Starting phenix.real_space_refine
on Fri Mar  6 02:37:47 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/6yrk_10890/03_2026/6yrk_10890.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/6yrk_10890/03_2026/6yrk_10890.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/6yrk_10890/03_2026/6yrk_10890.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/6yrk_10890/03_2026/6yrk_10890.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/6yrk_10890/03_2026/6yrk_10890.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/6yrk_10890/03_2026/6yrk_10890.cif"
  }
  resolution = 4.1
  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=   0.001
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 15058 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: 4
    Type Number    sf(0)   Gaussians
     S      19      5.16       5
     C    9490      2.51       5
     N    2544      2.21       5
     O    3005      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 58 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 15058
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5982
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 777, 5982
          Classifications: {'peptide': 777}
          Link IDs: {'PTRANS': 34, 'TRANS': 742}
          Chain breaks: 3
    Chain: "B"
      Number of atoms: 9076
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1160, 9076
          Classifications: {'peptide': 1160}
          Link IDs: {'PTRANS': 71, 'TRANS': 1088}
          Chain breaks: 5
  Time building chain proxies: 3.23, per 1000 atoms: 0.21
  Number of scatterers: 15058
  At special positions: 0
  Unit cell: (121.8, 99.75, 118.65, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      19     16.00
     O    3005      8.00
     N    2544      7.00
     C    9490      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.14
  Conformation dependent library (CDL) restraints added in 725.6 milliseconds
  

