Starting phenix.real_space_refine
on Sat May 10 22:55:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8toh_41452/05_2025/8toh_41452.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8toh_41452/05_2025/8toh_41452.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.29
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8toh_41452/05_2025/8toh_41452.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8toh_41452/05_2025/8toh_41452.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8toh_41452/05_2025/8toh_41452.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8toh_41452/05_2025/8toh_41452.cif"
  }
  resolution = 3.29
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.032
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      25      5.16       5
     C    4554      2.51       5
     N    1199      2.21       5
     O    1244      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 7022
  Number of models: 1
  Model: ""
    Number of chains: 1
    Chain: "A"
      Number of atoms: 7022
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 860, 7022
          Classifications: {'peptide': 860}
          Link IDs: {'PTRANS': 49, 'TRANS': 810}
          Chain breaks: 2
  Time building chain proxies: 4.98, per 1000 atoms: 0.71
  Number of scatterers: 7022
  At special positions: 0
  Unit cell: (72.8784, 76.1319, 115.825, 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      25     16.00
     O    1244      8.00
     N    1199      7.00
     C    4554      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: 1.74
  Conformation dependent library (CDL) restraints added in 937.6 milliseconds
  

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1600

  Finding SS restraints...
    Secondary structure from input PDB file:
      35 helices and 8 sheets defined
      47.1% alpha, 9.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.75
  Creating SS restraints...
    Processing helix  chain 'A' and resid 36 through 38
      No H-bonds generated for 'chain 'A' and resid 36 through 38'
    Processing helix  chain 'A' and resid 39 through 45
      removed outlier: 4.317A  pdb=" N   ALA A  43 " --> pdb=" O   ALA A  39 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 50 through 56
    Processing helix  chain 'A' and resid 72 through 77
      removed outlier: 3.598A  pdb=" N   THR A  76 " --> pdb=" O   ALA A  72 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 85
    Processing helix  chain 'A' and resid 88 through 96
      removed outlier: 3.866A  pdb=" N   THR A  92 " --> pdb=" O   SER A  88 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   HIS A  95 " --> pdb=" O   ASP A  91 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   HIS A  96 " --> pdb=" O   THR A  92 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 121 through 125
      removed outlier: 3.774A  pdb=" N   VAL A 124 " --> pdb=" O   THR A 121 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ALA A 125 " --> pdb=" O   GLY A 122 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 121 through 125'
    Processing helix  chain 'A' and resid 132 through 143
      removed outlier: 3.750A  pdb=" N   THR A 136 " --> pdb=" O   VAL A 132 " (cutoff:3.500A)
      removed outlier: 3.634A  pdb=" N   ALA A 138 " --> pdb=" O   ARG A 134 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 166 through 184
    Processing helix  chain 'A' and resid 198 through 203
      removed outlier: 4.187A  pdb=" N   ALA A 203 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 205 through 209
      removed outlier: 4.245A  pdb=" N   ALA A 208 " --> pdb=" O   GLY A 205 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 228
      removed outlier: 4.011A  pdb=" N   ASP A 214 " --> pdb=" O   ARG A 210 " (cutoff:3.500A)
      removed outlier: 3.571A  pdb=" N   ARG A 217 " --> pdb=" O   ALA A 213 " (cutoff:3.500A)
      removed outlier: 3.671A  pdb=" N   TYR A 219 " --> pdb=" O   HIS A 215 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   ALA A 220 " --> pdb=" O   PHE A 216 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 222 " --> pdb=" O   ASP A 218 " (cutoff:3.500A)
      removed outlier: 3.669A  pdb=" N   PHE A 224 " --> pdb=" O   ALA A 220 " (cutoff:3.500A)
      removed outlier: 3.934A  pdb=" N   ARG A 225 " --> pdb=" O   GLU A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 239 through 249
      removed outlier: 3.541A  pdb=" N   HIS A 246 " --> pdb=" O   VAL A 242 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   GLY A 247 " --> pdb=" O   VAL A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 260 through 286
      removed outlier: 3.962A  pdb=" N   GLY A 264 " --> pdb=" O   SER A 260 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   LEU A 266 " --> pdb=" O   ARG A 262 " (cutoff:3.500A)
      removed outlier: 3.729A  pdb=" N   LEU A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
      removed outlier: 3.784A  pdb=" N   THR A 284 " --> pdb=" O   HIS A 280 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 290
    Processing helix  chain 'A' and resid 309 through 324
      removed outlier: 3.552A  pdb=" N   VAL A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 333
      Proline residue:  A 330  - end of helix
      removed outlier: 3.639A  pdb=" N   ILE A 333 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 338 through 345
      removed outlier: 3.502A  pdb=" N   LYS A 342 " --> pdb=" O   PRO A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 353 through 361
      removed outlier: 3.666A  pdb=" N   LYS A 358 " --> pdb=" O   GLU A 354 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 386
      removed outlier: 3.558A  pdb=" N   PHE A 386 " --> pdb=" O   HIS A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 394 through 405
      removed outlier: 3.578A  pdb=" N   SER A 399 " --> pdb=" O   ARG A 395 " (cutoff:3.500A)
      removed outlier: 4.308A  pdb=" N   TRP A 400 " --> pdb=" O   GLN A 396 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 427 through 448
      removed outlier: 3.918A  pdb=" N   TYR A 432 " --> pdb=" O   ALA A 428 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   LEU A 442 " --> pdb=" O   ILE A 438 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 468 through 470
      No H-bonds generated for 'chain 'A' and resid 468 through 470'
    Processing helix  chain 'A' and resid 491 through 502
      removed outlier: 3.879A  pdb=" N   ILE A 501 " --> pdb=" O   TYR A 497 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   GLU A 502 " --> pdb=" O   GLN A 498 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 577 through 589
      removed outlier: 4.360A  pdb=" N   GLN A 581 " --> pdb=" O   ALA A 577 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   GLU A 587 " --> pdb=" O   ALA A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 603
    Processing helix  chain 'A' and resid 612 through 629
