Starting phenix.real_space_refine
on Sat Aug 23 09:41:35 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jqi_36573/08_2025/8jqi_36573_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jqi_36573/08_2025/8jqi_36573.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jqi_36573/08_2025/8jqi_36573_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jqi_36573/08_2025/8jqi_36573_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jqi_36573/08_2025/8jqi_36573.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jqi_36573/08_2025/8jqi_36573.map"
  }
  resolution = 4.1
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.064
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      63      5.16       5
     C    7121      2.51       5
     N    1917      2.21       5
     O    2079      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 11180
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 8716
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1062, 8716
          Classifications: {'peptide': 1062}
          Link IDs: {'PTRANS': 47, 'TRANS': 1014}
          Chain breaks: 4
    Chain: "B"
      Number of atoms: 2464
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 307, 2464
          Classifications: {'peptide': 307}
          Link IDs: {'PTRANS': 18, 'TRANS': 288}
  Time building chain proxies: 2.45, per 1000 atoms: 0.22
  Number of scatterers: 11180
  At special positions: 0
  Unit cell: (108.9, 102.3, 152.9, 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      63     16.00
     O    2079      8.00
     N    1917      7.00
     C    7121      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: 0.83
  Conformation dependent library (CDL) restraints added in 555.6 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2614

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 17 sheets defined
      35.2% alpha, 18.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 11 through 25
      removed outlier: 3.776A  pdb=" N   GLN A  17 " --> pdb=" O   TYR A  13 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 136
    Processing helix  chain 'A' and resid 137 through 154
      removed outlier: 3.909A  pdb=" N   ASP A 154 " --> pdb=" O   ILE A 150 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 163 through 173
      Proline residue:  A 171  - end of helix
    Processing helix  chain 'A' and resid 180 through 191
      removed outlier: 4.167A  pdb=" N   LYS A 184 " --> pdb=" O   ALA A 180 " (cutoff:3.500A)
      removed outlier: 3.644A  pdb=" N   ASP A 185 " --> pdb=" O   LYS A 181 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 199 through 223
      removed outlier: 5.839A  pdb=" N   SER A 216 " --> pdb=" O   GLU A 212 " (cutoff:3.500A)
      removed outlier: 6.543A  pdb=" N   ILE A 217 " --> pdb=" O   GLN A 213 " (cutoff:3.500A)
      removed outlier: 4.352A  pdb=" N   LEU A 218 " --> pdb=" O   GLN A 214 " (cutoff:3.500A)
      removed outlier: 3.884A  pdb=" N   LYS A 223 " --> pdb=" O   ASP A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 242 through 253
    Processing helix  chain 'A' and resid 256 through 260
    Processing helix  chain 'A' and resid 261 through 274
      removed outlier: 3.663A  pdb=" N   VAL A 265 " --> pdb=" O   ASP A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 287 through 296
    Processing helix  chain 'A' and resid 297 through 300
    Processing helix  chain 'A' and resid 303 through 307
      removed outlier: 3.713A  pdb=" N   TYR A 306 " --> pdb=" O   ASP A 303 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 311 through 315
      removed outlier: 3.662A  pdb=" N   ASN A 315 " --> pdb=" O   GLN A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 317 through 319
      No H-bonds generated for 'chain 'A' and resid 317 through 319'
    Processing helix  chain 'A' and resid 341 through 352
      removed outlier: 3.956A  pdb=" N   TYR A 345 " --> pdb=" O   SER A 341 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   GLY A 352 " --> pdb=" O   CYS A 348 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 382 through 392
    Processing helix  chain 'A' and resid 410 through 426
    Processing helix  chain 'A' and resid 427 through 429
      No H-bonds generated for 'chain 'A' and resid 427 through 429'
    Processing helix  chain 'A' and resid 539 through 554
      removed outlier: 3.666A  pdb=" N   THR A 554 " --> pdb=" O   TYR A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 609 through 620
      removed outlier: 4.001A  pdb=" N   LEU A 613 " --> pdb=" O   SER A 609 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 639 through 644
    Processing helix  chain 'A' and resid 652 through 663
    Processing helix  chain 'A' and resid 712 through 722
      removed outlier: 3.901A  pdb=" N   LYS A 722 " --> pdb=" O   SER A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 736 through 746
      removed outlier: 4.152A  pdb=" N   ARG A 742 " --> pdb=" O   GLU A 738 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 835 through 843
    Processing helix  chain 'A' and resid 845 through 849
    Processing helix  chain 'A' and resid 856 through 858
      No H-bonds generated for 'chain 'A' and resid 856 through 858'
    Processing helix  chain 'A' and resid 892 through 908
    Processing helix  chain 'A' and resid 927 through 934
    Processing helix  chain 'A' and resid 960 through 970
    Processing helix  chain 'A' and resid 970 through 979
    Processing helix  chain 'A' and resid 999 through 1005
    Processing helix  chain 'A' and resid 1018 through 1034
      removed outlier: 4.203A  pdb=" N   LEU A1030 " --> pdb=" O   ALA A1026 " (cutoff:3.500A)
      removed outlier: 6.101A  pdb=" N   ASN A1031 " --> pdb=" O   LEU A1027 " (cutoff:3.500A)
      removed outlier: 5.990A  pdb=" N   GLY A1032 " --> pdb=" O   PHE A1028 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   THR A1034 " --> pdb=" O   LEU A1030 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1040 through 1045
    Processing helix  chain 'A' and resid 1156 through 1158
      No H-bonds generated for 'chain 'A' and resid 1156 through 1158'
    Processing helix  chain 'B' and resid 521 through 539
    Processing helix  chain 'B' and resid 568 through 575
    Processing helix  chain 'B' and resid 596 through 617
    Processing helix  chain 'B' and resid 668 through 674
    Processing helix  chain 'B' and resid 678 through 695
    Processing helix  chain 'B' and resid 705 through 715
      removed outlier: 3.871A  pdb=" N   PHE B 710 " --> pdb=" O   VAL B 706 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   LYS B 711 " --> pdb=" O   GLU B 707 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 726 through 737