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3590

  Finding SS restraints...
    Secondary structure from input PDB file:
      62 helices and 30 sheets defined
      22.3% alpha, 19.3% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.61
  Creating SS restraints...
    Processing helix  chain 'A' and resid 54 through 58
    Processing helix  chain 'A' and resid 138 through 146
      removed outlier: 3.754A  pdb=" N   VAL A 144 " --> pdb=" O   ASP A 140 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 159 through 164
    Processing helix  chain 'A' and resid 170 through 176
    Processing helix  chain 'A' and resid 183 through 188
    Processing helix  chain 'A' and resid 236 through 243
    Processing helix  chain 'A' and resid 243 through 252
      removed outlier: 3.620A  pdb=" N   GLU A 247 " --> pdb=" O   THR A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 271 through 278
    Processing helix  chain 'A' and resid 289 through 299
    Processing helix  chain 'A' and resid 349 through 360
      removed outlier: 3.822A  pdb=" N   VAL A 356 " --> pdb=" O   GLN A 352 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   GLN A 359 " --> pdb=" O   PHE A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 444
    Processing helix  chain 'A' and resid 513 through 522
      removed outlier: 3.740A  pdb=" N   VAL A 517 " --> pdb=" O   GLU A 513 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 548 through 561
    Processing helix  chain 'A' and resid 581 through 583
      No H-bonds generated for 'chain 'A' and resid 581 through 583'
    Processing helix  chain 'A' and resid 596 through 605
      removed outlier: 6.402A  pdb=" N   ALA A 602 " --> pdb=" O   ASN A 599 " (cutoff:3.500A)
      removed outlier: 6.405A  pdb=" N   SER A 603 " --> pdb=" O   ARG A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 687 through 692
    Processing helix  chain 'A' and resid 694 through 696
      No H-bonds generated for 'chain 'A' and resid 694 through 696'
    Processing helix  chain 'A' and resid 717 through 719
      No H-bonds generated for 'chain 'A' and resid 717 through 719'
    Processing helix  chain 'A' and resid 751 through 755
      removed outlier: 3.878A  pdb=" N   THR A 754 " --> pdb=" O   GLN A 751 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   THR A 755 " --> pdb=" O   ALA A 752 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 751 through 755'
    Processing helix  chain 'B' and resid 99 through 103
      removed outlier: 3.866A  pdb=" N   SER B 102 " --> pdb=" O   ASN B  99 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 111 through 124
      removed outlier: 3.595A  pdb=" N   LEU B 115 " --> pdb=" O   ASN B 111 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   GLY B 124 " --> pdb=" O   LYS B 120 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 179 through 184
    Processing helix  chain 'B' and resid 207 through 213
      removed outlier: 4.052A  pdb=" N   LEU B 211 " --> pdb=" O   PRO B 207 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 214 through 216
      No H-bonds generated for 'chain 'B' and resid 214 through 216'
    Processing helix  chain 'B' and resid 312 through 317
    Processing helix  chain 'B' and resid 326 through 333
    Processing helix  chain 'B' and resid 362 through 368
      removed outlier: 4.162A  pdb=" N   MET B 366 " --> pdb=" O   ASP B 362 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 369 through 370
      No H-bonds generated for 'chain 'B' and resid 369 through 370'
    Processing helix  chain 'B' and resid 371 through 376
      removed outlier: 3.519A  pdb=" N   THR B 376 " --> pdb=" O   SER B 373 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 383 through 393
    Processing helix  chain 'B' and resid 405 through 409
      removed outlier: 3.685A  pdb=" N   TRP B 408 " --> pdb=" O   HIS B 405 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 411 through 416
      removed outlier: 3.552A  pdb=" N   LYS B 415 " --> pdb=" O   GLY B 412 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 429 through 433
    Processing helix  chain 'B' and resid 446 through 453
    Processing helix  chain 'B' and resid 505 through 509
    Processing helix  chain 'B' and resid 513 through 517
    Processing helix  chain 'B' and resid 567 through 573
      removed outlier: 4.261A  pdb=" N   LEU B 571 " --> pdb=" O   TYR B 568 " (cutoff:3.500A)
      removed outlier: 5.487A  pdb=" N   GLU B 572 " --> pdb=" O   ASP B 569 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 574 through 582
    Processing helix  chain 'B' and resid 604 through 608
    Processing helix  chain 'B' and resid 633 through 641
    Processing helix  chain 'B' and resid 661 through 670
    Processing helix  chain 'B' and resid 699 through 706
    Processing helix  chain 'B' and resid 713 through 717
    Processing helix  chain 'B' and resid 721 through 727
      removed outlier: 4.150A  pdb=" N   ASN B 727 " --> pdb=" O   ALA B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 739 through 744
      removed outlier: 3.533A  pdb=" N   TYR B 743 " --> pdb=" O   TRP B 740 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 758 through 768
      removed outlier: 3.784A  pdb=" N   ASP B 762 " --> pdb=" O   SER B 758 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   GLN B 763 " --> pdb=" O   SER B 759 " (cutoff:3.500A)
      removed outlier: 3.856A  pdb=" N   PHE B 764 " --> pdb=" O   THR B 760 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 808 through 810
      No H-bonds generated for 'chain 'B' and resid 808 through 810'
    Processing helix  chain 'B' and resid 863 through 865
      No H-bonds generated for 'chain 'B' and resid 863 through 865'
    Processing helix  chain 'B' and resid 896 through 900
    Processing helix  chain 'B' and resid 903 through 917
      removed outlier: 3.502A  pdb=" N   LEU B 912 " --> pdb=" O   ASN B 908 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 934 through 939
      removed outlier: 3.525A  pdb=" N   GLU B 938 " --> pdb=" O   ASN B 934 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 946 through 950
    Processing helix  chain 'B' and resid 961 through 969
    Processing helix  chain 'B' and resid 1051 through 1056
    Processing helix  chain 'B' and resid 1059 through 1062
    Processing helix  chain 'B' and resid 1081 through 1084
    Processing helix  chain 'B' and resid 1119 through 1123
      removed outlier: 3.758A  pdb=" N   ASN B1122 " --> pdb=" O   ASN B1119 " (cutoff:3.500A)
      removed outlier: 4.451A  pdb=" N   LYS B1123 " --> pdb=" O   THR B1120 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 1119 through 1123'
    Processing helix  chain 'B' and resid 1133 through 1136
    Processing helix  chain 'B' and resid 1137 through 1143
      removed outlier: 3.809A  pdb=" N   LEU B1143 " --> pdb=" O   SER B1139 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1145 through 1153
      removed outlier: 3.592A  pdb=" N   ILE B1149 " --> pdb=" O   THR B1145 " (cutoff:3.500A)
      removed outlier: 3.708A  pdb=" N   LYS B1152 " --> pdb=" O   ASN B1148 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1192 through 1203
    Processing helix  chain 'B' and resid 1207 through 1211
    Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31
    Processing sheet with id=AA2, first strand: chain 'A' and resid 64 through 72
      removed outlier: 5.683A  pdb=" N   ILE A  66 " --> pdb=" O   LYS A  81 " (cutoff:3.500A)
      removed outlier: 6.537A  pdb=" N   LYS A  81 " --> pdb=" O   ILE A  66 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ASP A  68 " --> pdb=" O   LEU A  79 " (cutoff:3.500A)
      removed outlier: 6.859A  pdb=" N   SER A 109 " --> pdb=" O   GLN A 131 " (cutoff:3.500A)
      removed outlier: 4.670A  pdb=" N   GLN A 131 " --> pdb=" O   SER A 109 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   VAL A 111 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 4.540A  pdb=" N   LYS A 129 " --> pdb=" O   VAL A 111 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   GLU A 113 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      removed outlier: 8.756A  pdb=" N   ASN A 335 " --> pdb=" O   LYS A 129 " (cutoff:3.500A)
      removed outlier: 6.578A  pdb=" N   GLN A 131 " --> pdb=" O   ASN A 335 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 89
    Processing sheet with id=AA4, first strand: chain 'A' and resid 213 through 214
      removed outlier: 4.221A  pdb=" N   GLY A 406 " --> pdb=" O   LEU A 425 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 223 through 225
    Processing sheet with id=AA6, first strand: chain 'A' and resid 282 through 283
    Processing sheet with id=AA7, first strand: chain 'A' and resid 301 through 304
    Processing sheet with id=AA8, first strand: chain 'A' and resid 343 through 345
      removed outlier: 6.589A  pdb=" N   ASN A 344 " --> pdb=" O   TRP A 570 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA8
    Processing sheet with id=AA9, first strand: chain 'A' and resid 383 through 391
      removed outlier: 4.907A  pdb=" N   ILE A 385 " --> pdb=" O   PHE A 400 " (cutoff:3.500A)
      removed outlier: 6.497A  pdb=" N   PHE A 400 " --> pdb=" O   ILE A 385 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLY A 387 " --> pdb=" O   SER A 398 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   SER A 398 " --> pdb=" O   GLY A 387 " (cutoff:3.500A)
      removed outlier: 5.056A  pdb=" N   ILE A 541 " --> pdb=" O   LYS A 401 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 457 through 459
    Processing sheet with id=AB2, first strand: chain 'A' and resid 585 through 586
      removed outlier: 4.769A  pdb=" N   LYS A 611 " --> pdb=" O   GLU A 586 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 626 through 633
      removed outlier: 4.367A  pdb=" N   LEU A 629 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL A 649 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ALA A 631 " --> pdb=" O   GLY A 647 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLY A 647 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   TYR A 646 " --> pdb=" O   PHE A 661 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   PHE A 661 " --> pdb=" O   TYR A 646 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 626 through 633
      removed outlier: 4.367A  pdb=" N   LEU A 629 " --> pdb=" O   VAL A 649 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   VAL A 649 " --> pdb=" O   LEU A 629 " (cutoff:3.500A)
      removed outlier: 4.504A  pdb=" N   ALA A 631 " --> pdb=" O   GLY A 647 " (cutoff:3.500A)
      removed outlier: 6.779A  pdb=" N   GLY A 647 " --> pdb=" O   ALA A 631 " (cutoff:3.500A)
      removed outlier: 5.296A  pdb=" N   TYR A 646 " --> pdb=" O   PHE A 661 " (cutoff:3.500A)
      removed outlier: 4.135A  pdb=" N   PHE A 661 " --> pdb=" O   TYR A 646 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 698 through 704
      removed outlier: 6.859A  pdb=" N   ILE A 713 " --> pdb=" O   LYS A 699 " (cutoff:3.500A)
      removed outlier: 4.317A  pdb=" N   VAL A 701 " --> pdb=" O   SER A 711 " (cutoff:3.500A)
      removed outlier: 6.474A  pdb=" N   SER A 711 " --> pdb=" O   VAL A 701 " (cutoff:3.500A)
      removed outlier: 4.388A  pdb=" N   TYR A 703 " --> pdb=" O   LEU A 709 " (cutoff:3.500A)
      removed outlier: 6.498A  pdb=" N   LEU A 709 " --> pdb=" O   TYR A 703 " (cutoff:3.500A)
      removed outlier: 7.093A  pdb=" N   PHE A 735 " --> pdb=" O   ILE A 769 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ILE A 769 " --> pdb=" O   PHE A 735 " (cutoff:3.500A)
      removed outlier: 7.904A  pdb=" N   VAL A 737 " --> pdb=" O   SER A 767 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 775 through 780
      removed outlier: 6.907A  pdb=" N   ILE A 790 " --> pdb=" O   THR A 777 " (cutoff:3.500A)
      removed outlier: 4.522A  pdb=" N   VAL A 779 " --> pdb=" O   ALA A 788 " (cutoff:3.500A)
      removed outlier: 6.345A  pdb=" N   ALA A 788 " --> pdb=" O   VAL A 779 " (cutoff:3.500A)
      removed outlier: 4.482A  pdb=" N   ILE A 801 " --> pdb=" O   ASP A 812 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 65 through 67
    Processing sheet with id=AB8, first strand: chain 'B' and resid 65 through 67
      removed outlier: 6.955A  pdb=" N   ARG B 132 " --> pdb=" O   LEU B 140 " (cutoff:3.500A)
    Processing sheet with id=AB9, first strand: chain 'B' and resid 164 through 165
    Processing sheet with id=AC1, first strand: chain 'B' and resid 187 through 193
      removed outlier: 6.539A  pdb=" N   LEU B 204 " --> pdb=" O   VAL B 189 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   VAL B 191 " --> pdb=" O   PHE B 202 " (cutoff:3.500A)
      removed outlier: 6.538A  pdb=" N   PHE B 202 " --> pdb=" O   VAL B 191 " (cutoff:3.500A)
      removed outlier: 4.966A  pdb=" N   GLN B 193 " --> pdb=" O   LEU B 200 " (cutoff:3.500A)
      removed outlier: 7.496A  pdb=" N   LEU B 200 " --> pdb=" O   GLN B 193 " (cutoff:3.500A)
      removed outlier: 7.211A  pdb=" N   ALA B 338 " --> pdb=" O   HIS B 360 " (cutoff:3.500A)
      removed outlier: 4.902A  pdb=" N   HIS B 360 " --> pdb=" O   ALA B 338 " (cutoff:3.500A)
      removed outlier: 6.568A  pdb=" N   VAL B 340 " --> pdb=" O   VAL B 358 " (cutoff:3.500A)
      removed outlier: 4.346A  pdb=" N   VAL B 358 " --> pdb=" O   VAL B 340 " (cutoff:3.500A)
      removed outlier: 6.103A  pdb=" N   SER B 342 " --> pdb=" O   GLY B 356 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 246 through 247
    Processing sheet with id=AC3, first strand: chain 'B' and resid 270 through 271
    Processing sheet with id=AC4, first strand: chain 'B' and resid 292 through 293
    Processing sheet with id=AC5, first strand: chain 'B' and resid 457 through 460
    Processing sheet with id=AC6, first strand: chain 'B' and resid 537 through 545
      removed outlier: 4.761A  pdb=" N   VAL B 539 " --> pdb=" O   THR B 554 " (cutoff:3.500A)
      removed outlier: 6.353A  pdb=" N   THR B 554 " --> pdb=" O   VAL B 539 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   GLY B 541 " --> pdb=" O   ALA B 552 " (cutoff:3.500A)
      removed outlier: 5.034A  pdb=" N   LEU B 549 " --> pdb=" O   LEU B 698 " (cutoff:3.500A)
      removed outlier: 6.660A  pdb=" N   ALA B 695 " --> pdb=" O   PHE B 750 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   PHE B 750 " --> pdb=" O   ALA B 695 " (cutoff:3.500A)
      removed outlier: 6.655A  pdb=" N   ILE B 697 " --> pdb=" O   GLN B 748 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 804 through 806
    Processing sheet with id=AC8, first strand: chain 'B' and resid 845 through 846
    Processing sheet with id=AC9, first strand: chain 'B' and resid 921 through 923
    Processing sheet with id=AD1, first strand: chain 'B' and resid 1013 through 1014
      removed outlier: 3.824A  pdb=" N   PHE B1020 " --> pdb=" O   PHE B1031 " (cutoff:3.500A)
      removed outlier: 8.543A  pdb=" N   GLY B1214 " --> pdb=" O   ILE B1044 " (cutoff:3.500A)
      removed outlier: 6.161A  pdb=" N   LEU B1046 " --> pdb=" O   GLY B1214 " (cutoff:3.500A)
    Processing sheet with id=AD2, first strand: chain 'B' and resid 1064 through 1069
      removed outlier: 5.071A  pdb=" N   LEU B1078 " --> pdb=" O   LYS B1065 " (cutoff:3.500A)
      removed outlier: 4.387A  pdb=" N   SER B1067 " --> pdb=" O   LYS B1076 " (cutoff:3.500A)
      removed outlier: 6.376A  pdb=" N   LYS B1076 " --> pdb=" O   SER B1067 " (cutoff:3.500A)
    Processing sheet with id=AD3, first strand: chain 'B' and resid 1228 through 1230

