Starting phenix.real_space_refine
on Thu Feb  5 11:24:17 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9h8v_51944/02_2026/9h8v_51944.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9h8v_51944/02_2026/9h8v_51944.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9h8v_51944/02_2026/9h8v_51944.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9h8v_51944/02_2026/9h8v_51944.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9h8v_51944/02_2026/9h8v_51944.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9h8v_51944/02_2026/9h8v_51944.cif"
  }
  resolution = 2.41
  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=  -0.004 sd=   0.044
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      96      5.16       5
     C   10634      2.51       5
     N    2780      2.21       5
     O    3138      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 16648
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 8324
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1039, 8324
          Classifications: {'peptide': 1039}
          Incomplete info: {'truncation_to_alanine': 9}
          Link IDs: {'PTRANS': 42, 'TRANS': 996}
          Unresolved non-hydrogen bonds: 48
          Unresolved non-hydrogen angles: 58
          Unresolved non-hydrogen dihedrals: 42
          Planarities with less than four sites: {'GLU:plan': 2, 'ARG:plan': 4, 'HIS:plan': 2}
          Unresolved non-hydrogen planarities: 38
  Restraints were copied for chains:
    B
  Time building chain proxies: 9.05, per 1000 atoms: 0.54
  Number of scatterers: 16648
  At special positions: 0
  Unit cell: (110.7, 145.96, 106.6, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      96     16.00
     O    3138      8.00
     N    2780      7.00
     C   10634      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: 1.49
  Conformation dependent library (CDL) restraints added in 719.6 milliseconds
  

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  3832

  Finding SS restraints...
    Secondary structure from input PDB file:
      84 helices and 28 sheets defined
      42.4% alpha, 17.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.85
  Creating SS restraints...
    Processing helix  chain 'A' and resid 13 through 16
    Processing helix  chain 'A' and resid 52 through 54
      No H-bonds generated for 'chain 'A' and resid 52 through 54'
    Processing helix  chain 'A' and resid 62 through 74
      removed outlier: 5.154A  pdb=" N   LYS A  71 " --> pdb=" O   TYR A  67 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   THR A  72 " --> pdb=" O   GLN A  68 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 164 through 176
      removed outlier: 7.649A  pdb=" N   GLN A 173 " --> pdb=" O   LYS A 169 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   THR A 174 " --> pdb=" O   ASN A 170 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 227 through 233
      removed outlier: 4.225A  pdb=" N   ILE A 231 " --> pdb=" O   ASP A 227 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 241 through 247
    Processing helix  chain 'A' and resid 248 through 254
      removed outlier: 3.538A  pdb=" N   LEU A 254 " --> pdb=" O   LYS A 250 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 299
      removed outlier: 3.592A  pdb=" N   LEU A 295 " --> pdb=" O   ASN A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 324
      removed outlier: 3.645A  pdb=" N   ALA A 319 " --> pdb=" O   ALA A 315 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 332 through 351
    Processing helix  chain 'A' and resid 393 through 400
    Processing helix  chain 'A' and resid 402 through 407
    Processing helix  chain 'A' and resid 408 through 411
    Processing helix  chain 'A' and resid 412 through 420
    Processing helix  chain 'A' and resid 440 through 448
    Processing helix  chain 'A' and resid 449 through 451
      No H-bonds generated for 'chain 'A' and resid 449 through 451'
    Processing helix  chain 'A' and resid 452 through 464
    Processing helix  chain 'A' and resid 468 through 481
    Processing helix  chain 'A' and resid 485 through 496
      removed outlier: 3.792A  pdb=" N   PHE A 489 " --> pdb=" O   ASP A 485 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 511 through 514
    Processing helix  chain 'A' and resid 515 through 527
      removed outlier: 3.671A  pdb=" N   LEU A 519 " --> pdb=" O   TYR A 515 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 536
    Processing helix  chain 'A' and resid 551 through 555
    Processing helix  chain 'A' and resid 571 through 574
    Processing helix  chain 'A' and resid 584 through 589
    Processing helix  chain 'A' and resid 596 through 611
    Processing helix  chain 'A' and resid 629 through 633
      removed outlier: 3.574A  pdb=" N   LEU A 632 " --> pdb=" O   TYR A 629 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 635 through 639
    Processing helix  chain 'A' and resid 643 through 663
    Processing helix  chain 'A' and resid 671 through 694
      removed outlier: 5.440A  pdb=" N   ASP A 689 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   ASN A 690 " --> pdb=" O   LEU A 686 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG A 693 " --> pdb=" O   ASP A 689 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 718
      removed outlier: 3.758A  pdb=" N   GLN A 717 " --> pdb=" O   ASP A 713 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY A 718 " --> pdb=" O   LYS A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 754
    Processing helix  chain 'A' and resid 790 through 797
    Processing helix  chain 'A' and resid 802 through 815
    Processing helix  chain 'A' and resid 836 through 845
      removed outlier: 3.727A  pdb=" N   LEU A 839 " --> pdb=" O   SER A 836 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   GLY A 840 " --> pdb=" O   PHE A 837 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ARG A 841 " --> pdb=" O   GLU A 838 " (cutoff:3.500A)
      removed outlier: 5.780A  pdb=" N   ALA A 842 " --> pdb=" O   LEU A 839 " (cutoff:3.500A)
      removed outlier: 3.515A  pdb=" N   PHE A 845 " --> pdb=" O   ALA A 842 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 857 through 870
    Processing helix  chain 'A' and resid 872 through 884
    Processing helix  chain 'A' and resid 885 through 888
    Processing helix  chain 'A' and resid 889 through 894
    Processing helix  chain 'A' and resid 925 through 940
      removed outlier: 3.999A  pdb=" N   GLU A 929 " --> pdb=" O   GLY A 925 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 960 through 964
    Processing helix  chain 'A' and resid 1019 through 1028
    Processing helix  chain 'B' and resid 13 through 16
    Processing helix  chain 'B' and resid 52 through 54
      No H-bonds generated for 'chain 'B' and resid 52 through 54'
    Processing helix  chain 'B' and resid 62 through 74
      removed outlier: 5.153A  pdb=" N   LYS B  71 " --> pdb=" O   TYR B  67 " (cutoff:3.500A)
      removed outlier: 5.576A  pdb=" N   THR B  72 " --> pdb=" O   GLN B  68 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 164 through 176
      removed outlier: 7.649A  pdb=" N   GLN B 173 " --> pdb=" O   LYS B 169 " (cutoff:3.500A)
      removed outlier: 6.890A  pdb=" N   THR B 174 " --> pdb=" O   ASN B 170 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 227 through 233
      removed outlier: 4.225A  pdb=" N   ILE B 231 " --> pdb=" O   ASP B 227 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 241 through 247
    Processing helix  chain 'B' and resid 248 through 254
      removed outlier: 3.538A  pdb=" N   LEU B 254 " --> pdb=" O   LYS B 250 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 291 through 299
      removed outlier: 3.592A  pdb=" N   LEU B 295 " --> pdb=" O   ASN B 291 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 304 through 324
      removed outlier: 3.645A  pdb=" N   ALA B 319 " --> pdb=" O   ALA B 315 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 332 through 351
