Starting phenix.real_space_refine
on Wed Mar  4 00:27:46 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7qks_14050/03_2026/7qks_14050.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7qks_14050/03_2026/7qks_14050.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.1
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7qks_14050/03_2026/7qks_14050.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7qks_14050/03_2026/7qks_14050.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7qks_14050/03_2026/7qks_14050.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7qks_14050/03_2026/7qks_14050.cif"
  }
  resolution = 3.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.005
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      47      5.16       5
     C    6011      2.51       5
     N    1541      2.21       5
     O    1740      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 9339
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 9300
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1199, 9300
          Classifications: {'peptide': 1199}
          Link IDs: {'PTRANS': 27, 'TRANS': 1171}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 39
          Unusual residues: {'9Z9': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.51, per 1000 atoms: 0.27
  Number of scatterers: 9339
  At special positions: 0
  Unit cell: (132.246, 105.462, 102.114, 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      47     16.00
     O    1740      8.00
     N    1541      7.00
     C    6011      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: 0.84
  Conformation dependent library (CDL) restraints added in 575.7 milliseconds
  

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2220

  Finding SS restraints...
    Secondary structure from input PDB file:
      58 helices and 4 sheets defined
      72.5% alpha, 8.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'A' and resid 32 through 42
    Processing helix  chain 'A' and resid 51 through 57
    Processing helix  chain 'A' and resid 58 through 59
      No H-bonds generated for 'chain 'A' and resid 58 through 59'
    Processing helix  chain 'A' and resid 60 through 62
      No H-bonds generated for 'chain 'A' and resid 60 through 62'
    Processing helix  chain 'A' and resid 63 through 80
      removed outlier: 3.588A  pdb=" N   ALA A  67 " --> pdb=" O   GLU A  63 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 82 through 100
      removed outlier: 4.000A  pdb=" N   LEU A  86 " --> pdb=" O   PRO A  82 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 159
      removed outlier: 3.592A  pdb=" N   HIS A 158 " --> pdb=" O   TRP A 154 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 160 through 168
    Processing helix  chain 'A' and resid 169 through 178
    Processing helix  chain 'A' and resid 179 through 188
      removed outlier: 3.555A  pdb=" N   ILE A 183 " --> pdb=" O   ASP A 179 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 188 through 212
      removed outlier: 3.676A  pdb=" N   GLY A 192 " --> pdb=" O   SER A 188 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 212 through 229
    Processing helix  chain 'A' and resid 230 through 261
      removed outlier: 3.756A  pdb=" N   ILE A 234 " --> pdb=" O   SER A 230 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 261 through 269
    Processing helix  chain 'A' and resid 270 through 283
      removed outlier: 3.682A  pdb=" N   PHE A 281 " --> pdb=" O   LYS A 277 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 283 through 326
      removed outlier: 3.648A  pdb=" N   LYS A 291 " --> pdb=" O   GLY A 287 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   PHE A 308 " --> pdb=" O   TRP A 304 " (cutoff:3.500A)
      removed outlier: 3.724A  pdb=" N   VAL A 323 " --> pdb=" O   SER A 319 " (cutoff:3.500A)
      removed outlier: 4.707A  pdb=" N   SER A 324 " --> pdb=" O   ARG A 320 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 345
    Processing helix  chain 'A' and resid 345 through 372
      removed outlier: 3.628A  pdb=" N   ALA A 349 " --> pdb=" O   ILE A 345 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   ILE A 351 " --> pdb=" O   GLY A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 434 through 442
      removed outlier: 4.406A  pdb=" N   ILE A 438 " --> pdb=" O   LYS A 434 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 460 through 462
      No H-bonds generated for 'chain 'A' and resid 460 through 462'
    Processing helix  chain 'A' and resid 463 through 470
    Processing helix  chain 'A' and resid 484 through 491
    Processing helix  chain 'A' and resid 492 through 494
      No H-bonds generated for 'chain 'A' and resid 492 through 494'
    Processing helix  chain 'A' and resid 502 through 517
    Processing helix  chain 'A' and resid 519 through 524
    Processing helix  chain 'A' and resid 528 through 532
      removed outlier: 4.169A  pdb=" N   ASP A 531 " --> pdb=" O   ASN A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 542 through 557
      removed outlier: 4.406A  pdb=" N   SER A 557 " --> pdb=" O   ARG A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 572 through 588
      removed outlier: 4.226A  pdb=" N   GLY A 577 " --> pdb=" O   THR A 573 " (cutoff:3.500A)
      removed outlier: 4.633A  pdb=" N   ILE A 578 " --> pdb=" O   ARG A 574 " (cutoff:3.500A)
      removed outlier: 3.656A  pdb=" N   VAL A 579 " --> pdb=" O   SER A 575 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 598 through 603
      removed outlier: 4.053A  pdb=" N   GLN A 603 " --> pdb=" O   SER A 600 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 621 through 627
    Processing helix  chain 'A' and resid 630 through 645
    Processing helix  chain 'A' and resid 698 through 706
      removed outlier: 3.730A  pdb=" N   LEU A 702 " --> pdb=" O   LEU A 698 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 709 through 741
      Proline residue:  A 715  - end of helix
      removed outlier: 4.065A  pdb=" N   PHE A 718 " --> pdb=" O   ILE A 714 " (cutoff:3.500A)
      removed outlier: 4.469A  pdb=" N   PHE A 727 " --> pdb=" O   ALA A 723 " (cutoff:3.500A)
      Proline residue:  A 728  - end of helix
      removed outlier: 4.132A  pdb=" N   LEU A 732 " --> pdb=" O   PRO A 728 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 745 through 747
      No H-bonds generated for 'chain 'A' and resid 745 through 747'
    Processing helix  chain 'A' and resid 748 through 802
      removed outlier: 3.664A  pdb=" N   PHE A 762 " --> pdb=" O   LYS A 758 " (cutoff:3.500A)
      removed outlier: 3.842A  pdb=" N   LEU A 771 " --> pdb=" O   GLY A 767 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   ARG A 802 " --> pdb=" O   LYS A 798 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 804 through 809
      removed outlier: 3.840A  pdb=" N   PHE A 808 " --> pdb=" O   ASP A 804 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   ASP A 809 " --> pdb=" O   MET A 805 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 804 through 809'
    Processing helix  chain 'A' and resid 810 through 813
    Processing helix  chain 'A' and resid 814 through 829
      Proline residue:  A 826  - end of helix
    Processing helix  chain 'A' and resid 830 through 833
    Processing helix  chain 'A' and resid 834 through 858