      removed outlier: 3.844A  pdb=" N   LEU A 616 " --> pdb=" O   ASN A 612 " (cutoff:3.500A)
      removed outlier: 3.761A  pdb=" N   TYR A 619 " --> pdb=" O   ILE A 615 " (cutoff:3.500A)
      removed outlier: 3.602A  pdb=" N   ARG A 620 " --> pdb=" O   LEU A 616 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 661 through 678
      removed outlier: 3.584A  pdb=" N   TYR A 669 " --> pdb=" O   ALA A 665 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   GLU A 676 " --> pdb=" O   LEU A 672 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 696 through 718
      removed outlier: 3.964A  pdb=" N   ASN A 702 " --> pdb=" O   SER A 698 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA A 708 " --> pdb=" O   LEU A 704 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 742 through 757
      removed outlier: 3.721A  pdb=" N   LYS A 746 " --> pdb=" O   SER A 742 " (cutoff:3.500A)
      removed outlier: 3.589A  pdb=" N   GLU A 750 " --> pdb=" O   LYS A 746 " (cutoff:3.500A)
      removed outlier: 3.668A  pdb=" N   ARG A 751 " --> pdb=" O   GLU A 747 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 771 through 781
    Processing helix  chain 'A' and resid 790 through 798
      removed outlier: 3.759A  pdb=" N   LYS A 795 " --> pdb=" O   GLU A 791 " (cutoff:3.500A)
      removed outlier: 3.976A  pdb=" N   LEU A 796 " --> pdb=" O   ASP A 792 " (cutoff:3.500A)
      removed outlier: 3.565A  pdb=" N   ILE A 797 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   GLN A 798 " --> pdb=" O   LYS A 794 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 850 through 864
      removed outlier: 3.555A  pdb=" N   LYS A 854 " --> pdb=" O   TRP A 850 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   VAL A 855 " --> pdb=" O   GLY A 851 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LYS A 860 " --> pdb=" O   LEU A 856 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 884 through 904
      removed outlier: 3.699A  pdb=" N   TYR A 889 " --> pdb=" O   GLN A 885 " (cutoff:3.500A)
      removed outlier: 4.079A  pdb=" N   GLN A 892 " --> pdb=" O   VAL A 888 " (cutoff:3.500A)
      removed outlier: 3.566A  pdb=" N   ALA A 901 " --> pdb=" O   GLU A 897 " (cutoff:3.500A)
      removed outlier: 4.016A  pdb=" N   HIS A 902 " --> pdb=" O   ALA A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 939 through 951
      removed outlier: 3.652A  pdb=" N   HIS A 943 " --> pdb=" O   ALA A 939 " (cutoff:3.500A)
      removed outlier: 3.703A  pdb=" N   ILE A 947 " --> pdb=" O   HIS A 943 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 66 through 69
      removed outlier: 7.840A  pdb=" N   ILE A 410 " --> pdb=" O   ILE A 453 " (cutoff:3.500A)
      removed outlier: 6.560A  pdb=" N   TYR A 455 " --> pdb=" O   ILE A 410 " (cutoff:3.500A)
      removed outlier: 6.472A  pdb=" N   ILE A 412 " --> pdb=" O   TYR A 455 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   ALA A 457 " --> pdb=" O   ILE A 412 " (cutoff:3.500A)
      removed outlier: 7.156A  pdb=" N   GLU A 414 " --> pdb=" O   ALA A 457 " (cutoff:3.500A)
      removed outlier: 3.539A  pdb=" N   LEU A 369 " --> pdb=" O   PHE A 411 " (cutoff:3.500A)
      removed outlier: 5.442A  pdb=" N   PHE A 366 " --> pdb=" O   VAL A 294 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ILE A 296 " --> pdb=" O   PHE A 366 " (cutoff:3.500A)
      removed outlier: 6.402A  pdb=" N   TRP A 234 " --> pdb=" O   SER A 295 " (cutoff:3.500A)
      removed outlier: 6.746A  pdb=" N   ALA A 297 " --> pdb=" O   TRP A 234 " (cutoff:3.500A)
      removed outlier: 7.183A  pdb=" N   THR A 236 " --> pdb=" O   ALA A 297 " (cutoff:3.500A)
      removed outlier: 12.037A  pdb=" N   SER A 299 " --> pdb=" O   THR A 236 " (cutoff:3.500A)
      removed outlier: 10.423A  pdb=" N   ASP A 238 " --> pdb=" O   SER A 299 " (cutoff:3.500A)
      removed outlier: 8.080A  pdb=" N   ILE A 235 " --> pdb=" O   PRO A 187 " (cutoff:3.500A)
      removed outlier: 6.524A  pdb=" N   VAL A 189 " --> pdb=" O   ILE A 235 " (cutoff:3.500A)
      removed outlier: 7.714A  pdb=" N   ILE A 237 " --> pdb=" O   VAL A 189 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   TYR A 147 " --> pdb=" O   VAL A 188 " (cutoff:3.500A)
      removed outlier: 7.727A  pdb=" N   THR A 190 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 6.870A  pdb=" N   PHE A 149 " --> pdb=" O   THR A 190 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 302 through 304
      removed outlier: 4.048A  pdb=" N   TRP A 302 " --> pdb=" O   SER A 391 " (cutoff:3.500A)
      removed outlier: 3.662A  pdb=" N   SER A 391 " --> pdb=" O   TRP A 302 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   LEU A 389 " --> pdb=" O   ASN A 304 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 419 through 420
    Processing sheet with id=AA4, first strand: chain 'A' and resid 594 through 595
      removed outlier: 5.807A  pdb=" N   VAL A 527 " --> pdb=" O   ARG A 594 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 634 through 635
      removed outlier: 5.701A  pdb=" N   VAL A 635 " --> pdb=" O   ILE A 685 " (cutoff:3.500A)
      removed outlier: 7.105A  pdb=" N   MET A 687 " --> pdb=" O   VAL A 635 " (cutoff:3.500A)
      removed outlier: 6.127A  pdb=" N   TRP A 684 " --> pdb=" O   SER A 727 " (cutoff:3.500A)
      removed outlier: 6.365A  pdb=" N   ALA A 729 " --> pdb=" O   TRP A 684 " (cutoff:3.500A)
      removed outlier: 7.037A  pdb=" N   THR A 686 " --> pdb=" O   ALA A 729 " (cutoff:3.500A)
      removed outlier: 11.642A  pdb=" N   GLN A 731 " --> pdb=" O   THR A 686 " (cutoff:3.500A)
      removed outlier: 11.204A  pdb=" N   ASN A 688 " --> pdb=" O   GLN A 731 " (cutoff:3.500A)
      removed outlier: 9.200A  pdb=" N   ALA A 805 " --> pdb=" O   ILE A 726 " (cutoff:3.500A)
      removed outlier: 7.030A  pdb=" N   ILE A 728 " --> pdb=" O   ALA A 805 " (cutoff:3.500A)
      removed outlier: 7.783A  pdb=" N   SER A 807 " --> pdb=" O   ILE A 728 " (cutoff:3.500A)
      removed outlier: 6.975A  pdb=" N   LEU A 730 " --> pdb=" O   SER A 807 " (cutoff:3.500A)
      removed outlier: 6.421A  pdb=" N   LEU A 804 " --> pdb=" O   TYR A 869 " (cutoff:3.500A)
      removed outlier: 6.094A  pdb=" N   ILE A 871 " --> pdb=" O   LEU A 804 " (cutoff:3.500A)
      removed outlier: 7.424A  pdb=" N   LEU A 806 " --> pdb=" O   ILE A 871 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 734 through 737
      removed outlier: 3.503A  pdb=" N   GLU A 736 " --> pdb=" O   ILE A 812 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   VAL A 814 " --> pdb=" O   GLU A 736 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 824 through 825
    Processing sheet with id=AA8, first strand: chain 'A' and resid 928 through 931
      removed outlier: 3.605A  pdb=" N   ARG A 929 " --> pdb=" O   GLU A 936 " (cutoff:3.500A)
      removed outlier: 3.554A  pdb=" N   GLU A 936 " --> pdb=" O   ARG A 929 " (cutoff:3.500A)

