.004   0.069   2601
  Dihedral  :  4.058  21.832   1980
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 6.30
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.53 %
    Favored  : 97.36 %
  Rotamer:
    Outliers :  1.56 %
    Allowed  : 16.81 %
    Favored  : 81.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.10 (0.20), residues: 1819
  helix:  2.57 (0.16), residues: 1067
  sheet:  0.79 (0.52), residues: 101
  loop : -0.55 (0.24), residues: 651

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.040   0.001   ARG A1082 
 TYR   0.010   0.001   TYR A 284 
 PHE   0.015   0.001   PHE A 553 
 TRP   0.011   0.001   TRP A1248 
 HIS   0.007   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00316 (15028)
  covalent geometry    : angle       0.62596 (20306)
  SS BOND              : bond        0.00108 (    1)
  SS BOND              : angle       0.33007 (    2)
  hydrogen bonds       : bond        0.04248 (  843)
  hydrogen bonds       : angle       3.75183 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  218 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 192
  time to evaluate  : 0.588 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8613 (mp0) cc_final: 0.8242 (mp0)
REVERT: A   78 LYS cc_start: 0.8084 (mptt) cc_final: 0.7669 (mmtt)
REVERT: A  141 ARG cc_start: 0.7888 (mtm-85) cc_final: 0.7609 (mmm-85)
REVERT: A  204 LYS cc_start: 0.9324 (mtpp) cc_final: 0.8824 (mppt)
REVERT: A  419 TYR cc_start: 0.8252 (m-10) cc_final: 0.7957 (m-10)
REVERT: A  426 LYS cc_start: 0.8984 (mttm) cc_final: 0.8766 (tmtt)
REVERT: A  469 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8096 (ptp)
REVERT: A  472 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.7790 (mtmm)
REVERT: A  531 GLU cc_start: 0.8459 (mp0) cc_final: 0.8110 (mp0)
REVERT: A  893 LYS cc_start: 0.9064 (mtmt) cc_final: 0.8748 (mttp)
REVERT: A 1032 MET cc_start: 0.8673 (mtt) cc_final: 0.8182 (mtt)
REVERT: A 1132 GLU cc_start: 0.8474 (pp20) cc_final: 0.8101 (pp20)
REVERT: A 1180 ARG cc_start: 0.9025 (mtt-85) cc_final: 0.8624 (ttm110)
REVERT: A 1245 MET cc_start: 0.8220 (ttp) cc_final: 0.7610 (ttt)
REVERT: A 1295 ARG cc_start: 0.8906 (mmm160) cc_final: 0.8629 (mtt180)
REVERT: A 1314 CYS cc_start: 0.8148 (m) cc_final: 0.7774 (m)
REVERT: A 1447 GLU cc_start: 0.8371 (tt0) cc_final: 0.8102 (tm-30)
REVERT: B  555 ARG cc_start: 0.8804 (ptp-110) cc_final: 0.8488 (ptp90)
REVERT: B  568 GLU cc_start: 0.8433 (tm-30) cc_final: 0.8104 (tm-30)
REVERT: C  531 MET cc_start: 0.9034 (tmm) cc_final: 0.8660 (ppp)
REVERT: C  549 LYS cc_start: 0.8120 (OUTLIER) cc_final: 0.7746 (ttmm)
REVERT: C  665 LYS cc_start: 0.8220 (OUTLIER) cc_final: 0.7603 (tttp)
REVERT: D  531 MET cc_start: 0.8833 (OUTLIER) cc_final: 0.8433 (ppp)
REVERT: D  581 LYS cc_start: 0.7863 (mtmm) cc_final: 0.7542 (mmpt)
  outliers start: 26
  outliers final: 14
  residues processed: 204
  average time/residue: 0.8112
  time to fit residues: 178.5911
Evaluate side-chains
  207 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 188
  time to evaluate  : 0.599 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  472 LYS
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  882 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain A residue 1294 LEU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain C residue  549 LYS
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  665 LYS
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain E residue  534 ASN
Chi-restraints excluded: chain E residue  575 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 178 optimal weight:    1.9990
   chunk 164 optimal weight:   10.0000
   chunk 89 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0970
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.0050
   chunk 88 optimal weight:    0.9980
   chunk 113 optimal weight:    0.5980
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    0.6980
   chunk 138 optimal weight:    0.7980
   overall best weight:    0.4192

