Starting phenix.real_space_refine
on Tue Nov 18 03:52:11 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/5yud_6845/11_2025/5yud_6845_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/5yud_6845/11_2025/5yud_6845.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.28
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/5yud_6845/11_2025/5yud_6845_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/5yud_6845/11_2025/5yud_6845_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/5yud_6845/11_2025/5yud_6845.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/5yud_6845/11_2025/5yud_6845.map"
  }
  resolution = 4.28
  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=   0.008
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 44 atoms to isotropic.
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P       3      5.49       5
     S      54      5.16       5
     C    6691      2.51       5
     N    1779      2.21       5
     O    1983      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10510
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 9943
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1238, 9943
          Classifications: {'peptide': 1238}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 50, 'TRANS': 1187}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 75, 536
          Classifications: {'peptide': 75}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 1, 'TRANS': 73}
    Chain: "A"
      Number of atoms: 31
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 31
          Unusual residues: {'ATP': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.77, per 1000 atoms: 0.26
  Number of scatterers: 10510
  At special positions: 0
  Unit cell: (92.7643, 118.895, 138.493, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      54     16.00
     P       3     15.00
     O    1983      8.00
     N    1779      7.00
     C    6691      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 1.08
  Conformation dependent library (CDL) restraints added in 545.5 milliseconds
  

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2510

  Finding SS restraints...
    Secondary structure from input PDB file:
      65 helices and 9 sheets defined
      48.0% alpha, 5.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 22 through 25
      removed outlier: 3.820A  pdb=" N   ALA A  25 " --> pdb=" O   GLU A  22 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 22 through 25'
    Processing helix  chain 'A' and resid 26 through 31
      removed outlier: 4.056A  pdb=" N   ASP A  30 " --> pdb=" O   LEU A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 36 through 51
      removed outlier: 3.807A  pdb=" N   GLU A  40 " --> pdb=" O   LYS A  36 " (cutoff:3.500A)
      removed outlier: 4.072A  pdb=" N   HIS A  43 " --> pdb=" O   GLU A  39 " (cutoff:3.500A)
      removed outlier: 4.260A  pdb=" N   LYS A  44 " --> pdb=" O   GLU A  40 " (cutoff:3.500A)
      removed outlier: 4.051A  pdb=" N   GLU A  45 " --> pdb=" O   GLU A  41 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   LYS A  50 " --> pdb=" O   ARG A  46 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 59 through 61
      No H-bonds generated for 'chain 'A' and resid 59 through 61'
    Processing helix  chain 'A' and resid 62 through 67
      removed outlier: 3.680A  pdb=" N   THR A  66 " --> pdb=" O   LYS A  62 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 77 through 85
      removed outlier: 3.728A  pdb=" N   ALA A  83 " --> pdb=" O   GLN A  79 " (cutoff:3.500A)
      removed outlier: 3.591A  pdb=" N   ALA A  84 " --> pdb=" O   GLU A  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 112 through 121
      removed outlier: 3.725A  pdb=" N   ARG A 116 " --> pdb=" O   LEU A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 144 through 149
      removed outlier: 4.376A  pdb=" N   MET A 148 " --> pdb=" O   ARG A 144 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   LEU A 149 " --> pdb=" O   PRO A 145 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 144 through 149'
    Processing helix  chain 'A' and resid 158 through 164
      removed outlier: 3.649A  pdb=" N   ARG A 162 " --> pdb=" O   GLU A 158 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 165 through 168
    Processing helix  chain 'A' and resid 177 through 184
      removed outlier: 3.656A  pdb=" N   LEU A 181 " --> pdb=" O   SER A 177 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 221
      removed outlier: 5.303A  pdb=" N   ALA A 218 " --> pdb=" O   TRP A 214 " (cutoff:3.500A)
      removed outlier: 4.436A  pdb=" N   LYS A 219 " --> pdb=" O   LYS A 215 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 224 through 229
    Processing helix  chain 'A' and resid 233 through 240
      removed outlier: 4.110A  pdb=" N   ALA A 237 " --> pdb=" O   SER A 233 " (cutoff:3.500A)
      removed outlier: 3.677A  pdb=" N   GLN A 238 " --> pdb=" O   GLU A 234 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 406 through 418
      removed outlier: 3.856A  pdb=" N   ASN A 410 " --> pdb=" O   GLN A 406 " (cutoff:3.500A)
      removed outlier: 3.676A  pdb=" N   TYR A 411 " --> pdb=" O   LEU A 407 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 454 through 461
      removed outlier: 3.711A  pdb=" N   SER A 460 " --> pdb=" O   PRO A 456 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 475 through 489
      removed outlier: 3.922A  pdb=" N   LEU A 480 " --> pdb=" O   LYS A 476 " (cutoff:3.500A)
      removed outlier: 3.760A  pdb=" N   ILE A 483 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   ALA A 484 " --> pdb=" O   LEU A 480 " (cutoff:3.500A)
      removed outlier: 3.961A  pdb=" N   SER A 489 " --> pdb=" O   PHE A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 492 through 498
      removed outlier: 4.178A  pdb=" N   TYR A 496 " --> pdb=" O   CYS A 492 " (cutoff:3.500A)
      removed outlier: 3.832A  pdb=" N   ARG A 497 " --> pdb=" O   PRO A 493 " (cutoff:3.500A)
      removed outlier: 4.458A  pdb=" N   PHE A 498 " --> pdb=" O   LEU A 494 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 492 through 498'
    Processing helix  chain 'A' and resid 516 through 524
      removed outlier: 4.604A  pdb=" N   GLN A 522 " --> pdb=" O   ILE A 518 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 535 through 542
      removed outlier: 3.543A  pdb=" N   LEU A 542 " --> pdb=" O   SER A 538 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 585 through 590
      removed outlier: 4.174A  pdb=" N   ILE A 589 " --> pdb=" O   ARG A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 615
      removed outlier: 3.819A  pdb=" N   THR A 607 " --> pdb=" O   PRO A 603 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   PHE A 615 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 620 through 631
      removed outlier: 3.971A  pdb=" N   ILE A 626 " --> pdb=" O   VAL A 622 " (cutoff:3.500A)
      removed outlier: 4.014A  pdb=" N   ILE A 627 " --> pdb=" O   GLU A 623 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 637
      removed outlier: 3.803A  pdb=" N   GLY A 637 " --> pdb=" O   LYS A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 641 through 650
      removed outlier: 3.729A  pdb=" N   VAL A 645 " --> pdb=" O   THR A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 664 through 680
      removed outlier: 3.696A  pdb=" N   GLN A 673 " --> pdb=" O   GLN A 669 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 683 through 703
      removed outlier: 3.581A  pdb=" N   GLN A 695 " --> pdb=" O   SER A 691 " (cutoff:3.500A)
      removed outlier: 4.561A  pdb=" N   LEU A 696 " --> pdb=" O   SER A 692 " (cutoff:3.500A)
      removed outlier: 3.689A  pdb=" N   ALA A 697 " --> pdb=" O   CYS A 693 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   THR A 699 " --> pdb=" O   GLN A 695 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   GLY A 700 " --> pdb=" O   LEU A 696 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   LEU A 701 " --> pdb=" O   ALA A 697 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   PHE A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 717
    Processing helix  chain 'A' and resid 718 through 722
      removed outlier: 3.993A  pdb=" N   GLU A 722 " --> pdb=" O   ASP A 719 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 723 through 728
      removed outlier: 3.898A  pdb=" N   LEU A 727 " --> pdb=" O   LYS A 723 " (cutoff:3.500A)
      removed outlier: 4.212A  pdb=" N   LEU A 728 " --> pdb=" O   LEU A 724 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 723 through 728'
    Processing helix  chain 'A' and resid 745 through 760
      removed outlier: 3.755A  pdb=" N   ALA A 754 " --> pdb=" O   GLU A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 769 through 777
      removed outlier: 3.798A  pdb=" N   ARG A 777 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 781 through 787
      removed outlier: 3.629A  pdb=" N   ALA A 785 " --> pdb=" O   SER A 781 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 800