    399 hydrogen bonds defined for protein.
    996 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 3.31

  Time building geometry restraints manager: 1.57 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3183
        1.33 -     1.45: 3878
        1.45 -     1.58: 8294
        1.58 -     1.70: 19
        1.70 -     1.82: 34
  Bond restraints: 15408
  Sorted by residual:
  bond pdb=" SD  MET B 537 "
       pdb=" CE  MET B 537 "
    ideal  model  delta    sigma   weight residual
    1.791  1.634  0.157 2.50e-02 1.60e+03 3.93e+01
  bond pdb=" SD  MET B 557 "
       pdb=" CE  MET B 557 "
    ideal  model  delta    sigma   weight residual
    1.791  1.642  0.149 2.50e-02 1.60e+03 3.56e+01
  bond pdb=" CA  PHE B1020 "
       pdb=" C   PHE B1020 "
    ideal  model  delta    sigma   weight residual
    1.522  1.594 -0.072 1.24e-02 6.50e+03 3.37e+01
  bond pdb=" SD  MET B 457 "
       pdb=" CE  MET B 457 "
    ideal  model  delta    sigma   weight residual
    1.791  1.658  0.133 2.50e-02 1.60e+03 2.81e+01
  bond pdb=" CA  ILE A 502 "
       pdb=" C   ILE A 502 "
    ideal  model  delta    sigma   weight residual
    1.522  1.587 -0.065 1.24e-02 6.50e+03 2.74e+01
  ... (remaining 15403 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.67: 18172
        2.67 -     5.35: 2428
        5.35 -     8.02: 325
        8.02 -    10.69: 25
       10.69 -    13.37: 4
  Bond angle restraints: 20954
  Sorted by residual:
  angle pdb=" CA  ASN B  99 "
        pdb=" CB  ASN B  99 "
        pdb=" CG  ASN B  99 "
      ideal   model   delta    sigma   weight residual
     112.60  121.90   -9.30 1.00e+00 1.00e+00 8.64e+01
  angle pdb=" CA  ASP B 701 "
        pdb=" CB  ASP B 701 "
        pdb=" CG  ASP B 701 "
      ideal   model   delta    sigma   weight residual
     112.60  121.13   -8.53 1.00e+00 1.00e+00 7.27e+01
  angle pdb=" C   ALA B 987 "
        pdb=" N   ASP B 988 "
        pdb=" CA  ASP B 988 "
      ideal   model   delta    sigma   weight residual
     121.02  133.40  -12.38 1.48e+00 4.57e-01 7.00e+01
  angle pdb=" C   GLN B 849 "
        pdb=" N   VAL B 850 "
        pdb=" CA  VAL B 850 "
      ideal   model   delta    sigma   weight residual
     120.77  131.47  -10.70 1.46e+00 4.69e-01 5.37e+01
  angle pdb=" N   GLN B 849 "
        pdb=" CA  GLN B 849 "
        pdb=" C   GLN B 849 "
      ideal   model   delta    sigma   weight residual
     111.56  101.53   10.03 1.38e+00 5.25e-01 5.28e+01
  ... (remaining 20949 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.86: 7902
       17.86 -    35.72: 807
       35.72 -    53.58: 305
       53.58 -    71.45: 108
       71.45 -    89.31: 40
  Dihedral angle restraints: 9162
    sinusoidal: 3583
      harmonic: 5579
  Sorted by residual:
  dihedral pdb=" C   ASP A 723 "
           pdb=" N   ASP A 723 "
           pdb=" CA  ASP A 723 "
           pdb=" CB  ASP A 723 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -112.13  -10.47     0      2.50e+00 1.60e-01 1.75e+01
  dihedral pdb=" N   ASN B 150 "
           pdb=" C   ASN B 150 "
           pdb=" CA  ASN B 150 "
           pdb=" CB  ASN B 150 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.22  -10.42     0      2.50e+00 1.60e-01 1.74e+01
  dihedral pdb=" C   GLN A 104 "
           pdb=" N   GLN A 104 "
           pdb=" CA  GLN A 104 "
           pdb=" CB  GLN A 104 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.58    9.98     0      2.50e+00 1.60e-01 1.59e+01
  ... (remaining 9159 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.078: 1010
       0.078 -    0.156: 832
       0.156 -    0.234: 392
       0.234 -    0.312: 78
       0.312 -    0.390: 6
  Chirality restraints: 2318
  Sorted by residual:
  chirality pdb=" CA  ALA B 538 "
            pdb=" N   ALA B 538 "
            pdb=" C   ALA B 538 "
            pdb=" CB  ALA B 538 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    2.87   -0.39 2.00e-01 2.50e+01 3.80e+00
  chirality pdb=" CA  ASN B 150 "
            pdb=" N   ASN B 150 "
            pdb=" C   ASN B 150 "
            pdb=" CB  ASN B 150 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.16    0.35 2.00e-01 2.50e+01 3.04e+00
  chirality pdb=" CA  LYS A 156 "
            pdb=" N   LYS A 156 "
            pdb=" C   LYS A 156 "
            pdb=" CB  LYS A 156 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.85   -0.34 2.00e-01 2.50e+01 2.94e+00
  ... (remaining 2315 not shown)

  Planarity restraints: 2742
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 658 "   -0.066 2.00e-02 2.50e+03   3.47e-02 2.41e+01
        pdb=" CG  TYR B 658 "    0.059 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 658 "    0.018 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 658 "    0.012 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 658 "    0.004 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 658 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 658 "   -0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR B 658 "   -0.034 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 669 "   -0.010 2.00e-02 2.50e+03   2.54e-02 1.61e+01
        pdb=" CG  TRP B 669 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 669 "   -0.006 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 669 "    0.011 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 669 "    0.044 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 669 "    0.011 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 669 "    0.030 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 669 "   -0.032 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 669 "    0.015 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 669 "   -0.025 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 408 "   -0.048 2.00e-02 2.50e+03   2.40e-02 1.44e+01
        pdb=" CG  TRP B 408 "    0.028 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 408 "    0.004 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 408 "    0.019 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 408 "   -0.004 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 408 "    0.008 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 408 "    0.034 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 408 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 408 "   -0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 408 "   -0.032 2.00e-02 2.50e+03
  ... (remaining 2739 not shown)