    228 hydrogen bonds defined for protein.
    657 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: 2.14

  Time building geometry restraints manager: 2.05 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 2248
        1.34 -     1.46: 1791
        1.46 -     1.58: 3168
        1.58 -     1.69: 0
        1.69 -     1.81: 42
  Bond restraints: 7249
  Sorted by residual:
  bond pdb=" C   TRP A 638 "
       pdb=" N   GLN A 639 "
    ideal  model  delta    sigma   weight residual
    1.329  1.358 -0.029 1.35e-02 5.49e+03 4.65e+00
  bond pdb=" CB  PRO A  35 "
       pdb=" CG  PRO A  35 "
    ideal  model  delta    sigma   weight residual
    1.492  1.573 -0.081 5.00e-02 4.00e+02 2.62e+00
  bond pdb=" C   ALA A 254 "
       pdb=" N   PRO A 255 "
    ideal  model  delta    sigma   weight residual
    1.328  1.346 -0.018 1.25e-02 6.40e+03 2.10e+00
  bond pdb=" CB  LYS A 329 "
       pdb=" CG  LYS A 329 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.34e+00
  bond pdb=" CB  GLN A 230 "
       pdb=" CG  GLN A 230 "
    ideal  model  delta    sigma   weight residual
    1.520  1.553 -0.033 3.00e-02 1.11e+03 1.22e+00
  ... (remaining 7244 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 9572
        1.52 -     3.04: 253
        3.04 -     4.57: 24
        4.57 -     6.09: 8
        6.09 -     7.61: 5
  Bond angle restraints: 9862
  Sorted by residual:
  angle pdb=" N   VAL A 132 "
        pdb=" CA  VAL A 132 "
        pdb=" C   VAL A 132 "
      ideal   model   delta    sigma   weight residual
     113.47  109.22    4.25 1.01e+00 9.80e-01 1.77e+01
  angle pdb=" CB  LYS A 329 "
        pdb=" CG  LYS A 329 "
        pdb=" CD  LYS A 329 "
      ideal   model   delta    sigma   weight residual
     111.30  118.91   -7.61 2.30e+00 1.89e-01 1.10e+01
  angle pdb=" CA  LYS A 329 "
        pdb=" CB  LYS A 329 "
        pdb=" CG  LYS A 329 "
      ideal   model   delta    sigma   weight residual
     114.10  120.54   -6.44 2.00e+00 2.50e-01 1.04e+01
  angle pdb=" CA  GLN A 230 "
        pdb=" CB  GLN A 230 "
        pdb=" CG  GLN A 230 "
      ideal   model   delta    sigma   weight residual
     114.10  119.61   -5.51 2.00e+00 2.50e-01 7.60e+00
  angle pdb=" CA  GLN A 731 "
        pdb=" CB  GLN A 731 "
        pdb=" CG  GLN A 731 "
      ideal   model   delta    sigma   weight residual
     114.10  119.58   -5.48 2.00e+00 2.50e-01 7.50e+00
  ... (remaining 9857 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.19: 3649
       15.19 -    30.37: 402
       30.37 -    45.55: 115
       45.55 -    60.74: 23
       60.74 -    75.92: 7
  Dihedral angle restraints: 4196
    sinusoidal: 1695
      harmonic: 2501
  Sorted by residual:
  dihedral pdb=" CA  HIS A 880 "
           pdb=" C   HIS A 880 "
           pdb=" N   ALA A 881 "
           pdb=" CA  ALA A 881 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.30   20.70     0      5.00e+00 4.00e-02 1.71e+01
  dihedral pdb=" CA  THR A 632 "
           pdb=" C   THR A 632 "
           pdb=" N   PRO A 633 "
           pdb=" CA  PRO A 633 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.49  -18.51     0      5.00e+00 4.00e-02 1.37e+01
  dihedral pdb=" CA  ILE A 438 "
           pdb=" C   ILE A 438 "
           pdb=" N   MET A 439 "
           pdb=" CA  MET A 439 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.31   17.69     0      5.00e+00 4.00e-02 1.25e+01
  ... (remaining 4193 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.029: 590
       0.029 -    0.057: 267
       0.057 -    0.086: 97
       0.086 -    0.115: 48
       0.115 -    0.143: 9
  Chirality restraints: 1011
  Sorted by residual:
  chirality pdb=" CA  ILE A 870 "
            pdb=" N   ILE A 870 "
            pdb=" C   ILE A 870 "
            pdb=" CB  ILE A 870 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.14 2.00e-01 2.50e+01 5.12e-01
  chirality pdb=" CA  ILE A 685 "
            pdb=" N   ILE A 685 "
            pdb=" C   ILE A 685 "
            pdb=" CB  ILE A 685 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.48e-01
  chirality pdb=" CA  TRP A 279 "
            pdb=" N   TRP A 279 "
            pdb=" C   TRP A 279 "
            pdb=" CB  TRP A 279 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.34e-01
  ... (remaining 1008 not shown)

  Planarity restraints: 1273
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A 279 "   -0.031 2.00e-02 2.50e+03   2.30e-02 1.32e+01
        pdb=" CG  TRP A 279 "    0.061 2.00e-02 2.50e+03
        pdb=" CD1 TRP A 279 "   -0.022 2.00e-02 2.50e+03
        pdb=" CD2 TRP A 279 "   -0.001 2.00e-02 2.50e+03
        pdb=" NE1 TRP A 279 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A 279 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP A 279 "    0.005 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A 279 "   -0.007 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A 279 "   -0.009 2.00e-02 2.50e+03
        pdb=" CH2 TRP A 279 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLU A 689 "    0.039 5.00e-02 4.00e+02   5.93e-02 5.63e+00
        pdb=" N   PRO A 690 "   -0.103 5.00e-02 4.00e+02
        pdb=" CA  PRO A 690 "    0.031 5.00e-02 4.00e+02
        pdb=" CD  PRO A 690 "    0.033 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER A 260 "   -0.026 5.00e-02 4.00e+02   3.97e-02 2.53e+00
        pdb=" N   PRO A 261 "    0.069 5.00e-02 4.00e+02
        pdb=" CA  PRO A 261 "   -0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO A 261 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 1270 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1209
        2.76 -     3.30: 7073
        3.30 -     3.83: 12180
        3.83 -     4.37: 14197
        4.37 -     4.90: 23515
  Nonbonded interactions: 58174
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 873 "
            pdb=" OH  TYR A 912 "
     model   vdw
     2.227 3.040
  nonbonded pdb=" O   SER A 596 "
            pdb=" OH  TYR A 619 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" NH2 ARG A 148 "
            pdb=" OD2 ASP A 238 "
     model   vdw
     2.241 3.120
  nonbonded pdb=" NH2 ARG A 134 "
            pdb=" O   ASP A 485 "
     model   vdw
     2.244 3.120
  nonbonded pdb=" OG1 THR A  92 "
            pdb=" NE2 GLN A 198 "
     model   vdw
     2.255 3.120
  ... (remaining 58169 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as 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:             1.820
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.300
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.150
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.030
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   25.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6433
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      :  0.003   0.081   7249  Z= 0.118
  Angle     :  0.582   7.611   9862  Z= 0.317
  Chirality :  0.041   0.143   1011
  Planarity :  0.004   0.059   1273
  Dihedral  : 14.462  75.924   2596
  Min Nonbonded Distance : 2.227