      removed outlier: 3.549A  pdb=" N   TYR A 794 " --> pdb=" O   ASN A 790 " (cutoff:3.500A)
      removed outlier: 3.790A  pdb=" N   TYR A 795 " --> pdb=" O   ILE A 791 " (cutoff:3.500A)
      removed outlier: 3.577A  pdb=" N   SER A 800 " --> pdb=" O   VAL A 796 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 803 through 815
      removed outlier: 4.420A  pdb=" N   THR A 807 " --> pdb=" O   LYS A 803 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   HIS A 811 " --> pdb=" O   THR A 807 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 830 through 835
    Processing helix  chain 'A' and resid 836 through 852
      removed outlier: 4.009A  pdb=" N   LEU A 840 " --> pdb=" O   PRO A 836 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 852 through 873
      removed outlier: 3.764A  pdb=" N   SER A 857 " --> pdb=" O   PRO A 853 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   GLU A 862 " --> pdb=" O   SER A 858 " (cutoff:3.500A)
      removed outlier: 3.711A  pdb=" N   HIS A 863 " --> pdb=" O   PHE A 859 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 880 through 889
      removed outlier: 4.165A  pdb=" N   PHE A 884 " --> pdb=" O   GLU A 880 " (cutoff:3.500A)
      removed outlier: 3.624A  pdb=" N   GLN A 887 " --> pdb=" O   PRO A 883 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 901
      removed outlier: 4.268A  pdb=" N   ASN A 900 " --> pdb=" O   LEU A 896 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 929 through 939
      removed outlier: 3.757A  pdb=" N   TYR A 932 " --> pdb=" O   TYR A 929 " (cutoff:3.500A)
      removed outlier: 4.578A  pdb=" N   TYR A 937 " --> pdb=" O   PHE A 934 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 956 through 978
      removed outlier: 3.923A  pdb=" N   ILE A 970 " --> pdb=" O   GLN A 966 " (cutoff:3.500A)
      removed outlier: 3.547A  pdb=" N   TYR A 974 " --> pdb=" O   ILE A 970 " (cutoff:3.500A)
      removed outlier: 3.932A  pdb=" N   ARG A 978 " --> pdb=" O   TYR A 974 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 988 through 993
    Processing helix  chain 'A' and resid 1008 through 1012
      removed outlier: 3.862A  pdb=" N   ALA A1011 " --> pdb=" O   ASN A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1013 through 1025
      removed outlier: 3.932A  pdb=" N   GLU A1022 " --> pdb=" O   GLN A1018 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   VAL A1023 " --> pdb=" O   VAL A1019 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   SER A1025 " --> pdb=" O   MET A1021 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1039 through 1049
      removed outlier: 3.884A  pdb=" N   SER A1043 " --> pdb=" O   GLY A1039 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   CYS A1045 " --> pdb=" O   LEU A1041 " (cutoff:3.500A)
      Proline residue:  A1046  - end of helix
    Processing helix  chain 'A' and resid 1069 through 1076
      removed outlier: 3.681A  pdb=" N   LEU A1076 " --> pdb=" O   LEU A1072 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1154
      removed outlier: 4.114A  pdb=" N   GLN A1152 " --> pdb=" O   VAL A1148 " (cutoff:3.500A)
      removed outlier: 4.571A  pdb=" N   ASN A1153 " --> pdb=" O   LYS A1149 " (cutoff:3.500A)
      removed outlier: 3.846A  pdb=" N   PHE A1154 " --> pdb=" O   PHE A1150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1155 through 1157
      No H-bonds generated for 'chain 'A' and resid 1155 through 1157'
    Processing helix  chain 'A' and resid 1173 through 1178
    Processing helix  chain 'A' and resid 1201 through 1205
      removed outlier: 3.969A  pdb=" N   PHE A1205 " --> pdb=" O   LEU A1202 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1220 through 1234
    Processing helix  chain 'A' and resid 1247 through 1252
      removed outlier: 4.030A  pdb=" N   GLN A1250 " --> pdb=" O   GLY A1247 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1253 through 1258
      removed outlier: 3.616A  pdb=" N   GLN A1258 " --> pdb=" O   LEU A1254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1259 through 1262
    Processing helix  chain 'A' and resid 1277 through 1288
    Processing helix  chain 'A' and resid 1306 through 1308
      No H-bonds generated for 'chain 'A' and resid 1306 through 1308'
    Processing helix  chain 'A' and resid 1309 through 1314
    Processing helix  chain 'A' and resid 1339 through 1344
      removed outlier: 3.836A  pdb=" N   LYS A1344 " --> pdb=" O   ALA A1340 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1345 through 1351
    Processing helix  chain 'A' and resid 1364 through 1374
    Processing helix  chain 'A' and resid 1397 through 1402
    Processing helix  chain 'C' and resid 426 through 444
      removed outlier: 4.757A  pdb=" N   ASN C 432 " --> pdb=" O   GLY C 428 " (cutoff:3.500A)
      removed outlier: 3.957A  pdb=" N   SER C 433 " --> pdb=" O   LEU C 429 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ALA C 439 " --> pdb=" O   LYS C 435 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   ILE C 443 " --> pdb=" O   ALA C 439 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA C 444 " --> pdb=" O   GLY C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 453 through 483
      removed outlier: 4.068A  pdb=" N   GLU C 462 " --> pdb=" O   ASP C 458 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   GLN C 473 " --> pdb=" O   ALA C 469 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 484 through 495
      removed outlier: 3.923A  pdb=" N   GLN C 488 " --> pdb=" O   ASN C 484 " (cutoff:3.500A)
      removed outlier: 4.077A  pdb=" N   LEU C 493 " --> pdb=" O   ASN C 489 " (cutoff:3.500A)
      removed outlier: 3.679A  pdb=" N   LEU C 494 " --> pdb=" O   VAL C 490 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88
    Processing sheet with id=AA2, first strand: chain 'A' and resid 186 through 188
    Processing sheet with id=AA3, first strand: chain 'A' and resid 440 through 441
    Processing sheet with id=AA4, first strand: chain 'A' and resid 469 through 470
      removed outlier: 6.647A  pdb=" N   PHE A 548 " --> pdb=" O   LEU A 578 " (cutoff:3.500A)
      removed outlier: 7.927A  pdb=" N   ALA A 580 " --> pdb=" O   PHE A 548 " (cutoff:3.500A)
      removed outlier: 6.619A  pdb=" N   LEU A 550 " --> pdb=" O   ALA A 580 " (cutoff:3.500A)
      removed outlier: 8.162A  pdb=" N   HIS A 582 " --> pdb=" O   LEU A 550 " (cutoff:3.500A)
      removed outlier: 3.531A  pdb=" N   ASP A 551 " --> pdb=" O   LEU A 504 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 730 through 731
    Processing sheet with id=AA6, first strand: chain 'A' and resid 892 through 895
      removed outlier: 5.878A  pdb=" N   LYS A 892 " --> pdb=" O   LEU A 914 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   SER A 916 " --> pdb=" O   LYS A 892 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   LEU A 894 " --> pdb=" O   SER A 916 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   LYS A 918 " --> pdb=" O   LEU A 894 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   LEU A 913 " --> pdb=" O   LYS A1001 " (cutoff:3.500A)
      removed outlier: 9.009A  pdb=" N   GLU A1003 " --> pdb=" O   LEU A 913 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ARG A 915 " --> pdb=" O   GLU A1003 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   GLN A1005 " --> pdb=" O   ARG A 915 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LEU A 917 " --> pdb=" O   GLN A1005 " (cutoff:3.500A)
      removed outlier: 7.586A  pdb=" N   ILE A 999 " --> pdb=" O   GLN A1028 " (cutoff:3.500A)
      removed outlier: 7.040A  pdb=" N   ILE A1030 " --> pdb=" O   ILE A 999 " (cutoff:3.500A)
      removed outlier: 8.920A  pdb=" N   LYS A1001 " --> pdb=" O   ILE A1030 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'A' and resid 892 through 895
      removed outlier: 5.878A  pdb=" N   LYS A 892 " --> pdb=" O   LEU A 914 " (cutoff:3.500A)
      removed outlier: 7.567A  pdb=" N   SER A 916 " --> pdb=" O   LYS A 892 " (cutoff:3.500A)
      removed outlier: 6.123A  pdb=" N   LEU A 894 " --> pdb=" O   SER A 916 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   LYS A 918 " --> pdb=" O   LEU A 894 " (cutoff:3.500A)
      removed outlier: 8.021A  pdb=" N   LEU A 913 " --> pdb=" O   LYS A1001 " (cutoff:3.500A)
      removed outlier: 9.009A  pdb=" N   GLU A1003 " --> pdb=" O   LEU A 913 " (cutoff:3.500A)
      removed outlier: 6.785A  pdb=" N   ARG A 915 " --> pdb=" O   GLU A1003 " (cutoff:3.500A)
      removed outlier: 7.949A  pdb=" N   GLN A1005 " --> pdb=" O   ARG A 915 " (cutoff:3.500A)
      removed outlier: 6.350A  pdb=" N   LEU A 917 " --> pdb=" O   GLN A1005 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   PHE A1032 " --> pdb=" O   SER A1059 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   CYS A1058 " --> pdb=" O   GLU A1083 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 1134 through 1135
      removed outlier: 6.627A  pdb=" N   LEU A1134 " --> pdb=" O   LYS A1163 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 1296 through 1299