  Histogram of nonbonded interaction distances:
        2.47 -     2.96: 6258
        2.96 -     3.44: 14739
        3.44 -     3.93: 27510
        3.93 -     4.41: 31715
        4.41 -     4.90: 51435
  Nonbonded interactions: 131657
  Sorted by model distance:
  nonbonded pdb=" N   SER B 856 "
            pdb=" N   THR B 857 "
     model   vdw
     2.473 2.560
  nonbonded pdb=" N   GLN B 849 "
            pdb=" N   VAL B 850 "
     model   vdw
     2.474 2.560
  nonbonded pdb=" ND2 ASN A 806 "
            pdb=" O   ASP B 701 "
     model   vdw
     2.481 3.120
  nonbonded pdb=" N   THR A 687 "
            pdb=" O   THR A 687 "
     model   vdw
     2.500 2.496
  nonbonded pdb=" O   GLN A 796 "
            pdb=" NE2 GLN A 796 "
     model   vdw
     2.503 3.120
  ... (remaining 131652 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.070
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.220
  Check model and map are aligned:         0.040
  Set scattering table:                    0.040
  Process input model:                     14.930
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.310
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.520
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.4598
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      :  0.014   0.157  15408  Z= 0.854
  Angle     :  1.850  13.366  20954  Z= 1.238
  Chirality :  0.119   0.390   2318
  Planarity :  0.008   0.038   2742
  Dihedral  : 18.902  89.307   5572
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 6.61
  Ramachandran Plot:
    Outliers :  0.47 %
    Allowed  :  6.36 %
    Favored  : 93.17 %
  Rotamer:
    Outliers : 12.77 %
    Allowed  : 10.93 %
    Favored  : 76.30 %
  Cbeta Deviations :  0.72 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.49 (0.16), residues: 1917
  helix: -2.78 (0.22), residues: 293
  sheet: -0.90 (0.27), residues: 301
  loop : -1.64 (0.15), residues: 1323

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.002   ARG A 537 
 TYR   0.066   0.010   TYR B 658 
 PHE   0.043   0.008   PHE A 397 
 TRP   0.059   0.011   TRP B1056 
 HIS   0.015   0.004   HIS B 381 

Details of bonding type rmsd
  covalent geometry    : bond        0.01354 (15408)
  covalent geometry    : angle       1.85022 (20954)
  hydrogen bonds       : bond        0.20871 (  389)
  hydrogen bonds       : angle       8.82561 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  530 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 216
    poor density    : 314
  time to evaluate  : 0.502 
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: A   84 ASP cc_start: 0.5026 (OUTLIER) cc_final: 0.4520 (t70)
REVERT: A  136 ASN cc_start: 0.1348 (OUTLIER) cc_final: -0.1533 (t0)
REVERT: A  189 ASN cc_start: 0.6164 (OUTLIER) cc_final: 0.5209 (m-40)
REVERT: A  254 SER cc_start: 0.2811 (OUTLIER) cc_final: 0.2584 (t)
REVERT: A  366 THR cc_start: 0.4866 (OUTLIER) cc_final: 0.4636 (p)
REVERT: A  670 SER cc_start: 0.2743 (OUTLIER) cc_final: 0.2281 (p)
REVERT: B  448 GLU cc_start: 0.2298 (OUTLIER) cc_final: 0.0943 (mt-10)
REVERT: B  683 VAL cc_start: 0.6851 (t) cc_final: 0.6605 (p)
REVERT: B 1136 ASN cc_start: 0.7041 (OUTLIER) cc_final: 0.6696 (m-40)
  outliers start: 216
  outliers final: 36
  residues processed: 491
  average time/residue: 0.1315
  time to fit residues: 93.2241
Evaluate side-chains
  196 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 152
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 98 optimal weight:    9.9990
   chunk 107 optimal weight:    0.9980
   chunk 10 optimal weight:    5.9990
   chunk 66 optimal weight:    1.9990
   chunk 130 optimal weight:    0.6980
   chunk 124 optimal weight:    4.9990
   chunk 103 optimal weight:    2.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:    6.9990
   chunk 91 optimal weight:    2.9990
   chunk 149 optimal weight:    4.9990
   overall best weight:    1.9386

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 131 GLN
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 189 ASN
A 194 ASN
** A 231 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 332 ASN
A 475 ASN
A 503 ASN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 599 ASN
A 660 ASN
A 662 ASN
A 722 HIS
A 748 ASN
B  59 GLN
B 196 HIS
B 360 HIS
B 382 HIS
B 395 GLN
** B 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 548 GLN
** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 631 ASN
B 735 ASN
B 745 ASN
B 967 HIS
B1011 ASN
B1050 GLN
B1108 GLN
B1119 ASN
B1235 ASN

Total number of N/Q/H flips: 26

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.086884 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.075481 restraints weight = 96476.877|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.077225 restraints weight = 65760.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.078475 restraints weight = 48605.022|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4070 r_free = 0.4070 target = 0.079404 restraints weight = 38597.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.080034 restraints weight = 32180.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6382
moved from start:          0.3967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15408  Z= 0.181
  Angle     :  0.707   7.821  20954  Z= 0.380
  Chirality :  0.047   0.217   2318
  Planarity :  0.005   0.061   2742
  Dihedral  :  5.476  36.606   2032
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 12.55
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  3.70 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.49 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.16 (0.18), residues: 1917
  helix: -0.93 (0.28), residues: 296
  sheet: -0.21 (0.27), residues: 346
  loop : -0.90 (0.16), residues: 1275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG B 835 
 TYR   0.030   0.002   TYR B 201 
 PHE   0.032   0.002   PHE B 761 
 TRP   0.025   0.002   TRP A 220 
 HIS   0.008   0.001   HIS A 722 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 (15408)
  covalent geometry    : angle       0.70659 (20954)
  hydrogen bonds       : bond        0.04266 (  389)
  hydrogen bonds       : angle       6.54931 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 184
  time to evaluate  : 0.494 
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: A  145 LEU cc_start: 0.8327 (mt) cc_final: 0.7319 (mt)
REVERT: A  763 LEU cc_start: 0.9432 (tt) cc_final: 0.8919 (tt)
REVERT: B  148 MET cc_start: -0.1520 (mmt) cc_final: -0.1863 (mmt)
REVERT: B  200 LEU cc_start: 0.8438 (mp) cc_final: 0.8118 (mp)
REVERT: B  374 TRP cc_start: 0.6360 (m100) cc_final: 0.6101 (m100)
REVERT: B  545 VAL cc_start: 0.7828 (t) cc_final: 0.7315 (p)
REVERT: B  635 ASP cc_start: 0.8452 (m-30) cc_final: 0.8001 (p0)
REVERT: B  702 LEU cc_start: 0.9163 (tp) cc_final: 0.8778 (tt)
REVERT: B  756 LEU cc_start: 0.7643 (mp) cc_final: 0.7142 (mm)
REVERT: B  757 ASP cc_start: 0.7948 (t0) cc_final: 0.7586 (p0)
REVERT: B 1004 TRP cc_start: 0.7269 (m100) cc_final: 0.6905 (m100)
  outliers start: 2
  outliers final: 1
  residues processed: 186
  average time/residue: 0.1187
  time to fit residues: 33.8889
Evaluate side-chains
  116 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 115
  time to evaluate  : 0.466 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 106 optimal weight:    0.0970
   chunk 141 optimal weight:    7.9990
   chunk 81 optimal weight:   10.0000
   chunk 149 optimal weight:    2.9990
   chunk 38 optimal weight:   20.0000
   chunk 51 optimal weight:    6.9990
   chunk 23 optimal weight:    8.9990
   chunk 156 optimal weight:    9.9990
   chunk 172 optimal weight:    1.9990
   chunk 99 optimal weight:   10.0000
   chunk 144 optimal weight:    4.9990
   overall best weight:    3.4186

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 183 GLN
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 524 ASN
** A 526 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN
** A 540 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B  59 GLN
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 302 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 405 HIS
B 576 ASN
** B 582 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1110 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.080720 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3829 r_free = 0.3829 target = 0.070111 restraints weight = 105022.612|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3871 r_free = 0.3871 target = 0.071699 restraints weight = 70458.523|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.072853 restraints weight = 52036.351|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.073691 restraints weight = 41247.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3940 r_free = 0.3940 target = 0.074283 restraints weight = 34438.211|
|-----------------------------------------------------------------------------|
r_work (final): 0.3947
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6628
moved from start:          0.5084