    Processing helix  chain 'A' and resid 858 through 894
      removed outlier: 4.125A  pdb=" N   VAL A 864 " --> pdb=" O   ARG A 860 " (cutoff:3.500A)
      removed outlier: 3.535A  pdb=" N   THR A 866 " --> pdb=" O   GLY A 862 " (cutoff:3.500A)
      removed outlier: 3.552A  pdb=" N   THR A 868 " --> pdb=" O   VAL A 864 " (cutoff:3.500A)
      removed outlier: 3.775A  pdb=" N   VAL A 869 " --> pdb=" O   CYS A 865 " (cutoff:3.500A)
      Proline residue:  A 870  - end of helix
      removed outlier: 3.861A  pdb=" N   VAL A 880 " --> pdb=" O   GLY A 876 " (cutoff:3.500A)
      removed outlier: 3.753A  pdb=" N   ILE A 890 " --> pdb=" O   PHE A 886 " (cutoff:3.500A)
      removed outlier: 4.286A  pdb=" N   LEU A 891 " --> pdb=" O   GLU A 887 " (cutoff:3.500A)
      removed outlier: 3.885A  pdb=" N   TYR A 894 " --> pdb=" O   ILE A 890 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 895 through 907
      removed outlier: 4.028A  pdb=" N   ALA A 907 " --> pdb=" O   GLU A 903 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 907 through 914
      removed outlier: 3.546A  pdb=" N   VAL A 911 " --> pdb=" O   ALA A 907 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 916 through 971
      removed outlier: 3.615A  pdb=" N   LYS A 933 " --> pdb=" O   LYS A 929 " (cutoff:3.500A)
      removed outlier: 3.687A  pdb=" N   ARG A 937 " --> pdb=" O   LYS A 933 " (cutoff:3.500A)
      removed outlier: 4.013A  pdb=" N   SER A 938 " --> pdb=" O   ARG A 934 " (cutoff:3.500A)
      removed outlier: 3.751A  pdb=" N   LEU A 944 " --> pdb=" O   SER A 940 " (cutoff:3.500A)
      removed outlier: 4.243A  pdb=" N   LEU A 945 " --> pdb=" O   ARG A 941 " (cutoff:3.500A)
      removed outlier: 4.580A  pdb=" N   ASN A 953 " --> pdb=" O   ILE A 949 " (cutoff:3.500A)
      Proline residue:  A 954  - end of helix
    Processing helix  chain 'A' and resid 974 through 993
    Processing helix  chain 'A' and resid 994 through 997
    Processing helix  chain 'A' and resid 998 through 1018
      removed outlier: 3.649A  pdb=" N   MET A1002 " --> pdb=" O   TYR A 998 " (cutoff:3.500A)
      removed outlier: 3.773A  pdb=" N   GLY A1003 " --> pdb=" O   ALA A 999 " (cutoff:3.500A)
      removed outlier: 3.805A  pdb=" N   LYS A1004 " --> pdb=" O   PRO A1000 " (cutoff:3.500A)
      removed outlier: 3.510A  pdb=" N   LYS A1006 " --> pdb=" O   MET A1002 " (cutoff:3.500A)
      removed outlier: 3.765A  pdb=" N   ALA A1009 " --> pdb=" O   ALA A1005 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1084 through 1091
      removed outlier: 3.876A  pdb=" N   GLY A1088 " --> pdb=" O   SER A1084 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1111
      No H-bonds generated for 'chain 'A' and resid 1109 through 1111'
    Processing helix  chain 'A' and resid 1112 through 1119
    Processing helix  chain 'A' and resid 1133 through 1139
    Processing helix  chain 'A' and resid 1140 through 1142
      No H-bonds generated for 'chain 'A' and resid 1140 through 1142'
    Processing helix  chain 'A' and resid 1153 through 1162
    Processing helix  chain 'A' and resid 1164 through 1171
    Processing helix  chain 'A' and resid 1187 through 1202
      removed outlier: 4.542A  pdb=" N   ARG A1202 " --> pdb=" O   ARG A1198 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1217 through 1232
      removed outlier: 3.764A  pdb=" N   MET A1222 " --> pdb=" O   SER A1218 " (cutoff:3.500A)
      removed outlier: 4.250A  pdb=" N   VAL A1223 " --> pdb=" O   GLU A1219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1266 through 1274
    Processing helix  chain 'A' and resid 1275 through 1288
    Processing sheet with id=AA1, first strand: chain 'A' and resid 405 through 418
      removed outlier: 6.821A  pdb=" N   VAL A 410 " --> pdb=" O   ARG A 401 " (cutoff:3.500A)
      removed outlier: 7.347A  pdb=" N   ARG A 401 " --> pdb=" O   VAL A 410 " (cutoff:3.500A)
      removed outlier: 6.986A  pdb=" N   SER A 412 " --> pdb=" O   THR A 399 " (cutoff:3.500A)
      removed outlier: 6.491A  pdb=" N   THR A 399 " --> pdb=" O   SER A 412 " (cutoff:3.500A)
      removed outlier: 4.874A  pdb=" N   PHE A 414 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
      removed outlier: 5.543A  pdb=" N   PHE A 395 " --> pdb=" O   LEU A 453 " (cutoff:3.500A)
      removed outlier: 6.805A  pdb=" N   LEU A 453 " --> pdb=" O   PHE A 395 " (cutoff:3.500A)
      removed outlier: 5.327A  pdb=" N   ASN A 397 " --> pdb=" O   GLU A 451 " (cutoff:3.500A)
      removed outlier: 5.017A  pdb=" N   GLU A 451 " --> pdb=" O   ASN A 397 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 471 through 474
      removed outlier: 6.260A  pdb=" N   ALA A 472 " --> pdb=" O   LEU A 563 " (cutoff:3.500A)
      removed outlier: 7.011A  pdb=" N   ASP A 565 " --> pdb=" O   ALA A 472 " (cutoff:3.500A)
      removed outlier: 6.760A  pdb=" N   VAL A 474 " --> pdb=" O   ASP A 565 " (cutoff:3.500A)
      removed outlier: 6.949A  pdb=" N   LEU A 562 " --> pdb=" O   ILE A 593 " (cutoff:3.500A)
      removed outlier: 7.552A  pdb=" N   ILE A 595 " --> pdb=" O   LEU A 562 " (cutoff:3.500A)
      removed outlier: 6.447A  pdb=" N   LEU A 564 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 6.408A  pdb=" N   ILE A 424 " --> pdb=" O   VAL A 594 " (cutoff:3.500A)
      removed outlier: 6.159A  pdb=" N   THR A 423 " --> pdb=" O   LEU A 607 " (cutoff:3.500A)
      removed outlier: 7.473A  pdb=" N   VAL A 609 " --> pdb=" O   THR A 423 " (cutoff:3.500A)
      removed outlier: 6.047A  pdb=" N   ALA A 425 " --> pdb=" O   VAL A 609 " (cutoff:3.500A)
      removed outlier: 7.187A  pdb=" N   LEU A 611 " --> pdb=" O   ALA A 425 " (cutoff:3.500A)
      removed outlier: 6.213A  pdb=" N   VAL A 427 " --> pdb=" O   LEU A 611 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   GLU A 618 " --> pdb=" O   VAL A 610 " (cutoff:3.500A)
      removed outlier: 6.862A  pdb=" N   SER A 612 " --> pdb=" O   ILE A 616 " (cutoff:3.500A)
      removed outlier: 5.620A  pdb=" N   ILE A 616 " --> pdb=" O   SER A 612 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 1058 through 1067
      removed outlier: 6.989A  pdb=" N   VAL A1059 " --> pdb=" O   ARG A1050 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   ARG A1050 " --> pdb=" O   VAL A1059 " (cutoff:3.500A)
      removed outlier: 6.728A  pdb=" N   THR A1061 " --> pdb=" O   THR A1048 " (cutoff:3.500A)
      removed outlier: 6.396A  pdb=" N   THR A1048 " --> pdb=" O   THR A1061 " (cutoff:3.500A)
      removed outlier: 5.083A  pdb=" N   LEU A1063 " --> pdb=" O   ASP A1046 " (cutoff:3.500A)
      removed outlier: 4.206A  pdb=" N   VAL A1047 " --> pdb=" O   SER A1098 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   SER A1098 " --> pdb=" O   VAL A1047 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1120 through 1123
      removed outlier: 6.466A  pdb=" N   ALA A1121 " --> pdb=" O   LEU A1208 " (cutoff:3.500A)
      removed outlier: 7.512A  pdb=" N   ASP A1210 " --> pdb=" O   ALA A1121 " (cutoff:3.500A)
      removed outlier: 6.815A  pdb=" N   VAL A1123 " --> pdb=" O   ASP A1210 " (cutoff:3.500A)
      removed outlier: 3.942A  pdb=" N   GLU A1263 " --> pdb=" O   VAL A1255 " (cutoff:3.500A)
      removed outlier: 6.330A  pdb=" N   ASP A1257 " --> pdb=" O   ILE A1261 " (cutoff:3.500A)
      removed outlier: 5.233A  pdb=" N   ILE A1261 " --> pdb=" O   ASP A1257 " (cutoff:3.500A)