    314 hydrogen bonds defined for protein.
    861 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.91

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.19 -     1.31: 1766
        1.31 -     1.44: 2799
        1.44 -     1.56: 6082
        1.56 -     1.69: 5
        1.69 -     1.81: 75
  Bond restraints: 10727
  Sorted by residual:
  bond pdb=" C4  ATP A1501 "
       pdb=" C5  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.388  1.468 -0.080 1.00e-02 1.00e+04 6.35e+01
  bond pdb=" C   TRP A  76 "
       pdb=" N   THR A  77 "
    ideal  model  delta    sigma   weight residual
    1.331  1.190  0.141 2.07e-02 2.33e+03 4.63e+01
  bond pdb=" C5  ATP A1501 "
       pdb=" C6  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.409  1.471 -0.062 1.00e-02 1.00e+04 3.82e+01
  bond pdb=" C5  ATP A1501 "
       pdb=" N7  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.387  1.334  0.053 1.00e-02 1.00e+04 2.78e+01
  bond pdb=" C4  ATP A1501 "
       pdb=" N9  ATP A1501 "
    ideal  model  delta    sigma   weight residual
    1.374  1.327  0.047 1.00e-02 1.00e+04 2.25e+01
  ... (remaining 10722 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.51: 14398
        5.51 -    11.01: 105
       11.01 -    16.52: 6
       16.52 -    22.03: 1
       22.03 -    27.53: 3
  Bond angle restraints: 14513
  Sorted by residual:
  angle pdb=" PB  ATP A1501 "
        pdb=" O3B ATP A1501 "
        pdb=" PG  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     139.87  112.34   27.53 1.00e+00 1.00e+00 7.58e+02
  angle pdb=" C   HIS A 907 "
        pdb=" N   PRO A 908 "
        pdb=" CA  PRO A 908 "
      ideal   model   delta    sigma   weight residual
     119.84   94.12   25.72 1.25e+00 6.40e-01 4.23e+02
  angle pdb=" N   TYR A 903 "
        pdb=" CA  TYR A 903 "
        pdb=" C   TYR A 903 "
      ideal   model   delta    sigma   weight residual
     113.41   90.76   22.65 1.22e+00 6.72e-01 3.45e+02
  angle pdb=" PA  ATP A1501 "
        pdb=" O3A ATP A1501 "
        pdb=" PB  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     136.83  119.36   17.47 1.00e+00 1.00e+00 3.05e+02
  angle pdb=" C5  ATP A1501 "
        pdb=" C4  ATP A1501 "
        pdb=" N3  ATP A1501 "
      ideal   model   delta    sigma   weight residual
     126.80  118.70    8.10 1.00e+00 1.00e+00 6.56e+01
  ... (remaining 14508 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.98: 6084
       15.98 -    31.97: 398
       31.97 -    47.95: 37
       47.95 -    63.93: 9
       63.93 -    79.92: 5
  Dihedral angle restraints: 6533
    sinusoidal: 2677
      harmonic: 3856
  Sorted by residual:
  dihedral pdb=" CA  HIS A1381 "
           pdb=" C   HIS A1381 "
           pdb=" N   PRO A1382 "
           pdb=" CA  PRO A1382 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -130.09  -49.91     0      5.00e+00 4.00e-02 9.96e+01
  dihedral pdb=" CA  GLN A 735 "
           pdb=" C   GLN A 735 "
           pdb=" N   ARG A 736 "
           pdb=" CA  ARG A 736 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  144.80   35.20     0      5.00e+00 4.00e-02 4.96e+01
  dihedral pdb=" CA  GLU A1141 "
           pdb=" C   GLU A1141 "
           pdb=" N   SER A1142 "
           pdb=" CA  SER A1142 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -145.39  -34.61     0      5.00e+00 4.00e-02 4.79e+01
  ... (remaining 6530 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.095: 1462
       0.095 -    0.191: 159
       0.191 -    0.286: 6
       0.286 -    0.381: 0
       0.381 -    0.477: 3
  Chirality restraints: 1630
  Sorted by residual:
  chirality pdb=" CA  ASP A 947 "
            pdb=" N   ASP A 947 "
            pdb=" C   ASP A 947 "
            pdb=" CB  ASP A 947 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.03    0.48 2.00e-01 2.50e+01 5.68e+00
  chirality pdb=" CA  TYR A 903 "
            pdb=" N   TYR A 903 "
            pdb=" C   TYR A 903 "
            pdb=" CB  TYR A 903 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.93   -0.42 2.00e-01 2.50e+01 4.39e+00
  chirality pdb=" CA  ILE A1273 "
            pdb=" N   ILE A1273 "
            pdb=" C   ILE A1273 "
            pdb=" CB  ILE A1273 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.02    0.42 2.00e-01 2.50e+01 4.32e+00
  ... (remaining 1627 not shown)

  Planarity restraints: 1865
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLN A 902 "   -0.027 2.00e-02 2.50e+03   5.69e-02 3.23e+01
        pdb=" C   GLN A 902 "    0.098 2.00e-02 2.50e+03
        pdb=" O   GLN A 902 "   -0.039 2.00e-02 2.50e+03
        pdb=" N   TYR A 903 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS A 907 "   -0.095 5.00e-02 4.00e+02   1.40e-01 3.16e+01
        pdb=" N   PRO A 908 "    0.241 5.00e-02 4.00e+02
        pdb=" CA  PRO A 908 "   -0.052 5.00e-02 4.00e+02
        pdb=" CD  PRO A 908 "   -0.094 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ASP A 947 "    0.021 2.00e-02 2.50e+03   4.27e-02 1.83e+01
        pdb=" C   ASP A 947 "   -0.074 2.00e-02 2.50e+03
        pdb=" O   ASP A 947 "    0.028 2.00e-02 2.50e+03
        pdb=" N   GLU A 948 "    0.025 2.00e-02 2.50e+03
  ... (remaining 1862 not shown)

  Histogram of nonbonded interaction distances:
        1.30 -     2.02: 11
        2.02 -     2.74: 1716
        2.74 -     3.46: 16973
        3.46 -     4.18: 25772
        4.18 -     4.90: 42157
  Nonbonded interactions: 86629
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 631 "
            pdb=" CD2 LEU A 635 "
     model   vdw
     1.301 3.460
  nonbonded pdb=" OG  SER A  59 "
            pdb=" CG1 VAL A 132 "
     model   vdw
     1.800 3.460
  nonbonded pdb=" CD2 LEU A1274 "
            pdb=" CD1 ILE A1299 "
     model   vdw
     1.821 3.880
  nonbonded pdb=" SG  CYS A 467 "
            pdb=" CD2 LEU A 593 "
     model   vdw
     1.889 3.820
  nonbonded pdb=" O   ASP A 947 "
            pdb=" N   TYR A 950 "
     model   vdw
     1.932 3.120
  ... (remaining 86624 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.530
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     11.690
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.270
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7563
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      :  0.012   0.826  10728  Z= 0.904
  Angle     :  1.307  27.532  14513  Z= 0.782
  Chirality :  0.060   0.477   1630
  Planarity :  0.007   0.140   1865
  Dihedral  : 10.622  79.916   4023
  Min Nonbonded Distance : 1.301

Molprobity Statistics.
  All-atom Clashscore : 55.14
  Ramachandran Plot:
    Outliers :  1.07 %
    Allowed  : 16.14 %
    Favored  : 82.79 %
  Rotamer:
    Outliers :  0.17 %
    Allowed  :  0.68 %
    Favored  : 99.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.48 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -5.50 (0.17), residues: 1307
  helix: -4.49 (0.12), residues: 424
  sheet: -3.01 (0.53), residues: 65
  loop : -3.40 (0.18), residues: 818

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG A 162 
 TYR   0.055   0.003   TYR A 950 
 PHE   0.031   0.004   PHE A1154 
 TRP   0.026   0.004   TRP A  76 
 HIS   0.012   0.003   HIS A  88 

Details of bonding type rmsd
  covalent geometry    : bond        0.00838 (10727)
  covalent geometry    : angle       1.30740 (14513)
  hydrogen bonds       : bond        0.38109 (  314)
  hydrogen bonds       : angle      10.52314 (  861)
  Misc. bond           : bond        0.82599 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  382 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 380
  time to evaluate  : 0.391 
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: symmetry clash
   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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  147 LYS cc_start: 0.9298 (mttt) cc_final: 0.8989 (mtpt)
REVERT: A  220 TRP cc_start: 0.8741 (m100) cc_final: 0.8458 (m100)
REVERT: A  418 HIS cc_start: 0.8442 (m-70) cc_final: 0.8147 (m-70)
REVERT: A  454 THR cc_start: 0.8189 (p) cc_final: 0.6868 (p)
REVERT: A  462 LEU cc_start: 0.8297 (tp) cc_final: 0.8052 (tp)
REVERT: A  548 PHE cc_start: 0.8310 (m-80) cc_final: 0.8022 (m-10)
REVERT: A  967 ASP cc_start: 0.9120 (m-30) cc_final: 0.8533 (m-30)
REVERT: A 1063 LEU cc_start: 0.8598 (tp) cc_final: 0.8316 (tp)
REVERT: A 1123 ARG cc_start: 0.7548 (mtt180) cc_final: 0.6565 (ptp90)
REVERT: A 1223 THR cc_start: 0.9079 (m) cc_final: 0.7267 (m)
REVERT: A 1226 LYS cc_start: 0.9434 (mttt) cc_final: 0.9148 (mttm)
  outliers start: 2
  outliers final: 1
  residues processed: 380
  average time/residue: 0.1424
  time to fit residues: 70.6808
Evaluate side-chains
  245 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 244
  time to evaluate  : 0.421 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 98 optimal weight:    0.9980
   chunk 107 optimal weight:    3.9990
   chunk 10 optimal weight:    1.9990
   chunk 66 optimal weight:    6.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.0970
   chunk 77 optimal weight:    0.8980
   chunk 122 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 55 optimal weight:    3.9990
   chunk 129 optimal weight:    1.9990
   overall best weight:    1.1982

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

Flipped N/Q/H residues before XYZ refinement:
A  33 GLN
A  88 HIS
A 174 HIS
A 206 ASN
A 406 GLN
A 418 HIS
A 444 HIS
A 499 GLN
A 663 GLN
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1097 ASN
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1236 ASN
A1261 GLN
A1322 ASN
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1375 ASN
** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.081082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3311 r_free = 0.3311 target = 0.067869 restraints weight = 46706.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.070041 restraints weight = 30506.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.071628 restraints weight = 21947.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.072773 restraints weight = 16823.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.073683 restraints weight = 13566.559|
|-----------------------------------------------------------------------------|
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.4130

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.108  10728  Z= 0.216
  Angle     :  0.947  14.435  14513  Z= 0.484
  Chirality :  0.052   0.323   1630
  Planarity :  0.006   0.045   1865
  Dihedral  : 10.239  75.623   1446
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 20.97
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 10.79 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.49 %
    Favored  : 96.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.98 (0.20), residues: 1307
  helix: -2.31 (0.19), residues: 499
  sheet: -3.31 (0.46), residues: 83
  loop : -2.88 (0.21), residues: 725