    Processing helix  chain 'B' and resid 746 through 762
    Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 55
      removed outlier: 6.474A  pdb=" N   THR A  37 " --> pdb=" O   SER A  32 " (cutoff:3.500A)
      removed outlier: 6.501A  pdb=" N   SER A  32 " --> pdb=" O   THR A  37 " (cutoff:3.500A)
      removed outlier: 3.720A  pdb=" N   SER A 110 " --> pdb=" O   PHE A  31 " (cutoff:3.500A)
      removed outlier: 7.202A  pdb=" N   THR A  97 " --> pdb=" O   ILE A  73 " (cutoff:3.500A)
      removed outlier: 5.218A  pdb=" N   ILE A  73 " --> pdb=" O   THR A  97 " (cutoff:3.500A)
      removed outlier: 7.190A  pdb=" N   LEU A  99 " --> pdb=" O   LYS A  71 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 160 through 162
    Processing sheet with id=AA3, first strand: chain 'A' and resid 240 through 241
    Processing sheet with id=AA4, first strand: chain 'A' and resid 938 through 939
      removed outlier: 5.813A  pdb=" N   LYS A 938 " --> pdb=" O   ILE A 955 " (cutoff:3.500A)
      removed outlier: 7.148A  pdb=" N   SER A 957 " --> pdb=" O   LYS A 938 " (cutoff:3.500A)
      removed outlier: 6.354A  pdb=" N   GLU A 954 " --> pdb=" O   LEU A 982 " (cutoff:3.500A)
      removed outlier: 7.362A  pdb=" N   ARG A 984 " --> pdb=" O   GLU A 954 " (cutoff:3.500A)
      removed outlier: 5.622A  pdb=" N   ARG A 956 " --> pdb=" O   ARG A 984 " (cutoff:3.500A)
      removed outlier: 7.094A  pdb=" N   TYR A 986 " --> pdb=" O   ARG A 956 " (cutoff:3.500A)
      removed outlier: 6.143A  pdb=" N   PHE A 958 " --> pdb=" O   TYR A 986 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   THR A 983 " --> pdb=" O   MET A1009 " (cutoff:3.500A)
      removed outlier: 7.117A  pdb=" N   ALA A1011 " --> pdb=" O   THR A 983 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   VAL A 985 " --> pdb=" O   ALA A1011 " (cutoff:3.500A)
      removed outlier: 7.915A  pdb=" N   VAL A1010 " --> pdb=" O   TYR A 321 " (cutoff:3.500A)
      removed outlier: 7.230A  pdb=" N   ILE A 323 " --> pdb=" O   VAL A1010 " (cutoff:3.500A)
      removed outlier: 8.005A  pdb=" N   LEU A1012 " --> pdb=" O   ILE A 323 " (cutoff:3.500A)
      removed outlier: 7.294A  pdb=" N   SER A 325 " --> pdb=" O   LEU A1012 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 355 through 358
      removed outlier: 6.400A  pdb=" N   ILE A 356 " --> pdb=" O   SER A 404 " (cutoff:3.500A)
      removed outlier: 6.315A  pdb=" N   VAL A 401 " --> pdb=" O   ILE A 452 " (cutoff:3.500A)
      removed outlier: 7.340A  pdb=" N   LYS A 454 " --> pdb=" O   VAL A 401 " (cutoff:3.500A)
      removed outlier: 6.414A  pdb=" N   LEU A 403 " --> pdb=" O   LYS A 454 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA5
    Processing sheet with id=AA6, first strand: chain 'A' and resid 360 through 361
      removed outlier: 3.767A  pdb=" N   VAL A 369 " --> pdb=" O   TRP A 361 " (cutoff:3.500A)
      removed outlier: 3.615A  pdb=" N   ILE A 370 " --> pdb=" O   ILE A 380 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   ILE A 380 " --> pdb=" O   ILE A 370 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 478 through 484
      removed outlier: 6.970A  pdb=" N   ARG A 493 " --> pdb=" O   ASP A 508 " (cutoff:3.500A)
      removed outlier: 4.776A  pdb=" N   ASP A 508 " --> pdb=" O   ARG A 493 " (cutoff:3.500A)
      removed outlier: 5.394A  pdb=" N   TYR A 495 " --> pdb=" O   SER A 506 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 563 through 565
    Processing sheet with id=AA9, first strand: chain 'A' and resid 577 through 579
    Processing sheet with id=AB1, first strand: chain 'A' and resid 590 through 593
      removed outlier: 3.620A  pdb=" N   LEU A 605 " --> pdb=" O   LEU A 601 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 622 through 623
    Processing sheet with id=AB3, first strand: chain 'A' and resid 647 through 648
      removed outlier: 3.925A  pdb=" N   LYS A 673 " --> pdb=" O   TYR A 648 " (cutoff:3.500A)
      removed outlier: 4.332A  pdb=" N   ALA A 668 " --> pdb=" O   ARG A 685 " (cutoff:3.500A)
      removed outlier: 3.600A  pdb=" N   ARG A 685 " --> pdb=" O   ALA A 668 " (cutoff:3.500A)
      removed outlier: 3.509A  pdb=" N   ALA A 708 " --> pdb=" O   LEU A 704 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'A' and resid 647 through 648
      removed outlier: 3.925A  pdb=" N   LYS A 673 " --> pdb=" O   TYR A 648 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'A' and resid 1120 through 1124
      removed outlier: 5.214A  pdb=" N   LEU A1063 " --> pdb=" O   ARG A1187 " (cutoff:3.500A)
      removed outlier: 7.216A  pdb=" N   ARG A1187 " --> pdb=" O   LEU A1063 " (cutoff:3.500A)
      removed outlier: 5.519A  pdb=" N   VAL A1065 " --> pdb=" O   GLU A1185 " (cutoff:3.500A)
      removed outlier: 7.396A  pdb=" N   GLU A1185 " --> pdb=" O   VAL A1065 " (cutoff:3.500A)
      removed outlier: 5.199A  pdb=" N   VAL A1067 " --> pdb=" O   PHE A1183 " (cutoff:3.500A)
      removed outlier: 6.108A  pdb=" N   PHE A1183 " --> pdb=" O   VAL A1067 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY A1069 " --> pdb=" O   LEU A1181 " (cutoff:3.500A)
      removed outlier: 5.506A  pdb=" N   ALA A1178 " --> pdb=" O   LEU A1167 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'A' and resid 1098 through 1100
      removed outlier: 3.518A  pdb=" N   ALA A1149 " --> pdb=" O   VAL A1136 " (cutoff:3.500A)
      removed outlier: 6.596A  pdb=" N   GLU A1138 " --> pdb=" O   PHE A1147 " (cutoff:3.500A)
      removed outlier: 6.316A  pdb=" N   PHE A1147 " --> pdb=" O   GLU A1138 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'B' and resid 478 through 486
      removed outlier: 5.453A  pdb=" N   LEU B 494 " --> pdb=" O   GLY B 481 " (cutoff:3.500A)
      removed outlier: 7.449A  pdb=" N   VAL B 492 " --> pdb=" O   PRO B 483 " (cutoff:3.500A)
      removed outlier: 7.404A  pdb=" N   GLY B 485 " --> pdb=" O   GLY B 490 " (cutoff:3.500A)
      removed outlier: 7.385A  pdb=" N   GLY B 490 " --> pdb=" O   GLY B 485 " (cutoff:3.500A)
      removed outlier: 6.597A  pdb=" N   TYR B 558 " --> pdb=" O   ALA B 550 " (cutoff:3.500A)
      removed outlier: 4.478A  pdb=" N   ALA B 550 " --> pdb=" O   TYR B 558 " (cutoff:3.500A)
      removed outlier: 6.732A  pdb=" N   ILE B 560 " --> pdb=" O   LEU B 548 " (cutoff:3.500A)
    Processing sheet with id=AB8, first strand: chain 'B' and resid 629 through 631

    426 hydrogen bonds defined for protein.
    1191 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: 2.53