    617 hydrogen bonds defined for protein.
    1815 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.82

  Time building geometry restraints manager: 1.16 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2087
        1.33 -     1.45: 1923
        1.45 -     1.57: 5412
        1.57 -     1.69: 0
        1.69 -     1.81: 78
  Bond restraints: 9500
  Sorted by residual:
  bond pdb=" N   VAL A1076 "
       pdb=" CA  VAL A1076 "
    ideal  model  delta    sigma   weight residual
    1.456  1.490 -0.035 1.11e-02 8.12e+03 9.76e+00
  bond pdb=" C   ARG A 405 "
       pdb=" N   PRO A 406 "
    ideal  model  delta    sigma   weight residual
    1.334  1.359 -0.026 8.40e-03 1.42e+04 9.45e+00
  bond pdb=" N   ILE A 346 "
       pdb=" CA  ILE A 346 "
    ideal  model  delta    sigma   weight residual
    1.461  1.497 -0.037 1.19e-02 7.06e+03 9.44e+00
  bond pdb=" N   ILE A 722 "
       pdb=" CA  ILE A 722 "
    ideal  model  delta    sigma   weight residual
    1.460  1.497 -0.037 1.19e-02 7.06e+03 9.44e+00
  bond pdb=" N   ILE A 176 "
       pdb=" CA  ILE A 176 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.19e-02 7.06e+03 8.99e+00
  ... (remaining 9495 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.82: 12308
        1.82 -     3.64: 488
        3.64 -     5.45: 53
        5.45 -     7.27: 6
        7.27 -     9.09: 2
  Bond angle restraints: 12857
  Sorted by residual:
  angle pdb=" N   LYS A 354 "
        pdb=" CA  LYS A 354 "
        pdb=" C   LYS A 354 "
      ideal   model   delta    sigma   weight residual
     111.07  106.92    4.15 1.07e+00 8.73e-01 1.50e+01
  angle pdb=" N   GLY A1174 "
        pdb=" CA  GLY A1174 "
        pdb=" C   GLY A1174 "
      ideal   model   delta    sigma   weight residual
     113.18  104.15    9.03 2.37e+00 1.78e-01 1.45e+01
  angle pdb=" CA  GLY A 170 "
        pdb=" C   GLY A 170 "
        pdb=" O   GLY A 170 "
      ideal   model   delta    sigma   weight residual
     120.45  116.61    3.84 1.02e+00 9.61e-01 1.41e+01
  angle pdb=" N   ASP A 179 "
        pdb=" CA  ASP A 179 "
        pdb=" C   ASP A 179 "
      ideal   model   delta    sigma   weight residual
     113.72  109.00    4.72 1.30e+00 5.92e-01 1.32e+01
  angle pdb=" N   ILE A 523 "
        pdb=" CA  ILE A 523 "
        pdb=" C   ILE A 523 "
      ideal   model   delta    sigma   weight residual
     111.45  108.09    3.36 9.30e-01 1.16e+00 1.31e+01
  ... (remaining 12852 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.27: 5434
       24.27 -    48.55: 294
       48.55 -    72.82: 31
       72.82 -    97.09: 6
       97.09 -   121.37: 4
  Dihedral angle restraints: 5769
    sinusoidal: 2307
      harmonic: 3462
  Sorted by residual:
  dihedral pdb=" C21 9Z9 A1301 "
           pdb=" C22 9Z9 A1301 "
           pdb=" C23 9Z9 A1301 "
           pdb=" C24 9Z9 A1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      77.99  -43.38  121.37     1      3.00e+01 1.11e-03 1.62e+01
  dihedral pdb=" C   PHE A 987 "
           pdb=" N   PHE A 987 "
           pdb=" CA  PHE A 987 "
           pdb=" CB  PHE A 987 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -132.39    9.79     0      2.50e+00 1.60e-01 1.53e+01
  dihedral pdb=" C18 9Z9 A1301 "
           pdb=" C17 9Z9 A1301 "
           pdb=" O20 9Z9 A1301 "
           pdb=" C21 9Z9 A1301 "
      ideal   model   delta sinusoidal    sigma   weight residual
     163.81  -92.29 -103.90     1      3.00e+01 1.11e-03 1.32e+01
  ... (remaining 5766 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.059: 1254
       0.059 -    0.118: 212
       0.118 -    0.177: 31
       0.177 -    0.236: 15
       0.236 -    0.295: 2
  Chirality restraints: 1514
  Sorted by residual:
  chirality pdb=" CA  PHE A 987 "
            pdb=" N   PHE A 987 "
            pdb=" C   PHE A 987 "
            pdb=" CB  PHE A 987 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.22    0.30 2.00e-01 2.50e+01 2.18e+00
  chirality pdb=" CA  LEU A1075 "
            pdb=" N   LEU A1075 "
            pdb=" C   LEU A1075 "
            pdb=" CB  LEU A1075 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.76   -0.25 2.00e-01 2.50e+01 1.55e+00
  chirality pdb=" CA  ASN A 706 "
            pdb=" N   ASN A 706 "
            pdb=" C   ASN A 706 "
            pdb=" CB  ASN A 706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.28    0.23 2.00e-01 2.50e+01 1.36e+00
  ... (remaining 1511 not shown)