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.059  15408  Z= 0.212
  Angle     :  0.693  12.677  20954  Z= 0.366
  Chirality :  0.047   0.201   2318
  Planarity :  0.005   0.045   2742
  Dihedral  :  5.420  34.330   2032
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 16.29
  Ramachandran Plot:
    Outliers :  0.10 %
    Allowed  :  4.80 %
    Favored  : 95.10 %
  Rotamer:
    Outliers :  0.12 %
    Allowed  :  3.49 %
    Favored  : 96.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.17 (0.18), residues: 1917
  helix: -0.73 (0.28), residues: 302
  sheet: -0.32 (0.28), residues: 340
  loop : -0.92 (0.16), residues: 1275

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.013   0.001   ARG B 835 
 TYR   0.023   0.002   TYR B 201 
 PHE   0.032   0.002   PHE A 373 
 TRP   0.022   0.002   TRP A 220 
 HIS   0.006   0.001   HIS A 175 

Details of bonding type rmsd
  covalent geometry    : bond        0.00459 (15408)
  covalent geometry    : angle       0.69254 (20954)
  hydrogen bonds       : bond        0.04127 (  389)
  hydrogen bonds       : angle       6.20076 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 154
  time to evaluate  : 0.633 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 MET cc_start: 0.8459 (tmm) cc_final: 0.8253 (tmm)
REVERT: A  378 PHE cc_start: 0.7682 (m-80) cc_final: 0.6770 (m-10)
REVERT: A  524 ASN cc_start: 0.6337 (OUTLIER) cc_final: 0.5231 (p0)
REVERT: A  805 ASN cc_start: 0.8467 (m110) cc_final: 0.8048 (m-40)
REVERT: B  190 GLU cc_start: 0.7382 (tm-30) cc_final: 0.6890 (tm-30)
REVERT: B  200 LEU cc_start: 0.8633 (mp) cc_final: 0.8317 (mp)
REVERT: B  740 TRP cc_start: 0.8984 (p-90) cc_final: 0.8507 (p-90)
REVERT: B  756 LEU cc_start: 0.8017 (mp) cc_final: 0.7754 (mp)
REVERT: B 1076 LYS cc_start: 0.8198 (mttp) cc_final: 0.7973 (mttp)
REVERT: B 1198 LYS cc_start: 0.9151 (tttt) cc_final: 0.8688 (ttmt)
  outliers start: 2
  outliers final: 1
  residues processed: 156
  average time/residue: 0.1086
  time to fit residues: 26.6304
Evaluate side-chains
  110 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 108
  time to evaluate  : 0.574 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 118 optimal weight:   10.0000
   chunk 172 optimal weight:    0.7980
   chunk 86 optimal weight:   10.0000
   chunk 119 optimal weight:    9.9990
   chunk 50 optimal weight:    6.9990
   chunk 46 optimal weight:    4.9990
   chunk 192 optimal weight:   10.0000
   chunk 159 optimal weight:    7.9990
   chunk 2 optimal weight:   10.0000
   chunk 142 optimal weight:   10.0000
   chunk 121 optimal weight:    6.9990
   overall best weight:    5.5588

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

Flipped N/Q/H residues before XYZ refinement:
A  73 ASN
A 171 GLN
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 344 ASN
A 354 GLN
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 526 ASN
A 531 GLN
A 540 GLN
** A 624 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 645 ASN
B 116 ASN
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 214 HIS
B 430 HIS
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 582 GLN
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 924 ASN
B1110 ASN

Total number of N/Q/H flips: 14

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3938 r_free = 0.3938 target = 0.071750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.061305 restraints weight = 108577.859|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.062637 restraints weight = 76312.832|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.063611 restraints weight = 58328.323|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3753 r_free = 0.3753 target = 0.064290 restraints weight = 47972.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.064793 restraints weight = 41588.114|
|-----------------------------------------------------------------------------|
r_work (final): 0.3753
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6925
moved from start:          0.6921

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.099  15408  Z= 0.304
  Angle     :  0.816  14.357  20954  Z= 0.430
  Chirality :  0.050   0.252   2318
  Planarity :  0.006   0.051   2742
  Dihedral  :  6.183  37.065   2032
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 25.74
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  6.10 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  5.02 %
    Favored  : 94.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.67 (0.18), residues: 1917
  helix: -1.28 (0.26), residues: 308
  sheet: -0.58 (0.28), residues: 335
  loop : -1.24 (0.16), residues: 1274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 835 
 TYR   0.029   0.003   TYR B 450 
 PHE   0.028   0.003   PHE A 594 
 TRP   0.033   0.003   TRP B1004 
 HIS   0.009   0.002   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00650 (15408)
  covalent geometry    : angle       0.81551 (20954)
  hydrogen bonds       : bond        0.04772 (  389)
  hydrogen bonds       : angle       6.86814 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 144
  time to evaluate  : 0.566 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  320 MET cc_start: 0.8131 (ptm) cc_final: 0.7323 (ptt)
REVERT: A  785 GLU cc_start: 0.9342 (pp20) cc_final: 0.9036 (pp20)
REVERT: A  796 GLN cc_start: 0.8236 (tp-100) cc_final: 0.8030 (pp30)
REVERT: A  801 ILE cc_start: 0.6776 (tt) cc_final: 0.6539 (tt)
REVERT: B  148 MET cc_start: -0.0811 (mmt) cc_final: -0.1020 (mmt)
REVERT: B  200 LEU cc_start: 0.8757 (mp) cc_final: 0.8485 (mp)
REVERT: B  462 ASN cc_start: 0.9541 (p0) cc_final: 0.9249 (p0)
REVERT: B  490 LYS cc_start: 0.8988 (mptt) cc_final: 0.8683 (mptt)
REVERT: B  548 GLN cc_start: 0.8512 (mm110) cc_final: 0.8291 (mm-40)
REVERT: B  588 ASP cc_start: 0.8314 (m-30) cc_final: 0.8054 (m-30)
REVERT: B  740 TRP cc_start: 0.9266 (p-90) cc_final: 0.8600 (p-90)
REVERT: B  761 PHE cc_start: 0.8108 (t80) cc_final: 0.7410 (t80)
REVERT: B 1004 TRP cc_start: 0.7387 (m100) cc_final: 0.7025 (m-10)
REVERT: B 1198 LYS cc_start: 0.9285 (tttt) cc_final: 0.8801 (ttmt)
  outliers start: 3
  outliers final: 0
  residues processed: 147
  average time/residue: 0.1173
  time to fit residues: 26.6097
Evaluate side-chains
  100 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 100
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 164 optimal weight:    2.9990
   chunk 148 optimal weight:    7.9990
   chunk 166 optimal weight:   10.0000
   chunk 98 optimal weight:    0.8980
   chunk 133 optimal weight:    5.9990
   chunk 131 optimal weight:    0.9980
   chunk 146 optimal weight:    4.9990
   chunk 136 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 32 optimal weight:    9.9990
   chunk 109 optimal weight:    0.8980
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 369 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN
A 660 ASN
A 766 GLN
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 453 ASN
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 748 GLN
** B 908 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1003 ASN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4014 r_free = 0.4014 target = 0.073556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3743 r_free = 0.3743 target = 0.062851 restraints weight = 104553.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.064343 restraints weight = 70717.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.065351 restraints weight = 53047.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3832 r_free = 0.3832 target = 0.066066 restraints weight = 43191.522|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.3846 r_free = 0.3846 target = 0.066554 restraints weight = 37005.035|
|-----------------------------------------------------------------------------|
r_work (final): 0.3839
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6805
moved from start:          0.6907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15408  Z= 0.140
  Angle     :  0.620  11.831  20954  Z= 0.327
  Chirality :  0.045   0.187   2318
  Planarity :  0.004   0.076   2742
  Dihedral  :  5.553  34.861   2032
  Min Nonbonded Distance : 2.393

Molprobity Statistics.
  All-atom Clashscore : 16.12
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  4.90 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.66 %
    Favored  : 97.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.35 (0.18), residues: 1917
  helix: -0.91 (0.29), residues: 303
  sheet: -0.41 (0.29), residues: 327
  loop : -1.04 (0.16), residues: 1287