  Time building geometry restraints manager: 1.14 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: 2434
        1.33 -     1.45: 2538
        1.45 -     1.57: 6365
        1.57 -     1.69: 0
        1.69 -     1.81: 101
  Bond restraints: 11438
  Sorted by residual:
  bond pdb=" CA  LYS A 598 "
       pdb=" C   LYS A 598 "
    ideal  model  delta    sigma   weight residual
    1.526  1.474  0.052 1.42e-02 4.96e+03 1.35e+01
  bond pdb=" C   TYR A1036 "
       pdb=" N   VAL A1037 "
    ideal  model  delta    sigma   weight residual
    1.332  1.293  0.039 1.23e-02 6.61e+03 1.01e+01
  bond pdb=" CA  TYR A1036 "
       pdb=" C   TYR A1036 "
    ideal  model  delta    sigma   weight residual
    1.522  1.486  0.036 1.19e-02 7.06e+03 9.16e+00
  bond pdb=" C   TYR A 600 "
       pdb=" N   LEU A 601 "
    ideal  model  delta    sigma   weight residual
    1.335  1.373 -0.038 1.35e-02 5.49e+03 7.74e+00
  bond pdb=" CA  TYR A1036 "
       pdb=" CB  TYR A1036 "
    ideal  model  delta    sigma   weight residual
    1.532  1.489  0.042 1.74e-02 3.30e+03 5.88e+00
  ... (remaining 11433 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.94: 14814
        1.94 -     3.89: 550
        3.89 -     5.83: 63
        5.83 -     7.78: 16
        7.78 -     9.72: 3
  Bond angle restraints: 15446
  Sorted by residual:
  angle pdb=" N   ILE B 648 "
        pdb=" CA  ILE B 648 "
        pdb=" C   ILE B 648 "
      ideal   model   delta    sigma   weight residual
     111.91  106.64    5.27 8.90e-01 1.26e+00 3.50e+01
  angle pdb=" C   LYS A 223 "
        pdb=" CA  LYS A 223 "
        pdb=" CB  LYS A 223 "
      ideal   model   delta    sigma   weight residual
     116.54  110.05    6.49 1.15e+00 7.56e-01 3.18e+01
  angle pdb=" N   ASP A 633 "
        pdb=" CA  ASP A 633 "
        pdb=" C   ASP A 633 "
      ideal   model   delta    sigma   weight residual
     108.47  118.19   -9.72 1.79e+00 3.12e-01 2.95e+01
  angle pdb=" N   ILE A 229 "
        pdb=" CA  ILE A 229 "
        pdb=" C   ILE A 229 "
      ideal   model   delta    sigma   weight residual
     111.56  107.91    3.65 8.60e-01 1.35e+00 1.80e+01
  angle pdb=" N   ASN A 604 "
        pdb=" CA  ASN A 604 "
        pdb=" C   ASN A 604 "
      ideal   model   delta    sigma   weight residual
     111.36  106.75    4.61 1.09e+00 8.42e-01 1.79e+01
  ... (remaining 15441 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 6307
       17.99 -    35.98: 549
       35.98 -    53.97: 81
       53.97 -    71.96: 13
       71.96 -    89.96: 11
  Dihedral angle restraints: 6961
    sinusoidal: 2928
      harmonic: 4033
  Sorted by residual:
  dihedral pdb=" CA  PHE B 694 "
           pdb=" C   PHE B 694 "
           pdb=" N   THR B 695 "
           pdb=" CA  THR B 695 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  154.61   25.39     0      5.00e+00 4.00e-02 2.58e+01
  dihedral pdb=" CA  PHE A 577 "
           pdb=" C   PHE A 577 "
           pdb=" N   TRP A 578 "
           pdb=" CA  TRP A 578 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.15   19.85     0      5.00e+00 4.00e-02 1.58e+01
  dihedral pdb=" CA  TYR A 321 "
           pdb=" C   TYR A 321 "
           pdb=" N   TRP A 322 "
           pdb=" CA  TRP A 322 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  160.80   19.20     0      5.00e+00 4.00e-02 1.47e+01
  ... (remaining 6958 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.051: 1237
       0.051 -    0.102: 342
       0.102 -    0.154: 80
       0.154 -    0.205: 2
       0.205 -    0.256: 2
  Chirality restraints: 1663
  Sorted by residual:
  chirality pdb=" CB  ILE A 453 "
            pdb=" CA  ILE A 453 "
            pdb=" CG1 ILE A 453 "
            pdb=" CG2 ILE A 453 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.39    0.26 2.00e-01 2.50e+01 1.64e+00
  chirality pdb=" CB  ILE A 487 "
            pdb=" CA  ILE A 487 "
            pdb=" CG1 ILE A 487 "
            pdb=" CG2 ILE A 487 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.21 2.00e-01 2.50e+01 1.11e+00
  chirality pdb=" CG  LEU B 767 "
            pdb=" CB  LEU B 767 "
            pdb=" CD1 LEU B 767 "
            pdb=" CD2 LEU B 767 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.78    0.20 2.00e-01 2.50e+01 9.53e-01
  ... (remaining 1660 not shown)

  Planarity restraints: 1987
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP A1003 "    0.025 2.00e-02 2.50e+03   2.39e-02 1.43e+01
        pdb=" CG  TRP A1003 "   -0.064 2.00e-02 2.50e+03
        pdb=" CD1 TRP A1003 "    0.031 2.00e-02 2.50e+03
        pdb=" CD2 TRP A1003 "   -0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP A1003 "   -0.002 2.00e-02 2.50e+03
        pdb=" CE2 TRP A1003 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE3 TRP A1003 "    0.006 2.00e-02 2.50e+03
        pdb=" CZ2 TRP A1003 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP A1003 "    0.004 2.00e-02 2.50e+03
        pdb=" CH2 TRP A1003 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B 577 "    0.271 9.50e-02 1.11e+02   1.21e-01 9.10e+00
        pdb=" NE  ARG B 577 "   -0.017 2.00e-02 2.50e+03
        pdb=" CZ  ARG B 577 "   -0.000 2.00e-02 2.50e+03
        pdb=" NH1 ARG B 577 "   -0.003 2.00e-02 2.50e+03
        pdb=" NH2 ARG B 577 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 597 "   -0.012 2.00e-02 2.50e+03   2.44e-02 5.95e+00
        pdb=" C   LEU A 597 "    0.042 2.00e-02 2.50e+03
        pdb=" O   LEU A 597 "   -0.016 2.00e-02 2.50e+03
        pdb=" N   LYS A 598 "   -0.014 2.00e-02 2.50e+03
  ... (remaining 1984 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 2102
        2.76 -     3.30: 12078
        3.30 -     3.83: 19524
        3.83 -     4.37: 23240
        4.37 -     4.90: 36678
  Nonbonded interactions: 93622
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG A 589 "
            pdb=" OD2 ASP B 755 "
     model   vdw
     2.226 3.120
  nonbonded pdb=" ND2 ASN A 978 "
            pdb=" O   GLY A1006 "
     model   vdw
     2.229 3.120
  nonbonded pdb=" OE1 GLU A 407 "
            pdb=" NE2 HIS A 455 "
     model   vdw
     2.237 3.120
  nonbonded pdb=" O   THR B 678 "
            pdb=" OG  SER B 681 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" OD1 ASP A 362 "
            pdb=" NE2 GLN A 413 "
     model   vdw
     2.246 3.120
  ... (remaining 93617 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.01 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.100
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     11.790
  Find NCS groups from input model:        0.050
  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:             0.000
  Load rotamer database and sin/cos tables:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.530
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7343
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   0.057  11438  Z= 0.269
  Angle     :  0.846   9.719  15446  Z= 0.490
  Chirality :  0.048   0.256   1663
  Planarity :  0.006   0.121   1987
  Dihedral  : 13.610  89.955   4347
  Min Nonbonded Distance : 2.226