    Processing helix  chain 'B' and resid 393 through 400
    Processing helix  chain 'B' and resid 402 through 407
    Processing helix  chain 'B' and resid 408 through 411
    Processing helix  chain 'B' and resid 412 through 420
    Processing helix  chain 'B' and resid 440 through 448
    Processing helix  chain 'B' and resid 449 through 451
      No H-bonds generated for 'chain 'B' and resid 449 through 451'
    Processing helix  chain 'B' and resid 452 through 464
    Processing helix  chain 'B' and resid 468 through 481
    Processing helix  chain 'B' and resid 485 through 496
      removed outlier: 3.792A  pdb=" N   PHE B 489 " --> pdb=" O   ASP B 485 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 511 through 514
    Processing helix  chain 'B' and resid 515 through 527
      removed outlier: 3.671A  pdb=" N   LEU B 519 " --> pdb=" O   TYR B 515 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 530 through 536
    Processing helix  chain 'B' and resid 551 through 555
    Processing helix  chain 'B' and resid 571 through 574
    Processing helix  chain 'B' and resid 584 through 589
    Processing helix  chain 'B' and resid 596 through 611
    Processing helix  chain 'B' and resid 629 through 633
      removed outlier: 3.574A  pdb=" N   LEU B 632 " --> pdb=" O   TYR B 629 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 635 through 639
    Processing helix  chain 'B' and resid 643 through 663
    Processing helix  chain 'B' and resid 671 through 694
      removed outlier: 5.440A  pdb=" N   ASP B 689 " --> pdb=" O   ARG B 685 " (cutoff:3.500A)
      removed outlier: 5.279A  pdb=" N   ASN B 690 " --> pdb=" O   LEU B 686 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ARG B 693 " --> pdb=" O   ASP B 689 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 697 through 718
      removed outlier: 3.758A  pdb=" N   GLN B 717 " --> pdb=" O   ASP B 713 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLY B 718 " --> pdb=" O   LYS B 714 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 728 through 754
    Processing helix  chain 'B' and resid 790 through 797
    Processing helix  chain 'B' and resid 802 through 815
    Processing helix  chain 'B' and resid 836 through 845
      removed outlier: 3.727A  pdb=" N   LEU B 839 " --> pdb=" O   SER B 836 " (cutoff:3.500A)
      removed outlier: 4.218A  pdb=" N   GLY B 840 " --> pdb=" O   PHE B 837 " (cutoff:3.500A)
      removed outlier: 6.751A  pdb=" N   ARG B 841 " --> pdb=" O   GLU B 838 " (cutoff:3.500A)
      removed outlier: 5.779A  pdb=" N   ALA B 842 " --> pdb=" O   LEU B 839 " (cutoff:3.500A)
      removed outlier: 3.517A  pdb=" N   PHE B 845 " --> pdb=" O   ALA B 842 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 857 through 870
    Processing helix  chain 'B' and resid 872 through 884
    Processing helix  chain 'B' and resid 885 through 888
    Processing helix  chain 'B' and resid 889 through 894
    Processing helix  chain 'B' and resid 925 through 940
      removed outlier: 4.014A  pdb=" N   GLU B 929 " --> pdb=" O   GLY B 925 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 960 through 964
    Processing helix  chain 'B' and resid 1019 through 1028
    Processing sheet with id=AA1, first strand: chain 'A' and resid 8 through 11
      removed outlier: 4.199A  pdb=" N   THR A  95 " --> pdb=" O   GLN A 110 " (cutoff:3.500A)
      removed outlier: 3.803A  pdb=" N   GLY A 104 " --> pdb=" O   HIS A 101 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   GLY A 131 " --> pdb=" O   GLN A 288 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   ARG A 192 " --> pdb=" O   GLN A 180 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 20 through 22
      removed outlier: 3.535A  pdb=" N   SER A  47 " --> pdb=" O   TYR A  37 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL A  39 " --> pdb=" O   VAL A  45 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   VAL A  45 " --> pdb=" O   VAL A  39 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 86
    Processing sheet with id=AA4, first strand: chain 'A' and resid 328 through 329
      removed outlier: 3.913A  pdb=" N   HIS A 999 " --> pdb=" O   ALA A1036 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 352 through 356
      removed outlier: 3.657A  pdb=" N   LYS A 360 " --> pdb=" O   LEU A 356 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 391 through 392
    Processing sheet with id=AA7, first strand: chain 'A' and resid 437 through 438
    Processing sheet with id=AA8, first strand: chain 'A' and resid 548 through 549
      removed outlier: 4.482A  pdb=" N   ASN A 548 " --> pdb=" O   ASN A 570 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 556 through 559
    Processing sheet with id=AB1, first strand: chain 'A' and resid 619 through 620
      removed outlier: 6.315A  pdb=" N   TYR A 763 " --> pdb=" O   PRO A 783 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL A 765 " --> pdb=" O   PHE A 781 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   PHE A 781 " --> pdb=" O   VAL A 765 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   GLU A 767 " --> pdb=" O   LEU A 779 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 666 through 670
    Processing sheet with id=AB3, first strand: chain 'A' and resid 819 through 820
    Processing sheet with id=AB4, first strand: chain 'A' and resid 855 through 856
    Processing sheet with id=AB5, first strand: chain 'A' and resid 944 through 947
    Processing sheet with id=AB6, first strand: chain 'B' and resid 8 through 11
      removed outlier: 4.199A  pdb=" N   THR B  95 " --> pdb=" O   GLN B 110 " (cutoff:3.500A)
      removed outlier: 3.806A  pdb=" N   GLY B 104 " --> pdb=" O   HIS B 101 " (cutoff:3.500A)
      removed outlier: 4.194A  pdb=" N   GLY B 131 " --> pdb=" O   GLN B 288 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   ARG B 192 " --> pdb=" O   GLN B 180 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 20 through 22
      removed outlier: 3.535A  pdb=" N   SER B  47 " --> pdb=" O   TYR B  37 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   VAL B  39 " --> pdb=" O   VAL B  45 " (cutoff:3.500A)
      removed outlier: 4.858A  pdb=" N   VAL B  45 " --> pdb=" O   VAL B  39 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 84 through 86
    Processing sheet with id=AB9, first strand: chain 'B' and resid 328 through 329
      removed outlier: 3.913A  pdb=" N   HIS B 999 " --> pdb=" O   ALA B1036 " (cutoff:3.500A)
    Processing sheet with id=AC1, first strand: chain 'B' and resid 352 through 356
      removed outlier: 3.657A  pdb=" N   LYS B 360 " --> pdb=" O   LEU B 356 " (cutoff:3.500A)
    Processing sheet with id=AC2, first strand: chain 'B' and resid 391 through 392
    Processing sheet with id=AC3, first strand: chain 'B' and resid 437 through 438
    Processing sheet with id=AC4, first strand: chain 'B' and resid 548 through 549
      removed outlier: 4.483A  pdb=" N   ASN B 548 " --> pdb=" O   ASN B 570 " (cutoff:3.500A)
    Processing sheet with id=AC5, first strand: chain 'B' and resid 556 through 559
    Processing sheet with id=AC6, first strand: chain 'B' and resid 619 through 620
      removed outlier: 6.315A  pdb=" N   TYR B 763 " --> pdb=" O   PRO B 783 " (cutoff:3.500A)
      removed outlier: 6.917A  pdb=" N   VAL B 765 " --> pdb=" O   PHE B 781 " (cutoff:3.500A)
      removed outlier: 7.272A  pdb=" N   PHE B 781 " --> pdb=" O   VAL B 765 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   GLU B 767 " --> pdb=" O   LEU B 779 " (cutoff:3.500A)
    Processing sheet with id=AC7, first strand: chain 'B' and resid 666 through 670
    Processing sheet with id=AC8, first strand: chain 'B' and resid 819 through 820
    Processing sheet with id=AC9, first strand: chain 'B' and resid 855 through 856
    Processing sheet with id=AD1, first strand: chain 'B' and resid 944 through 947