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

Flipped N/Q/H residues before XYZ refinement:
A 860 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 651 GLN
D 522 ASN
** D 591 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3788 r_free = 0.3788 target = 0.126934 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3051 r_free = 0.3051 target = 0.077566 restraints weight = 24508.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.3034 rms_B_bonded: 2.87
r_work: 0.2883 rms_B_bonded: 3.47 restraints_weight: 0.5000
r_work (final): 0.2883
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8110
moved from start:          0.3533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053  15029  Z= 0.120
  Angle     :  0.603  13.067  20308  Z= 0.301
  Chirality :  0.041   0.149   2305
  Planarity :  0.004   0.051   2601
  Dihedral  :  3.965  20.676   1980
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 6.57
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.64 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 17.29 %
    Favored  : 81.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.15 (0.20), residues: 1819
  helix:  2.60 (0.16), residues: 1070
  sheet:  0.87 (0.53), residues: 101
  loop : -0.52 (0.24), residues: 648

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG C 555 
 TYR   0.009   0.001   TYR A 284 
 PHE   0.016   0.001   PHE A 553 
 TRP   0.012   0.001   TRP A1248 
 HIS   0.007   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 (15028)
  covalent geometry    : angle       0.60323 (20306)
  SS BOND              : bond        0.00100 (    1)
  SS BOND              : angle       0.34195 (    2)
  hydrogen bonds       : bond        0.03932 (  843)
  hydrogen bonds       : angle       3.68129 ( 2421)