Molprobity Statistics.
  All-atom Clashscore : 13.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.14 %
    Favored  : 99.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.67 (0.28), residues: 854
  helix: -0.54 (0.29), residues: 316
  sheet: -0.66 (0.59), residues: 85
  loop : -1.61 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A 279 
 HIS   0.006   0.001   HIS A 146 
 PHE   0.016   0.001   PHE A 332 
 TYR   0.011   0.001   TYR A 531 
 ARG   0.003   0.000   ARG A 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.31200 (  228)
  hydrogen bonds       : angle      10.20215 (  657)
  covalent geometry    : bond        0.00258 ( 7249)
  covalent geometry    : angle       0.58209 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  131 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 131
  time to evaluate  : 0.671 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  230 GLN cc_start: 0.6649 (tm-30) cc_final: 0.6379 (pt0)
REVERT: A  262 ARG cc_start: 0.7336 (tmt-80) cc_final: 0.7117 (tpt90)
REVERT: A  266 LEU cc_start: 0.8012 (tp) cc_final: 0.7564 (tp)
REVERT: A  386 PHE cc_start: 0.7884 (m-80) cc_final: 0.7608 (m-80)
REVERT: A  502 GLU cc_start: 0.7071 (mp0) cc_final: 0.6867 (mp0)
  outliers start: 0
  outliers final: 0
  residues processed: 131
  average time/residue: 0.1840
  time to fit residues: 32.9033
Evaluate side-chains
  127 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.729 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 72 optimal weight:    3.9990
   chunk 65 optimal weight:    0.5980
   chunk 36 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 43 optimal weight:    0.1980
   chunk 34 optimal weight:    0.8980
   chunk 67 optimal weight:    0.7980
   chunk 26 optimal weight:    4.9990
   chunk 40 optimal weight:    2.9990
   chunk 50 optimal weight:    4.9990
   chunk 78 optimal weight:    0.8980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 396 GLN
A 608 GLN
A 902 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4503 r_free = 0.4503 target = 0.197145 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.176020 restraints weight = 11036.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.4303 rms_B_bonded: 3.65
r_work: 0.4169 rms_B_bonded: 4.36 restraints_weight: 0.5000
r_work (final): 0.4169
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6489
moved from start:          0.1598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   7249  Z= 0.155
  Angle     :  0.614   7.142   9862  Z= 0.319
  Chirality :  0.045   0.168   1011
  Planarity :  0.005   0.040   1273
  Dihedral  :  4.878  22.706    946
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 13.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  0.95 %
    Allowed  :  9.69 %
    Favored  : 89.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (0.28), residues: 854
  helix:  0.07 (0.28), residues: 333
  sheet: -0.35 (0.57), residues: 87
  loop : -1.77 (0.29), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 279 
 HIS   0.011   0.001   HIS A 275 
 PHE   0.015   0.001   PHE A 861 
 TYR   0.018   0.001   TYR A 531 
 ARG   0.004   0.000   ARG A 671 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05645 (  228)
  hydrogen bonds       : angle       6.26948 (  657)
  covalent geometry    : bond        0.00340 ( 7249)
  covalent geometry    : angle       0.61393 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 142
  time to evaluate  : 0.778 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   95 HIS cc_start: 0.8031 (m-70) cc_final: 0.7819 (m170)
REVERT: A  234 TRP cc_start: 0.6038 (m100) cc_final: 0.4364 (m100)
REVERT: A  262 ARG cc_start: 0.7522 (tmt-80) cc_final: 0.7002 (tpt90)
REVERT: A  360 ILE cc_start: 0.7694 (tt) cc_final: 0.7345 (tt)
REVERT: A  386 PHE cc_start: 0.7900 (m-80) cc_final: 0.7532 (m-80)
REVERT: A  435 LYS cc_start: 0.7796 (tttt) cc_final: 0.7509 (tttm)
REVERT: A  439 MET cc_start: 0.7267 (mmp) cc_final: 0.6758 (mmp)
REVERT: A  502 GLU cc_start: 0.7507 (mp0) cc_final: 0.7068 (mp0)
REVERT: A  744 LYS cc_start: 0.8574 (tptp) cc_final: 0.8315 (tptp)
REVERT: A  803 PHE cc_start: 0.6641 (p90) cc_final: 0.5883 (p90)
  outliers start: 7
  outliers final: 4
  residues processed: 145
  average time/residue: 0.2021
  time to fit residues: 39.1708
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 137
  time to evaluate  : 0.698 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  886 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 80 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 63 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9980
   chunk 0 optimal weight:    6.9990
   chunk 46 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 42 optimal weight:    4.9990
   overall best weight:    1.0382

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
A 283 ASN
A 388 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4484 r_free = 0.4484 target = 0.195287 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4264 r_free = 0.4264 target = 0.174248 restraints weight = 11027.250|
|-----------------------------------------------------------------------------|
r_work (start): 0.4259 rms_B_bonded: 3.64
r_work: 0.4124 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.4124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6570
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   7249  Z= 0.184
  Angle     :  0.611   8.201   9862  Z= 0.319
  Chirality :  0.045   0.170   1011
  Planarity :  0.004   0.043   1273
  Dihedral  :  5.084  22.777    946
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 14.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.49 %
    Favored  : 92.51 %
  Rotamer:
    Outliers :  2.59 %
    Allowed  : 13.51 %
    Favored  : 83.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.19 (0.29), residues: 854
  helix:  0.29 (0.29), residues: 326
  sheet: -0.53 (0.56), residues: 87
  loop : -1.72 (0.29), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 850 
 HIS   0.015   0.001   HIS A 275 
 PHE   0.022   0.002   PHE A 861 
 TYR   0.020   0.002   TYR A 531 
 ARG   0.005   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04801 (  228)
  hydrogen bonds       : angle       5.72075 (  657)
  covalent geometry    : bond        0.00401 ( 7249)
  covalent geometry    : angle       0.61130 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 146
  time to evaluate  : 0.745 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7634 (tpp-160) cc_final: 0.7361 (tpp-160)
REVERT: A   52 GLU cc_start: 0.7033 (mt-10) cc_final: 0.6318 (mt-10)
REVERT: A  262 ARG cc_start: 0.7548 (tmt-80) cc_final: 0.7095 (tmt-80)
REVERT: A  386 PHE cc_start: 0.7934 (m-80) cc_final: 0.7525 (m-80)
REVERT: A  415 ASN cc_start: 0.8511 (t0) cc_final: 0.8269 (t0)
REVERT: A  744 LYS cc_start: 0.8566 (tptp) cc_final: 0.8284 (tptp)
REVERT: A  746 LYS cc_start: 0.8367 (mttp) cc_final: 0.8094 (mttp)
REVERT: A  803 PHE cc_start: 0.6697 (p90) cc_final: 0.6015 (p90)
REVERT: A  925 PHE cc_start: 0.6328 (OUTLIER) cc_final: 0.6098 (m-80)
REVERT: A  941 MET cc_start: 0.4905 (tpp) cc_final: 0.4618 (tpt)
  outliers start: 19
  outliers final: 11
  residues processed: 152
  average time/residue: 0.2102
  time to fit residues: 42.1008
Evaluate side-chains
  144 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 132
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  283 ASN
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 41 optimal weight:    2.9990
   chunk 65 optimal weight:    0.6980
   chunk 80 optimal weight:    0.6980
   chunk 56 optimal weight:    0.6980
   chunk 31 optimal weight:    0.0060
   chunk 55 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9990
   chunk 37 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0770
   chunk 13 optimal weight:    0.9990
   overall best weight:    0.4354