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.025   0.001   ARG A 765 
 TYR   0.055   0.003   TYR A 950 
 PHE   0.019   0.002   PHE A1291 
 TRP   0.019   0.002   TRP A 214 
 HIS   0.011   0.002   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00443 (10727)
  covalent geometry    : angle       0.94682 (14513)
  hydrogen bonds       : bond        0.07216 (  314)
  hydrogen bonds       : angle       7.33883 (  861)
  Misc. bond           : bond        0.00463 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  336 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 335
  time to evaluate  : 0.444 
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: symmetry clash
   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: symmetry clash
   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   47 MET cc_start: 0.9374 (mmp) cc_final: 0.9048 (mmp)
REVERT: A   50 LYS cc_start: 0.9582 (mttt) cc_final: 0.9358 (mttp)
REVERT: A   53 PHE cc_start: 0.8196 (m-10) cc_final: 0.7606 (m-10)
REVERT: A   68 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7471 (mm-30)
REVERT: A   96 GLN cc_start: 0.8724 (tt0) cc_final: 0.8295 (tm-30)
REVERT: A  220 TRP cc_start: 0.8517 (m100) cc_final: 0.8199 (m100)
REVERT: A  437 ASP cc_start: 0.8490 (m-30) cc_final: 0.8195 (m-30)
REVERT: A  550 LEU cc_start: 0.8493 (mp) cc_final: 0.8291 (mp)
REVERT: A  552 ASP cc_start: 0.6152 (t0) cc_final: 0.5433 (m-30)
REVERT: A  553 TYR cc_start: 0.7971 (p90) cc_final: 0.7486 (p90)
REVERT: A  577 LEU cc_start: 0.9248 (mt) cc_final: 0.9013 (mt)
REVERT: A  635 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8160 (pp)
REVERT: A  749 GLN cc_start: 0.9018 (tt0) cc_final: 0.8485 (tp40)
REVERT: A  795 TYR cc_start: 0.8757 (m-10) cc_final: 0.8414 (m-10)
REVERT: A  889 LEU cc_start: 0.9580 (mt) cc_final: 0.9317 (pp)
REVERT: A  894 LEU cc_start: 0.9396 (mt) cc_final: 0.8941 (mp)
REVERT: A  939 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8806 (mm-30)
REVERT: A  941 LEU cc_start: 0.9258 (pt) cc_final: 0.8770 (pp)
REVERT: A  967 ASP cc_start: 0.9287 (m-30) cc_final: 0.9041 (m-30)
REVERT: A  977 ILE cc_start: 0.9726 (mt) cc_final: 0.9498 (tp)
REVERT: A 1013 ASP cc_start: 0.8396 (m-30) cc_final: 0.8194 (m-30)
REVERT: A 1024 PHE cc_start: 0.9348 (m-10) cc_final: 0.8943 (m-80)
REVERT: A 1041 LEU cc_start: 0.9744 (mm) cc_final: 0.9307 (tt)
REVERT: A 1208 LEU cc_start: 0.8578 (mt) cc_final: 0.8368 (mt)
REVERT: A 1239 GLU cc_start: 0.9313 (pt0) cc_final: 0.8622 (pt0)
REVERT: A 1270 PHE cc_start: 0.8498 (m-80) cc_final: 0.8248 (m-10)
REVERT: A 1369 GLU cc_start: 0.9122 (mm-30) cc_final: 0.8920 (tt0)
REVERT: A 1380 ARG cc_start: 0.8597 (tmt170) cc_final: 0.8365 (tmt-80)
REVERT: A 1389 ILE cc_start: 0.8453 (mt) cc_final: 0.7898 (mt)
REVERT: C  429 LEU cc_start: 0.9308 (tp) cc_final: 0.9103 (tt)
REVERT: C  432 ASN cc_start: 0.9610 (m-40) cc_final: 0.9081 (m110)
REVERT: C  454 ILE cc_start: 0.9274 (pt) cc_final: 0.9035 (mm)
REVERT: C  456 ASP cc_start: 0.8946 (t0) cc_final: 0.8646 (t0)
  outliers start: 1
  outliers final: 0
  residues processed: 336
  average time/residue: 0.1319
  time to fit residues: 58.7609
Evaluate side-chains
  252 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 251
  time to evaluate  : 0.339 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 79 optimal weight:    4.9990
   chunk 45 optimal weight:    2.9990
   chunk 105 optimal weight:    0.0010
   chunk 68 optimal weight:    0.2980
   chunk 30 optimal weight:    5.9990
   chunk 106 optimal weight:    9.9990
   chunk 22 optimal weight:    2.9990
   chunk 89 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 123 optimal weight:    6.9990
   chunk 75 optimal weight:    8.9990
   overall best weight:    2.2592

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1036 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1097 ASN
A1099 HIS
A1271 HIS
A1296 ASN
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1348 GLN
** C 432 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 474 GLN
C 482 GLN
** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.079670 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.066505 restraints weight = 46714.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.068592 restraints weight = 30310.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 20)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.070152 restraints weight = 21805.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3378 r_free = 0.3378 target = 0.071307 restraints weight = 16711.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3396 r_free = 0.3396 target = 0.072187 restraints weight = 13431.471|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8015
moved from start:          0.5035

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  10728  Z= 0.201
  Angle     :  0.839  12.464  14513  Z= 0.433
  Chirality :  0.048   0.227   1630
  Planarity :  0.005   0.061   1865
  Dihedral  :  9.982  79.793   1446
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 22.73
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 11.40 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.26 %
    Favored  : 95.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.52 (0.21), residues: 1307
  helix: -1.67 (0.21), residues: 503
  sheet: -3.25 (0.48), residues: 83
  loop : -2.80 (0.21), residues: 721

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.019   0.001   ARG A1235 
 TYR   0.038   0.002   TYR A 950 
 PHE   0.021   0.002   PHE A 954 
 TRP   0.015   0.002   TRP A 214 
 HIS   0.013   0.002   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00447 (10727)
  covalent geometry    : angle       0.83939 (14513)
  hydrogen bonds       : bond        0.05735 (  314)
  hydrogen bonds       : angle       6.84529 (  861)
  Misc. bond           : bond        0.00058 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  290 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 290
  time to evaluate  : 0.435 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   20 LEU cc_start: 0.9079 (tp) cc_final: 0.8587 (tt)
REVERT: A   49 MET cc_start: 0.8849 (mtm) cc_final: 0.8307 (mtt)
REVERT: A   65 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8452 (mmmm)
REVERT: A   68 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7255 (mm-30)
REVERT: A   96 GLN cc_start: 0.8579 (tt0) cc_final: 0.7986 (tp-100)
REVERT: A  115 GLU cc_start: 0.9201 (tt0) cc_final: 0.8988 (tt0)
REVERT: A  148 MET cc_start: 0.7904 (mmt) cc_final: 0.7699 (mmt)
REVERT: A  215 LYS cc_start: 0.9057 (tppt) cc_final: 0.7965 (tptt)
REVERT: A  216 GLU cc_start: 0.8934 (mm-30) cc_final: 0.7762 (mm-30)
REVERT: A  220 TRP cc_start: 0.8561 (m100) cc_final: 0.8315 (m-90)
REVERT: A  437 ASP cc_start: 0.8337 (m-30) cc_final: 0.8034 (m-30)
REVERT: A  469 GLU cc_start: 0.8360 (mt-10) cc_final: 0.8044 (mt-10)
REVERT: A  479 PHE cc_start: 0.9570 (t80) cc_final: 0.9345 (t80)
REVERT: A  550 LEU cc_start: 0.8608 (mp) cc_final: 0.8316 (mp)
REVERT: A  552 ASP cc_start: 0.6338 (t0) cc_final: 0.5290 (m-30)
REVERT: A  553 TYR cc_start: 0.7987 (p90) cc_final: 0.7434 (p90)
REVERT: A  597 LEU cc_start: 0.9027 (mt) cc_final: 0.8577 (mt)
REVERT: A  598 GLU cc_start: 0.8346 (pm20) cc_final: 0.7993 (pm20)
REVERT: A  795 TYR cc_start: 0.8707 (m-10) cc_final: 0.8190 (m-10)
REVERT: A  894 LEU cc_start: 0.9264 (mt) cc_final: 0.8640 (mp)
REVERT: A  967 ASP cc_start: 0.9290 (m-30) cc_final: 0.9059 (m-30)
REVERT: A  977 ILE cc_start: 0.9612 (mt) cc_final: 0.9364 (tp)
REVERT: A 1024 PHE cc_start: 0.9430 (m-10) cc_final: 0.9206 (m-80)
REVERT: A 1080 GLN cc_start: 0.8963 (mt0) cc_final: 0.8748 (mt0)
REVERT: A 1092 GLU cc_start: 0.9073 (mm-30) cc_final: 0.8326 (pp20)
REVERT: A 1114 LYS cc_start: 0.8977 (mttt) cc_final: 0.8372 (tttt)
REVERT: A 1177 LEU cc_start: 0.9316 (mt) cc_final: 0.8989 (mt)
REVERT: A 1270 PHE cc_start: 0.8480 (m-80) cc_final: 0.8252 (m-10)
REVERT: A 1276 ASP cc_start: 0.9100 (t0) cc_final: 0.8867 (t0)
REVERT: A 1335 ARG cc_start: 0.8104 (mtm180) cc_final: 0.7869 (mtp180)
REVERT: A 1356 LEU cc_start: 0.8903 (tt) cc_final: 0.8641 (tt)
REVERT: A 1389 ILE cc_start: 0.8142 (mt) cc_final: 0.7927 (mt)
REVERT: C  432 ASN cc_start: 0.9625 (m-40) cc_final: 0.9113 (m110)
REVERT: C  456 ASP cc_start: 0.8918 (t0) cc_final: 0.8639 (t0)
REVERT: C  463 VAL cc_start: 0.9484 (t) cc_final: 0.9223 (t)
  outliers start: 0
  outliers final: 0
  residues processed: 290
  average time/residue: 0.1288
  time to fit residues: 49.9561
Evaluate side-chains
  225 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 225
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 74 optimal weight:    5.9990
   chunk 20 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 13 optimal weight:    5.9990
   chunk 61 optimal weight:    1.9990
   chunk 95 optimal weight:    4.9990
   chunk 3 optimal weight:    1.9990
   chunk 96 optimal weight:    0.2980
   chunk 113 optimal weight:    7.9990
   chunk 53 optimal weight:    9.9990
   chunk 92 optimal weight:    6.9990
   overall best weight:    2.2588

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 778 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1007 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1036 ASN
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1315 GLN
A1348 GLN
C 488 GLN
C 489 ASN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3562 r_free = 0.3562 target = 0.079785 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.066504 restraints weight = 46902.178|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.068551 restraints weight = 30345.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.070082 restraints weight = 21972.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.071258 restraints weight = 16863.637|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.072109 restraints weight = 13582.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3398
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8019
moved from start:          0.5577