Molprobity Statistics.
  All-atom Clashscore : 25.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.13 %
    Favored  : 98.79 %
  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 aren not related in a simple way.
  whole: -1.03 (0.22), residues: 1357
  helix:  0.13 (0.24), residues: 438
  sheet: -1.22 (0.37), residues: 209
  loop : -0.97 (0.22), residues: 710

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 147 
 TYR   0.031   0.002   TYR A 100 
 PHE   0.024   0.003   PHE A1000 
 TRP   0.064   0.003   TRP A1003 
 HIS   0.009   0.002   HIS A 494 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 (11438)
  covalent geometry    : angle       0.84648 (15446)
  hydrogen bonds       : bond        0.12822 (  425)
  hydrogen bonds       : angle       7.45281 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  176 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 175
  time to evaluate  : 0.530 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   72 GLU cc_start: 0.9061 (pp20) cc_final: 0.8611 (pp20)
REVERT: A  171 PRO cc_start: 0.8022 (Cg_exo) cc_final: 0.7639 (Cg_endo)
REVERT: A  331 LEU cc_start: 0.8788 (mt) cc_final: 0.8535 (mt)
REVERT: A  483 MET cc_start: 0.8122 (mmm) cc_final: 0.7743 (mmt)
REVERT: A  845 LEU cc_start: 0.8817 (tp) cc_final: 0.8409 (tp)
REVERT: A  946 ASN cc_start: 0.8403 (t0) cc_final: 0.8181 (t0)
REVERT: B  515 MET cc_start: 0.4842 (ptt) cc_final: 0.4605 (pmm)
REVERT: B  583 TYR cc_start: 0.5286 (m-80) cc_final: 0.5005 (p90)
REVERT: B  717 HIS cc_start: 0.8252 (m-70) cc_final: 0.7824 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 176
  average time/residue: 0.1056
  time to fit residues: 26.2495
Evaluate side-chains
  120 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 119
  time to evaluate  : 0.438 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    6.9990
   chunk 10 optimal weight:    2.9990
   chunk 66 optimal weight:    0.9990
   chunk 130 optimal weight:   10.0000
   chunk 124 optimal weight:    0.0170
   chunk 103 optimal weight:    3.9990
   chunk 77 optimal weight:    3.9990
   chunk 122 optimal weight:   10.0000
   chunk 91 optimal weight:    0.3980
   chunk 55 optimal weight:    1.9990
   overall best weight:    1.2824

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

Flipped N/Q/H residues before XYZ refinement:
A  17 GLN
** A 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 616 HIS
** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4244 r_free = 0.4244 target = 0.123962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3796 r_free = 0.3796 target = 0.097665 restraints weight = 41044.347|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.100029 restraints weight = 22979.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101595 restraints weight = 14939.125|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3893 r_free = 0.3893 target = 0.102728 restraints weight = 10777.249|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.103520 restraints weight = 8354.689|
|-----------------------------------------------------------------------------|
r_work (final): 0.3874
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3875
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3875 r_free = 0.3875    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.01   number of occupancies < 0.1:        7 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3872 r_free = 0.3872    target_work(ls_wunit_k1) = 0.101         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
r_final: 0.3872
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7156
moved from start:          0.1324

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  11438  Z= 0.139
  Angle     :  0.610   8.516  15446  Z= 0.321
  Chirality :  0.044   0.145   1663
  Planarity :  0.004   0.050   1987
  Dihedral  :  4.952  22.210   1504
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.88 %
    Favored  : 96.12 %
  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 aren not related in a simple way.
  whole: -0.63 (0.22), residues: 1357
  helix:  0.70 (0.24), residues: 457
  sheet: -1.16 (0.36), residues: 208
  loop : -0.89 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG B 577 
 TYR   0.022   0.002   TYR A 600 
 PHE   0.031   0.002   PHE A 421 
 TRP   0.033   0.002   TRP A1003 
 HIS   0.005   0.001   HIS A 455 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 (11438)
  covalent geometry    : angle       0.60965 (15446)
  hydrogen bonds       : bond        0.04039 (  425)
  hydrogen bonds       : angle       6.09899 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 168
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LEU cc_start: 0.9096 (mt) cc_final: 0.8803 (mt)
REVERT: A  845 LEU cc_start: 0.8739 (tp) cc_final: 0.8324 (tp)
REVERT: B  515 MET cc_start: 0.5785 (ptt) cc_final: 0.5394 (pmm)
REVERT: B  583 TYR cc_start: 0.4778 (m-80) cc_final: 0.4268 (p90)
REVERT: B  717 HIS cc_start: 0.8175 (m-70) cc_final: 0.7608 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0951
  time to fit residues: 22.5364
Evaluate side-chains
  121 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.415 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 5 optimal weight:    9.9990
   chunk 73 optimal weight:    1.9990
   chunk 11 optimal weight:    0.9980
   chunk 4 optimal weight:    4.9990
   chunk 98 optimal weight:    0.0980
   chunk 36 optimal weight:    6.9990
   chunk 124 optimal weight:    0.6980
   chunk 24 optimal weight:    6.9990
   chunk 23 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9990
   chunk 104 optimal weight:    0.6980
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A 131 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 214 GLN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 604 ASN
** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1022 GLN
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 589 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4253 r_free = 0.4253 target = 0.123895 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.097711 restraints weight = 41444.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.100038 restraints weight = 22401.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3890 r_free = 0.3890 target = 0.101584 restraints weight = 14108.113|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.102707 restraints weight = 9911.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.103489 restraints weight = 7562.013|
|-----------------------------------------------------------------------------|
r_work (final): 0.3906
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3906
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3906 r_free = 0.3906    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       21 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3906 r_free = 0.3906    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.3906
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7142
moved from start:          0.1882