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

Flipped N/Q/H residues before XYZ refinement:
A 198 GLN
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4513 r_free = 0.4513 target = 0.198152 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.176593 restraints weight = 11181.484|
|-----------------------------------------------------------------------------|
r_work (start): 0.4289 rms_B_bonded: 3.72
r_work: 0.4152 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6514
moved from start:          0.2354

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7249  Z= 0.118
  Angle     :  0.562   7.712   9862  Z= 0.291
  Chirality :  0.043   0.166   1011
  Planarity :  0.004   0.066   1273
  Dihedral  :  4.854  22.471    946
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  3.14 %
    Allowed  : 14.73 %
    Favored  : 82.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.14 (0.29), residues: 854
  helix:  0.46 (0.29), residues: 331
  sheet: -0.85 (0.55), residues: 97
  loop : -1.74 (0.29), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP A 850 
 HIS   0.009   0.001   HIS A 275 
 PHE   0.022   0.001   PHE A 861 
 TYR   0.020   0.001   TYR A 531 
 ARG   0.003   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03831 (  228)
  hydrogen bonds       : angle       5.35139 (  657)
  covalent geometry    : bond        0.00265 ( 7249)
  covalent geometry    : angle       0.56227 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.686 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7574 (tpp-160) cc_final: 0.7302 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6913 (mt-10) cc_final: 0.6313 (mt-10)
REVERT: A  262 ARG cc_start: 0.7499 (tmt-80) cc_final: 0.6971 (tpt170)
REVERT: A  390 GLU cc_start: 0.7481 (mp0) cc_final: 0.7264 (mp0)
REVERT: A  397 LEU cc_start: 0.7856 (OUTLIER) cc_final: 0.7606 (tt)
REVERT: A  404 GLU cc_start: 0.7973 (tp30) cc_final: 0.7522 (tp30)
REVERT: A  431 MET cc_start: 0.7560 (OUTLIER) cc_final: 0.7301 (ttm)
REVERT: A  502 GLU cc_start: 0.7550 (mp0) cc_final: 0.7056 (mp0)
REVERT: A  744 LYS cc_start: 0.8515 (tptp) cc_final: 0.8300 (tptm)
REVERT: A  803 PHE cc_start: 0.6733 (p90) cc_final: 0.6068 (p90)
REVERT: A  900 LYS cc_start: 0.8075 (mtpp) cc_final: 0.7853 (mtpp)
REVERT: A  925 PHE cc_start: 0.6261 (OUTLIER) cc_final: 0.6050 (m-80)
REVERT: A  946 LYS cc_start: 0.7554 (mmmm) cc_final: 0.7337 (ttmm)
  outliers start: 23
  outliers final: 11
  residues processed: 144
  average time/residue: 0.1822
  time to fit residues: 35.6587
Evaluate side-chains
  142 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 128
  time to evaluate  : 0.769 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  397 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  886 LEU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 78 optimal weight:    2.9990
   chunk 3 optimal weight:    4.9990
   chunk 67 optimal weight:    3.9990
   chunk 68 optimal weight:    1.9990
   chunk 83 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 6 optimal weight:    5.9990
   chunk 4 optimal weight:    0.9990
   chunk 18 optimal weight:    0.9990
   overall best weight:    1.1990

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

Flipped N/Q/H residues before XYZ refinement:
A 902 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4470 r_free = 0.4470 target = 0.193873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4246 r_free = 0.4246 target = 0.172532 restraints weight = 11036.880|
|-----------------------------------------------------------------------------|
r_work (start): 0.4245 rms_B_bonded: 3.64
r_work: 0.4109 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6610
moved from start:          0.2715

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   7249  Z= 0.202
  Angle     :  0.638   7.823   9862  Z= 0.333
  Chirality :  0.046   0.162   1011
  Planarity :  0.005   0.048   1273
  Dihedral  :  5.169  22.455    946
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 14.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.73 %
    Favored  : 92.27 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 15.96 %
    Favored  : 81.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.27 (0.29), residues: 854
  helix:  0.42 (0.29), residues: 331
  sheet: -0.73 (0.57), residues: 87
  loop : -1.93 (0.29), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.002   TRP A 850 
 HIS   0.011   0.001   HIS A 275 
 PHE   0.020   0.002   PHE A 861 
 TYR   0.021   0.002   TYR A 531 
 ARG   0.004   0.000   ARG A 387 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04455 (  228)
  hydrogen bonds       : angle       5.45877 (  657)
  covalent geometry    : bond        0.00442 ( 7249)
  covalent geometry    : angle       0.63783 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  164 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 143
  time to evaluate  : 0.687 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7730 (tpp-160) cc_final: 0.7458 (tpp-160)
REVERT: A   81 GLN cc_start: 0.7419 (mp10) cc_final: 0.7169 (mp10)
REVERT: A  151 ILE cc_start: 0.5581 (OUTLIER) cc_final: 0.5332 (mm)
REVERT: A  262 ARG cc_start: 0.7544 (tmt-80) cc_final: 0.7047 (tmt-80)
REVERT: A  380 LEU cc_start: 0.7777 (tp) cc_final: 0.7485 (tt)
REVERT: A  386 PHE cc_start: 0.7934 (m-80) cc_final: 0.7701 (m-80)
REVERT: A  436 LYS cc_start: 0.8097 (tptp) cc_final: 0.7744 (tptp)
REVERT: A  443 LYS cc_start: 0.8122 (mttm) cc_final: 0.7804 (mttm)
REVERT: A  450 VAL cc_start: 0.8231 (OUTLIER) cc_final: 0.7626 (t)
REVERT: A  502 GLU cc_start: 0.7611 (mp0) cc_final: 0.7398 (mp0)
REVERT: A  803 PHE cc_start: 0.6704 (p90) cc_final: 0.6026 (p90)
REVERT: A  925 PHE cc_start: 0.6594 (OUTLIER) cc_final: 0.6339 (m-80)
  outliers start: 21
  outliers final: 12
  residues processed: 151
  average time/residue: 0.2177
  time to fit residues: 43.0859
Evaluate side-chains
  147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 132
  time to evaluate  : 0.755 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  253 LEU
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  848 VAL
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 1 optimal weight:    0.0570
   chunk 24 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   chunk 83 optimal weight:    4.9990
   chunk 27 optimal weight:    0.9990
   chunk 40 optimal weight:    0.7980
   chunk 62 optimal weight:    0.4980
   chunk 56 optimal weight:    0.2980
   chunk 42 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9990
   overall best weight:    0.4098