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG B 817 
 TYR   0.016   0.002   TYR B 344 
 PHE   0.023   0.002   PHE B 761 
 TRP   0.026   0.001   TRP B 503 
 HIS   0.004   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 (15408)
  covalent geometry    : angle       0.62005 (20954)
  hydrogen bonds       : bond        0.03498 (  389)
  hydrogen bonds       : angle       6.32247 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 143
  time to evaluate  : 0.602 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  796 GLN cc_start: 0.8265 (tp-100) cc_final: 0.8050 (pp30)
REVERT: A  801 ILE cc_start: 0.6920 (tt) cc_final: 0.6582 (tt)
REVERT: B  190 GLU cc_start: 0.7127 (tm-30) cc_final: 0.5669 (tm-30)
REVERT: B  200 LEU cc_start: 0.8377 (mp) cc_final: 0.7849 (mp)
REVERT: B  344 TYR cc_start: 0.9262 (m-80) cc_final: 0.9032 (m-80)
REVERT: B  462 ASN cc_start: 0.9562 (p0) cc_final: 0.9347 (p0)
REVERT: B  465 PHE cc_start: 0.7630 (m-10) cc_final: 0.7250 (m-80)
REVERT: B  548 GLN cc_start: 0.8377 (mm110) cc_final: 0.8154 (mm110)
REVERT: B  588 ASP cc_start: 0.8101 (m-30) cc_final: 0.7768 (m-30)
REVERT: B  740 TRP cc_start: 0.9223 (p-90) cc_final: 0.8276 (p-90)
REVERT: B  761 PHE cc_start: 0.7955 (t80) cc_final: 0.7449 (t80)
REVERT: B 1004 TRP cc_start: 0.7346 (m100) cc_final: 0.6031 (m100)
REVERT: B 1198 LYS cc_start: 0.9250 (tttt) cc_final: 0.8839 (ttmt)
REVERT: B 1221 MET cc_start: 0.3987 (ppp) cc_final: 0.3738 (ppp)
  outliers start: 1
  outliers final: 1
  residues processed: 144
  average time/residue: 0.1080
  time to fit residues: 24.1845
Evaluate side-chains
  101 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 100
  time to evaluate  : 0.515 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 44 optimal weight:    5.9990
   chunk 42 optimal weight:    6.9990
   chunk 71 optimal weight:    8.9990
   chunk 160 optimal weight:    5.9990
   chunk 111 optimal weight:   10.0000
   chunk 118 optimal weight:    7.9990
   chunk 138 optimal weight:    0.0570
   chunk 52 optimal weight:    0.0060
   chunk 105 optimal weight:   10.0000
   chunk 191 optimal weight:    7.9990
   chunk 22 optimal weight:    4.9990
   overall best weight:    3.4120

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 190 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN
A 624 ASN
A 766 GLN
** B 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 252 GLN
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 908 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 = 0.3941 r_free = 0.3941 target = 0.071035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.060883 restraints weight = 108489.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.062178 restraints weight = 73060.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.063092 restraints weight = 55936.625|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.063773 restraints weight = 46039.233|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.064288 restraints weight = 39788.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.3766
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6906
moved from start:          0.7527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.064  15408  Z= 0.201
  Angle     :  0.674  14.045  20954  Z= 0.351
  Chirality :  0.046   0.200   2318
  Planarity :  0.005   0.070   2742
  Dihedral  :  5.682  32.868   2032
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 20.10
  Ramachandran Plot:
    Outliers :  0.05 %
    Allowed  :  5.79 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  2.07 %
    Favored  : 97.87 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.11 %

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: -1.45 (0.18), residues: 1917
  helix: -1.01 (0.29), residues: 304
  sheet: -0.65 (0.28), residues: 330
  loop : -1.05 (0.17), residues: 1283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 817 
 TYR   0.022   0.002   TYR A 439 
 PHE   0.028   0.002   PHE B 761 
 TRP   0.022   0.002   TRP A 220 
 HIS   0.005   0.001   HIS A 473 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (15408)
  covalent geometry    : angle       0.67413 (20954)
  hydrogen bonds       : bond        0.03740 (  389)
  hydrogen bonds       : angle       6.50390 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  141 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 140
  time to evaluate  : 0.564 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  126 MET cc_start: 0.8566 (tmm) cc_final: 0.8149 (tmm)
REVERT: A  596 ARG cc_start: 0.8627 (mpt180) cc_final: 0.8150 (mpt180)
REVERT: A  784 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8708 (mp0)
REVERT: A  785 GLU cc_start: 0.9331 (pp20) cc_final: 0.9021 (pp20)
REVERT: A  796 GLN cc_start: 0.8472 (tp-100) cc_final: 0.8246 (pp30)
REVERT: B  200 LEU cc_start: 0.8450 (mp) cc_final: 0.7923 (mp)
REVERT: B  344 TYR cc_start: 0.9268 (m-80) cc_final: 0.8962 (m-80)
REVERT: B  462 ASN cc_start: 0.9571 (p0) cc_final: 0.9327 (p0)
REVERT: B  548 GLN cc_start: 0.8535 (mm110) cc_final: 0.8222 (mm110)
REVERT: B  588 ASP cc_start: 0.8253 (m-30) cc_final: 0.7979 (m-30)
REVERT: B  728 GLN cc_start: 0.8145 (pp30) cc_final: 0.7743 (pp30)
REVERT: B  740 TRP cc_start: 0.9364 (p-90) cc_final: 0.8360 (p-90)
REVERT: B  761 PHE cc_start: 0.8094 (t80) cc_final: 0.7679 (t80)
REVERT: B 1004 TRP cc_start: 0.7486 (m100) cc_final: 0.6923 (m100)
REVERT: B 1024 LEU cc_start: 0.9249 (tp) cc_final: 0.8913 (tt)
REVERT: B 1198 LYS cc_start: 0.9348 (tttt) cc_final: 0.8887 (ttmt)
  outliers start: 1
  outliers final: 0
  residues processed: 141
  average time/residue: 0.1164
  time to fit residues: 25.6916
Evaluate side-chains
  102 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.575 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 72 optimal weight:    5.9990
   chunk 77 optimal weight:    0.9980
   chunk 84 optimal weight:    5.9990
   chunk 150 optimal weight:    5.9990
   chunk 15 optimal weight:    4.9990
   chunk 102 optimal weight:    5.9990
   chunk 105 optimal weight:   10.0000
   chunk 14 optimal weight:    5.9990
   chunk 95 optimal weight:    9.9990
   chunk 56 optimal weight:    6.9990
   chunk 24 optimal weight:    1.9990
   overall best weight:    3.9988

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 473 HIS
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN
A 766 GLN
** B  59 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 126 GLN
B 193 GLN
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 924 ASN
B1110 ASN