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061  10728  Z= 0.191
  Angle     :  0.823  11.798  14513  Z= 0.418
  Chirality :  0.047   0.280   1630
  Planarity :  0.005   0.053   1865
  Dihedral  :  9.771  72.470   1446
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 21.54
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 11.40 %
    Favored  : 88.14 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.83 %
    Favored  : 96.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.22 (0.21), residues: 1307
  helix: -1.30 (0.21), residues: 505
  sheet: -3.34 (0.50), residues: 78
  loop : -2.71 (0.22), residues: 724

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A1380 
 TYR   0.057   0.002   TYR A 950 
 PHE   0.018   0.002   PHE A1160 
 TRP   0.016   0.002   TRP A1391 
 HIS   0.008   0.002   HIS A 582 

Details of bonding type rmsd
  covalent geometry    : bond        0.00426 (10727)
  covalent geometry    : angle       0.82305 (14513)
  hydrogen bonds       : bond        0.04896 (  314)
  hydrogen bonds       : angle       6.50844 (  861)
  Misc. bond           : bond        0.00009 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  282 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 281
  time to evaluate  : 0.458 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   39 GLU cc_start: 0.9252 (mp0) cc_final: 0.8890 (mp0)
REVERT: A   65 LYS cc_start: 0.8876 (mmmm) cc_final: 0.8420 (mmmm)
REVERT: A   68 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7376 (mm-30)
REVERT: A   77 THR cc_start: 0.9430 (m) cc_final: 0.8997 (p)
REVERT: A   96 GLN cc_start: 0.8607 (tt0) cc_final: 0.8060 (tp-100)
REVERT: A  216 GLU cc_start: 0.8989 (mm-30) cc_final: 0.8176 (mp0)
REVERT: A  239 TYR cc_start: 0.8315 (m-80) cc_final: 0.7890 (m-80)
REVERT: A  479 PHE cc_start: 0.9572 (t80) cc_final: 0.9308 (t80)
REVERT: A  537 SER cc_start: 0.9249 (m) cc_final: 0.8952 (p)
REVERT: A  552 ASP cc_start: 0.6356 (t0) cc_final: 0.4933 (m-30)
REVERT: A  597 LEU cc_start: 0.8860 (mt) cc_final: 0.8508 (mt)
REVERT: A  598 GLU cc_start: 0.8341 (pm20) cc_final: 0.7886 (pm20)
REVERT: A  768 ASP cc_start: 0.9047 (t0) cc_final: 0.8725 (t0)
REVERT: A  784 LYS cc_start: 0.8987 (mmtt) cc_final: 0.8772 (mmtt)
REVERT: A  939 GLU cc_start: 0.9067 (mm-30) cc_final: 0.8808 (mm-30)
REVERT: A  941 LEU cc_start: 0.9326 (pt) cc_final: 0.8730 (pp)
REVERT: A  967 ASP cc_start: 0.9326 (m-30) cc_final: 0.9122 (m-30)
REVERT: A 1024 PHE cc_start: 0.9376 (m-10) cc_final: 0.9127 (m-80)
REVERT: A 1080 GLN cc_start: 0.8863 (mt0) cc_final: 0.8640 (mt0)
REVERT: A 1092 GLU cc_start: 0.9060 (mm-30) cc_final: 0.8371 (pp20)
REVERT: A 1102 LEU cc_start: 0.9269 (mt) cc_final: 0.9032 (mt)
REVERT: A 1114 LYS cc_start: 0.8983 (mttt) cc_final: 0.8388 (tttt)
REVERT: A 1177 LEU cc_start: 0.9156 (mt) cc_final: 0.8911 (mp)
REVERT: A 1276 ASP cc_start: 0.8904 (t0) cc_final: 0.8659 (t0)
REVERT: A 1335 ARG cc_start: 0.8021 (mtm180) cc_final: 0.7776 (mtp180)
REVERT: A 1381 HIS cc_start: 0.8054 (p90) cc_final: 0.7751 (p90)
REVERT: A 1389 ILE cc_start: 0.8201 (mt) cc_final: 0.7920 (mt)
REVERT: C  432 ASN cc_start: 0.9580 (m-40) cc_final: 0.9111 (m110)
REVERT: C  437 ASP cc_start: 0.9153 (m-30) cc_final: 0.8916 (m-30)
REVERT: C  463 VAL cc_start: 0.9502 (t) cc_final: 0.9232 (t)
REVERT: C  473 GLN cc_start: 0.8854 (mp10) cc_final: 0.8604 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 281
  average time/residue: 0.1209
  time to fit residues: 46.1081
Evaluate side-chains
  213 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 213
  time to evaluate  : 0.404 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 49 optimal weight:    0.6980
   chunk 100 optimal weight:    9.9990
   chunk 94 optimal weight:   10.0000
   chunk 11 optimal weight:    0.3980
   chunk 44 optimal weight:    0.9990
   chunk 28 optimal weight:    6.9990
   chunk 61 optimal weight:   30.0000
   chunk 85 optimal weight:    1.9990
   chunk 4 optimal weight:    9.9990
   chunk 121 optimal weight:    0.9990
   chunk 10 optimal weight:    0.9980
   overall best weight:    0.8184

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
A 206 ASN
A 418 HIS
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 GLN
A 778 GLN
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1348 GLN
** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 474 GLN
C 488 GLN
C 489 ASN

Total number of N/Q/H flips: 9

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.082600 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.069057 restraints weight = 45534.352|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.071210 restraints weight = 29936.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.072777 restraints weight = 21660.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.073954 restraints weight = 16726.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.074850 restraints weight = 13534.158|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.6203

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.058  10728  Z= 0.148
  Angle     :  0.801  10.590  14513  Z= 0.398
  Chirality :  0.046   0.199   1630
  Planarity :  0.005   0.103   1865
  Dihedral  :  9.376  73.971   1446
  Min Nonbonded Distance : 2.411

Molprobity Statistics.
  All-atom Clashscore : 17.82
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  : 10.86 %
    Favored  : 88.60 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  2.90 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.04 (0.22), residues: 1307
  helix: -1.08 (0.21), residues: 518
  sheet: -3.36 (0.46), residues: 88
  loop : -2.63 (0.23), residues: 701

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 915 
 TYR   0.038   0.002   TYR A 950 
 PHE   0.020   0.002   PHE A1035 
 TRP   0.014   0.002   TRP A 214 
 HIS   0.010   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 (10727)
  covalent geometry    : angle       0.80071 (14513)
  hydrogen bonds       : bond        0.04272 (  314)
  hydrogen bonds       : angle       6.35812 (  861)
  Misc. bond           : bond        0.00030 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  281 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 280
  time to evaluate  : 0.421 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: 0.8500 (mpp) cc_final: 0.8158 (mpp)
REVERT: A   96 GLN cc_start: 0.8624 (tt0) cc_final: 0.7961 (tp-100)
REVERT: A  418 HIS cc_start: 0.8425 (m90) cc_final: 0.8100 (m90)
REVERT: A  479 PHE cc_start: 0.9520 (t80) cc_final: 0.9280 (t80)
REVERT: A  550 LEU cc_start: 0.8452 (mp) cc_final: 0.8075 (mp)
REVERT: A  552 ASP cc_start: 0.6285 (t0) cc_final: 0.4887 (m-30)
REVERT: A  598 GLU cc_start: 0.8530 (pm20) cc_final: 0.8124 (pm20)
REVERT: A  635 LEU cc_start: 0.8605 (pp) cc_final: 0.8122 (pp)
REVERT: A  784 LYS cc_start: 0.8940 (mmtt) cc_final: 0.8681 (mmtt)
REVERT: A  939 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8733 (mm-30)
REVERT: A  941 LEU cc_start: 0.9300 (pt) cc_final: 0.8972 (pp)
REVERT: A 1024 PHE cc_start: 0.9431 (m-10) cc_final: 0.9074 (m-80)
REVERT: A 1092 GLU cc_start: 0.9008 (mm-30) cc_final: 0.8335 (pp20)
REVERT: A 1102 LEU cc_start: 0.9206 (mt) cc_final: 0.8970 (mt)
REVERT: A 1114 LYS cc_start: 0.8934 (mttt) cc_final: 0.8421 (tttt)
REVERT: A 1276 ASP cc_start: 0.8793 (t0) cc_final: 0.8532 (t0)
REVERT: A 1326 LEU cc_start: 0.8885 (tp) cc_final: 0.8512 (pp)
REVERT: A 1335 ARG cc_start: 0.7865 (mtm180) cc_final: 0.7564 (mtm180)
REVERT: A 1358 ARG cc_start: 0.7730 (mpp80) cc_final: 0.7462 (mpp80)
REVERT: C  432 ASN cc_start: 0.9537 (m-40) cc_final: 0.9100 (m110)
REVERT: C  437 ASP cc_start: 0.9074 (m-30) cc_final: 0.8813 (m-30)
REVERT: C  455 GLU cc_start: 0.8777 (mp0) cc_final: 0.8461 (mp0)
REVERT: C  456 ASP cc_start: 0.8899 (t70) cc_final: 0.8599 (t0)
REVERT: C  463 VAL cc_start: 0.9496 (t) cc_final: 0.9197 (t)
REVERT: C  466 MET cc_start: 0.8669 (ppp) cc_final: 0.8458 (ppp)
  outliers start: 1
  outliers final: 0
  residues processed: 280
  average time/residue: 0.1152
  time to fit residues: 44.3227
Evaluate side-chains
  210 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 210
  time to evaluate  : 0.417 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 116 optimal weight:    0.0020
   chunk 58 optimal weight:    0.9990
   chunk 124 optimal weight:    0.7980
   chunk 17 optimal weight:   10.0000
   chunk 45 optimal weight:    1.9990
   chunk 35 optimal weight:    1.9990
   chunk 9 optimal weight:   10.0000
   chunk 123 optimal weight:    7.9990
   chunk 100 optimal weight:    6.9990
   chunk 46 optimal weight:    0.7980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
A 206 ASN
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 778 GLN
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1348 GLN
** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 441 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 474 GLN
** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.083692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.069986 restraints weight = 45501.682|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.072212 restraints weight = 29660.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.073827 restraints weight = 21276.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.075024 restraints weight = 16299.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.075929 restraints weight = 13109.737|
|-----------------------------------------------------------------------------|
r_work (final): 0.3477
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7941
moved from start:          0.6677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  10728  Z= 0.143
  Angle     :  0.779   9.956  14513  Z= 0.389
  Chirality :  0.045   0.186   1630
  Planarity :  0.005   0.063   1865
  Dihedral  :  9.137  79.191   1446
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 17.59
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  : 10.71 %
    Favored  : 88.75 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.47 %
    Favored  : 97.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.81 (0.22), residues: 1307
  helix: -0.84 (0.22), residues: 510
  sheet: -3.34 (0.48), residues: 86
  loop : -2.52 (0.23), residues: 711