  Planarity restraints: 1608
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A1092 "   -0.256 9.50e-02 1.11e+02   1.15e-01 8.06e+00
        pdb=" NE  ARG A1092 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  ARG A1092 "    0.002 2.00e-02 2.50e+03
        pdb=" NH1 ARG A1092 "    0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG A1092 "   -0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 344 "    0.013 2.00e-02 2.50e+03   2.65e-02 7.02e+00
        pdb=" C   LEU A 344 "   -0.046 2.00e-02 2.50e+03
        pdb=" O   LEU A 344 "    0.017 2.00e-02 2.50e+03
        pdb=" N   ILE A 345 "    0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG A 372 "   -0.232 9.50e-02 1.11e+02   1.04e-01 6.67e+00
        pdb=" NE  ARG A 372 "    0.013 2.00e-02 2.50e+03
        pdb=" CZ  ARG A 372 "    0.005 2.00e-02 2.50e+03
        pdb=" NH1 ARG A 372 "    0.001 2.00e-02 2.50e+03
        pdb=" NH2 ARG A 372 "   -0.009 2.00e-02 2.50e+03
  ... (remaining 1605 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 972
        2.75 -     3.29: 9394
        3.29 -     3.82: 15174
        3.82 -     4.36: 18529
        4.36 -     4.90: 32404
  Nonbonded interactions: 76473
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU A 142 "
            pdb=" NH2 ARG A 889 "
     model   vdw
     2.210 3.120
  nonbonded pdb=" O   GLY A 862 "
            pdb=" OG1 THR A 866 "
     model   vdw
     2.221 3.040
  nonbonded pdb=" O   ILE A1090 "
            pdb=" OH  TYR A1116 "
     model   vdw
     2.228 3.040
  nonbonded pdb=" O   VAL A 939 "
            pdb=" OG1 THR A 943 "
     model   vdw
     2.317 3.040
  nonbonded pdb=" O   LYS A 909 "
            pdb=" OG  SER A 913 "
     model   vdw
     2.346 3.040
  ... (remaining 76468 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:             2.360
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.290
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.420
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.400
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8374
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   9500  Z= 0.343
  Angle     :  0.738   9.091  12857  Z= 0.506
  Chirality :  0.050   0.295   1514
  Planarity :  0.007   0.115   1608
  Dihedral  : 14.589 121.366   3549
  Min Nonbonded Distance : 2.210

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  3.66 %
    Favored  : 96.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.65 (0.24), residues: 1193
  helix:  1.06 (0.18), residues: 779
  sheet: -1.59 (0.78), residues: 48
  loop : -0.50 (0.33), residues: 366

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A1019 
 TYR   0.025   0.001   TYR A 248 
 PHE   0.021   0.001   PHE A 119 
 TRP   0.006   0.001   TRP A 955 
 HIS   0.004   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00506 ( 9500)
  covalent geometry    : angle       0.73828 (12857)
  hydrogen bonds       : bond        0.14880 (  617)
  hydrogen bonds       : angle       5.78263 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 117
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  165 ASP cc_start: 0.7896 (m-30) cc_final: 0.7452 (m-30)
REVERT: A 1248 GLN cc_start: 0.8532 (tt0) cc_final: 0.8294 (tp40)
  outliers start: 1
  outliers final: 1
  residues processed: 118
  average time/residue: 0.1045
  time to fit residues: 16.9150
Evaluate side-chains
  95 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 94
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  372 ARG
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 108 optimal weight:    0.0980
   chunk 49 optimal weight:    0.0870
   chunk 97 optimal weight:    0.8980
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    0.2980
   chunk 5 optimal weight:    0.9980
   chunk 33 optimal weight:    2.9990
   chunk 65 optimal weight:    0.2980
   chunk 62 optimal weight:    0.1980
   chunk 51 optimal weight:    0.9990
   chunk 117 optimal weight:    5.9990
   overall best weight:    0.1958

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

Flipped N/Q/H residues before XYZ refinement:
A 196 GLN
A 637 GLN
A1242 HIS
A1248 GLN
A1267 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.136000 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.104169 restraints weight = 11891.313|
|-----------------------------------------------------------------------------|
r_work (start): 0.3246 rms_B_bonded: 1.84
r_work: 0.3106 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2965 rms_B_bonded: 3.91 restraints_weight: 0.2500
r_work (final): 0.2965
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8510
moved from start:          0.1195

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9500  Z= 0.105
  Angle     :  0.462   8.258  12857  Z= 0.240
  Chirality :  0.037   0.134   1514
  Planarity :  0.004   0.046   1608
  Dihedral  :  6.129 107.700   1395
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 5.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  :  7.22 %
    Favored  : 92.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.55 (0.25), residues: 1193
  helix:  1.79 (0.19), residues: 784
  sheet: -1.40 (0.81), residues: 48
  loop : -0.22 (0.33), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A1274 
 TYR   0.021   0.001   TYR A 248 
 PHE   0.022   0.001   PHE A1167 
 TRP   0.005   0.001   TRP A 955 
 HIS   0.004   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00196 ( 9500)
  covalent geometry    : angle       0.46214 (12857)
  hydrogen bonds       : bond        0.04368 (  617)
  hydrogen bonds       : angle       4.19591 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  122 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 115
  time to evaluate  : 0.346 
Fit side-chains
REVERT: A   90 ASP cc_start: 0.8606 (t70) cc_final: 0.8157 (t0)
REVERT: A  725 MET cc_start: 0.7130 (mmp) cc_final: 0.6752 (mtp)
REVERT: A 1017 ASP cc_start: 0.8392 (t0) cc_final: 0.8147 (t0)
REVERT: A 1046 ASP cc_start: 0.8175 (t70) cc_final: 0.7666 (t0)
REVERT: A 1050 ARG cc_start: 0.7384 (mtp85) cc_final: 0.7072 (mtp85)
REVERT: A 1054 ARG cc_start: 0.7425 (mtm180) cc_final: 0.7144 (mpp80)
REVERT: A 1168 ILE cc_start: 0.8006 (OUTLIER) cc_final: 0.7753 (mp)
REVERT: A 1248 GLN cc_start: 0.8891 (tt0) cc_final: 0.8257 (tp40)
  outliers start: 7
  outliers final: 4
  residues processed: 119
  average time/residue: 0.1045
  time to fit residues: 17.1114
Evaluate side-chains
  107 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 102
  time to evaluate  : 0.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1201 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 91 optimal weight:    0.9990
   chunk 97 optimal weight:    0.0270
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    0.0270
   chunk 60 optimal weight:    3.9990
   chunk 78 optimal weight:    0.4980
   chunk 52 optimal weight:    0.3980
   chunk 38 optimal weight:    0.4980
   chunk 45 optimal weight:    0.9990
   chunk 20 optimal weight:    3.9990
   overall best weight:    0.2896