    794 hydrogen bonds defined for protein.
    2196 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: 3.85

  Time building geometry restraints manager: 1.99 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 5448
        1.34 -     1.46: 2787
        1.46 -     1.57: 8635
        1.57 -     1.69: 0
        1.69 -     1.81: 166
  Bond restraints: 17036
  Sorted by residual:
  bond pdb=" C   CYS A  44 "
       pdb=" O   CYS A  44 "
    ideal  model  delta    sigma   weight residual
    1.235  1.221  0.015 1.26e-02 6.30e+03 1.35e+00
  bond pdb=" C   CYS B  44 "
       pdb=" O   CYS B  44 "
    ideal  model  delta    sigma   weight residual
    1.235  1.221  0.015 1.26e-02 6.30e+03 1.35e+00
  bond pdb=" CA  GLY A 481 "
       pdb=" C   GLY A 481 "
    ideal  model  delta    sigma   weight residual
    1.514  1.530 -0.015 1.41e-02 5.03e+03 1.17e+00
  bond pdb=" CA  GLY B 481 "
       pdb=" C   GLY B 481 "
    ideal  model  delta    sigma   weight residual
    1.514  1.530 -0.015 1.41e-02 5.03e+03 1.17e+00
  bond pdb=" CB  ILE B 704 "
       pdb=" CG2 ILE B 704 "
    ideal  model  delta    sigma   weight residual
    1.521  1.488  0.033 3.30e-02 9.18e+02 9.91e-01
  ... (remaining 17031 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.46: 22699
        1.46 -     2.92: 251
        2.92 -     4.38: 56
        4.38 -     5.84: 6
        5.84 -     7.30: 2
  Bond angle restraints: 23014
  Sorted by residual:
  angle pdb=" C   GLN A  43 "
        pdb=" N   CYS A  44 "
        pdb=" CA  CYS A  44 "
      ideal   model   delta    sigma   weight residual
     121.54  128.84   -7.30 1.91e+00 2.74e-01 1.46e+01
  angle pdb=" C   GLN B  43 "
        pdb=" N   CYS B  44 "
        pdb=" CA  CYS B  44 "
      ideal   model   delta    sigma   weight residual
     121.54  128.81   -7.27 1.91e+00 2.74e-01 1.45e+01
  angle pdb=" CA  CYS B  44 "
        pdb=" C   CYS B  44 "
        pdb=" N   VAL B  45 "
      ideal   model   delta    sigma   weight residual
     116.84  120.73   -3.89 1.71e+00 3.42e-01 5.17e+00
  angle pdb=" CA  CYS A  44 "
        pdb=" C   CYS A  44 "
        pdb=" N   VAL A  45 "
      ideal   model   delta    sigma   weight residual
     116.84  120.73   -3.89 1.71e+00 3.42e-01 5.17e+00
  angle pdb=" C   GLN A 948 "
        pdb=" N   GLU A 949 "
        pdb=" CA  GLU A 949 "
      ideal   model   delta    sigma   weight residual
     121.54  125.64   -4.10 1.91e+00 2.74e-01 4.62e+00
  ... (remaining 23009 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.96: 9754
       17.96 -    35.93: 350
       35.93 -    53.89: 56
       53.89 -    71.86: 8
       71.86 -    89.82: 2
  Dihedral angle restraints: 10170
    sinusoidal: 4140
      harmonic: 6030
  Sorted by residual:
  dihedral pdb=" CA  GLN A  43 "
           pdb=" C   GLN A  43 "
           pdb=" N   CYS A  44 "
           pdb=" CA  CYS A  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.78   19.22     0      5.00e+00 4.00e-02 1.48e+01
  dihedral pdb=" CA  GLN B  43 "
           pdb=" C   GLN B  43 "
           pdb=" N   CYS B  44 "
           pdb=" CA  CYS B  44 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.81   19.19     0      5.00e+00 4.00e-02 1.47e+01
  dihedral pdb=" CA  LYS B 368 "
           pdb=" C   LYS B 368 "
           pdb=" N   HIS B 369 "
           pdb=" CA  HIS B 369 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -164.55  -15.45     0      5.00e+00 4.00e-02 9.54e+00
  ... (remaining 10167 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.028: 1429
       0.028 -    0.056: 632
       0.056 -    0.084: 207
       0.084 -    0.112: 129
       0.112 -    0.141: 27
  Chirality restraints: 2424
  Sorted by residual:
  chirality pdb=" CA  CYS A  44 "
            pdb=" N   CYS A  44 "
            pdb=" C   CYS A  44 "
            pdb=" CB  CYS A  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CA  CYS B  44 "
            pdb=" N   CYS B  44 "
            pdb=" C   CYS B  44 "
            pdb=" CB  CYS B  44 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.37    0.14 2.00e-01 2.50e+01 4.94e-01
  chirality pdb=" CA  VAL A 991 "
            pdb=" N   VAL A 991 "
            pdb=" C   VAL A 991 "
            pdb=" CB  VAL A 991 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.22e-01
  ... (remaining 2421 not shown)

  Planarity restraints: 3004
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET B 168 "   -0.009 2.00e-02 2.50e+03   1.80e-02 3.25e+00
        pdb=" C   MET B 168 "    0.031 2.00e-02 2.50e+03
        pdb=" O   MET B 168 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LYS B 169 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 168 "   -0.009 2.00e-02 2.50e+03   1.80e-02 3.25e+00
        pdb=" C   MET A 168 "    0.031 2.00e-02 2.50e+03
        pdb=" O   MET A 168 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   LYS A 169 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 125 "   -0.021 5.00e-02 4.00e+02   3.22e-02 1.66e+00
        pdb=" N   PRO A 126 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO A 126 "   -0.017 5.00e-02 4.00e+02
        pdb=" CD  PRO A 126 "   -0.018 5.00e-02 4.00e+02
  ... (remaining 3001 not shown)

  Histogram of nonbonded interaction distances:
        2.20 -     2.74: 1391
        2.74 -     3.28: 16551
        3.28 -     3.82: 29121
        3.82 -     4.36: 35782
        4.36 -     4.90: 61359
  Nonbonded interactions: 144204
  Sorted by model distance:
  nonbonded pdb=" OH  TYR B 629 "
            pdb=" O   GLU B 851 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" OH  TYR A 629 "
            pdb=" O   GLU A 851 "
     model   vdw
     2.197 3.040
  nonbonded pdb=" O   LEU B 535 "
            pdb=" OG1 THR B 596 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" O   LEU A 535 "
            pdb=" OG1 THR A 596 "
     model   vdw
     2.210 3.040
  nonbonded pdb=" OG  SER A 196 "
            pdb=" OD1 ASP A 198 "
     model   vdw
     2.223 3.040
  ... (remaining 144199 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: 0.03
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.940
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.290
  Check model and map are aligned:         0.060
  Set scattering table:                    0.050
  Process input model:                     23.230
  Find NCS groups from input model:        0.130
  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:6.620
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.370
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8661
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033  17036  Z= 0.157
  Angle     :  0.443   7.297  23014  Z= 0.238
  Chirality :  0.041   0.141   2424
  Planarity :  0.003   0.032   3004
  Dihedral  :  9.621  89.822   6338
  Min Nonbonded Distance : 2.197

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.03 %
    Favored  : 97.97 %
  Rotamer:
    Outliers :  0.57 %
    Allowed  :  3.42 %
    Favored  : 96.01 %
  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:  1.03 (0.19), residues: 2074
  helix:  1.81 (0.20), residues: 738
  sheet:  0.78 (0.30), residues: 308
  loop : -0.13 (0.19), residues: 1028

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG B 895 
 TYR   0.013   0.001   TYR B  38 
 PHE   0.012   0.001   PHE A 930 
 TRP   0.009   0.001   TRP A  35 
 HIS   0.002   0.001   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (17036)
  covalent geometry    : angle       0.44251 (23014)
  hydrogen bonds       : bond        0.16025 (  794)
  hydrogen bonds       : angle       7.16808 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  317 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 307
  time to evaluate  : 0.695 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   99 GLN cc_start: 0.8485 (mt0) cc_final: 0.8111 (mp10)
REVERT: A  108 GLU cc_start: 0.8134 (mt-10) cc_final: 0.7769 (mt-10)
REVERT: A  452 LYS cc_start: 0.9409 (ttmt) cc_final: 0.9085 (ttmm)
REVERT: A  501 ASN cc_start: 0.7451 (p0) cc_final: 0.7118 (p0)
REVERT: A  736 GLU cc_start: 0.8578 (mt-10) cc_final: 0.8325 (mt-10)
REVERT: B  433 GLU cc_start: 0.8627 (mt-10) cc_final: 0.8301 (mt-10)
REVERT: B  484 TRP cc_start: 0.7067 (p-90) cc_final: 0.6756 (p-90)
REVERT: B  817 ASP cc_start: 0.8356 (t70) cc_final: 0.7978 (t0)
REVERT: B  822 GLU cc_start: 0.8872 (mp0) cc_final: 0.8567 (mp0)
REVERT: B  966 GLU cc_start: 0.8924 (tp30) cc_final: 0.8673 (tp30)
  outliers start: 10
  outliers final: 6
  residues processed: 312
  average time/residue: 0.8160
  time to fit residues: 277.4236
Evaluate side-chains
  203 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 197
  time to evaluate  : 0.696 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  336 ASP
Chi-restraints excluded: chain A residue  611 THR
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  611 THR
Chi-restraints excluded: chain B residue 1011 THR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 98 optimal weight:    0.0070
   chunk 194 optimal weight:    5.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    6.9990
   chunk 66 optimal weight:    3.9990
   chunk 130 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 103 optimal weight:    8.9990
   chunk 200 optimal weight:    6.9990
   chunk 77 optimal weight:    5.9990
   chunk 122 optimal weight:    9.9990
   overall best weight:    4.0006

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

Flipped N/Q/H residues before XYZ refinement:
A  64 HIS
B 399 ASN
B 987 HIS
B1044 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2830 r_free = 0.2830 target = 0.060556 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2564 r_free = 0.2564 target = 0.047877 restraints weight = 39246.724|
|-----------------------------------------------------------------------------|
r_work (start): 0.2496 rms_B_bonded: 2.72
r_work: 0.2356 rms_B_bonded: 2.91 restraints_weight: 0.5000
r_work: 0.2234 rms_B_bonded: 4.69 restraints_weight: 0.2500
r_work (final): 0.2234
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9130
moved from start:          0.5051