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A  63 
 TYR   0.054   0.002   TYR A 950 
 PHE   0.017   0.001   PHE A 954 
 TRP   0.035   0.002   TRP A1391 
 HIS   0.006   0.001   HIS A 799 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 (10727)
  covalent geometry    : angle       0.77858 (14513)
  hydrogen bonds       : bond        0.04122 (  314)
  hydrogen bonds       : angle       6.23529 (  861)
  Misc. bond           : bond        0.00019 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  268 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 268
  time to evaluate  : 0.378 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   49 MET cc_start: 0.8539 (mpp) cc_final: 0.8148 (mpp)
REVERT: A   96 GLN cc_start: 0.8636 (tt0) cc_final: 0.7952 (tp-100)
REVERT: A  115 GLU cc_start: 0.9149 (tt0) cc_final: 0.8850 (tt0)
REVERT: A  418 HIS cc_start: 0.8458 (m90) cc_final: 0.8145 (m-70)
REVERT: A  458 VAL cc_start: 0.9677 (t) cc_final: 0.9426 (t)
REVERT: A  469 GLU cc_start: 0.8897 (pp20) cc_final: 0.8402 (tm-30)
REVERT: A  597 LEU cc_start: 0.8604 (mt) cc_final: 0.8242 (mt)
REVERT: A  635 LEU cc_start: 0.8394 (pp) cc_final: 0.7802 (pp)
REVERT: A  784 LYS cc_start: 0.8991 (mmtt) cc_final: 0.8643 (mmtm)
REVERT: A  824 ASN cc_start: 0.7938 (t0) cc_final: 0.7177 (t0)
REVERT: A  905 ARG cc_start: 0.8856 (ttm-80) cc_final: 0.8458 (ttm-80)
REVERT: A  939 GLU cc_start: 0.8998 (mm-30) cc_final: 0.8714 (mm-30)
REVERT: A  941 LEU cc_start: 0.9324 (pt) cc_final: 0.8931 (pp)
REVERT: A  967 ASP cc_start: 0.9405 (m-30) cc_final: 0.9205 (m-30)
REVERT: A 1024 PHE cc_start: 0.9423 (m-10) cc_final: 0.9054 (m-80)
REVERT: A 1092 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8323 (pp20)
REVERT: A 1102 LEU cc_start: 0.9218 (mt) cc_final: 0.9010 (mt)
REVERT: A 1114 LYS cc_start: 0.8938 (mttt) cc_final: 0.8452 (tttt)
REVERT: A 1276 ASP cc_start: 0.8663 (t0) cc_final: 0.8451 (t0)
REVERT: A 1326 LEU cc_start: 0.8943 (tp) cc_final: 0.8494 (pp)
REVERT: A 1335 ARG cc_start: 0.7661 (mtm180) cc_final: 0.7280 (mtp180)
REVERT: A 1356 LEU cc_start: 0.8920 (pt) cc_final: 0.8604 (pt)
REVERT: A 1358 ARG cc_start: 0.7653 (mpp80) cc_final: 0.7163 (mpp80)
REVERT: C  432 ASN cc_start: 0.9458 (m-40) cc_final: 0.9015 (m110)
REVERT: C  437 ASP cc_start: 0.9099 (m-30) cc_final: 0.8766 (m-30)
REVERT: C  455 GLU cc_start: 0.8742 (mp0) cc_final: 0.8460 (mp0)
REVERT: C  456 ASP cc_start: 0.8846 (t70) cc_final: 0.8601 (t0)
REVERT: C  463 VAL cc_start: 0.9501 (t) cc_final: 0.9172 (t)
REVERT: C  470 GLN cc_start: 0.8812 (mt0) cc_final: 0.8550 (mt0)
REVERT: C  473 GLN cc_start: 0.8816 (mp10) cc_final: 0.8492 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 268
  average time/residue: 0.1146
  time to fit residues: 42.2101
Evaluate side-chains
  207 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 207
  time to evaluate  : 0.414 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 94 optimal weight:    7.9990
   chunk 93 optimal weight:    1.9990
   chunk 110 optimal weight:    7.9990
   chunk 13 optimal weight:    0.7980
   chunk 4 optimal weight:    4.9990
   chunk 74 optimal weight:    6.9990
   chunk 44 optimal weight:    0.0980
   chunk 121 optimal weight:    8.9990
   chunk 129 optimal weight:    3.9990
   chunk 57 optimal weight:    0.7980
   chunk 126 optimal weight:    6.9990
   overall best weight:    1.5384

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

Flipped N/Q/H residues before XYZ refinement:
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 778 GLN
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1339 GLN
A1348 GLN
** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 441 GLN
C 474 GLN
** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3607 r_free = 0.3607 target = 0.081868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.068421 restraints weight = 46442.271|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.070607 restraints weight = 30415.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3401 r_free = 0.3401 target = 0.072176 restraints weight = 21862.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3424 r_free = 0.3424 target = 0.073319 restraints weight = 16791.546|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.074213 restraints weight = 13557.230|
|-----------------------------------------------------------------------------|
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.6791

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055  10728  Z= 0.153
  Angle     :  0.796  11.621  14513  Z= 0.395
  Chirality :  0.046   0.267   1630
  Planarity :  0.005   0.061   1865
  Dihedral  :  8.996  78.295   1446
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 19.06
  Ramachandran Plot:
    Outliers :  0.54 %
    Allowed  : 11.25 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.96 %
    Favored  : 98.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.67 (0.23), residues: 1307
  helix: -0.62 (0.22), residues: 514
  sheet: -3.44 (0.40), residues: 123
  loop : -2.41 (0.24), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 915 
 TYR   0.048   0.002   TYR A 950 
 PHE   0.024   0.001   PHE A 954 
 TRP   0.024   0.002   TRP A1391 
 HIS   0.006   0.001   HIS A 799 

Details of bonding type rmsd
  covalent geometry    : bond        0.00345 (10727)
  covalent geometry    : angle       0.79606 (14513)
  hydrogen bonds       : bond        0.03932 (  314)
  hydrogen bonds       : angle       6.06446 (  861)
  Misc. bond           : bond        0.00048 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  248 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 248
  time to evaluate  : 0.432 
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: symmetry clash
   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: symmetry clash
   revert: symmetry clash
REVERT: A   39 GLU cc_start: 0.8400 (pm20) cc_final: 0.7995 (pm20)
REVERT: A   49 MET cc_start: 0.8560 (mpp) cc_final: 0.8122 (mpp)
REVERT: A   77 THR cc_start: 0.9487 (m) cc_final: 0.9241 (p)
REVERT: A   96 GLN cc_start: 0.8679 (tt0) cc_final: 0.7937 (tp40)
REVERT: A  115 GLU cc_start: 0.9164 (tt0) cc_final: 0.8872 (tt0)
REVERT: A  156 TYR cc_start: 0.8459 (m-10) cc_final: 0.8251 (m-80)
REVERT: A  216 GLU cc_start: 0.8953 (mm-30) cc_final: 0.8556 (mm-30)
REVERT: A  418 HIS cc_start: 0.8464 (m90) cc_final: 0.8167 (m-70)
REVERT: A  543 GLN cc_start: 0.7772 (pp30) cc_final: 0.7502 (pp30)
REVERT: A  635 LEU cc_start: 0.8245 (pp) cc_final: 0.7846 (pp)
REVERT: A  830 ASP cc_start: 0.8911 (p0) cc_final: 0.8686 (p0)
REVERT: A  905 ARG cc_start: 0.8866 (ttm-80) cc_final: 0.8560 (ttm-80)
REVERT: A  939 GLU cc_start: 0.9063 (mm-30) cc_final: 0.8764 (mm-30)
REVERT: A  941 LEU cc_start: 0.9391 (pt) cc_final: 0.9049 (pp)
REVERT: A  967 ASP cc_start: 0.9406 (m-30) cc_final: 0.9204 (m-30)
REVERT: A  992 LEU cc_start: 0.9006 (mt) cc_final: 0.8635 (mt)
REVERT: A 1022 GLU cc_start: 0.8726 (pp20) cc_final: 0.8256 (pp20)
REVERT: A 1024 PHE cc_start: 0.9427 (m-10) cc_final: 0.9029 (m-80)
REVERT: A 1114 LYS cc_start: 0.9001 (mttt) cc_final: 0.8630 (tttt)
REVERT: A 1196 MET cc_start: 0.8842 (ptp) cc_final: 0.8373 (ptp)
REVERT: A 1276 ASP cc_start: 0.8628 (t0) cc_final: 0.8373 (t0)
REVERT: A 1281 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8392 (mt-10)
REVERT: A 1326 LEU cc_start: 0.8958 (tp) cc_final: 0.8466 (pp)
REVERT: A 1335 ARG cc_start: 0.7787 (mtm180) cc_final: 0.7483 (mtp180)
REVERT: A 1356 LEU cc_start: 0.8951 (pt) cc_final: 0.8596 (pt)
REVERT: A 1358 ARG cc_start: 0.7499 (mpp80) cc_final: 0.7008 (mpp80)
REVERT: A 1365 LEU cc_start: 0.7726 (tp) cc_final: 0.7401 (tp)
REVERT: A 1389 ILE cc_start: 0.8013 (mt) cc_final: 0.7774 (mt)
REVERT: C  432 ASN cc_start: 0.9393 (m-40) cc_final: 0.9006 (m110)
REVERT: C  437 ASP cc_start: 0.9092 (m-30) cc_final: 0.8768 (m-30)
REVERT: C  455 GLU cc_start: 0.8696 (mp0) cc_final: 0.8398 (mp0)
REVERT: C  456 ASP cc_start: 0.8785 (t70) cc_final: 0.8566 (t0)
REVERT: C  463 VAL cc_start: 0.9499 (t) cc_final: 0.9176 (t)
REVERT: C  470 GLN cc_start: 0.8842 (mt0) cc_final: 0.8577 (mt0)
REVERT: C  473 GLN cc_start: 0.8809 (mp10) cc_final: 0.8531 (mp10)
  outliers start: 0
  outliers final: 0
  residues processed: 248
  average time/residue: 0.1179
  time to fit residues: 39.9959
Evaluate side-chains
  203 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 203
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 73 optimal weight:    9.9990
   chunk 15 optimal weight:    4.9990
   chunk 22 optimal weight:    7.9990
   chunk 119 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 45 optimal weight:    3.9990
   chunk 49 optimal weight:    0.7980
   chunk 58 optimal weight:    0.7980
   chunk 14 optimal weight:    2.9990
   chunk 114 optimal weight:    1.9990
   chunk 7 optimal weight:    8.9990
   overall best weight:    2.1186