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

Flipped N/Q/H residues before XYZ refinement:
A1242 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.136484 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.102589 restraints weight = 11935.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3244 rms_B_bonded: 2.02
r_work: 0.3115 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.2966 rms_B_bonded: 4.30 restraints_weight: 0.2500
r_work (final): 0.2966
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8496
moved from start:          0.1552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.021   9500  Z= 0.096
  Angle     :  0.429   7.307  12857  Z= 0.222
  Chirality :  0.036   0.134   1514
  Planarity :  0.003   0.043   1608
  Dihedral  :  5.514  94.334   1391
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.26 %
    Favored  : 98.74 %
  Rotamer:
    Outliers :  0.99 %
    Allowed  :  9.00 %
    Favored  : 90.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.25), residues: 1193
  helix:  2.13 (0.19), residues: 783
  sheet: -1.27 (0.83), residues: 48
  loop : -0.12 (0.34), residues: 362

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 598 
 TYR   0.020   0.001   TYR A 248 
 PHE   0.025   0.001   PHE A1167 
 TRP   0.006   0.001   TRP A 213 
 HIS   0.003   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00184 ( 9500)
  covalent geometry    : angle       0.42926 (12857)
  hydrogen bonds       : bond        0.03985 (  617)
  hydrogen bonds       : angle       3.87807 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 117
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A   90 ASP cc_start: 0.8616 (t70) cc_final: 0.8147 (t0)
REVERT: A  165 ASP cc_start: 0.8511 (m-30) cc_final: 0.8111 (m-30)
REVERT: A 1046 ASP cc_start: 0.8107 (t70) cc_final: 0.7464 (t0)
REVERT: A 1050 ARG cc_start: 0.7422 (mtp85) cc_final: 0.6893 (mtp85)
REVERT: A 1154 ASP cc_start: 0.7837 (m-30) cc_final: 0.7378 (t0)
REVERT: A 1168 ILE cc_start: 0.8026 (OUTLIER) cc_final: 0.7749 (mp)
REVERT: A 1248 GLN cc_start: 0.8902 (tt0) cc_final: 0.8239 (tp40)
  outliers start: 10
  outliers final: 6
  residues processed: 122
  average time/residue: 0.1031
  time to fit residues: 17.4989
Evaluate side-chains
  108 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 101
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1239 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 111 optimal weight:    2.9990
   chunk 98 optimal weight:    2.9990
   chunk 104 optimal weight:    0.6980
   chunk 35 optimal weight:    4.9990
   chunk 51 optimal weight:    0.7980
   chunk 46 optimal weight:    3.9990
   chunk 75 optimal weight:    5.9990
   chunk 72 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 20 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   overall best weight:    2.0986

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

Flipped N/Q/H residues before XYZ refinement:
A1137 ASN
A1242 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.129612 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3103 r_free = 0.3103 target = 0.094536 restraints weight = 11973.502|
|-----------------------------------------------------------------------------|
r_work (start): 0.3038 rms_B_bonded: 2.03
r_work: 0.2915 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2770 rms_B_bonded: 3.97 restraints_weight: 0.2500
r_work (final): 0.2770
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8500
moved from start:          0.1467

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.040   9500  Z= 0.233
  Angle     :  0.531  10.207  12857  Z= 0.273
  Chirality :  0.041   0.134   1514
  Planarity :  0.004   0.043   1608
  Dihedral  :  5.715  91.881   1391
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.10 %
    Favored  : 97.90 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 10.78 %
    Favored  : 87.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.56 (0.25), residues: 1193
  helix:  1.75 (0.18), residues: 786
  sheet: -1.43 (0.80), residues: 48
  loop : -0.12 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1050 
 TYR   0.027   0.002   TYR A 248 
 PHE   0.023   0.002   PHE A 979 
 TRP   0.006   0.001   TRP A 316 
 HIS   0.007   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00563 ( 9500)
  covalent geometry    : angle       0.53134 (12857)
  hydrogen bonds       : bond        0.05195 (  617)
  hydrogen bonds       : angle       4.14150 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 97
  time to evaluate  : 0.348 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8049 (tp30) cc_final: 0.7627 (mt-10)
REVERT: A  165 ASP cc_start: 0.8565 (m-30) cc_final: 0.8157 (m-30)
REVERT: A 1046 ASP cc_start: 0.8016 (t70) cc_final: 0.7352 (t0)
REVERT: A 1154 ASP cc_start: 0.7792 (m-30) cc_final: 0.7398 (t0)
REVERT: A 1168 ILE cc_start: 0.7942 (OUTLIER) cc_final: 0.7653 (mp)
REVERT: A 1248 GLN cc_start: 0.8876 (tt0) cc_final: 0.8119 (tp40)
  outliers start: 19
  outliers final: 14
  residues processed: 111
  average time/residue: 0.0970
  time to fit residues: 15.1462
Evaluate side-chains
  108 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 93
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  351 ILE
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  604 ASN
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  866 THR
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue  949 ILE
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1201 ILE
Chi-restraints excluded: chain A residue 1239 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 114 optimal weight:    2.9990
   chunk 35 optimal weight:    0.9980
   chunk 83 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 59 optimal weight:    5.9990
   chunk 63 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 100 optimal weight:    0.9980
   chunk 27 optimal weight:    0.7980
   chunk 73 optimal weight:    0.8980
   chunk 81 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A1137 ASN
A1242 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.131533 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.096374 restraints weight = 11791.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.3103 rms_B_bonded: 2.11
r_work: 0.2976 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.2827 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.2827
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8515
moved from start:          0.1538