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.024  11438  Z= 0.113
  Angle     :  0.572   6.218  15446  Z= 0.300
  Chirality :  0.042   0.165   1663
  Planarity :  0.004   0.051   1987
  Dihedral  :  4.677  19.229   1504
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 13.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.98 %
    Favored  : 96.02 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.07 %
    Favored  : 96.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.45 (0.22), residues: 1357
  helix:  0.88 (0.24), residues: 458
  sheet: -1.04 (0.36), residues: 207
  loop : -0.82 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 577 
 TYR   0.020   0.001   TYR A 206 
 PHE   0.025   0.002   PHE A1028 
 TRP   0.043   0.002   TRP A1003 
 HIS   0.004   0.001   HIS A 408 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 (11438)
  covalent geometry    : angle       0.57210 (15446)
  hydrogen bonds       : bond        0.03544 (  425)
  hydrogen bonds       : angle       5.77212 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 168
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LEU cc_start: 0.9137 (mt) cc_final: 0.8806 (mt)
REVERT: A  483 MET cc_start: 0.8097 (mmm) cc_final: 0.7873 (mmt)
REVERT: A  495 TYR cc_start: 0.7215 (t80) cc_final: 0.6822 (t80)
REVERT: A  592 MET cc_start: 0.1465 (ptp) cc_final: 0.1059 (ptp)
REVERT: A  845 LEU cc_start: 0.8721 (tp) cc_final: 0.8372 (tp)
REVERT: A 1003 TRP cc_start: 0.8702 (m-90) cc_final: 0.8442 (m-90)
REVERT: A 1012 LEU cc_start: 0.9426 (mm) cc_final: 0.9053 (mm)
REVERT: B  515 MET cc_start: 0.5478 (ptt) cc_final: 0.4977 (pmm)
REVERT: B  583 TYR cc_start: 0.5294 (m-80) cc_final: 0.4710 (p90)
REVERT: B  701 TYR cc_start: 0.4874 (m-80) cc_final: 0.4528 (m-10)
REVERT: B  717 HIS cc_start: 0.8052 (m-70) cc_final: 0.7659 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 168
  average time/residue: 0.0972
  time to fit residues: 22.6571
Evaluate side-chains
  117 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 117
  time to evaluate  : 0.316 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 100 optimal weight:    0.6980
   chunk 114 optimal weight:    6.9990
   chunk 22 optimal weight:    6.9990
   chunk 117 optimal weight:    5.9990
   chunk 44 optimal weight:    2.9990
   chunk 130 optimal weight:    9.9990
   chunk 126 optimal weight:    9.9990
   chunk 20 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 91 optimal weight:    6.9990
   chunk 80 optimal weight:    1.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 571 ASN
** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 744 ASN
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 606 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.121732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.096225 restraints weight = 42171.036|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3820 r_free = 0.3820 target = 0.098647 restraints weight = 22877.482|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.100260 restraints weight = 14429.847|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3873 r_free = 0.3873 target = 0.101376 restraints weight = 10102.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.102104 restraints weight = 7710.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.3855
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3855
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3855 r_free = 0.3855    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.3855
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7174
moved from start:          0.2204

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034  11438  Z= 0.139
  Angle     :  0.590   7.768  15446  Z= 0.307
  Chirality :  0.043   0.203   1663
  Planarity :  0.004   0.050   1987
  Dihedral  :  4.625  18.723   1504
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 15.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  3.64 %
    Favored  : 96.28 %
  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 aren not related in a simple way.
  whole: -0.40 (0.22), residues: 1357
  helix:  0.92 (0.24), residues: 461
  sheet: -1.01 (0.36), residues: 203
  loop : -0.81 (0.23), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 147 
 TYR   0.021   0.001   TYR A 206 
 PHE   0.020   0.002   PHE A 187 
 TRP   0.026   0.002   TRP A1003 
 HIS   0.005   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 (11438)
  covalent geometry    : angle       0.58953 (15446)
  hydrogen bonds       : bond        0.03514 (  425)
  hydrogen bonds       : angle       5.64905 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 156
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  331 LEU cc_start: 0.9119 (mt) cc_final: 0.8751 (mt)
REVERT: A  495 TYR cc_start: 0.7798 (t80) cc_final: 0.7165 (t80)
REVERT: A  592 MET cc_start: 0.1530 (ptp) cc_final: 0.1162 (ptp)
REVERT: A  845 LEU cc_start: 0.8701 (tp) cc_final: 0.8269 (tp)
REVERT: A 1003 TRP cc_start: 0.8825 (m-90) cc_final: 0.8468 (m-90)
REVERT: A 1012 LEU cc_start: 0.9483 (mm) cc_final: 0.9102 (mm)
REVERT: B  468 ASP cc_start: 0.5627 (t0) cc_final: 0.5349 (m-30)
REVERT: B  515 MET cc_start: 0.6128 (ptt) cc_final: 0.5807 (pmm)
REVERT: B  701 TYR cc_start: 0.4549 (m-80) cc_final: 0.4191 (m-10)
REVERT: B  717 HIS cc_start: 0.7924 (m-70) cc_final: 0.7508 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 157
  average time/residue: 0.0835
  time to fit residues: 19.2229
Evaluate side-chains
  118 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 118
  time to evaluate  : 0.443 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 21 optimal weight:    0.0270
   chunk 58 optimal weight:    8.9990
   chunk 65 optimal weight:   10.0000
   chunk 4 optimal weight:    3.9990
   chunk 132 optimal weight:    5.9990
   chunk 31 optimal weight:    5.9990
   chunk 134 optimal weight:   10.0000
   chunk 19 optimal weight:    0.6980
   chunk 80 optimal weight:    0.9990
   chunk 117 optimal weight:    0.0000
   chunk 33 optimal weight:    0.7980
   overall best weight:    0.5044

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 637 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** 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 = 0.4258 r_free = 0.4258 target = 0.124379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3812 r_free = 0.3812 target = 0.098587 restraints weight = 41273.009|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3860 r_free = 0.3860 target = 0.101046 restraints weight = 22676.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3892 r_free = 0.3892 target = 0.102692 restraints weight = 14410.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3913 r_free = 0.3913 target = 0.103803 restraints weight = 10177.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3927 r_free = 0.3927 target = 0.104587 restraints weight = 7802.005|
|-----------------------------------------------------------------------------|
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3900
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3900 r_free = 0.3900    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3900 r_free = 0.3900    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
r_final: 0.3900
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7098
moved from start:          0.2602

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032  11438  Z= 0.110
  Angle     :  0.566   7.782  15446  Z= 0.293
  Chirality :  0.043   0.148   1663
  Planarity :  0.004   0.052   1987
  Dihedral  :  4.456  18.603   1504
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 12.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.75 %
    Favored  : 97.25 %
  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 aren not related in a simple way.
  whole: -0.31 (0.23), residues: 1357
  helix:  0.99 (0.25), residues: 461
  sheet: -0.85 (0.36), residues: 203
  loop : -0.77 (0.23), residues: 693

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 564 
 TYR   0.019   0.001   TYR A 206 
 PHE   0.025   0.001   PHE A1028 
 TRP   0.021   0.001   TRP A1003 
 HIS   0.005   0.001   HIS A 701 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (11438)
  covalent geometry    : angle       0.56613 (15446)
  hydrogen bonds       : bond        0.03342 (  425)
  hydrogen bonds       : angle       5.43522 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 169
  time to evaluate  : 0.319 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ILE cc_start: 0.8038 (pt) cc_final: 0.7800 (pt)
REVERT: A  269 MET cc_start: 0.8667 (mmp) cc_final: 0.8439 (mmp)
REVERT: A  331 LEU cc_start: 0.9047 (mt) cc_final: 0.8616 (mt)
REVERT: A  351 MET cc_start: 0.9102 (mtp) cc_final: 0.8408 (mtp)
REVERT: A  483 MET cc_start: 0.7990 (mmm) cc_final: 0.7684 (mmt)
REVERT: A  495 TYR cc_start: 0.7819 (t80) cc_final: 0.7370 (t80)
REVERT: A  592 MET cc_start: 0.1420 (ptp) cc_final: 0.1162 (ptp)
REVERT: A  845 LEU cc_start: 0.8650 (tp) cc_final: 0.8277 (tp)
REVERT: A 1003 TRP cc_start: 0.8806 (m-90) cc_final: 0.8379 (m-90)
REVERT: B  468 ASP cc_start: 0.5677 (t0) cc_final: 0.5389 (m-30)
REVERT: B  515 MET cc_start: 0.6003 (ptt) cc_final: 0.5717 (pmm)
REVERT: B  701 TYR cc_start: 0.4596 (m-80) cc_final: 0.4191 (m-80)
REVERT: B  717 HIS cc_start: 0.7816 (m-70) cc_final: 0.7396 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 169
  average time/residue: 0.0858
  time to fit residues: 20.9226
Evaluate side-chains
  121 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 121
  time to evaluate  : 0.340 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 6 optimal weight:    1.9990
   chunk 1 optimal weight:   10.0000
   chunk 45 optimal weight:    0.9990
   chunk 84 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 99 optimal weight:    2.9990
   chunk 111 optimal weight:    6.9990
   chunk 28 optimal weight:    0.7980
   chunk 115 optimal weight:    5.9990
   chunk 132 optimal weight:    0.0050
   chunk 37 optimal weight:    5.9990
   overall best weight:    0.7600