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.069  17036  Z= 0.345
  Angle     :  0.706  10.509  23014  Z= 0.377
  Chirality :  0.049   0.198   2424
  Planarity :  0.005   0.045   3004
  Dihedral  :  4.797  44.108   2332
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.13 %
    Favored  : 96.87 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  :  8.95 %
    Favored  : 88.60 %
  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:  0.62 (0.18), residues: 2074
  helix:  1.23 (0.19), residues: 736
  sheet:  0.66 (0.31), residues: 284
  loop : -0.18 (0.19), residues: 1054

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 841 
 TYR   0.025   0.002   TYR A  38 
 PHE   0.024   0.002   PHE A 495 
 TRP   0.014   0.001   TRP B  35 
 HIS   0.007   0.001   HIS A  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00783 (17036)
  covalent geometry    : angle       0.70556 (23014)
  hydrogen bonds       : bond        0.04877 (  794)
  hydrogen bonds       : angle       5.80637 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  216 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 43
    poor density    : 173
  time to evaluate  : 0.570 
Fit side-chains
REVERT: A  145 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8299 (pp20)
REVERT: A  433 GLU cc_start: 0.9101 (mm-30) cc_final: 0.8528 (mt-10)
REVERT: A  452 LYS cc_start: 0.9432 (ttmt) cc_final: 0.9157 (ttmm)
REVERT: A  459 LEU cc_start: 0.9128 (mt) cc_final: 0.8882 (mp)
REVERT: A  501 ASN cc_start: 0.8432 (p0) cc_final: 0.7608 (p0)
REVERT: A  533 GLU cc_start: 0.9131 (tp30) cc_final: 0.8884 (mp0)
REVERT: A  635 MET cc_start: 0.9429 (mtp) cc_final: 0.9204 (ttp)
REVERT: A  662 GLN cc_start: 0.9368 (tt0) cc_final: 0.9001 (tt0)
REVERT: A  719 VAL cc_start: 0.9469 (m) cc_final: 0.9255 (p)
REVERT: A  802 GLU cc_start: 0.8765 (OUTLIER) cc_final: 0.8459 (tm-30)
REVERT: A  966 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8579 (tp30)
REVERT: B  433 GLU cc_start: 0.9270 (mt-10) cc_final: 0.8439 (mt-10)
REVERT: B  484 TRP cc_start: 0.7201 (p-90) cc_final: 0.6608 (p-90)
REVERT: B  501 ASN cc_start: 0.7953 (p0) cc_final: 0.6839 (p0)
REVERT: B  645 GLU cc_start: 0.9344 (mp0) cc_final: 0.9037 (mp0)
REVERT: B  822 GLU cc_start: 0.9246 (mp0) cc_final: 0.8882 (mp0)
REVERT: B  948 GLN cc_start: 0.8524 (tm-30) cc_final: 0.8080 (tm-30)
REVERT: B  966 GLU cc_start: 0.9292 (tp30) cc_final: 0.8935 (tp30)
  outliers start: 43
  outliers final: 7
  residues processed: 201
  average time/residue: 0.8246
  time to fit residues: 180.9674
Evaluate side-chains
  157 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 148
  time to evaluate  : 0.691 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  145 GLU
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  597 LEU
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  430 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 88 optimal weight:    0.7980
   chunk 160 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 110 optimal weight:    3.9990
   chunk 69 optimal weight:    6.9990
   chunk 105 optimal weight:    0.5980
   chunk 140 optimal weight:    0.9980
   chunk 42 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 104 optimal weight:    0.7980
   chunk 157 optimal weight:    2.9990
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2868 r_free = 0.2868 target = 0.062527 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2600 r_free = 0.2600 target = 0.049682 restraints weight = 38735.016|
|-----------------------------------------------------------------------------|
r_work (start): 0.2577 rms_B_bonded: 2.75
r_work: 0.2445 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2328 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9121
moved from start:          0.5063

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  17036  Z= 0.112
  Angle     :  0.515  12.570  23014  Z= 0.272
  Chirality :  0.042   0.139   2424
  Planarity :  0.003   0.032   3004
  Dihedral  :  4.199  23.736   2325
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 4.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  : 10.15 %
    Favored  : 88.03 %
  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:  0.69 (0.19), residues: 2074
  helix:  1.40 (0.19), residues: 752
  sheet:  0.63 (0.30), residues: 302
  loop : -0.24 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 327 
 TYR   0.018   0.001   TYR B  38 
 PHE   0.011   0.001   PHE A 527 
 TRP   0.010   0.001   TRP B  35 
 HIS   0.002   0.000   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (17036)
  covalent geometry    : angle       0.51546 (23014)
  hydrogen bonds       : bond        0.03736 (  794)
  hydrogen bonds       : angle       5.40918 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  190 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 158
  time to evaluate  : 0.687 
Fit side-chains
REVERT: A  258 MET cc_start: 0.8636 (ttm) cc_final: 0.8057 (tpt)
REVERT: A  433 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8646 (mt-10)
REVERT: A  452 LYS cc_start: 0.9397 (ttmt) cc_final: 0.9121 (ttmm)
REVERT: A  501 ASN cc_start: 0.8131 (p0) cc_final: 0.7354 (p0)
REVERT: A  662 GLN cc_start: 0.9349 (tt0) cc_final: 0.9081 (tt0)
REVERT: A  682 LEU cc_start: 0.9556 (tp) cc_final: 0.9322 (mt)
REVERT: A  802 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.8364 (tm-30)
REVERT: A  966 GLU cc_start: 0.9007 (mm-30) cc_final: 0.8490 (tp30)
REVERT: B  171 MET cc_start: 0.9016 (ptm) cc_final: 0.8769 (ptm)
REVERT: B  341 TYR cc_start: 0.8979 (OUTLIER) cc_final: 0.8634 (t80)
REVERT: B  433 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8654 (mt-10)
REVERT: B  484 TRP cc_start: 0.7172 (p-90) cc_final: 0.6586 (p-90)
REVERT: B  501 ASN cc_start: 0.7671 (p0) cc_final: 0.6867 (p0)
REVERT: B  692 MET cc_start: 0.8877 (OUTLIER) cc_final: 0.8664 (mmp)
REVERT: B  822 GLU cc_start: 0.9259 (mp0) cc_final: 0.8917 (mp0)
REVERT: B  949 GLU cc_start: 0.8756 (pp20) cc_final: 0.8458 (pp20)
REVERT: B  966 GLU cc_start: 0.9229 (tp30) cc_final: 0.8856 (tp30)
  outliers start: 32
  outliers final: 8
  residues processed: 177
  average time/residue: 0.8108
  time to fit residues: 157.0708
Evaluate side-chains
  151 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 140
  time to evaluate  : 0.644 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  739 LEU
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  692 MET
Chi-restraints excluded: chain B residue  762 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 52 optimal weight:    2.9990
   chunk 163 optimal weight:    4.9990
   chunk 90 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 95 optimal weight:    0.0170
   chunk 0 optimal weight:    8.9990
   chunk 149 optimal weight:    2.9990
   chunk 143 optimal weight:    3.9990
   chunk 115 optimal weight:    4.9990
   chunk 1 optimal weight:    4.9990
   overall best weight:    1.8024

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

Flipped N/Q/H residues before XYZ refinement:
B 688 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2832 r_free = 0.2832 target = 0.060812 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2558 r_free = 0.2558 target = 0.047938 restraints weight = 38933.238|
|-----------------------------------------------------------------------------|
r_work (start): 0.2566 rms_B_bonded: 2.78
r_work: 0.2435 rms_B_bonded: 2.92 restraints_weight: 0.5000
r_work: 0.2319 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.2319
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9144
moved from start:          0.5304