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9500  Z= 0.127
  Angle     :  0.465   9.302  12857  Z= 0.237
  Chirality :  0.037   0.129   1514
  Planarity :  0.003   0.042   1608
  Dihedral  :  5.441  85.179   1391
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 4.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.76 %
    Favored  : 98.24 %
  Rotamer:
    Outliers :  1.48 %
    Allowed  : 11.97 %
    Favored  : 86.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.81 (0.25), residues: 1193
  helix:  1.98 (0.19), residues: 784
  sheet: -1.35 (0.80), residues: 48
  loop : -0.09 (0.34), residues: 361

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1050 
 TYR   0.023   0.001   TYR A 248 
 PHE   0.014   0.001   PHE A 979 
 TRP   0.008   0.001   TRP A 213 
 HIS   0.005   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 9500)
  covalent geometry    : angle       0.46478 (12857)
  hydrogen bonds       : bond        0.04498 (  617)
  hydrogen bonds       : angle       3.97206 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 101
  time to evaluate  : 0.353 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8081 (tp30) cc_final: 0.7670 (mt-10)
REVERT: A  165 ASP cc_start: 0.8606 (m-30) cc_final: 0.8271 (m-30)
REVERT: A 1046 ASP cc_start: 0.8050 (t70) cc_final: 0.7361 (t0)
REVERT: A 1050 ARG cc_start: 0.7293 (mtp85) cc_final: 0.6868 (mtp85)
REVERT: A 1154 ASP cc_start: 0.7739 (m-30) cc_final: 0.7380 (t0)
REVERT: A 1168 ILE cc_start: 0.7874 (OUTLIER) cc_final: 0.7585 (mp)
REVERT: A 1248 GLN cc_start: 0.8866 (tt0) cc_final: 0.8130 (tp40)
  outliers start: 15
  outliers final: 11
  residues processed: 110
  average time/residue: 0.0978
  time to fit residues: 15.0950
Evaluate side-chains
  109 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 97
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  866 THR
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Chi-restraints excluded: chain A residue 1239 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 54 optimal weight:    5.9990
   chunk 30 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 1 optimal weight:    5.9990
   chunk 32 optimal weight:    0.7980
   chunk 118 optimal weight:    0.9990
   chunk 93 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 58 optimal weight:    1.9990
   chunk 77 optimal weight:    0.7980
   chunk 102 optimal weight:    2.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A1137 ASN
A1242 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.132842 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.099571 restraints weight = 11826.387|
|-----------------------------------------------------------------------------|
r_work (start): 0.3165 rms_B_bonded: 1.96
r_work: 0.3026 rms_B_bonded: 2.39 restraints_weight: 0.5000
r_work: 0.2881 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2881
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8450
moved from start:          0.1649

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9500  Z= 0.123
  Angle     :  0.467  10.342  12857  Z= 0.234
  Chirality :  0.037   0.130   1514
  Planarity :  0.003   0.041   1608
  Dihedral  :  5.126  73.878   1391
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 4.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.84 %
    Favored  : 98.16 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 12.36 %
    Favored  : 86.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.92 (0.25), residues: 1193
  helix:  2.07 (0.19), residues: 785
  sheet: -1.17 (0.69), residues: 58
  loop : -0.06 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1050 
 TYR   0.023   0.001   TYR A 248 
 PHE   0.014   0.001   PHE A 979 
 TRP   0.008   0.001   TRP A 213 
 HIS   0.005   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00277 ( 9500)
  covalent geometry    : angle       0.46738 (12857)
  hydrogen bonds       : bond        0.04346 (  617)
  hydrogen bonds       : angle       3.88345 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 104
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8055 (tp30) cc_final: 0.7585 (mt-10)
REVERT: A  165 ASP cc_start: 0.8545 (m-30) cc_final: 0.8158 (m-30)
REVERT: A 1046 ASP cc_start: 0.7996 (t70) cc_final: 0.7666 (t0)
REVERT: A 1154 ASP cc_start: 0.7722 (m-30) cc_final: 0.7358 (t0)
REVERT: A 1168 ILE cc_start: 0.7801 (OUTLIER) cc_final: 0.7514 (mp)
REVERT: A 1173 GLU cc_start: 0.6189 (OUTLIER) cc_final: 0.5822 (pm20)
REVERT: A 1248 GLN cc_start: 0.8868 (tt0) cc_final: 0.8109 (tp40)
  outliers start: 16
  outliers final: 12
  residues processed: 115
  average time/residue: 0.1039
  time to fit residues: 16.6414
Evaluate side-chains
  115 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 101
  time to evaluate  : 0.231 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1173 GLU
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Chi-restraints excluded: chain A residue 1239 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 80 optimal weight:    0.6980
   chunk 100 optimal weight:    2.9990
   chunk 89 optimal weight:    2.9990
   chunk 0 optimal weight:    6.9990
   chunk 105 optimal weight:    2.9990
   chunk 73 optimal weight:    0.8980
   chunk 58 optimal weight:    5.9990
   chunk 5 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 87 optimal weight:    1.9990
   chunk 88 optimal weight:    0.7980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.133326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.100113 restraints weight = 11774.392|
|-----------------------------------------------------------------------------|
r_work (start): 0.3172 rms_B_bonded: 1.97
r_work: 0.3031 rms_B_bonded: 2.41 restraints_weight: 0.5000
r_work: 0.2887 rms_B_bonded: 3.92 restraints_weight: 0.2500
r_work (final): 0.2887
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8446
moved from start:          0.1708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   9500  Z= 0.119
  Angle     :  0.461   8.799  12857  Z= 0.232
  Chirality :  0.037   0.130   1514
  Planarity :  0.003   0.039   1608
  Dihedral  :  4.538  53.528   1391
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 4.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.36 %
    Favored  : 85.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.96 (0.25), residues: 1193
  helix:  2.09 (0.19), residues: 791
  sheet: -1.08 (0.70), residues: 58
  loop : -0.06 (0.35), residues: 344