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 491 GLN ** 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 = 0.4259 r_free = 0.4259 target = 0.124575 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3811 r_free = 0.3811 target = 0.098606 restraints weight = 41966.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.101141 restraints weight = 22909.241|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3894 r_free = 0.3894 target = 0.102800 restraints weight = 14526.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3918 r_free = 0.3918 target = 0.103992 restraints weight = 10235.998|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3932 r_free = 0.3932 target = 0.104796 restraints weight = 7809.017|
|-----------------------------------------------------------------------------|
r_work (final): 0.3903
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3903
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       26 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3903 r_free = 0.3903    target_work(ls_wunit_k1) = 0.103         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.3903
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7102
moved from start:          0.2820

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029  11438  Z= 0.110
  Angle     :  0.564   6.407  15446  Z= 0.294
  Chirality :  0.043   0.148   1663
  Planarity :  0.004   0.052   1987
  Dihedral  :  4.360  18.728   1504
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 13.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.86 %
    Favored  : 98.14 %
  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 aren not related in a simple way.
  whole: -0.26 (0.23), residues: 1357
  helix:  0.96 (0.24), residues: 461
  sheet: -0.81 (0.38), residues: 193
  loop : -0.71 (0.23), residues: 703

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 493 
 TYR   0.023   0.001   TYR A 206 
 PHE   0.016   0.001   PHE A 187 
 TRP   0.015   0.001   TRP A 578 
 HIS   0.005   0.001   HIS A 616 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 (11438)
  covalent geometry    : angle       0.56440 (15446)
  hydrogen bonds       : bond        0.03308 (  425)
  hydrogen bonds       : angle       5.39478 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  159 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 159
  time to evaluate  : 0.337 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ILE cc_start: 0.8125 (pt) cc_final: 0.7892 (pt)
REVERT: A  313 ASP cc_start: 0.7903 (m-30) cc_final: 0.7692 (m-30)
REVERT: A  331 LEU cc_start: 0.9027 (mt) cc_final: 0.8637 (mt)
REVERT: A  351 MET cc_start: 0.9079 (mtp) cc_final: 0.8552 (mtp)
REVERT: A  592 MET cc_start: 0.1724 (ptp) cc_final: 0.1474 (ptp)
REVERT: A  845 LEU cc_start: 0.8697 (tp) cc_final: 0.8248 (tp)
REVERT: A 1003 TRP cc_start: 0.8815 (m-10) cc_final: 0.8386 (m-90)
REVERT: B  515 MET cc_start: 0.6085 (ptt) cc_final: 0.5845 (pmm)
REVERT: B  701 TYR cc_start: 0.4721 (m-80) cc_final: 0.4333 (m-80)
REVERT: B  717 HIS cc_start: 0.7781 (m-70) cc_final: 0.7376 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 159
  average time/residue: 0.0937
  time to fit residues: 21.4926
Evaluate side-chains
  110 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 110
  time to evaluate  : 0.258 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 9 optimal weight:    5.9990
   chunk 75 optimal weight:    7.9990
   chunk 101 optimal weight:    0.9990
   chunk 79 optimal weight:    9.9990
   chunk 95 optimal weight:    0.7980
   chunk 112 optimal weight:    6.9990
   chunk 109 optimal weight:    6.9990
   chunk 135 optimal weight:    5.9990
   chunk 5 optimal weight:    5.9990
   chunk 108 optimal weight:   10.0000
   chunk 111 optimal weight:    3.9990
   overall best weight:    3.5588

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

Flipped N/Q/H residues before XYZ refinement:
A 203 HIS
** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 701 HIS
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 491 GLN
B 679 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4156 r_free = 0.4156 target = 0.118347 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3689 r_free = 0.3689 target = 0.092520 restraints weight = 42632.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.094761 restraints weight = 24381.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.096249 restraints weight = 16012.799|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 50)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.097270 restraints weight = 11665.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.097933 restraints weight = 9194.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.3773
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3772
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3772 r_free = 0.3772    target_work(ls_wunit_k1) = 0.096         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.3772
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7295
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.053  11438  Z= 0.220
  Angle     :  0.678   6.937  15446  Z= 0.360
  Chirality :  0.046   0.194   1663
  Planarity :  0.005   0.047   1987
  Dihedral  :  4.915  23.668   1504
  Min Nonbonded Distance : 2.387

Molprobity Statistics.
  All-atom Clashscore : 20.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.31 %
    Favored  : 94.69 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  1.94 %
    Favored  : 97.98 %
  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 aren not related in a simple way.
  whole: -0.68 (0.22), residues: 1357
  helix:  0.61 (0.24), residues: 457
  sheet: -1.14 (0.38), residues: 194
  loop : -0.91 (0.23), residues: 706

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 235 
 TYR   0.023   0.002   TYR A 206 
 PHE   0.019   0.002   PHE A1000 
 TRP   0.040   0.002   TRP A 578 
 HIS   0.011   0.002   HIS A 203 