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3900 r_free = 0.3900 target = 0.069776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.059699 restraints weight = 108673.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.061021 restraints weight = 75289.807|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.061946 restraints weight = 57240.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.062611 restraints weight = 46996.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3738 r_free = 0.3738 target = 0.063117 restraints weight = 40534.332|
|-----------------------------------------------------------------------------|
r_work (final): 0.3726
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.8197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.050  15408  Z= 0.218
  Angle     :  0.698  12.865  20954  Z= 0.364
  Chirality :  0.046   0.182   2318
  Planarity :  0.005   0.066   2742
  Dihedral  :  5.831  32.729   2032
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 21.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.99 %
    Favored  : 93.01 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.30 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.66 (0.18), residues: 1917
  helix: -1.20 (0.28), residues: 317
  sheet: -0.87 (0.28), residues: 333
  loop : -1.16 (0.17), residues: 1267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG B 817 
 TYR   0.040   0.002   TYR A 469 
 PHE   0.024   0.002   PHE A 786 
 TRP   0.024   0.002   TRP B 503 
 HIS   0.005   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00478 (15408)
  covalent geometry    : angle       0.69797 (20954)
  hydrogen bonds       : bond        0.03863 (  389)
  hydrogen bonds       : angle       6.63371 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  133 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 132
  time to evaluate  : 0.502 
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: A  596 ARG cc_start: 0.8788 (mpt180) cc_final: 0.8143 (mtp180)
REVERT: A  785 GLU cc_start: 0.9379 (pp20) cc_final: 0.9087 (tm-30)
REVERT: A  796 GLN cc_start: 0.8616 (tp-100) cc_final: 0.8365 (pp30)
REVERT: A  801 ILE cc_start: 0.6978 (tt) cc_final: 0.6741 (tt)
REVERT: B  148 MET cc_start: 0.1025 (mmt) cc_final: 0.0768 (mmt)
REVERT: B  190 GLU cc_start: 0.6788 (tm-30) cc_final: 0.6226 (tm-30)
REVERT: B  200 LEU cc_start: 0.8515 (mp) cc_final: 0.7974 (mp)
REVERT: B  344 TYR cc_start: 0.9225 (m-80) cc_final: 0.8881 (m-80)
REVERT: B  450 TYR cc_start: 0.9218 (t80) cc_final: 0.8753 (t80)
REVERT: B  462 ASN cc_start: 0.9568 (p0) cc_final: 0.9323 (p0)
REVERT: B  490 LYS cc_start: 0.8990 (mptt) cc_final: 0.8735 (mptt)
REVERT: B  548 GLN cc_start: 0.8570 (mm110) cc_final: 0.8261 (mm110)
REVERT: B  588 ASP cc_start: 0.8230 (m-30) cc_final: 0.7999 (m-30)
REVERT: B  740 TRP cc_start: 0.9363 (p-90) cc_final: 0.8367 (p-90)
REVERT: B  756 LEU cc_start: 0.8182 (mp) cc_final: 0.7968 (mp)
REVERT: B  761 PHE cc_start: 0.8105 (t80) cc_final: 0.7447 (t80)
REVERT: B 1004 TRP cc_start: 0.7724 (m100) cc_final: 0.6760 (m100)
REVERT: B 1182 ILE cc_start: 0.6982 (pt) cc_final: 0.6767 (pt)
REVERT: B 1198 LYS cc_start: 0.9350 (tttt) cc_final: 0.8934 (ttmt)
  outliers start: 1
  outliers final: 0
  residues processed: 133
  average time/residue: 0.1085
  time to fit residues: 22.7392
Evaluate side-chains
  105 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 105
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 113 optimal weight:    6.9990
   chunk 138 optimal weight:    0.9980
   chunk 103 optimal weight:    3.9990
   chunk 65 optimal weight:    6.9990
   chunk 175 optimal weight:    9.9990
   chunk 171 optimal weight:    0.1980
   chunk 70 optimal weight:    3.9990
   chunk 64 optimal weight:    2.9990
   chunk 184 optimal weight:    7.9990
   chunk 161 optimal weight:    0.8980
   chunk 112 optimal weight:    7.9990
   overall best weight:    1.8184

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 190 GLN
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 423 GLN
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 531 GLN
B  59 GLN
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B1110 ASN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.071441 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.061296 restraints weight = 107897.177|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.062678 restraints weight = 73304.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.063601 restraints weight = 55165.813|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3772 r_free = 0.3772 target = 0.064320 restraints weight = 45166.705|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.064857 restraints weight = 38714.414|
|-----------------------------------------------------------------------------|
r_work (final): 0.3778
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6903
moved from start:          0.8250

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  15408  Z= 0.139
  Angle     :  0.608   9.835  20954  Z= 0.320
  Chirality :  0.045   0.189   2318
  Planarity :  0.004   0.050   2742
  Dihedral  :  5.519  30.143   2032
  Min Nonbonded Distance : 2.472

Molprobity Statistics.
  All-atom Clashscore : 16.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  0.06 %
    Allowed  :  1.24 %
    Favored  : 98.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -1.46 (0.18), residues: 1917
  helix: -0.98 (0.29), residues: 311
  sheet: -0.77 (0.28), residues: 333
  loop : -1.03 (0.17), residues: 1273

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 488 
 TYR   0.016   0.002   TYR A 439 
 PHE   0.021   0.002   PHE B 761 
 TRP   0.026   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00311 (15408)
  covalent geometry    : angle       0.60783 (20954)
  hydrogen bonds       : bond        0.03293 (  389)
  hydrogen bonds       : angle       6.31098 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 130
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  596 ARG cc_start: 0.8671 (mpt180) cc_final: 0.8107 (mtp180)
REVERT: A  785 GLU cc_start: 0.9353 (pp20) cc_final: 0.8979 (tm-30)
REVERT: A  796 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8216 (pp30)
REVERT: A  801 ILE cc_start: 0.7142 (tt) cc_final: 0.6884 (tt)
REVERT: B  200 LEU cc_start: 0.8435 (mp) cc_final: 0.7869 (mp)
REVERT: B  344 TYR cc_start: 0.9272 (m-80) cc_final: 0.8823 (m-80)
REVERT: B  366 MET cc_start: 0.7466 (tpp) cc_final: 0.7117 (tpt)
REVERT: B  462 ASN cc_start: 0.9535 (p0) cc_final: 0.9307 (p0)
REVERT: B  490 LYS cc_start: 0.8998 (mptt) cc_final: 0.8784 (mptt)
REVERT: B  548 GLN cc_start: 0.8456 (mm110) cc_final: 0.8195 (mm110)
REVERT: B  588 ASP cc_start: 0.8257 (m-30) cc_final: 0.8001 (m-30)
REVERT: B  740 TRP cc_start: 0.9357 (p-90) cc_final: 0.8294 (p-90)
REVERT: B  761 PHE cc_start: 0.8042 (t80) cc_final: 0.7503 (t80)
REVERT: B  997 LEU cc_start: 0.8484 (tp) cc_final: 0.8264 (tp)
REVERT: B 1004 TRP cc_start: 0.7601 (m100) cc_final: 0.6701 (m100)
REVERT: B 1024 LEU cc_start: 0.9283 (tp) cc_final: 0.8961 (tt)
REVERT: B 1182 ILE cc_start: 0.6915 (pt) cc_final: 0.6689 (pt)
REVERT: B 1198 LYS cc_start: 0.9342 (tttt) cc_final: 0.8960 (ttmt)
  outliers start: 1
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1151
  time to fit residues: 23.3141
Evaluate side-chains
  102 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 102
  time to evaluate  : 0.566 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 134 optimal weight:    7.9990
   chunk 165 optimal weight:    7.9990
   chunk 31 optimal weight:   20.0000
   chunk 57 optimal weight:    9.9990
   chunk 90 optimal weight:    4.9990
   chunk 39 optimal weight:    5.9990
   chunk 123 optimal weight:    7.9990
   chunk 64 optimal weight:    0.8980
   chunk 98 optimal weight:    6.9990
   chunk 50 optimal weight:   10.0000
   chunk 38 optimal weight:    7.9990
   overall best weight:    5.3788

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 HIS
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 380 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 196 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 456 ASN
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 634 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 924 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.068093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.058399 restraints weight = 112435.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.059670 restraints weight = 78893.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.060472 restraints weight = 60943.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.061082 restraints weight = 50557.919|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 22)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.061543 restraints weight = 44235.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7067
moved from start:          0.9052

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.061  15408  Z= 0.276
  Angle     :  0.777  13.727  20954  Z= 0.405
  Chirality :  0.049   0.267   2318
  Planarity :  0.006   0.055   2742
  Dihedral  :  6.201  31.450   2032
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 26.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.77 %
    Favored  : 99.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.05 %

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: -2.01 (0.18), residues: 1917
  helix: -1.71 (0.26), residues: 335
  sheet: -1.06 (0.28), residues: 341
  loop : -1.32 (0.17), residues: 1241