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1050 
 TYR   0.022   0.001   TYR A 248 
 PHE   0.013   0.001   PHE A 979 
 TRP   0.008   0.001   TRP A 213 
 HIS   0.005   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 9500)
  covalent geometry    : angle       0.46096 (12857)
  hydrogen bonds       : bond        0.04273 (  617)
  hydrogen bonds       : angle       3.84443 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 104
  time to evaluate  : 0.341 
Fit side-chains
REVERT: A  165 ASP cc_start: 0.8544 (m-30) cc_final: 0.8161 (m-30)
REVERT: A  189 GLU cc_start: 0.8293 (OUTLIER) cc_final: 0.7483 (pm20)
REVERT: A  366 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8287 (mp)
REVERT: A 1046 ASP cc_start: 0.8017 (t70) cc_final: 0.7550 (t0)
REVERT: A 1154 ASP cc_start: 0.7695 (m-30) cc_final: 0.7347 (t0)
REVERT: A 1168 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7508 (mp)
REVERT: A 1173 GLU cc_start: 0.6286 (OUTLIER) cc_final: 0.5914 (pm20)
REVERT: A 1248 GLN cc_start: 0.8886 (tt0) cc_final: 0.8123 (tp40)
  outliers start: 19
  outliers final: 14
  residues processed: 117
  average time/residue: 0.1016
  time to fit residues: 16.7673
Evaluate side-chains
  119 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 101
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1173 GLU
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Chi-restraints excluded: chain A residue 1239 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 64 optimal weight:    0.7980
   chunk 5 optimal weight:    0.0770
   chunk 30 optimal weight:    1.9990
   chunk 51 optimal weight:    0.0980
   chunk 27 optimal weight:    0.7980
   chunk 104 optimal weight:    2.9990
   chunk 118 optimal weight:    5.9990
   chunk 86 optimal weight:    0.6980
   chunk 17 optimal weight:    1.9990
   chunk 82 optimal weight:    1.9990
   chunk 70 optimal weight:    4.9990
   overall best weight:    0.4938

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

Flipped N/Q/H residues before XYZ refinement:
A  42 GLN
A 463 ASN
** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1163 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.134758 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.099981 restraints weight = 11733.860|
|-----------------------------------------------------------------------------|
r_work (start): 0.3154 rms_B_bonded: 2.02
r_work: 0.3037 rms_B_bonded: 2.45 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 3.99 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8426
moved from start:          0.1838

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9500  Z= 0.102
  Angle     :  0.449   8.271  12857  Z= 0.225
  Chirality :  0.037   0.132   1514
  Planarity :  0.003   0.038   1608
  Dihedral  :  3.950  42.996   1391
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 4.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.98 %
    Allowed  : 12.76 %
    Favored  : 85.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.12 (0.25), residues: 1193
  helix:  2.24 (0.19), residues: 786
  sheet: -1.00 (0.70), residues: 58
  loop : -0.07 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A1050 
 TYR   0.021   0.001   TYR A 248 
 PHE   0.011   0.001   PHE A 979 
 TRP   0.009   0.001   TRP A 213 
 HIS   0.004   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00214 ( 9500)
  covalent geometry    : angle       0.44909 (12857)
  hydrogen bonds       : bond        0.04029 (  617)
  hydrogen bonds       : angle       3.75502 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  123 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 0.371 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8044 (tp30) cc_final: 0.7624 (mt-10)
REVERT: A   90 ASP cc_start: 0.8588 (t70) cc_final: 0.8347 (t70)
REVERT: A  165 ASP cc_start: 0.8527 (m-30) cc_final: 0.8177 (m-30)
REVERT: A  366 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8180 (mp)
REVERT: A 1046 ASP cc_start: 0.8046 (t70) cc_final: 0.7560 (t0)
REVERT: A 1154 ASP cc_start: 0.7670 (m-30) cc_final: 0.7342 (t0)
REVERT: A 1168 ILE cc_start: 0.7791 (OUTLIER) cc_final: 0.7503 (mp)
REVERT: A 1173 GLU cc_start: 0.6328 (OUTLIER) cc_final: 0.5955 (pm20)
REVERT: A 1248 GLN cc_start: 0.8913 (tt0) cc_final: 0.8146 (tp40)
  outliers start: 20
  outliers final: 13
  residues processed: 117
  average time/residue: 0.1022
  time to fit residues: 16.6918
Evaluate side-chains
  116 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  462 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1173 GLU
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Chi-restraints excluded: chain A residue 1239 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 115 optimal weight:    5.9990
   chunk 116 optimal weight:    6.9990
   chunk 61 optimal weight:    0.0980
   chunk 68 optimal weight:    3.9990
   chunk 29 optimal weight:    0.9980
   chunk 106 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 74 optimal weight:    0.8980
   chunk 65 optimal weight:    1.9990
   chunk 14 optimal weight:    2.9990
   chunk 62 optimal weight:    6.9990
   overall best weight:    1.1984

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

Flipped N/Q/H residues before XYZ refinement:
A1163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.132025 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3164 r_free = 0.3164 target = 0.098550 restraints weight = 11826.282|
|-----------------------------------------------------------------------------|
r_work (start): 0.3152 rms_B_bonded: 1.97
r_work: 0.3013 rms_B_bonded: 2.40 restraints_weight: 0.5000
r_work: 0.2869 rms_B_bonded: 3.89 restraints_weight: 0.2500
r_work (final): 0.2869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8465
moved from start:          0.1757

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   9500  Z= 0.153
  Angle     :  0.489   9.017  12857  Z= 0.246
  Chirality :  0.038   0.127   1514
  Planarity :  0.003   0.039   1608
  Dihedral  :  4.057  42.885   1391
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.01 %
    Favored  : 97.99 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.76 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.99 (0.25), residues: 1193
  helix:  2.09 (0.18), residues: 793
  sheet: -1.01 (0.70), residues: 58
  loop : -0.02 (0.35), residues: 342

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A1274 
 TYR   0.025   0.001   TYR A 248 
 PHE   0.017   0.001   PHE A 979 
 TRP   0.007   0.001   TRP A 213 
 HIS   0.006   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00360 ( 9500)
  covalent geometry    : angle       0.48891 (12857)
  hydrogen bonds       : bond        0.04527 (  617)
  hydrogen bonds       : angle       3.86241 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 104
  time to evaluate  : 0.350 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8038 (tp30) cc_final: 0.7585 (mt-10)
REVERT: A  165 ASP cc_start: 0.8552 (m-30) cc_final: 0.8162 (m-30)
REVERT: A  189 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7485 (pm20)
REVERT: A  366 LEU cc_start: 0.8637 (OUTLIER) cc_final: 0.8373 (mp)
REVERT: A 1046 ASP cc_start: 0.7988 (t70) cc_final: 0.7666 (t0)
REVERT: A 1100 GLN cc_start: 0.7918 (mt0) cc_final: 0.7485 (mt0)
REVERT: A 1154 ASP cc_start: 0.7690 (m-30) cc_final: 0.7363 (t0)
REVERT: A 1168 ILE cc_start: 0.7810 (OUTLIER) cc_final: 0.7525 (mp)
REVERT: A 1173 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.5963 (pm20)
REVERT: A 1248 GLN cc_start: 0.8909 (tt0) cc_final: 0.8150 (tp40)
  outliers start: 21
  outliers final: 14
  residues processed: 118
  average time/residue: 0.0987
  time to fit residues: 16.1691
Evaluate side-chains
  120 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 102
  time to evaluate  : 0.334 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  189 GLU
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1173 GLU
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Chi-restraints excluded: chain A residue 1239 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 94 optimal weight:    3.9990
   chunk 61 optimal weight:    7.9990
   chunk 76 optimal weight:    0.9980
   chunk 105 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 31 optimal weight:    0.0980
   chunk 66 optimal weight:    0.7980
   chunk 5 optimal weight:    0.2980
   chunk 9 optimal weight:    0.9980
   chunk 87 optimal weight:    0.8980
   chunk 95 optimal weight:   10.0000
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A1163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.134214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3202 r_free = 0.3202 target = 0.101052 restraints weight = 11748.628|
|-----------------------------------------------------------------------------|
r_work (start): 0.3153 rms_B_bonded: 1.94
r_work: 0.3017 rms_B_bonded: 2.37 restraints_weight: 0.5000
r_work: 0.2875 rms_B_bonded: 3.85 restraints_weight: 0.2500
r_work (final): 0.2875
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.1859