Details of bonding type rmsd
  covalent geometry    : bond        0.00484 (11438)
  covalent geometry    : angle       0.67777 (15446)
  hydrogen bonds       : bond        0.03871 (  425)
  hydrogen bonds       : angle       5.79447 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 151
  time to evaluate  : 0.260 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ILE cc_start: 0.8430 (pt) cc_final: 0.8229 (pt)
REVERT: A  210 MET cc_start: 0.8142 (mtm) cc_final: 0.7807 (mtm)
REVERT: A  331 LEU cc_start: 0.9288 (mt) cc_final: 0.8937 (mt)
REVERT: A  351 MET cc_start: 0.8984 (mtp) cc_final: 0.8208 (mtp)
REVERT: A  357 GLU cc_start: 0.6861 (tt0) cc_final: 0.6652 (tt0)
REVERT: A  415 ARG cc_start: 0.7750 (mmt180) cc_final: 0.7041 (mmt180)
REVERT: A  483 MET cc_start: 0.8163 (mmm) cc_final: 0.7855 (mmt)
REVERT: A  592 MET cc_start: 0.2038 (ptp) cc_final: 0.1613 (ptp)
REVERT: A  729 MET cc_start: 0.7832 (ppp) cc_final: 0.7574 (ppp)
REVERT: A  845 LEU cc_start: 0.8633 (tp) cc_final: 0.8164 (tp)
REVERT: A  905 GLU cc_start: 0.8669 (mp0) cc_final: 0.8459 (mp0)
REVERT: A 1003 TRP cc_start: 0.9063 (m-10) cc_final: 0.8441 (m-90)
REVERT: A 1021 MET cc_start: 0.8436 (tpp) cc_final: 0.7966 (tpp)
REVERT: B  468 ASP cc_start: 0.5708 (t0) cc_final: 0.5487 (m-30)
REVERT: B  515 MET cc_start: 0.6392 (ptt) cc_final: 0.6132 (pmm)
REVERT: B  701 TYR cc_start: 0.4978 (m-80) cc_final: 0.4555 (m-80)
REVERT: B  717 HIS cc_start: 0.7913 (m-70) cc_final: 0.7573 (m-70)
  outliers start: 1
  outliers final: 1
  residues processed: 152
  average time/residue: 0.0898
  time to fit residues: 19.7132
Evaluate side-chains
  112 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 111
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 97 optimal weight:    8.9990
   chunk 66 optimal weight:    0.6980
   chunk 22 optimal weight:    2.9990
   chunk 121 optimal weight:    0.0010
   chunk 57 optimal weight:    5.9990
   chunk 135 optimal weight:    9.9990
   chunk 119 optimal weight:    2.9990
   chunk 36 optimal weight:    9.9990
   chunk 112 optimal weight:   10.0000
   chunk 1 optimal weight:    9.9990
   chunk 49 optimal weight:    9.9990
   overall best weight:    2.5392

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A1013 ASN ** 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 = 0.4172 r_free = 0.4172 target = 0.119171 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.3707 r_free = 0.3707 target = 0.093208 restraints weight = 44318.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3754 r_free = 0.3754 target = 0.095483 restraints weight = 25074.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3785 r_free = 0.3785 target = 0.096966 restraints weight = 16383.200|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.098031 restraints weight = 11877.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3821 r_free = 0.3821 target = 0.098749 restraints weight = 9289.221|
|-----------------------------------------------------------------------------|
r_work (final): 0.3793
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3793
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3793 r_free = 0.3793    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3793 r_free = 0.3793    target_work(ls_wunit_k1) = 0.097         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
r_final: 0.3793
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7283
moved from start:          0.3085

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036  11438  Z= 0.172
  Angle     :  0.633   8.787  15446  Z= 0.334
  Chirality :  0.045   0.175   1663
  Planarity :  0.004   0.048   1987
  Dihedral  :  4.836  22.988   1504
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 17.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.62 %
    Favored  : 98.38 %
  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 aren not related in a simple way.
  whole: -0.73 (0.22), residues: 1357
  helix:  0.65 (0.24), residues: 458
  sheet: -1.31 (0.36), residues: 207
  loop : -0.94 (0.23), residues: 692

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 347 
 TYR   0.034   0.002   TYR A 206 
 PHE   0.036   0.002   PHE A1028 
 TRP   0.033   0.002   TRP A 578 
 HIS   0.006   0.001   HIS A1025 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 (11438)
  covalent geometry    : angle       0.63291 (15446)
  hydrogen bonds       : bond        0.03633 (  425)
  hydrogen bonds       : angle       5.65425 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 153
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   61 ILE cc_start: 0.8386 (pt) cc_final: 0.8146 (pt)
REVERT: A  173 ILE cc_start: 0.8477 (pt) cc_final: 0.8271 (pt)
REVERT: A  331 LEU cc_start: 0.9249 (mt) cc_final: 0.8869 (mt)
REVERT: A  351 MET cc_start: 0.8960 (mtp) cc_final: 0.8180 (mtp)
REVERT: A  357 GLU cc_start: 0.6954 (tt0) cc_final: 0.6410 (tt0)
REVERT: A  483 MET cc_start: 0.8246 (mmm) cc_final: 0.8007 (mmt)
REVERT: A  579 ARG cc_start: 0.8941 (ptm-80) cc_final: 0.8167 (tmm-80)
REVERT: A  592 MET cc_start: 0.1969 (ptp) cc_final: 0.1565 (ptp)
REVERT: A  845 LEU cc_start: 0.8632 (tp) cc_final: 0.8167 (tp)
REVERT: A 1003 TRP cc_start: 0.9070 (m-10) cc_final: 0.8509 (m-90)
REVERT: A 1021 MET cc_start: 0.8446 (tpp) cc_final: 0.8058 (tpp)
REVERT: B  717 HIS cc_start: 0.8017 (m-70) cc_final: 0.7731 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 153
  average time/residue: 0.0950
  time to fit residues: 21.1011
Evaluate side-chains
  111 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 124 optimal weight:    0.9990
   chunk 9 optimal weight:    4.9990
   chunk 134 optimal weight:    7.9990
   chunk 126 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 88 optimal weight:    0.8980
   chunk 59 optimal weight:   20.0000
   chunk 118 optimal weight:    5.9990
   chunk 75 optimal weight:    0.0980
   chunk 33 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   overall best weight:    1.3986

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
A 990 GLN
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.120300 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3741 r_free = 0.3741 target = 0.094760 restraints weight = 41310.910|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3787 r_free = 0.3787 target = 0.097102 restraints weight = 23301.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3818 r_free = 0.3818 target = 0.098663 restraints weight = 15092.464|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3840 r_free = 0.3840 target = 0.099752 restraints weight = 10882.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.100514 restraints weight = 8440.069|
|-----------------------------------------------------------------------------|
r_work (final): 0.3831
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3831
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3831 r_free = 0.3831    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       27 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3830 r_free = 0.3830    target_work(ls_wunit_k1) = 0.099         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.3830
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7213
moved from start:          0.3361

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033  11438  Z= 0.133
  Angle     :  0.623   8.329  15446  Z= 0.326
  Chirality :  0.044   0.222   1663
  Planarity :  0.004   0.048   1987
  Dihedral  :  4.700  21.861   1504
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.20 %
    Favored  : 95.80 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  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 aren not related in a simple way.
  whole: -0.81 (0.22), residues: 1357
  helix:  0.60 (0.24), residues: 464
  sheet: -1.45 (0.35), residues: 212
  loop : -0.97 (0.23), residues: 681