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037  17036  Z= 0.170
  Angle     :  0.527  11.811  23014  Z= 0.278
  Chirality :  0.042   0.157   2424
  Planarity :  0.004   0.047   3004
  Dihedral  :  4.159  25.480   2325
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 4.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.80 %
    Favored  : 97.20 %
  Rotamer:
    Outliers :  1.82 %
    Allowed  :  9.92 %
    Favored  : 88.26 %
  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:  0.77 (0.19), residues: 2074
  helix:  1.52 (0.20), residues: 752
  sheet:  0.58 (0.29), residues: 302
  loop : -0.21 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG B 112 
 TYR   0.017   0.001   TYR A  38 
 PHE   0.015   0.001   PHE A 930 
 TRP   0.008   0.001   TRP B  35 
 HIS   0.003   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00384 (17036)
  covalent geometry    : angle       0.52680 (23014)
  hydrogen bonds       : bond        0.03777 (  794)
  hydrogen bonds       : angle       5.25167 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  179 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 147
  time to evaluate  : 0.651 
Fit side-chains
   revert: symmetry clash
REVERT: A  417 GLU cc_start: 0.9363 (OUTLIER) cc_final: 0.9075 (tp30)
REVERT: A  433 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8787 (mt-10)
REVERT: A  452 LYS cc_start: 0.9340 (ttmt) cc_final: 0.9067 (ttmm)
REVERT: A  501 ASN cc_start: 0.8284 (p0) cc_final: 0.7725 (p0)
REVERT: A  662 GLN cc_start: 0.9317 (tt0) cc_final: 0.9056 (tt0)
REVERT: A  682 LEU cc_start: 0.9572 (tp) cc_final: 0.9341 (mt)
REVERT: A  802 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8378 (tm-30)
REVERT: A  948 GLN cc_start: 0.9240 (mm-40) cc_final: 0.8925 (mp10)
REVERT: A  966 GLU cc_start: 0.9070 (mm-30) cc_final: 0.8618 (tp30)
REVERT: B  108 GLU cc_start: 0.9147 (mt-10) cc_final: 0.8915 (mt-10)
REVERT: B  171 MET cc_start: 0.9018 (ptm) cc_final: 0.8764 (ptm)
REVERT: B  341 TYR cc_start: 0.9043 (OUTLIER) cc_final: 0.8688 (t80)
REVERT: B  417 GLU cc_start: 0.9308 (OUTLIER) cc_final: 0.9015 (tp30)
REVERT: B  433 GLU cc_start: 0.9294 (mt-10) cc_final: 0.8615 (mt-10)
REVERT: B  484 TRP cc_start: 0.7213 (p-90) cc_final: 0.6576 (p-90)
REVERT: B  501 ASN cc_start: 0.8021 (p0) cc_final: 0.7471 (p0)
REVERT: B  645 GLU cc_start: 0.9297 (mp0) cc_final: 0.9065 (mp0)
REVERT: B  736 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8788 (mt-10)
REVERT: B  822 GLU cc_start: 0.9206 (mp0) cc_final: 0.8844 (mp0)
REVERT: B  966 GLU cc_start: 0.9212 (tp30) cc_final: 0.8851 (tp30)
  outliers start: 32
  outliers final: 10
  residues processed: 166
  average time/residue: 0.8616
  time to fit residues: 155.9793
Evaluate side-chains
  146 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 132
  time to evaluate  : 0.710 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  722 LYS
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  762 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 115 optimal weight:    0.0170
   chunk 172 optimal weight:    5.9990
   chunk 24 optimal weight:    4.9990
   chunk 12 optimal weight:    0.8980
   chunk 58 optimal weight:    3.9990
   chunk 53 optimal weight:    6.9990
   chunk 30 optimal weight:    0.9980
   chunk 168 optimal weight:    4.9990
   chunk 9 optimal weight:    8.9990
   chunk 89 optimal weight:    5.9990
   chunk 183 optimal weight:    6.9990
   overall best weight:    2.1822

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2825 r_free = 0.2825 target = 0.060714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2562 r_free = 0.2562 target = 0.048023 restraints weight = 39078.966|
|-----------------------------------------------------------------------------|
r_work (start): 0.2552 rms_B_bonded: 2.70
r_work: 0.2423 rms_B_bonded: 2.85 restraints_weight: 0.5000
r_work: 0.2306 rms_B_bonded: 4.61 restraints_weight: 0.2500
r_work (final): 0.2306
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9186
moved from start:          0.5456

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034  17036  Z= 0.191
  Angle     :  0.540  12.554  23014  Z= 0.283
  Chirality :  0.043   0.162   2424
  Planarity :  0.003   0.041   3004
  Dihedral  :  4.168  26.530   2325
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 10.43 %
    Favored  : 87.97 %
  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:  0.74 (0.18), residues: 2074
  helix:  1.52 (0.20), residues: 752
  sheet:  0.48 (0.29), residues: 302
  loop : -0.22 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 327 
 TYR   0.017   0.001   TYR A  38 
 PHE   0.016   0.001   PHE A 930 
 TRP   0.009   0.001   TRP B  35 
 HIS   0.003   0.001   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00434 (17036)
  covalent geometry    : angle       0.53976 (23014)
  hydrogen bonds       : bond        0.03790 (  794)
  hydrogen bonds       : angle       5.23709 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  170 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 142
  time to evaluate  : 0.731 
Fit side-chains
REVERT: A  341 TYR cc_start: 0.9136 (OUTLIER) cc_final: 0.8453 (t80)
REVERT: A  417 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.9012 (tp30)
REVERT: A  433 GLU cc_start: 0.9177 (mm-30) cc_final: 0.8896 (mt-10)
REVERT: A  452 LYS cc_start: 0.9303 (ttmt) cc_final: 0.9017 (ttmm)
REVERT: A  501 ASN cc_start: 0.8329 (p0) cc_final: 0.7884 (p0)
REVERT: A  662 GLN cc_start: 0.9330 (tt0) cc_final: 0.9116 (tt0)
REVERT: A  682 LEU cc_start: 0.9585 (tp) cc_final: 0.9355 (mt)
REVERT: A  802 GLU cc_start: 0.8738 (OUTLIER) cc_final: 0.8398 (tm-30)
REVERT: A  966 GLU cc_start: 0.9113 (mm-30) cc_final: 0.8713 (tp30)
REVERT: B  108 GLU cc_start: 0.9211 (mt-10) cc_final: 0.8984 (mt-10)
REVERT: B  112 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.8468 (mpp-170)
REVERT: B  341 TYR cc_start: 0.9067 (OUTLIER) cc_final: 0.8723 (t80)
REVERT: B  417 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.9004 (tp30)
REVERT: B  433 GLU cc_start: 0.9272 (mt-10) cc_final: 0.8558 (mt-10)
REVERT: B  451 VAL cc_start: 0.9374 (OUTLIER) cc_final: 0.9060 (p)
REVERT: B  484 TRP cc_start: 0.7306 (p-90) cc_final: 0.6686 (p-90)
REVERT: B  501 ASN cc_start: 0.7951 (p0) cc_final: 0.7339 (p0)
REVERT: B  685 ARG cc_start: 0.9006 (ttp80) cc_final: 0.8795 (mtm110)
REVERT: B  822 GLU cc_start: 0.9164 (mp0) cc_final: 0.8799 (mp0)
REVERT: B  966 GLU cc_start: 0.9206 (tp30) cc_final: 0.8837 (tp30)
  outliers start: 28
  outliers final: 11
  residues processed: 158
  average time/residue: 0.8421
  time to fit residues: 145.2141
Evaluate side-chains
  157 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 139
  time to evaluate  : 0.689 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  197 MET
Chi-restraints excluded: chain A residue  341 TYR
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  479 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  112 ARG
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  479 VAL
Chi-restraints excluded: chain B residue  762 THR
Chi-restraints excluded: chain B residue  872 LEU
Chi-restraints excluded: chain B residue 1009 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 117 optimal weight:    2.9990
   chunk 41 optimal weight:    2.9990
   chunk 128 optimal weight:    0.9990
   chunk 9 optimal weight:    3.9990
   chunk 13 optimal weight:    6.9990
   chunk 124 optimal weight:    3.9990
   chunk 15 optimal weight:    0.7980
   chunk 88 optimal weight:    2.9990
   chunk 147 optimal weight:    6.9990
   chunk 29 optimal weight:    0.6980
   chunk 55 optimal weight:    0.8980
   overall best weight:    1.2784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2848 r_free = 0.2848 target = 0.061422 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2587 r_free = 0.2587 target = 0.048849 restraints weight = 38749.793|
|-----------------------------------------------------------------------------|
r_work (start): 0.2596 rms_B_bonded: 2.72
r_work: 0.2469 rms_B_bonded: 2.86 restraints_weight: 0.5000
r_work: 0.2354 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.2354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9167
moved from start:          0.5545