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

Flipped N/Q/H residues before XYZ refinement:
A  95 HIS
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 902 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4508 r_free = 0.4508 target = 0.198068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.176919 restraints weight = 11059.533|
|-----------------------------------------------------------------------------|
r_work (start): 0.4290 rms_B_bonded: 3.66
r_work: 0.4156 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6506
moved from start:          0.2735

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7249  Z= 0.116
  Angle     :  0.574   7.311   9862  Z= 0.297
  Chirality :  0.042   0.167   1011
  Planarity :  0.004   0.049   1273
  Dihedral  :  4.830  22.283    946
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 12.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.03 %
    Favored  : 92.97 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 17.74 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.23 (0.29), residues: 854
  helix:  0.56 (0.29), residues: 332
  sheet: -1.15 (0.56), residues: 94
  loop : -1.90 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A 850 
 HIS   0.010   0.001   HIS A  95 
 PHE   0.013   0.001   PHE A 801 
 TYR   0.017   0.001   TYR A 531 
 ARG   0.002   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03451 (  228)
  hydrogen bonds       : angle       5.16776 (  657)
  covalent geometry    : bond        0.00265 ( 7249)
  covalent geometry    : angle       0.57360 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  155 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 134
  time to evaluate  : 0.728 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7682 (tpp-160) cc_final: 0.7395 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6318 (mt-10)
REVERT: A  188 VAL cc_start: 0.8017 (t) cc_final: 0.7402 (m)
REVERT: A  230 GLN cc_start: 0.7049 (tm-30) cc_final: 0.6721 (pt0)
REVERT: A  234 TRP cc_start: 0.6135 (m100) cc_final: 0.4021 (m100)
REVERT: A  262 ARG cc_start: 0.7449 (tmt-80) cc_final: 0.7003 (tmt-80)
REVERT: A  436 LYS cc_start: 0.8003 (tptp) cc_final: 0.7676 (tptp)
REVERT: A  702 ASN cc_start: 0.7871 (t0) cc_final: 0.7649 (t0)
REVERT: A  744 LYS cc_start: 0.8461 (tptp) cc_final: 0.8244 (tptm)
REVERT: A  803 PHE cc_start: 0.6733 (p90) cc_final: 0.6102 (p90)
REVERT: A  900 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7786 (mtpp)
REVERT: A  925 PHE cc_start: 0.6415 (OUTLIER) cc_final: 0.5948 (m-10)
REVERT: A  946 LYS cc_start: 0.7548 (mmmm) cc_final: 0.7315 (ttmm)
  outliers start: 21
  outliers final: 15
  residues processed: 141
  average time/residue: 0.1837
  time to fit residues: 35.1411
Evaluate side-chains
  145 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 129
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  151 ILE
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  836 ILE
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  899 LEU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 37 optimal weight:    0.5980
   chunk 41 optimal weight:    1.9990
   chunk 66 optimal weight:    1.9990
   chunk 82 optimal weight:    0.0770
   chunk 46 optimal weight:    0.0980
   chunk 28 optimal weight:    0.1980
   chunk 30 optimal weight:    2.9990
   chunk 43 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9990
   chunk 76 optimal weight:    0.8980
   chunk 11 optimal weight:    2.9990
   overall best weight:    0.3738

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

Flipped N/Q/H residues before XYZ refinement:
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4519 r_free = 0.4519 target = 0.198939 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4300 r_free = 0.4300 target = 0.177903 restraints weight = 11038.167|
|-----------------------------------------------------------------------------|
r_work (start): 0.4301 rms_B_bonded: 3.62
r_work: 0.4167 rms_B_bonded: 4.42 restraints_weight: 0.5000
r_work (final): 0.4167
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6487
moved from start:          0.2852

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   7249  Z= 0.109
  Angle     :  0.555   7.111   9862  Z= 0.287
  Chirality :  0.042   0.161   1011
  Planarity :  0.004   0.050   1273
  Dihedral  :  4.697  21.649    946
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 11.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.56 %
    Favored  : 93.44 %
  Rotamer:
    Outliers :  2.18 %
    Allowed  : 18.55 %
    Favored  : 79.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.29), residues: 854
  helix:  0.62 (0.30), residues: 333
  sheet: -1.09 (0.56), residues: 94
  loop : -1.87 (0.29), residues: 427

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.024   0.001   TRP A 850 
 HIS   0.009   0.001   HIS A 275 
 PHE   0.014   0.001   PHE A 861 
 TYR   0.016   0.001   TYR A 531 
 ARG   0.001   0.000   ARG A 887 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03226 (  228)
  hydrogen bonds       : angle       5.01772 (  657)
  covalent geometry    : bond        0.00250 ( 7249)
  covalent geometry    : angle       0.55528 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 131
  time to evaluate  : 0.661 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7600 (tpp-160) cc_final: 0.7333 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6933 (mt-10) cc_final: 0.6283 (mp0)
REVERT: A  188 VAL cc_start: 0.7951 (t) cc_final: 0.7728 (p)
REVERT: A  234 TRP cc_start: 0.6123 (m100) cc_final: 0.4139 (m100)
REVERT: A  262 ARG cc_start: 0.7458 (tmt-80) cc_final: 0.7030 (tmt-80)
REVERT: A  404 GLU cc_start: 0.7896 (tp30) cc_final: 0.7481 (tp30)
REVERT: A  436 LYS cc_start: 0.7951 (tptp) cc_final: 0.7634 (tptp)
REVERT: A  502 GLU cc_start: 0.7600 (mp0) cc_final: 0.7143 (mp0)
REVERT: A  588 MET cc_start: 0.2955 (tpt) cc_final: 0.2694 (tpt)
REVERT: A  645 GLN cc_start: 0.7572 (mt0) cc_final: 0.7362 (mt0)
REVERT: A  702 ASN cc_start: 0.7877 (t0) cc_final: 0.7609 (t0)
REVERT: A  744 LYS cc_start: 0.8456 (tptp) cc_final: 0.8245 (tptm)
REVERT: A  803 PHE cc_start: 0.6729 (p90) cc_final: 0.6107 (p90)
REVERT: A  848 VAL cc_start: 0.8193 (t) cc_final: 0.7964 (t)
REVERT: A  900 LYS cc_start: 0.8016 (mtpp) cc_final: 0.7751 (mtpp)
REVERT: A  946 LYS cc_start: 0.7565 (mmmm) cc_final: 0.7336 (ttmm)
  outliers start: 16
  outliers final: 11
  residues processed: 139
  average time/residue: 0.1871
  time to fit residues: 35.1390
Evaluate side-chains
  140 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 129
  time to evaluate  : 0.674 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  747 GLU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 66 optimal weight:    0.9990
   chunk 54 optimal weight:    0.0010
   chunk 35 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 14 optimal weight:    0.9980
   chunk 8 optimal weight:    7.9990
   chunk 25 optimal weight:    2.9990
   chunk 65 optimal weight:    0.8980
   chunk 43 optimal weight:    0.0040
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.5798