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

Flipped N/Q/H residues before XYZ refinement:
A  79 GLN
A 107 ASN
A 206 ASN
** A 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 778 GLN
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1348 GLN
** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 474 GLN
** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.081013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.067476 restraints weight = 46249.287|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.069636 restraints weight = 30081.505|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.071187 restraints weight = 21618.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.072337 restraints weight = 16608.874|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.073179 restraints weight = 13407.681|
|-----------------------------------------------------------------------------|
r_work (final): 0.3421
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8004
moved from start:          0.6905

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  10728  Z= 0.177
  Angle     :  0.822  12.788  14513  Z= 0.410
  Chirality :  0.047   0.266   1630
  Planarity :  0.005   0.081   1865
  Dihedral  :  8.983  78.703   1446
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 20.64
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 11.02 %
    Favored  : 88.52 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.45 %
    Favored  : 98.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.16 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.68 (0.22), residues: 1307
  helix: -0.60 (0.22), residues: 523
  sheet: -3.46 (0.42), residues: 114
  loop : -2.49 (0.23), residues: 670

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.017   0.001   ARG A 417 
 TYR   0.036   0.002   TYR A 950 
 PHE   0.021   0.002   PHE A 954 
 TRP   0.019   0.002   TRP A1391 
 HIS   0.005   0.001   HIS A 799 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 (10727)
  covalent geometry    : angle       0.82202 (14513)
  hydrogen bonds       : bond        0.04008 (  314)
  hydrogen bonds       : angle       5.99064 (  861)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  247 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 247
  time to evaluate  : 0.425 
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: symmetry clash
   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: symmetry clash
REVERT: A   43 HIS cc_start: 0.9146 (m90) cc_final: 0.8918 (m90)
REVERT: A   49 MET cc_start: 0.8388 (mpp) cc_final: 0.8149 (mpp)
REVERT: A   77 THR cc_start: 0.9486 (m) cc_final: 0.9141 (p)
REVERT: A   96 GLN cc_start: 0.8662 (tt0) cc_final: 0.7919 (tp40)
REVERT: A  115 GLU cc_start: 0.9168 (tt0) cc_final: 0.8869 (tt0)
REVERT: A  156 TYR cc_start: 0.8582 (m-10) cc_final: 0.8336 (m-80)
REVERT: A  216 GLU cc_start: 0.8966 (mm-30) cc_final: 0.8545 (mm-30)
REVERT: A  418 HIS cc_start: 0.8456 (m90) cc_final: 0.8134 (m-70)
REVERT: A  469 GLU cc_start: 0.8931 (pp20) cc_final: 0.8634 (pp20)
REVERT: A  635 LEU cc_start: 0.8247 (pp) cc_final: 0.7991 (pp)
REVERT: A  939 GLU cc_start: 0.9086 (mm-30) cc_final: 0.8780 (mm-30)
REVERT: A  941 LEU cc_start: 0.9438 (pt) cc_final: 0.9141 (pp)
REVERT: A  992 LEU cc_start: 0.9025 (mt) cc_final: 0.8674 (mt)
REVERT: A 1022 GLU cc_start: 0.8710 (pp20) cc_final: 0.8236 (pp20)
REVERT: A 1024 PHE cc_start: 0.9436 (m-10) cc_final: 0.9050 (m-80)
REVERT: A 1114 LYS cc_start: 0.8939 (mttt) cc_final: 0.8415 (tttt)
REVERT: A 1123 ARG cc_start: 0.8167 (mtt180) cc_final: 0.6752 (ptp-170)
REVERT: A 1196 MET cc_start: 0.8792 (ptp) cc_final: 0.8441 (ptp)
REVERT: A 1276 ASP cc_start: 0.8599 (t0) cc_final: 0.8332 (t0)
REVERT: A 1281 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8413 (mt-10)
REVERT: A 1356 LEU cc_start: 0.8952 (pt) cc_final: 0.8612 (tt)
REVERT: A 1365 LEU cc_start: 0.7672 (tp) cc_final: 0.7348 (tp)
REVERT: C  437 ASP cc_start: 0.9104 (m-30) cc_final: 0.8748 (m-30)
REVERT: C  455 GLU cc_start: 0.8643 (mp0) cc_final: 0.8326 (mp0)
REVERT: C  463 VAL cc_start: 0.9495 (t) cc_final: 0.9207 (t)
REVERT: C  466 MET cc_start: 0.8871 (ppp) cc_final: 0.8665 (ppp)
REVERT: C  470 GLN cc_start: 0.8894 (mt0) cc_final: 0.8617 (mt0)
REVERT: C  473 GLN cc_start: 0.8818 (mp10) cc_final: 0.8576 (mp10)
REVERT: C  474 GLN cc_start: 0.9455 (tp40) cc_final: 0.9254 (tp-100)
  outliers start: 0
  outliers final: 0
  residues processed: 247
  average time/residue: 0.1178
  time to fit residues: 39.8836
Evaluate side-chains
  200 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 200
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    1.9990
   chunk 42 optimal weight:    8.9990
   chunk 21 optimal weight:    3.9990
   chunk 56 optimal weight:    3.9990
   chunk 90 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 81 optimal weight:    0.5980
   chunk 73 optimal weight:    8.9990
   chunk 69 optimal weight:    0.9990
   chunk 25 optimal weight:    3.9990
   overall best weight:    1.7188

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

Flipped N/Q/H residues before XYZ refinement:
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 778 GLN
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1348 GLN
** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.081590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.068124 restraints weight = 46248.187|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 19)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.070269 restraints weight = 30241.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.071824 restraints weight = 21795.194|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.072986 restraints weight = 16747.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.073878 restraints weight = 13493.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3430
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7987
moved from start:          0.7088

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  10728  Z= 0.157
  Angle     :  0.805  11.414  14513  Z= 0.398
  Chirality :  0.046   0.270   1630
  Planarity :  0.005   0.072   1865
  Dihedral  :  8.837  79.570   1446
  Min Nonbonded Distance : 2.358

Molprobity Statistics.
  All-atom Clashscore : 19.35
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 11.32 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.02 %
    Favored  : 98.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.56 (0.23), residues: 1307
  helix: -0.48 (0.23), residues: 516
  sheet: -3.43 (0.43), residues: 112
  loop : -2.41 (0.23), residues: 679

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 417 
 TYR   0.040   0.002   TYR A 950 
 PHE   0.028   0.002   PHE A 954 
 TRP   0.018   0.002   TRP A1391 
 HIS   0.005   0.001   HIS A 799 