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  17036  Z= 0.132
  Angle     :  0.508  13.479  23014  Z= 0.266
  Chirality :  0.041   0.150   2424
  Planarity :  0.003   0.041   3004
  Dihedral  :  4.065  25.775   2325
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 4.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.23 %
    Favored  : 87.29 %
  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:  0.73 (0.19), residues: 2074
  helix:  1.53 (0.19), residues: 764
  sheet:  0.43 (0.29), residues: 302
  loop : -0.25 (0.19), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 327 
 TYR   0.015   0.001   TYR A  38 
 PHE   0.013   0.001   PHE A 930 
 TRP   0.008   0.001   TRP B  35 
 HIS   0.002   0.001   HIS B 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 (17036)
  covalent geometry    : angle       0.50779 (23014)
  hydrogen bonds       : bond        0.03487 (  794)
  hydrogen bonds       : angle       5.15562 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  173 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 147
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
REVERT: A  341 TYR cc_start: 0.9119 (OUTLIER) cc_final: 0.8641 (t80)
REVERT: A  417 GLU cc_start: 0.9319 (OUTLIER) cc_final: 0.8994 (tp30)
REVERT: A  433 GLU cc_start: 0.9156 (mm-30) cc_final: 0.8938 (mt-10)
REVERT: A  452 LYS cc_start: 0.9280 (ttmt) cc_final: 0.8989 (ttmm)
REVERT: A  501 ASN cc_start: 0.8255 (p0) cc_final: 0.7858 (p0)
REVERT: A  662 GLN cc_start: 0.9350 (tt0) cc_final: 0.9094 (tt0)
REVERT: A  682 LEU cc_start: 0.9592 (tp) cc_final: 0.9366 (mt)
REVERT: A  802 GLU cc_start: 0.8696 (OUTLIER) cc_final: 0.8336 (tm-30)
REVERT: A  948 GLN cc_start: 0.9213 (mm-40) cc_final: 0.9008 (mp10)
REVERT: A  966 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8708 (tp30)
REVERT: B  108 GLU cc_start: 0.9203 (mt-10) cc_final: 0.8979 (mt-10)
REVERT: B  112 ARG cc_start: 0.8697 (OUTLIER) cc_final: 0.8277 (mpp-170)
REVERT: B  258 MET cc_start: 0.8273 (tpt) cc_final: 0.7579 (mtt)
REVERT: B  341 TYR cc_start: 0.9022 (OUTLIER) cc_final: 0.8545 (t80)
REVERT: B  417 GLU cc_start: 0.9269 (OUTLIER) cc_final: 0.8955 (tp30)
REVERT: B  433 GLU cc_start: 0.9268 (mt-10) cc_final: 0.8559 (mt-10)
REVERT: B  451 VAL cc_start: 0.9363 (OUTLIER) cc_final: 0.9053 (p)
REVERT: B  484 TRP cc_start: 0.7316 (p-90) cc_final: 0.6682 (p-90)
REVERT: B  501 ASN cc_start: 0.8027 (p0) cc_final: 0.7582 (p0)
REVERT: B  685 ARG cc_start: 0.9037 (ttp80) cc_final: 0.8751 (mtm110)
REVERT: B  822 GLU cc_start: 0.9149 (mp0) cc_final: 0.8798 (mp0)
REVERT: B  948 GLN cc_start: 0.9237 (mm110) cc_final: 0.8793 (tm-30)
REVERT: B  949 GLU cc_start: 0.8942 (pp20) cc_final: 0.8559 (pp20)
REVERT: B  966 GLU cc_start: 0.9191 (tp30) cc_final: 0.8785 (tp30)
  outliers start: 26
  outliers final: 12
  residues processed: 164
  average time/residue: 0.8486
  time to fit residues: 151.9449
Evaluate side-chains
  151 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 132
  time to evaluate  : 0.671 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  341 TYR
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  522 ASP
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  112 ARG
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  197 MET
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  692 MET
Chi-restraints excluded: chain B residue  762 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 169 optimal weight:    7.9990
   chunk 27 optimal weight:    7.9990
   chunk 13 optimal weight:    0.9990
   chunk 108 optimal weight:    2.9990
   chunk 25 optimal weight:    6.9990
   chunk 109 optimal weight:    0.7980
   chunk 85 optimal weight:    4.9990
   chunk 41 optimal weight:    3.9990
   chunk 102 optimal weight:    2.9990
   chunk 155 optimal weight:    6.9990
   chunk 48 optimal weight:    4.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
B  64 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2812 r_free = 0.2812 target = 0.059872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2536 r_free = 0.2536 target = 0.047082 restraints weight = 38921.316|
|-----------------------------------------------------------------------------|
r_work (start): 0.2577 rms_B_bonded: 2.75
r_work: 0.2447 rms_B_bonded: 2.89 restraints_weight: 0.5000
r_work: 0.2331 rms_B_bonded: 4.67 restraints_weight: 0.2500
r_work (final): 0.2331
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9188
moved from start:          0.5627

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.041  17036  Z= 0.205
  Angle     :  0.553  14.544  23014  Z= 0.286
  Chirality :  0.043   0.149   2424
  Planarity :  0.003   0.052   3004
  Dihedral  :  4.140  27.293   2325
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 5.03
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.31 %
    Allowed  : 11.63 %
    Favored  : 87.06 %
  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:  0.76 (0.19), residues: 2074
  helix:  1.55 (0.20), residues: 752
  sheet:  0.43 (0.29), residues: 302
  loop : -0.20 (0.19), residues: 1020

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 327 
 TYR   0.016   0.001   TYR A  38 
 PHE   0.017   0.001   PHE A 930 
 TRP   0.008   0.001   TRP B  35 
 HIS   0.003   0.001   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00469 (17036)
  covalent geometry    : angle       0.55275 (23014)
  hydrogen bonds       : bond        0.03755 (  794)
  hydrogen bonds       : angle       5.17822 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 137
  time to evaluate  : 0.680 
Fit side-chains
REVERT: A  341 TYR cc_start: 0.9132 (OUTLIER) cc_final: 0.8467 (t80)
REVERT: A  417 GLU cc_start: 0.9340 (OUTLIER) cc_final: 0.9027 (tp30)
REVERT: A  433 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8918 (mt-10)
REVERT: A  452 LYS cc_start: 0.9283 (ttmt) cc_final: 0.8983 (ttmm)
REVERT: A  501 ASN cc_start: 0.8304 (p0) cc_final: 0.7873 (p0)
REVERT: A  682 LEU cc_start: 0.9602 (tp) cc_final: 0.9379 (mt)
REVERT: A  722 LYS cc_start: 0.9130 (ptmm) cc_final: 0.8928 (ptmm)
REVERT: A  802 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8351 (tm-30)
REVERT: A  948 GLN cc_start: 0.9223 (mm-40) cc_final: 0.9005 (mp10)
REVERT: A  966 GLU cc_start: 0.9090 (mm-30) cc_final: 0.8696 (tp30)
REVERT: B  108 GLU cc_start: 0.9193 (mt-10) cc_final: 0.8972 (mt-10)
REVERT: B  112 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.8325 (mpp-170)
REVERT: B  341 TYR cc_start: 0.9082 (OUTLIER) cc_final: 0.8404 (t80)
REVERT: B  417 GLU cc_start: 0.9295 (OUTLIER) cc_final: 0.9015 (tp30)
REVERT: B  433 GLU cc_start: 0.9285 (mt-10) cc_final: 0.8557 (mt-10)
REVERT: B  451 VAL cc_start: 0.9356 (OUTLIER) cc_final: 0.9026 (p)
REVERT: B  484 TRP cc_start: 0.7373 (p-90) cc_final: 0.6736 (p-90)
REVERT: B  501 ASN cc_start: 0.8085 (p0) cc_final: 0.7564 (p0)
REVERT: B  685 ARG cc_start: 0.9039 (ttp80) cc_final: 0.8836 (mtm110)
REVERT: B  822 GLU cc_start: 0.9148 (mp0) cc_final: 0.8781 (mp0)
REVERT: B  948 GLN cc_start: 0.9283 (mm110) cc_final: 0.8798 (tm-30)
REVERT: B  949 GLU cc_start: 0.8944 (pp20) cc_final: 0.8552 (pp20)
REVERT: B  966 GLU cc_start: 0.9187 (tp30) cc_final: 0.8781 (tp30)
  outliers start: 23
  outliers final: 12
  residues processed: 153
  average time/residue: 0.8335
  time to fit residues: 139.2383
Evaluate side-chains
  154 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 135
  time to evaluate  : 0.595 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  341 TYR
Chi-restraints excluded: chain A residue  417 GLU
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  112 ARG
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  522 ASP
Chi-restraints excluded: chain B residue  692 MET
Chi-restraints excluded: chain B residue  762 THR
Chi-restraints excluded: chain B residue  872 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 148 optimal weight:    6.9990
   chunk 166 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 193 optimal weight:    0.1980
   chunk 15 optimal weight:    1.9990
   chunk 98 optimal weight:    0.0030
   chunk 162 optimal weight:    2.9990
   chunk 118 optimal weight:    3.9990
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    8.9990
   chunk 34 optimal weight:    4.9990
   overall best weight:    1.1994