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 902 HIS
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4504 r_free = 0.4504 target = 0.197098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.175764 restraints weight = 11089.341|
|-----------------------------------------------------------------------------|
r_work (start): 0.4271 rms_B_bonded: 3.69
r_work: 0.4134 rms_B_bonded: 4.48 restraints_weight: 0.5000
r_work (final): 0.4134
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6518
moved from start:          0.2957

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   7249  Z= 0.126
  Angle     :  0.573   6.991   9862  Z= 0.297
  Chirality :  0.043   0.165   1011
  Planarity :  0.004   0.051   1273
  Dihedral  :  4.752  21.473    946
  Min Nonbonded Distance : 2.523

Molprobity Statistics.
  All-atom Clashscore : 12.39
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.14 %
    Favored  : 92.86 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 18.83 %
    Favored  : 78.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.29), residues: 854
  helix:  0.62 (0.30), residues: 332
  sheet: -1.07 (0.56), residues: 94
  loop : -1.86 (0.29), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.026   0.001   TRP A 850 
 HIS   0.006   0.001   HIS A 943 
 PHE   0.017   0.001   PHE A 861 
 TYR   0.017   0.001   TYR A 219 
 ARG   0.004   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03305 (  228)
  hydrogen bonds       : angle       5.05167 (  657)
  covalent geometry    : bond        0.00288 ( 7249)
  covalent geometry    : angle       0.57254 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.693 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7644 (tpp-160) cc_final: 0.7383 (tpp-160)
REVERT: A   52 GLU cc_start: 0.6965 (mt-10) cc_final: 0.6301 (mt-10)
REVERT: A  188 VAL cc_start: 0.7965 (t) cc_final: 0.7729 (p)
REVERT: A  234 TRP cc_start: 0.6171 (m100) cc_final: 0.4177 (m100)
REVERT: A  262 ARG cc_start: 0.7523 (tmt-80) cc_final: 0.7039 (tmt-80)
REVERT: A  366 PHE cc_start: 0.7429 (p90) cc_final: 0.7184 (p90)
REVERT: A  404 GLU cc_start: 0.7916 (tp30) cc_final: 0.7518 (tp30)
REVERT: A  436 LYS cc_start: 0.7906 (tptp) cc_final: 0.7595 (tptp)
REVERT: A  450 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7475 (t)
REVERT: A  702 ASN cc_start: 0.7882 (t0) cc_final: 0.7599 (t0)
REVERT: A  744 LYS cc_start: 0.8463 (tptp) cc_final: 0.8247 (tptm)
REVERT: A  803 PHE cc_start: 0.6725 (p90) cc_final: 0.6048 (p90)
REVERT: A  900 LYS cc_start: 0.8015 (mtpp) cc_final: 0.7750 (mtpp)
REVERT: A  925 PHE cc_start: 0.6470 (OUTLIER) cc_final: 0.6252 (m-80)
REVERT: A  941 MET cc_start: 0.5035 (tpp) cc_final: 0.4619 (tpt)
REVERT: A  946 LYS cc_start: 0.7600 (mmmm) cc_final: 0.7381 (ttmm)
  outliers start: 17
  outliers final: 11
  residues processed: 135
  average time/residue: 0.1887
  time to fit residues: 34.8104
Evaluate side-chains
  139 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 126
  time to evaluate  : 0.687 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 0 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 39 optimal weight:    0.5980
   chunk 22 optimal weight:    4.9990
   chunk 64 optimal weight:    0.3980
   chunk 75 optimal weight:    2.9990
   chunk 16 optimal weight:    0.6980
   chunk 77 optimal weight:    0.7980
   chunk 12 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 902 HIS
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4505 r_free = 0.4505 target = 0.197487 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.4284 r_free = 0.4284 target = 0.176185 restraints weight = 11040.212|
|-----------------------------------------------------------------------------|
r_work (start): 0.4279 rms_B_bonded: 3.71
r_work: 0.4143 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.4143
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6534
moved from start:          0.3054

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   7249  Z= 0.134
  Angle     :  0.577   7.191   9862  Z= 0.298
  Chirality :  0.043   0.160   1011
  Planarity :  0.004   0.052   1273
  Dihedral  :  4.834  21.373    946
  Min Nonbonded Distance : 2.517

Molprobity Statistics.
  All-atom Clashscore : 12.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.91 %
    Favored  : 93.09 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 17.60 %
    Favored  : 79.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.15 (0.29), residues: 854
  helix:  0.59 (0.30), residues: 334
  sheet: -0.84 (0.55), residues: 100
  loop : -1.92 (0.29), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.001   TRP A 850 
 HIS   0.006   0.001   HIS A 943 
 PHE   0.017   0.001   PHE A 861 
 TYR   0.019   0.001   TYR A 531 
 ARG   0.004   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03372 (  228)
  hydrogen bonds       : angle       5.07013 (  657)
  covalent geometry    : bond        0.00304 ( 7249)
  covalent geometry    : angle       0.57713 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 131
  time to evaluate  : 0.779 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7643 (tpp-160) cc_final: 0.7391 (tpp-160)
REVERT: A   52 GLU cc_start: 0.7023 (mt-10) cc_final: 0.6319 (mt-10)
REVERT: A  188 VAL cc_start: 0.7984 (t) cc_final: 0.7740 (p)
REVERT: A  234 TRP cc_start: 0.6188 (m100) cc_final: 0.4198 (m100)
REVERT: A  262 ARG cc_start: 0.7544 (tmt-80) cc_final: 0.7036 (tmt-80)
REVERT: A  404 GLU cc_start: 0.7879 (tp30) cc_final: 0.7461 (tp30)
REVERT: A  436 LYS cc_start: 0.7912 (tptp) cc_final: 0.7603 (tptp)
REVERT: A  450 VAL cc_start: 0.8177 (OUTLIER) cc_final: 0.7527 (t)
REVERT: A  502 GLU cc_start: 0.7623 (OUTLIER) cc_final: 0.6793 (mp0)
REVERT: A  645 GLN cc_start: 0.7638 (mt0) cc_final: 0.7431 (mt0)
REVERT: A  702 ASN cc_start: 0.7874 (t0) cc_final: 0.7574 (t0)
REVERT: A  744 LYS cc_start: 0.8481 (tptp) cc_final: 0.8280 (tptm)
REVERT: A  803 PHE cc_start: 0.6739 (p90) cc_final: 0.6052 (p90)
REVERT: A  900 LYS cc_start: 0.8074 (mtpp) cc_final: 0.7797 (mtpp)
REVERT: A  925 PHE cc_start: 0.6531 (OUTLIER) cc_final: 0.6320 (m-80)
REVERT: A  946 LYS cc_start: 0.7582 (mmmm) cc_final: 0.7362 (ttmm)
  outliers start: 22
  outliers final: 14
  residues processed: 142
  average time/residue: 0.1967
  time to fit residues: 37.9813
Evaluate side-chains
  144 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 127
  time to evaluate  : 0.737 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  389 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  521 CYS
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 73 optimal weight:    0.9980
   chunk 49 optimal weight:    1.9990
   chunk 37 optimal weight:    0.5980
   chunk 76 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 38 optimal weight:    0.5980
   chunk 61 optimal weight:    3.9990
   chunk 79 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 83 optimal weight:    2.9990
   chunk 21 optimal weight:    2.9990
   overall best weight:    0.7782