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 582 
 TYR   0.031   0.001   TYR A 206 
 PHE   0.027   0.002   PHE A 421 
 TRP   0.029   0.002   TRP A 578 
 HIS   0.005   0.001   HIS A1025 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (11438)
  covalent geometry    : angle       0.62340 (15446)
  hydrogen bonds       : bond        0.03638 (  425)
  hydrogen bonds       : angle       5.59712 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  152 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 152
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ILE cc_start: 0.8509 (pt) cc_final: 0.8293 (pt)
REVERT: A  331 LEU cc_start: 0.9159 (mt) cc_final: 0.8776 (mt)
REVERT: A  357 GLU cc_start: 0.6861 (tt0) cc_final: 0.6224 (tt0)
REVERT: A  483 MET cc_start: 0.8345 (mmm) cc_final: 0.8109 (mmt)
REVERT: A  579 ARG cc_start: 0.8681 (ptm-80) cc_final: 0.8183 (tmm-80)
REVERT: A  582 ARG cc_start: 0.8536 (ttt-90) cc_final: 0.8308 (ttt90)
REVERT: A  592 MET cc_start: 0.1907 (ptp) cc_final: 0.1494 (ptp)
REVERT: A  845 LEU cc_start: 0.8625 (tp) cc_final: 0.8181 (tp)
REVERT: A 1003 TRP cc_start: 0.8958 (m-10) cc_final: 0.8450 (m-90)
REVERT: A 1021 MET cc_start: 0.8336 (tpp) cc_final: 0.7927 (tpp)
REVERT: B  717 HIS cc_start: 0.8022 (m-70) cc_final: 0.7713 (m-70)
  outliers start: 0
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0945
  time to fit residues: 20.7932
Evaluate side-chains
  114 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 114
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 99 optimal weight:    0.0050
   chunk 44 optimal weight:    6.9990
   chunk 131 optimal weight:    0.0070
   chunk 35 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 133 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 130 optimal weight:    0.2980
   chunk 127 optimal weight:    9.9990
   chunk 113 optimal weight:    4.9990
   chunk 119 optimal weight:   10.0000
   overall best weight:    1.0616

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

Flipped N/Q/H residues before XYZ refinement:
A 214 GLN
** A1013 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A1031 ASN
A1039 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.121339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3757 r_free = 0.3757 target = 0.095681 restraints weight = 42040.758|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.098076 restraints weight = 23594.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.099655 restraints weight = 15263.225|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.100780 restraints weight = 10970.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3870 r_free = 0.3870 target = 0.101482 restraints weight = 8503.329|
|-----------------------------------------------------------------------------|
r_work (final): 0.3847
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3847
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3847 r_free = 0.3847    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3847 r_free = 0.3847    target_work(ls_wunit_k1) = 0.100         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.3847
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7189
moved from start:          0.3529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  11438  Z= 0.122
  Angle     :  0.614   8.289  15446  Z= 0.320
  Chirality :  0.044   0.228   1663
  Planarity :  0.004   0.048   1987
  Dihedral  :  4.608  22.131   1504
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 15.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.05 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.08 %
    Allowed  :  0.49 %
    Favored  : 99.43 %
  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 aren not related in a simple way.
  whole: -0.76 (0.22), residues: 1357
  helix:  0.64 (0.24), residues: 465
  sheet: -1.34 (0.36), residues: 204
  loop : -0.99 (0.22), residues: 688

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 347 
 TYR   0.037   0.001   TYR A 206 
 PHE   0.031   0.002   PHE A 421 
 TRP   0.041   0.002   TRP A 578 
 HIS   0.004   0.001   HIS A1150 

Details of bonding type rmsd
  covalent geometry    : bond        0.00269 (11438)
  covalent geometry    : angle       0.61365 (15446)
  hydrogen bonds       : bond        0.03586 (  425)
  hydrogen bonds       : angle       5.52705 ( 1191)

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

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

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2714 Ramachandran restraints generated.
    1357 Oldfield, 0 Emsley, 1357 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 152
  time to evaluate  : 0.329 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  173 ILE cc_start: 0.8485 (pt) cc_final: 0.8269 (pt)
REVERT: A  331 LEU cc_start: 0.9066 (mt) cc_final: 0.8677 (mt)
REVERT: A  357 GLU cc_start: 0.6861 (tt0) cc_final: 0.6307 (tt0)
REVERT: A  483 MET cc_start: 0.8363 (mmm) cc_final: 0.7929 (mmt)
REVERT: A  592 MET cc_start: 0.1864 (ptp) cc_final: 0.1436 (ptp)
REVERT: A  845 LEU cc_start: 0.8623 (tp) cc_final: 0.8164 (tp)
REVERT: A 1003 TRP cc_start: 0.8950 (m-10) cc_final: 0.8430 (m-90)
REVERT: A 1021 MET cc_start: 0.8298 (tpp) cc_final: 0.8046 (tpp)
REVERT: A 1031 ASN cc_start: 0.8404 (OUTLIER) cc_final: 0.7935 (t0)
REVERT: B  717 HIS cc_start: 0.7989 (m-70) cc_final: 0.7688 (m-70)
  outliers start: 1
  outliers final: 0
  residues processed: 152
  average time/residue: 0.0996
  time to fit residues: 21.9687
Evaluate side-chains
  115 residues out of total 1237 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 114
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 136
   random chunks:
   chunk 95 optimal weight:    0.8980
   chunk 114 optimal weight:    0.0770
   chunk 126 optimal weight:    0.0470
   chunk 100 optimal weight:    1.9990
   chunk 89 optimal weight:    0.8980
   chunk 22 optimal weight:    8.9990
   chunk 111 optimal weight:    0.5980
   chunk 55 optimal weight:    5.9990
   chunk 85 optimal weight:    0.0000
   chunk 38 optimal weight:    4.9990
   chunk 54 optimal weight:    5.9990
   overall best weight:    0.3240

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

Flipped N/Q/H residues before XYZ refinement:
** A 214 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1013 ASN ** 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 = 0.4237 r_free = 0.4237 target = 0.123064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3804 r_free = 0.3804 target = 0.098036 restraints weight = 42116.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.100485 restraints weight = 23307.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3885 r_free = 0.3885 target = 0.102117 restraints weight = 14892.629|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3907 r_free = 0.3907 target = 0.103269 restraints weight = 10551.204|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.104083 restraints weight = 8043.458|
|-----------------------------------------------------------------------------|
r_work (final): 0.3893
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3893
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3893 r_free = 0.3893    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3893 r_free = 0.3893    target_work(ls_wunit_k1) = 0.102         |
| occupancies: max = 1.00  min = 0.00   number of occupancies < 0.1:       29 |
|-----------------------------------------------------------------------------|
r_final: 0.3893
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7130
moved from start:          0.3790

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.045  11438  Z= 0.114
  Angle     :  0.630  18.118  15446  Z= 0.321
  Chirality :  0.044   0.223   1663
  Planarity :  0.004   0.047   1987
  Dihedral  :  4.510  22.373   1504
  Min Nonbonded Distance : 2.378

Molprobity Statistics.
  All-atom Clashscore : 13.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.83 %
    Favored  : 96.17 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.24 %
    Favored  : 99.76 %
  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 aren not related in a simple way.
  whole: -0.69 (0.22), residues: 1357
  helix:  0.66 (0.24), residues: 465
  sheet: -1.26 (0.36), residues: 210
  loop : -0.93 (0.23), residues: 682

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 347 
 TYR   0.039   0.001   TYR A 206 
 PHE   0.031   0.001   PHE A 421 
 TRP   0.030   0.002   TRP A 578 
 HIS   0.004   0.001   HIS A1025 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 (11438)
  covalent geometry    : angle       0.62989 (15446)
  hydrogen bonds       : bond        0.03473 (  425)
  hydrogen bonds       : angle       5.46657 ( 1191)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1811.06 seconds
wall clock time: 32 minutes 10.39 seconds (1930.39 seconds total)