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2795 r_free = 0.2795 target = 0.060691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2483 r_free = 0.2483 target = 0.047038 restraints weight = 36850.357|
|-----------------------------------------------------------------------------|
r_work (start): 0.2510 rms_B_bonded: 2.84
r_work: 0.2360 rms_B_bonded: 2.98 restraints_weight: 0.5000
r_work: 0.2229 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2229
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9109
moved from start:          0.5694

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  17036  Z= 0.128
  Angle     :  0.513  14.804  23014  Z= 0.267
  Chirality :  0.041   0.149   2424
  Planarity :  0.003   0.049   3004
  Dihedral  :  4.036  26.003   2325
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 4.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.97 %
    Favored  : 86.55 %
  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:  0.76 (0.19), residues: 2074
  helix:  1.57 (0.19), residues: 758
  sheet:  0.39 (0.29), residues: 302
  loop : -0.21 (0.19), residues: 1014

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 327 
 TYR   0.015   0.001   TYR B  38 
 PHE   0.012   0.001   PHE B 527 
 TRP   0.007   0.001   TRP A  35 
 HIS   0.002   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 (17036)
  covalent geometry    : angle       0.51306 (23014)
  hydrogen bonds       : bond        0.03412 (  794)
  hydrogen bonds       : angle       5.10521 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  167 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 141
  time to evaluate  : 0.701 
Fit side-chains
REVERT: A  301 GLU cc_start: 0.8084 (pm20) cc_final: 0.7803 (pm20)
REVERT: A  341 TYR cc_start: 0.9091 (OUTLIER) cc_final: 0.8578 (t80)
REVERT: A  433 GLU cc_start: 0.9186 (mm-30) cc_final: 0.8906 (mt-10)
REVERT: A  452 LYS cc_start: 0.9288 (ttmt) cc_final: 0.8992 (ttmm)
REVERT: A  501 ASN cc_start: 0.8228 (p0) cc_final: 0.7682 (p0)
REVERT: A  682 LEU cc_start: 0.9576 (tp) cc_final: 0.9358 (mt)
REVERT: A  722 LYS cc_start: 0.9217 (ptmm) cc_final: 0.8995 (ptmm)
REVERT: A  802 GLU cc_start: 0.8714 (OUTLIER) cc_final: 0.8363 (tm-30)
REVERT: A  948 GLN cc_start: 0.9304 (mm-40) cc_final: 0.9065 (mp10)
REVERT: A  966 GLU cc_start: 0.9119 (mm-30) cc_final: 0.8705 (tp30)
REVERT: B  108 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8955 (mt-10)
REVERT: B  112 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.8279 (mpp-170)
REVERT: B  258 MET cc_start: 0.8227 (tpt) cc_final: 0.7531 (mtp)
REVERT: B  341 TYR cc_start: 0.9009 (OUTLIER) cc_final: 0.8600 (t80)
REVERT: B  417 GLU cc_start: 0.9264 (OUTLIER) cc_final: 0.8943 (tp30)
REVERT: B  433 GLU cc_start: 0.9312 (mt-10) cc_final: 0.8553 (mt-10)
REVERT: B  451 VAL cc_start: 0.9297 (OUTLIER) cc_final: 0.8951 (p)
REVERT: B  484 TRP cc_start: 0.7223 (p-90) cc_final: 0.6556 (p-90)
REVERT: B  501 ASN cc_start: 0.8024 (p0) cc_final: 0.7539 (p0)
REVERT: B  685 ARG cc_start: 0.9046 (ttp80) cc_final: 0.8829 (mtm110)
REVERT: B  822 GLU cc_start: 0.9175 (mp0) cc_final: 0.8791 (mp0)
REVERT: B  966 GLU cc_start: 0.9185 (tp30) cc_final: 0.8754 (tp30)
  outliers start: 26
  outliers final: 10
  residues processed: 159
  average time/residue: 0.7759
  time to fit residues: 134.8707
Evaluate side-chains
  149 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 133
  time to evaluate  : 0.530 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  341 TYR
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain A residue  857 LEU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  112 ARG
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  430 LEU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  692 MET
Chi-restraints excluded: chain B residue  762 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 63 optimal weight:    2.9990
   chunk 91 optimal weight:    6.9990
   chunk 79 optimal weight:    0.7980
   chunk 65 optimal weight:    4.9990
   chunk 8 optimal weight:    0.1980
   chunk 93 optimal weight:    3.9990
   chunk 187 optimal weight:    6.9990
   chunk 53 optimal weight:    6.9990
   chunk 175 optimal weight:    0.8980
   chunk 120 optimal weight:    0.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    1.1784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2786 r_free = 0.2786 target = 0.060477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2475 r_free = 0.2475 target = 0.046893 restraints weight = 37048.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.2515 rms_B_bonded: 2.84
r_work: 0.2364 rms_B_bonded: 2.99 restraints_weight: 0.5000
r_work: 0.2232 rms_B_bonded: 4.83 restraints_weight: 0.2500
r_work (final): 0.2232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9104
moved from start:          0.5730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.046  17036  Z= 0.129
  Angle     :  0.530  14.970  23014  Z= 0.273
  Chirality :  0.041   0.161   2424
  Planarity :  0.003   0.058   3004
  Dihedral  :  4.003  26.102   2325
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 4.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  1.14 %
    Allowed  : 12.14 %
    Favored  : 86.72 %
  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:  0.83 (0.19), residues: 2074
  helix:  1.58 (0.19), residues: 758
  sheet:  0.53 (0.29), residues: 314
  loop : -0.18 (0.20), residues: 1002