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 902 HIS
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4496 r_free = 0.4496 target = 0.196851 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.175214 restraints weight = 11261.267|
|-----------------------------------------------------------------------------|
r_work (start): 0.4265 rms_B_bonded: 3.75
r_work: 0.4126 rms_B_bonded: 4.54 restraints_weight: 0.5000
r_work (final): 0.4126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6561
moved from start:          0.3147

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   7249  Z= 0.150
  Angle     :  0.611  11.089   9862  Z= 0.313
  Chirality :  0.044   0.173   1011
  Planarity :  0.004   0.053   1273
  Dihedral  :  4.958  21.657    946
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 13.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.26 %
    Favored  : 92.74 %
  Rotamer:
    Outliers :  2.46 %
    Allowed  : 18.83 %
    Favored  : 78.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.17 (0.29), residues: 854
  helix:  0.55 (0.30), residues: 333
  sheet: -0.85 (0.55), residues: 100
  loop : -1.90 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 850 
 HIS   0.006   0.001   HIS A 943 
 PHE   0.019   0.001   PHE A 861 
 TYR   0.020   0.002   TYR A 531 
 ARG   0.003   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03518 (  228)
  hydrogen bonds       : angle       5.12046 (  657)
  covalent geometry    : bond        0.00338 ( 7249)
  covalent geometry    : angle       0.61130 ( 9862)

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

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

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1708 Ramachandran restraints generated.
    854 Oldfield, 0 Emsley, 854 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  144 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 126
  time to evaluate  : 0.753 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   44 ARG cc_start: 0.7694 (tpp-160) cc_final: 0.7427 (tpp-160)
REVERT: A   52 GLU cc_start: 0.7069 (mt-10) cc_final: 0.5852 (pt0)
REVERT: A  234 TRP cc_start: 0.6207 (m100) cc_final: 0.4172 (m100)
REVERT: A  262 ARG cc_start: 0.7610 (tmt-80) cc_final: 0.7017 (tmt-80)
REVERT: A  404 GLU cc_start: 0.7912 (tp30) cc_final: 0.7494 (tp30)
REVERT: A  436 LYS cc_start: 0.7940 (tptp) cc_final: 0.7618 (tptp)
REVERT: A  450 VAL cc_start: 0.8198 (OUTLIER) cc_final: 0.7543 (t)
REVERT: A  502 GLU cc_start: 0.7617 (OUTLIER) cc_final: 0.6775 (mp0)
REVERT: A  645 GLN cc_start: 0.7661 (mt0) cc_final: 0.7455 (mt0)
REVERT: A  702 ASN cc_start: 0.7889 (t0) cc_final: 0.7568 (t0)
REVERT: A  744 LYS cc_start: 0.8500 (tptp) cc_final: 0.8232 (tptm)
REVERT: A  803 PHE cc_start: 0.6756 (p90) cc_final: 0.6059 (p90)
REVERT: A  900 LYS cc_start: 0.8080 (mtpp) cc_final: 0.7801 (mtpp)
REVERT: A  925 PHE cc_start: 0.6568 (OUTLIER) cc_final: 0.6357 (m-80)
REVERT: A  946 LYS cc_start: 0.7598 (mmmm) cc_final: 0.7365 (ttmm)
  outliers start: 18
  outliers final: 12
  residues processed: 136
  average time/residue: 0.1900
  time to fit residues: 35.0485
Evaluate side-chains
  141 residues out of total 733 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 126
  time to evaluate  : 0.739 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  242 VAL
Chi-restraints excluded: chain A residue  273 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  371 PHE
Chi-restraints excluded: chain A residue  375 LEU
Chi-restraints excluded: chain A residue  394 LEU
Chi-restraints excluded: chain A residue  431 MET
Chi-restraints excluded: chain A residue  439 MET
Chi-restraints excluded: chain A residue  442 LEU
Chi-restraints excluded: chain A residue  450 VAL
Chi-restraints excluded: chain A residue  502 GLU
Chi-restraints excluded: chain A residue  518 THR
Chi-restraints excluded: chain A residue  662 THR
Chi-restraints excluded: chain A residue  747 GLU
Chi-restraints excluded: chain A residue  925 PHE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 86
   random chunks:
   chunk 38 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 21 optimal weight:    1.9990
   chunk 39 optimal weight:    0.0670
   chunk 53 optimal weight:    2.9990
   chunk 16 optimal weight:    4.9990
   chunk 10 optimal weight:    2.9990
   chunk 43 optimal weight:    0.7980
   chunk 58 optimal weight:    0.0980
   chunk 72 optimal weight:    2.9990
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.7920

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

Flipped N/Q/H residues before XYZ refinement:
** A 230 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 239 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 943 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4493 r_free = 0.4493 target = 0.196731 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.175325 restraints weight = 11045.780|
|-----------------------------------------------------------------------------|
r_work (start): 0.4266 rms_B_bonded: 3.69
r_work: 0.4130 rms_B_bonded: 4.45 restraints_weight: 0.5000
r_work (final): 0.4130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6557
moved from start:          0.3204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   7249  Z= 0.152
  Angle     :  0.610  11.311   9862  Z= 0.313
  Chirality :  0.044   0.192   1011
  Planarity :  0.004   0.053   1273
  Dihedral  :  4.987  21.654    946
  Min Nonbonded Distance : 2.513

Molprobity Statistics.
  All-atom Clashscore : 12.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.38 %
    Favored  : 92.62 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 19.24 %
    Favored  : 78.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.16 (0.29), residues: 854
  helix:  0.58 (0.30), residues: 332
  sheet: -0.92 (0.55), residues: 100
  loop : -1.88 (0.30), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.001   TRP A 850 
 HIS   0.006   0.001   HIS A 943 
 PHE   0.019   0.001   PHE A 861 
 TYR   0.020   0.002   TYR A 531 
 ARG   0.003   0.000   ARG A 134 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03567 (  228)
  hydrogen bonds       : angle       5.11562 (  657)
  covalent geometry    : bond        0.00345 ( 7249)
  covalent geometry    : angle       0.61043 ( 9862)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3554.89 seconds
wall clock time: 62 minutes 25.44 seconds (3745.44 seconds total)