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024   9500  Z= 0.110
  Angle     :  0.461   8.339  12857  Z= 0.232
  Chirality :  0.037   0.134   1514
  Planarity :  0.003   0.037   1608
  Dihedral  :  3.952  38.259   1391
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.68 %
    Favored  : 98.32 %
  Rotamer:
    Outliers :  1.88 %
    Allowed  : 12.96 %
    Favored  : 85.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.14 (0.25), residues: 1193
  helix:  2.25 (0.18), residues: 786
  sheet: -0.93 (0.70), residues: 58
  loop : -0.04 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A1050 
 TYR   0.021   0.001   TYR A 248 
 PHE   0.011   0.001   PHE A 979 
 TRP   0.009   0.001   TRP A 213 
 HIS   0.004   0.001   HIS A 103 

Details of bonding type rmsd
  covalent geometry    : bond        0.00235 ( 9500)
  covalent geometry    : angle       0.46060 (12857)
  hydrogen bonds       : bond        0.04142 (  617)
  hydrogen bonds       : angle       3.79044 ( 1815)

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

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

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2386 Ramachandran restraints generated.
    1193 Oldfield, 0 Emsley, 1193 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 102
  time to evaluate  : 0.243 
Fit side-chains
REVERT: A   40 GLU cc_start: 0.8000 (tp30) cc_final: 0.7579 (mt-10)
REVERT: A   90 ASP cc_start: 0.8549 (t70) cc_final: 0.8277 (t70)
REVERT: A  165 ASP cc_start: 0.8528 (m-30) cc_final: 0.8147 (m-30)
REVERT: A  366 LEU cc_start: 0.8560 (OUTLIER) cc_final: 0.8205 (mp)
REVERT: A 1046 ASP cc_start: 0.7969 (t70) cc_final: 0.7630 (t0)
REVERT: A 1154 ASP cc_start: 0.7667 (m-30) cc_final: 0.7305 (t0)
REVERT: A 1168 ILE cc_start: 0.7767 (OUTLIER) cc_final: 0.7483 (mp)
REVERT: A 1173 GLU cc_start: 0.6317 (OUTLIER) cc_final: 0.5947 (pm20)
REVERT: A 1248 GLN cc_start: 0.8884 (tt0) cc_final: 0.8119 (tp40)
  outliers start: 19
  outliers final: 14
  residues processed: 114
  average time/residue: 0.1026
  time to fit residues: 16.4255
Evaluate side-chains
  114 residues out of total 1011 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 97
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 ILE
Chi-restraints excluded: chain A residue  223 MET
Chi-restraints excluded: chain A residue  229 SER
Chi-restraints excluded: chain A residue  299 MET
Chi-restraints excluded: chain A residue  366 LEU
Chi-restraints excluded: chain A residue  505 VAL
Chi-restraints excluded: chain A residue  578 ILE
Chi-restraints excluded: chain A residue  589 THR
Chi-restraints excluded: chain A residue  592 THR
Chi-restraints excluded: chain A residue  619 THR
Chi-restraints excluded: chain A residue  940 SER
Chi-restraints excluded: chain A residue 1143 ILE
Chi-restraints excluded: chain A residue 1168 ILE
Chi-restraints excluded: chain A residue 1173 GLU
Chi-restraints excluded: chain A residue 1185 MET
Chi-restraints excluded: chain A residue 1201 ILE
Chi-restraints excluded: chain A residue 1239 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 119
   random chunks:
   chunk 77 optimal weight:    0.7980
   chunk 108 optimal weight:   10.0000
   chunk 30 optimal weight:    2.9990
   chunk 104 optimal weight:    0.8980
   chunk 63 optimal weight:    1.9990
   chunk 32 optimal weight:    2.9990
   chunk 44 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 33 optimal weight:    2.9990
   chunk 102 optimal weight:    6.9990
   chunk 15 optimal weight:    0.0770
   overall best weight:    0.7140

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

Flipped N/Q/H residues before XYZ refinement:
** A 633 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A1163 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.133992 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3169 r_free = 0.3169 target = 0.099047 restraints weight = 11710.270|
|-----------------------------------------------------------------------------|
r_work (start): 0.3158 rms_B_bonded: 2.01
r_work: 0.3038 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.2893 rms_B_bonded: 4.01 restraints_weight: 0.2500
r_work (final): 0.2893
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8461
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   9500  Z= 0.116
  Angle     :  0.462   8.303  12857  Z= 0.233
  Chirality :  0.038   0.153   1514
  Planarity :  0.003   0.038   1608
  Dihedral  :  3.939  35.960   1391
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 4.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.59 %
    Favored  : 98.41 %
  Rotamer:
    Outliers :  2.08 %
    Allowed  : 12.96 %
    Favored  : 84.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.17 (0.25), residues: 1193
  helix:  2.24 (0.18), residues: 789
  sheet: -0.88 (0.70), residues: 58
  loop :  0.02 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A1274 
 TYR   0.022   0.001   TYR A 248 
 PHE   0.013   0.001   PHE A 979 
 TRP   0.008   0.001   TRP A 213 
 HIS   0.007   0.001   HIS A 633 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 9500)
  covalent geometry    : angle       0.46170 (12857)
  hydrogen bonds       : bond        0.04182 (  617)
  hydrogen bonds       : angle       3.78252 ( 1815)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2499.06 seconds
wall clock time: 43 minutes 20.99 seconds (2600.99 seconds total)