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 327 
 TYR   0.015   0.001   TYR A  38 
 PHE   0.012   0.001   PHE A 930 
 TRP   0.007   0.001   TRP B  35 
 HIS   0.002   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00294 (17036)
  covalent geometry    : angle       0.53004 (23014)
  hydrogen bonds       : bond        0.03393 (  794)
  hydrogen bonds       : angle       5.06717 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 140
  time to evaluate  : 0.723 
Fit side-chains
   revert: symmetry clash
REVERT: A  301 GLU cc_start: 0.8099 (pm20) cc_final: 0.7824 (pm20)
REVERT: A  433 GLU cc_start: 0.9172 (mm-30) cc_final: 0.8896 (mt-10)
REVERT: A  451 VAL cc_start: 0.9473 (OUTLIER) cc_final: 0.9264 (p)
REVERT: A  452 LYS cc_start: 0.9280 (ttmt) cc_final: 0.8975 (ttmm)
REVERT: A  501 ASN cc_start: 0.8156 (p0) cc_final: 0.7618 (p0)
REVERT: A  682 LEU cc_start: 0.9593 (tp) cc_final: 0.9381 (mt)
REVERT: A  722 LYS cc_start: 0.9229 (ptmm) cc_final: 0.9028 (ptmm)
REVERT: A  802 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8350 (tm-30)
REVERT: A  966 GLU cc_start: 0.9131 (mm-30) cc_final: 0.8722 (tp30)
REVERT: B  108 GLU cc_start: 0.9176 (mt-10) cc_final: 0.8958 (mt-10)
REVERT: B  112 ARG cc_start: 0.8715 (OUTLIER) cc_final: 0.8288 (mpp-170)
REVERT: B  341 TYR cc_start: 0.9002 (OUTLIER) cc_final: 0.8503 (t80)
REVERT: B  417 GLU cc_start: 0.9270 (OUTLIER) cc_final: 0.8945 (tp30)
REVERT: B  433 GLU cc_start: 0.9323 (mt-10) cc_final: 0.8576 (mt-10)
REVERT: B  451 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8928 (p)
REVERT: B  484 TRP cc_start: 0.7243 (p-90) cc_final: 0.6580 (p-90)
REVERT: B  501 ASN cc_start: 0.7973 (p0) cc_final: 0.7499 (p0)
REVERT: B  685 ARG cc_start: 0.9050 (ttp80) cc_final: 0.8833 (mtm110)
REVERT: B  822 GLU cc_start: 0.9155 (mp0) cc_final: 0.8776 (mp0)
REVERT: B  966 GLU cc_start: 0.9214 (tp30) cc_final: 0.8792 (tp30)
  outliers start: 20
  outliers final: 8
  residues processed: 153
  average time/residue: 0.8465
  time to fit residues: 141.1691
Evaluate side-chains
  149 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 135
  time to evaluate  : 0.625 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  112 ARG
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  692 MET
Chi-restraints excluded: chain B residue  762 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 151 optimal weight:    5.9990
   chunk 142 optimal weight:    0.6980
   chunk 189 optimal weight:    0.9990
   chunk 167 optimal weight:    3.9990
   chunk 106 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 202 optimal weight:    7.9990
   chunk 159 optimal weight:    4.9990
   chunk 85 optimal weight:    4.9990
   chunk 119 optimal weight:    4.9990
   chunk 5 optimal weight:    0.6980
   overall best weight:    2.0786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2762 r_free = 0.2762 target = 0.059348 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.2446 r_free = 0.2446 target = 0.045737 restraints weight = 37266.202|
|-----------------------------------------------------------------------------|
r_work (start): 0.2486 rms_B_bonded: 2.81
r_work: 0.2335 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2203 rms_B_bonded: 4.77 restraints_weight: 0.2500
r_work (final): 0.2203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9121
moved from start:          0.5747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045  17036  Z= 0.185
  Angle     :  0.561  14.914  23014  Z= 0.289
  Chirality :  0.042   0.158   2424
  Planarity :  0.003   0.064   3004
  Dihedral  :  4.093  27.358   2325
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.46 %
    Favored  : 97.54 %
  Rotamer:
    Outliers :  0.97 %
    Allowed  : 12.20 %
    Favored  : 86.83 %
  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:  0.80 (0.19), residues: 2074
  helix:  1.55 (0.20), residues: 752
  sheet:  0.52 (0.29), residues: 314
  loop : -0.19 (0.20), residues: 1008

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 327 
 TYR   0.016   0.001   TYR B  38 
 PHE   0.015   0.001   PHE A 930 
 TRP   0.007   0.001   TRP A  35 
 HIS   0.002   0.001   HIS A 369 

Details of bonding type rmsd
  covalent geometry    : bond        0.00423 (17036)
  covalent geometry    : angle       0.56066 (23014)
  hydrogen bonds       : bond        0.03641 (  794)
  hydrogen bonds       : angle       5.12340 ( 2196)

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

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

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  4148 Ramachandran restraints generated.
    2074 Oldfield, 0 Emsley, 2074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 136
  time to evaluate  : 0.608 
Fit side-chains
REVERT: A  145 GLU cc_start: 0.8900 (pm20) cc_final: 0.8563 (pp20)
REVERT: A  301 GLU cc_start: 0.8089 (pm20) cc_final: 0.7818 (pm20)
REVERT: A  433 GLU cc_start: 0.9198 (mm-30) cc_final: 0.8876 (mt-10)
REVERT: A  451 VAL cc_start: 0.9465 (OUTLIER) cc_final: 0.9230 (p)
REVERT: A  452 LYS cc_start: 0.9268 (ttmt) cc_final: 0.8949 (ttmm)
REVERT: A  501 ASN cc_start: 0.8258 (p0) cc_final: 0.7675 (p0)
REVERT: A  682 LEU cc_start: 0.9578 (tp) cc_final: 0.9359 (mt)
REVERT: A  722 LYS cc_start: 0.9222 (ptmm) cc_final: 0.9021 (ptmm)
REVERT: A  802 GLU cc_start: 0.8709 (OUTLIER) cc_final: 0.8354 (tm-30)
REVERT: A  966 GLU cc_start: 0.9151 (mm-30) cc_final: 0.8756 (tp30)
REVERT: B  108 GLU cc_start: 0.9189 (mt-10) cc_final: 0.8957 (mt-10)
REVERT: B  112 ARG cc_start: 0.8733 (OUTLIER) cc_final: 0.8319 (mpp-170)
REVERT: B  258 MET cc_start: 0.8306 (mmm) cc_final: 0.7487 (mtp)
REVERT: B  417 GLU cc_start: 0.9283 (OUTLIER) cc_final: 0.8993 (tp30)
REVERT: B  433 GLU cc_start: 0.9313 (mt-10) cc_final: 0.8561 (mt-10)
REVERT: B  451 VAL cc_start: 0.9279 (OUTLIER) cc_final: 0.8920 (p)
REVERT: B  484 TRP cc_start: 0.7260 (p-90) cc_final: 0.6629 (p-90)
REVERT: B  501 ASN cc_start: 0.8126 (p0) cc_final: 0.7644 (p0)
REVERT: B  685 ARG cc_start: 0.9059 (ttp80) cc_final: 0.8838 (mtm110)
REVERT: B  822 GLU cc_start: 0.9176 (mp0) cc_final: 0.8773 (mp0)
REVERT: B  966 GLU cc_start: 0.9196 (tp30) cc_final: 0.8777 (tp30)
  outliers start: 17
  outliers final: 9
  residues processed: 147
  average time/residue: 0.7501
  time to fit residues: 120.6226
Evaluate side-chains
  144 residues out of total 1772 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 130
  time to evaluate  : 0.654 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   84 THR
Chi-restraints excluded: chain A residue  181 VAL
Chi-restraints excluded: chain A residue  451 VAL
Chi-restraints excluded: chain A residue  762 THR
Chi-restraints excluded: chain A residue  802 GLU
Chi-restraints excluded: chain B residue   84 THR
Chi-restraints excluded: chain B residue  112 ARG
Chi-restraints excluded: chain B residue  181 VAL
Chi-restraints excluded: chain B residue  341 TYR
Chi-restraints excluded: chain B residue  347 VAL
Chi-restraints excluded: chain B residue  417 GLU
Chi-restraints excluded: chain B residue  451 VAL
Chi-restraints excluded: chain B residue  692 MET
Chi-restraints excluded: chain B residue  762 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 206
   random chunks:
   chunk 171 optimal weight:    0.7980
   chunk 114 optimal weight:    5.9990
   chunk 187 optimal weight:    5.9990
   chunk 41 optimal weight:    1.9990
   chunk 106 optimal weight:    2.9990
   chunk 31 optimal weight:    3.9990
   chunk 54 optimal weight:    5.9990
   chunk 104 optimal weight:    0.6980
   chunk 92 optimal weight:    0.6980
   chunk 86 optimal weight:    2.9990
   chunk 122 optimal weight:    0.0470
   overall best weight:    0.8480

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.2808 r_free = 0.2808 target = 0.061394 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.2504 r_free = 0.2504 target = 0.047942 restraints weight = 36626.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.2535 rms_B_bonded: 2.78
r_work: 0.2385 rms_B_bonded: 2.96 restraints_weight: 0.5000
r_work: 0.2254 rms_B_bonded: 4.80 restraints_weight: 0.2500
r_work (final): 0.2254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.9097
moved from start:          0.5787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.049  17036  Z= 0.110
  Angle     :  0.530  14.729  23014  Z= 0.273
  Chirality :  0.041   0.160   2424
  Planarity :  0.003   0.061   3004
  Dihedral  :  3.981  25.672   2325
  Min Nonbonded Distance : 2.474

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.51 %
    Favored  : 97.49 %
  Rotamer:
    Outliers :  0.74 %
    Allowed  : 12.60 %
    Favored  : 86.66 %
  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:  0.79 (0.19), residues: 2074
  helix:  1.56 (0.19), residues: 760
  sheet:  0.52 (0.29), residues: 314
  loop : -0.23 (0.20), residues: 1000

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.000   ARG A 327 
 TYR   0.015   0.001   TYR A  38 
 PHE   0.012   0.001   PHE B 527 
 TRP   0.007   0.001   TRP A  35 
 HIS   0.002   0.001   HIS B  96 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (17036)
  covalent geometry    : angle       0.53016 (23014)
  hydrogen bonds       : bond        0.03285 (  794)
  hydrogen bonds       : angle       5.04190 ( 2196)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 6300.36 seconds
wall clock time: 108 minutes 6.78 seconds (6486.78 seconds total)