Details of bonding type rmsd
  covalent geometry    : bond        0.00351 (10727)
  covalent geometry    : angle       0.80500 (14513)
  hydrogen bonds       : bond        0.03834 (  314)
  hydrogen bonds       : angle       5.86024 (  861)
  Misc. bond           : bond        0.00006 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  246 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 246
  time to evaluate  : 0.351 
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: symmetry clash
   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: symmetry clash
REVERT: A   49 MET cc_start: 0.8391 (mpp) cc_final: 0.8150 (mpp)
REVERT: A   77 THR cc_start: 0.9511 (m) cc_final: 0.9127 (p)
REVERT: A   96 GLN cc_start: 0.8618 (tt0) cc_final: 0.8001 (tp-100)
REVERT: A  115 GLU cc_start: 0.9161 (tt0) cc_final: 0.8905 (tt0)
REVERT: A  156 TYR cc_start: 0.8563 (m-10) cc_final: 0.8190 (m-80)
REVERT: A  216 GLU cc_start: 0.9050 (mm-30) cc_final: 0.8596 (mm-30)
REVERT: A  418 HIS cc_start: 0.8313 (m90) cc_final: 0.7971 (m-70)
REVERT: A  469 GLU cc_start: 0.8958 (pp20) cc_final: 0.8297 (tm-30)
REVERT: A  635 LEU cc_start: 0.8325 (pp) cc_final: 0.7968 (pp)
REVERT: A  939 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8696 (mm-30)
REVERT: A  941 LEU cc_start: 0.9383 (pt) cc_final: 0.9058 (pp)
REVERT: A 1022 GLU cc_start: 0.8690 (pp20) cc_final: 0.8331 (pp20)
REVERT: A 1024 PHE cc_start: 0.9419 (m-10) cc_final: 0.8995 (m-80)
REVERT: A 1114 LYS cc_start: 0.8918 (mttt) cc_final: 0.8427 (tttt)
REVERT: A 1123 ARG cc_start: 0.8177 (mtt180) cc_final: 0.6768 (ptp-170)
REVERT: A 1196 MET cc_start: 0.8724 (ptp) cc_final: 0.8414 (ptp)
REVERT: A 1276 ASP cc_start: 0.8480 (t0) cc_final: 0.8234 (t0)
REVERT: A 1281 GLU cc_start: 0.8846 (mt-10) cc_final: 0.8396 (mt-10)
REVERT: A 1326 LEU cc_start: 0.8940 (tp) cc_final: 0.8397 (pp)
REVERT: A 1356 LEU cc_start: 0.8892 (pt) cc_final: 0.8316 (pt)
REVERT: A 1358 ARG cc_start: 0.7637 (mpp80) cc_final: 0.7225 (mpp80)
REVERT: A 1365 LEU cc_start: 0.7818 (tp) cc_final: 0.7483 (tp)
REVERT: A 1389 ILE cc_start: 0.8189 (mt) cc_final: 0.7957 (mt)
REVERT: C  432 ASN cc_start: 0.9711 (m-40) cc_final: 0.9240 (m110)
REVERT: C  437 ASP cc_start: 0.9083 (m-30) cc_final: 0.8799 (m-30)
REVERT: C  455 GLU cc_start: 0.8818 (mp0) cc_final: 0.8492 (mp0)
REVERT: C  456 ASP cc_start: 0.8799 (t0) cc_final: 0.8581 (t0)
REVERT: C  463 VAL cc_start: 0.9499 (t) cc_final: 0.9212 (t)
REVERT: C  466 MET cc_start: 0.8969 (ppp) cc_final: 0.8768 (ppp)
REVERT: C  470 GLN cc_start: 0.8839 (mt0) cc_final: 0.8582 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 246
  average time/residue: 0.1173
  time to fit residues: 39.4662
Evaluate side-chains
  196 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 196
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 111 optimal weight:    5.9990
   chunk 124 optimal weight:    0.7980
   chunk 80 optimal weight:    0.9980
   chunk 109 optimal weight:    2.9990
   chunk 48 optimal weight:    9.9990
   chunk 95 optimal weight:    0.0170
   chunk 49 optimal weight:    0.9990
   chunk 101 optimal weight:    4.9990
   chunk 36 optimal weight:    8.9990
   chunk 23 optimal weight:    2.9990
   overall best weight:    1.1622

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

Flipped N/Q/H residues before XYZ refinement:
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 663 GLN
A 778 GLN
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1339 GLN
A1348 GLN
** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.082637 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.069078 restraints weight = 45465.031|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.071227 restraints weight = 29959.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.072775 restraints weight = 21701.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.073899 restraints weight = 16742.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3450 r_free = 0.3450 target = 0.074814 restraints weight = 13652.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3449
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7967
moved from start:          0.7290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  10728  Z= 0.146
  Angle     :  0.811  12.486  14513  Z= 0.402
  Chirality :  0.046   0.256   1630
  Planarity :  0.005   0.055   1865
  Dihedral  :  8.680  81.072   1446
  Min Nonbonded Distance : 2.355

Molprobity Statistics.
  All-atom Clashscore : 19.16
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 11.25 %
    Favored  : 88.29 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.23), residues: 1307
  helix: -0.39 (0.23), residues: 509
  sheet: -3.45 (0.40), residues: 123
  loop : -2.34 (0.24), residues: 675

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.022   0.001   ARG A 417 
 TYR   0.035   0.002   TYR A 138 
 PHE   0.020   0.001   PHE A 954 
 TRP   0.010   0.002   TRP A1391 
 HIS   0.004   0.001   HIS A 799 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10727)
  covalent geometry    : angle       0.81068 (14513)
  hydrogen bonds       : bond        0.03752 (  314)
  hydrogen bonds       : angle       5.80720 (  861)
  Misc. bond           : bond        0.00012 (    1)

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

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

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2614 Ramachandran restraints generated.
    1307 Oldfield, 0 Emsley, 1307 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  244 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 244
  time to evaluate  : 0.420 
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: symmetry clash
   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: symmetry clash
REVERT: A   49 MET cc_start: 0.8417 (mpp) cc_final: 0.8145 (mpp)
REVERT: A   96 GLN cc_start: 0.8589 (tt0) cc_final: 0.7872 (tp-100)
REVERT: A  115 GLU cc_start: 0.9142 (tt0) cc_final: 0.8877 (tt0)
REVERT: A  156 TYR cc_start: 0.8585 (m-10) cc_final: 0.8250 (m-80)
REVERT: A  216 GLU cc_start: 0.8903 (mm-30) cc_final: 0.8483 (mm-30)
REVERT: A  469 GLU cc_start: 0.8867 (pp20) cc_final: 0.8657 (pp20)
REVERT: A  628 TYR cc_start: 0.8878 (m-10) cc_final: 0.8439 (m-10)
REVERT: A  635 LEU cc_start: 0.8175 (pp) cc_final: 0.7887 (pp)
REVERT: A  939 GLU cc_start: 0.8983 (mm-30) cc_final: 0.8673 (mm-30)
REVERT: A  941 LEU cc_start: 0.9393 (pt) cc_final: 0.9060 (pp)
REVERT: A  967 ASP cc_start: 0.9335 (m-30) cc_final: 0.9083 (m-30)
REVERT: A 1022 GLU cc_start: 0.8736 (pp20) cc_final: 0.8377 (pp20)
REVERT: A 1024 PHE cc_start: 0.9401 (m-10) cc_final: 0.8995 (m-80)
REVERT: A 1114 LYS cc_start: 0.8890 (mttt) cc_final: 0.8449 (tttt)
REVERT: A 1123 ARG cc_start: 0.8241 (mtt180) cc_final: 0.6720 (ptp-170)
REVERT: A 1277 ASP cc_start: 0.8702 (t70) cc_final: 0.8250 (t0)
REVERT: A 1281 GLU cc_start: 0.8824 (mt-10) cc_final: 0.8185 (mt-10)
REVERT: A 1339 GLN cc_start: 0.8278 (mm-40) cc_final: 0.6993 (mm-40)
REVERT: A 1356 LEU cc_start: 0.8911 (pt) cc_final: 0.8592 (tt)
REVERT: A 1365 LEU cc_start: 0.7783 (tp) cc_final: 0.7429 (tp)
REVERT: A 1389 ILE cc_start: 0.8290 (mt) cc_final: 0.8079 (mt)
REVERT: C  432 ASN cc_start: 0.9697 (m-40) cc_final: 0.9210 (m110)
REVERT: C  437 ASP cc_start: 0.9059 (m-30) cc_final: 0.8722 (m-30)
REVERT: C  463 VAL cc_start: 0.9506 (t) cc_final: 0.9222 (t)
REVERT: C  470 GLN cc_start: 0.8807 (mt0) cc_final: 0.8409 (mt0)
  outliers start: 0
  outliers final: 0
  residues processed: 244
  average time/residue: 0.1124
  time to fit residues: 37.8331
Evaluate side-chains
  199 residues out of total 1174 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 199
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 130
   random chunks:
   chunk 93 optimal weight:    0.9990
   chunk 38 optimal weight:    6.9990
   chunk 108 optimal weight:    0.9980
   chunk 37 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 101 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 47 optimal weight:    3.9990
   chunk 106 optimal weight:    0.3980
   chunk 71 optimal weight:    3.9990
   chunk 28 optimal weight:    0.9990
   overall best weight:    1.4786

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

Flipped N/Q/H residues before XYZ refinement:
A 418 HIS
** A 544 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 584 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 778 GLN
** A 922 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1097 ASN
** A1169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1348 GLN
** A1375 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 441 GLN
C 474 GLN
** C 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.082521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.068869 restraints weight = 45632.864|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 23)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.071015 restraints weight = 29919.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.072592 restraints weight = 21571.420|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.073751 restraints weight = 16611.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.074672 restraints weight = 13450.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3448
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7974
moved from start:          0.7420

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042  10728  Z= 0.154
  Angle     :  0.816  11.149  14513  Z= 0.405
  Chirality :  0.046   0.249   1630
  Planarity :  0.005   0.050   1865
  Dihedral  :  8.671  86.443   1446
  Min Nonbonded Distance : 2.362

Molprobity Statistics.
  All-atom Clashscore : 19.16
  Ramachandran Plot:
    Outliers :  0.46 %
    Allowed  : 11.32 %
    Favored  : 88.22 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.60 %
    Favored  : 99.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 1.96 %
    Twisted General : 0.08 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.23), residues: 1307
  helix: -0.37 (0.23), residues: 506
  sheet: -3.47 (0.40), residues: 123
  loop : -2.34 (0.24), residues: 678

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 417 
 TYR   0.055   0.002   TYR A 950 
 PHE   0.029   0.002   PHE A 954 
 TRP   0.011   0.002   TRP A1391 
 HIS   0.013   0.001   HIS A 418 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (10727)
  covalent geometry    : angle       0.81605 (14513)
  hydrogen bonds       : bond        0.03779 (  314)
  hydrogen bonds       : angle       5.83221 (  861)
  Misc. bond           : bond        0.00010 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1795.33 seconds
wall clock time: 32 minutes 2.22 seconds (1922.22 seconds total)