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

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

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3638 Ramachandran restraints generated.
    1819 Oldfield, 0 Emsley, 1819 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  215 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 196
  time to evaluate  : 0.629 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   14 GLU cc_start: 0.8606 (mp0) cc_final: 0.8225 (mp0)
REVERT: A   78 LYS cc_start: 0.8100 (mptt) cc_final: 0.7656 (mmtt)
REVERT: A  204 LYS cc_start: 0.9340 (mtpp) cc_final: 0.8864 (mppt)
REVERT: A  419 TYR cc_start: 0.8233 (m-10) cc_final: 0.7949 (m-10)
REVERT: A  426 LYS cc_start: 0.8965 (mttm) cc_final: 0.8750 (tmtt)
REVERT: A  469 MET cc_start: 0.8757 (OUTLIER) cc_final: 0.8098 (ptp)
REVERT: A  472 LYS cc_start: 0.8396 (OUTLIER) cc_final: 0.7796 (mtmm)
REVERT: A  513 GLU cc_start: 0.8553 (pm20) cc_final: 0.8332 (pm20)
REVERT: A  531 GLU cc_start: 0.8439 (mp0) cc_final: 0.8084 (mp0)
REVERT: A  893 LYS cc_start: 0.9049 (mtmt) cc_final: 0.8733 (mttp)
REVERT: A 1032 MET cc_start: 0.8627 (mtt) cc_final: 0.8126 (mtt)
REVERT: A 1066 GLN cc_start: 0.8641 (tt0) cc_final: 0.8295 (tp40)
REVERT: A 1132 GLU cc_start: 0.8454 (pp20) cc_final: 0.8090 (pp20)
REVERT: A 1180 ARG cc_start: 0.9020 (mtt-85) cc_final: 0.8580 (ttm110)
REVERT: A 1225 MET cc_start: 0.8337 (mtm) cc_final: 0.8083 (mtm)
REVERT: A 1245 MET cc_start: 0.8226 (ttp) cc_final: 0.7642 (ttt)
REVERT: A 1295 ARG cc_start: 0.8883 (mmm160) cc_final: 0.8593 (mtt180)
REVERT: A 1314 CYS cc_start: 0.8103 (m) cc_final: 0.7740 (m)
REVERT: A 1447 GLU cc_start: 0.8361 (tt0) cc_final: 0.8081 (tm-30)
REVERT: B  555 ARG cc_start: 0.8807 (ptp-110) cc_final: 0.8558 (ptp90)
REVERT: B  568 GLU cc_start: 0.8445 (tm-30) cc_final: 0.8078 (tm-30)
REVERT: C  531 MET cc_start: 0.9042 (tmm) cc_final: 0.8667 (ppp)
REVERT: C  549 LYS cc_start: 0.8005 (OUTLIER) cc_final: 0.7647 (tttt)
REVERT: C  665 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7553 (tttp)
REVERT: D  531 MET cc_start: 0.8816 (OUTLIER) cc_final: 0.8474 (ppp)
REVERT: E  535 HIS cc_start: 0.8895 (m90) cc_final: 0.8357 (m90)
  outliers start: 19
  outliers final: 14
  residues processed: 206
  average time/residue: 0.7532
  time to fit residues: 167.8712
Evaluate side-chains
  210 residues out of total 1666 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 191
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  237 MET
Chi-restraints excluded: chain A residue  289 MET
Chi-restraints excluded: chain A residue  357 PHE
Chi-restraints excluded: chain A residue  358 SER
Chi-restraints excluded: chain A residue  469 MET
Chi-restraints excluded: chain A residue  472 LYS
Chi-restraints excluded: chain A residue  521 LEU
Chi-restraints excluded: chain A residue  882 THR
Chi-restraints excluded: chain A residue  979 ILE
Chi-restraints excluded: chain A residue 1291 THR
Chi-restraints excluded: chain A residue 1294 LEU
Chi-restraints excluded: chain B residue  529 LEU
Chi-restraints excluded: chain B residue  573 SER
Chi-restraints excluded: chain C residue  549 LYS
Chi-restraints excluded: chain C residue  572 VAL
Chi-restraints excluded: chain C residue  597 VAL
Chi-restraints excluded: chain C residue  665 LYS
Chi-restraints excluded: chain D residue  531 MET
Chi-restraints excluded: chain E residue  534 ASN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 182
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 56 optimal weight:    0.5980
   chunk 172 optimal weight:    0.8980
   chunk 76 optimal weight:    0.5980
   chunk 133 optimal weight:   50.0000
   chunk 167 optimal weight:    0.6980
   chunk 160 optimal weight:    0.4980
   chunk 153 optimal weight:    3.9990
   chunk 125 optimal weight:    1.9990
   chunk 141 optimal weight:   10.0000
   chunk 86 optimal weight:    0.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A  66 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 860 GLN
** A1237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 651 GLN
D 522 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.126304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3046 r_free = 0.3046 target = 0.077306 restraints weight = 24723.073|
|-----------------------------------------------------------------------------|
r_work (start): 0.3037 rms_B_bonded: 2.79
r_work: 0.2892 rms_B_bonded: 3.37 restraints_weight: 0.5000
r_work (final): 0.2892
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.3594

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  15029  Z= 0.131
  Angle     :  0.613  12.705  20308  Z= 0.305
  Chirality :  0.042   0.150   2305
  Planarity :  0.004   0.047   2601
  Dihedral  :  3.923  20.778   1980
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 6.36
  Ramachandran Plot:
    Outliers :  0.11 %
    Allowed  :  2.31 %
    Favored  : 97.58 %
  Rotamer:
    Outliers :  1.38 %
    Allowed  : 17.47 %
    Favored  : 81.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  2.13 (0.20), residues: 1819
  helix:  2.55 (0.16), residues: 1075
  sheet:  0.83 (0.52), residues: 101
  loop : -0.50 (0.24), residues: 643

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG C 555 
 TYR   0.011   0.001   TYR A 284 
 PHE   0.016   0.001   PHE A 553 
 TRP   0.011   0.001   TRP A1248 
 HIS   0.006   0.001   HIS B 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 (15028)
  covalent geometry    : angle       0.61294 (20306)
  SS BOND              : bond        0.00134 (    1)
  SS BOND              : angle       0.33755 (    2)
  hydrogen bonds       : bond        0.04070 (  843)
  hydrogen bonds       : angle       3.70092 ( 2421)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5811.86 seconds
wall clock time: 99 minutes 46.49 seconds (5986.49 seconds total)