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG B 488 
 TYR   0.038   0.003   TYR A 469 
 PHE   0.033   0.003   PHE A 786 
 TRP   0.025   0.002   TRP B 503 
 HIS   0.009   0.002   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00592 (15408)
  covalent geometry    : angle       0.77702 (20954)
  hydrogen bonds       : bond        0.04279 (  389)
  hydrogen bonds       : angle       6.90934 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 126
  time to evaluate  : 0.615 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  596 ARG cc_start: 0.8861 (mpt180) cc_final: 0.7923 (mtp180)
REVERT: A  639 MET cc_start: 0.8508 (ppp) cc_final: 0.8216 (ppp)
REVERT: A  796 GLN cc_start: 0.8685 (tp-100) cc_final: 0.8308 (pp30)
REVERT: A  800 ASP cc_start: 0.8335 (m-30) cc_final: 0.7901 (m-30)
REVERT: A  801 ILE cc_start: 0.7063 (tt) cc_final: 0.6722 (tt)
REVERT: B  148 MET cc_start: 0.1500 (mmt) cc_final: 0.1261 (mmt)
REVERT: B  170 PHE cc_start: 0.6061 (m-80) cc_final: 0.4382 (m-80)
REVERT: B  200 LEU cc_start: 0.8563 (mp) cc_final: 0.7942 (mp)
REVERT: B  344 TYR cc_start: 0.9278 (m-80) cc_final: 0.8891 (m-80)
REVERT: B  366 MET cc_start: 0.7642 (tpp) cc_final: 0.7218 (tpt)
REVERT: B  462 ASN cc_start: 0.9576 (p0) cc_final: 0.9304 (p0)
REVERT: B  490 LYS cc_start: 0.9003 (mptt) cc_final: 0.8792 (mptt)
REVERT: B  518 ASN cc_start: 0.8500 (t0) cc_final: 0.7859 (t0)
REVERT: B  740 TRP cc_start: 0.9368 (p-90) cc_final: 0.8653 (p-90)
REVERT: B  761 PHE cc_start: 0.8386 (t80) cc_final: 0.7828 (t80)
REVERT: B 1004 TRP cc_start: 0.7827 (m100) cc_final: 0.7472 (m100)
REVERT: B 1137 MET cc_start: 0.8365 (pmm) cc_final: 0.8116 (pmm)
REVERT: B 1198 LYS cc_start: 0.9353 (tttt) cc_final: 0.8921 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 126
  average time/residue: 0.1185
  time to fit residues: 23.0110
Evaluate side-chains
  97 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 97
  time to evaluate  : 0.596 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 157 optimal weight:    6.9990
   chunk 111 optimal weight:    1.9990
   chunk 119 optimal weight:    1.9990
   chunk 10 optimal weight:    9.9990
   chunk 52 optimal weight:    0.1980
   chunk 9 optimal weight:    8.9990
   chunk 70 optimal weight:    5.9990
   chunk 20 optimal weight:    6.9990
   chunk 101 optimal weight:    0.7980
   chunk 163 optimal weight:    5.9990
   chunk 175 optimal weight:    0.8980
   overall best weight:    1.1784

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 HIS
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 423 GLN
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 924 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.070399 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.059939 restraints weight = 107665.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.061313 restraints weight = 73970.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.062219 restraints weight = 57053.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3745 r_free = 0.3745 target = 0.062901 restraints weight = 46861.029|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.063426 restraints weight = 40348.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3748
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6942
moved from start:          0.8871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.075  15408  Z= 0.132
  Angle     :  0.633   8.451  20954  Z= 0.330
  Chirality :  0.045   0.180   2318
  Planarity :  0.005   0.047   2742
  Dihedral  :  5.621  29.472   2032
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 16.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.89 %
    Favored  : 94.11 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.30 %
    Favored  : 99.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.72 (0.18), residues: 1917
  helix: -1.39 (0.27), residues: 323
  sheet: -0.94 (0.28), residues: 334
  loop : -1.14 (0.17), residues: 1260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG B1036 
 TYR   0.019   0.002   TYR A 469 
 PHE   0.026   0.002   PHE B 761 
 TRP   0.023   0.001   TRP A 220 
 HIS   0.005   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 (15408)
  covalent geometry    : angle       0.63251 (20954)
  hydrogen bonds       : bond        0.03282 (  389)
  hydrogen bonds       : angle       6.41716 (  996)

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

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

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  3834 Ramachandran restraints generated.
    1917 Oldfield, 0 Emsley, 1917 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 130
  time to evaluate  : 0.526 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  172 ARG cc_start: 0.7433 (mtp180) cc_final: 0.6708 (mtt180)
REVERT: A  596 ARG cc_start: 0.8860 (mpt180) cc_final: 0.8025 (mtp180)
REVERT: A  639 MET cc_start: 0.8607 (ppp) cc_final: 0.8267 (ppp)
REVERT: A  796 GLN cc_start: 0.8631 (tp-100) cc_final: 0.8261 (pp30)
REVERT: A  800 ASP cc_start: 0.8552 (m-30) cc_final: 0.8195 (m-30)
REVERT: A  801 ILE cc_start: 0.7058 (tt) cc_final: 0.6775 (tp)
REVERT: B  148 MET cc_start: 0.1989 (mmt) cc_final: 0.1769 (mmt)
REVERT: B  200 LEU cc_start: 0.8559 (mp) cc_final: 0.8017 (mp)
REVERT: B  366 MET cc_start: 0.7624 (tpp) cc_final: 0.7093 (tpt)
REVERT: B  462 ASN cc_start: 0.9520 (p0) cc_final: 0.9258 (p0)
REVERT: B  490 LYS cc_start: 0.9046 (mptt) cc_final: 0.8821 (mptt)
REVERT: B  518 ASN cc_start: 0.8466 (t0) cc_final: 0.7934 (t0)
REVERT: B  740 TRP cc_start: 0.9355 (p-90) cc_final: 0.8276 (p-90)
REVERT: B  761 PHE cc_start: 0.8137 (t80) cc_final: 0.7794 (t80)
REVERT: B 1137 MET cc_start: 0.8340 (pmm) cc_final: 0.7970 (pmm)
REVERT: B 1198 LYS cc_start: 0.9358 (tttt) cc_final: 0.8954 (ttmt)
  outliers start: 0
  outliers final: 0
  residues processed: 130
  average time/residue: 0.1194
  time to fit residues: 23.6274
Evaluate side-chains
  101 residues out of total 1692 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 101
  time to evaluate  : 0.573 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 193
   random chunks:
   chunk 157 optimal weight:    4.9990
   chunk 32 optimal weight:   10.0000
   chunk 39 optimal weight:    9.9990
   chunk 12 optimal weight:    0.9990
   chunk 10 optimal weight:    6.9990
   chunk 20 optimal weight:    0.0770
   chunk 91 optimal weight:    4.9990
   chunk 79 optimal weight:    0.0030
   chunk 162 optimal weight:    0.0050
   chunk 62 optimal weight:    2.9990
   chunk 133 optimal weight:    0.8980
   overall best weight:    0.3964

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 175 HIS
** A 180 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 273 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 371 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 492 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 508 ASN
** B 360 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 590 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 620 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 773 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.072602 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.061969 restraints weight = 103382.722|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3750 r_free = 0.3750 target = 0.063318 restraints weight = 70527.454|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3774 r_free = 0.3774 target = 0.064311 restraints weight = 54556.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3793 r_free = 0.3793 target = 0.065050 restraints weight = 44491.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.065598 restraints weight = 38108.842|
|-----------------------------------------------------------------------------|
r_work (final): 0.3792
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6869
moved from start:          0.8787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15408  Z= 0.114
  Angle     :  0.600   7.585  20954  Z= 0.313
  Chirality :  0.044   0.179   2318
  Planarity :  0.004   0.048   2742
  Dihedral  :  5.235  26.696   2032
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 13.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.84 %
    Favored  : 94.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.35 %
    Favored  : 99.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.47 (0.19), residues: 1917
  helix: -0.96 (0.29), residues: 309
  sheet: -0.77 (0.29), residues: 332
  loop : -1.04 (0.17), residues: 1276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG B 488 
 TYR   0.024   0.002   TYR B 505 
 PHE   0.024   0.002   PHE B 761 
 TRP   0.043   0.001   TRP A 220 
 HIS   0.003   0.001   HIS A 371 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 (15408)
  covalent geometry    : angle       0.59990 (20954)
  hydrogen bonds       : bond        0.03273 (  389)
  hydrogen bonds       : angle       6.14328 (  996)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2296.98 seconds
wall clock time: 40 minutes 53.37 seconds (2453.37 seconds total)