Starting phenix.real_space_refine
on Fri Aug 22 19:20:17 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gua_34271/08_2025/8gua_34271.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gua_34271/08_2025/8gua_34271.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gua_34271/08_2025/8gua_34271.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gua_34271/08_2025/8gua_34271.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gua_34271/08_2025/8gua_34271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gua_34271/08_2025/8gua_34271.map"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.055
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: 5
    Type Number    sf(0)   Gaussians
     S      62      5.16       5
     C    4481      2.51       5
     N    1204      2.21       5
     O    1267      1.98       5
     F       3      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 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: 7017
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 6987
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 855, 6987
          Classifications: {'peptide': 855}
          Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 814}
          Chain breaks: 7
    Chain: "A"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'1LT': 1}
          Classifications: {'undetermined': 1}
  Residues with excluded nonbonded symmetry interactions: 4
    residue:
      pdb=" N   ILE A 932 " occ=0.50
      ... (6 atoms not shown)
      pdb=" CD1 ILE A 932 " occ=0.50
    residue:
      pdb=" N   ASP A 933 " occ=0.50
      ... (6 atoms not shown)
      pdb=" OD2 ASP A 933 " occ=0.50
    residue:
      pdb=" N   PHE A 934 " occ=0.50
      ... (9 atoms not shown)
      pdb=" CZ  PHE A 934 " occ=0.50
    residue:
      pdb=" N   GLY A 935 " occ=0.50
      ... (2 atoms not shown)
      pdb=" O   GLY A 935 " occ=0.50
  Time building chain proxies: 1.71, per 1000 atoms: 0.24
  Number of scatterers: 7017
  At special positions: 0
  Unit cell: (79.254, 95.319, 103.887, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      62     16.00
     F       3      9.00
     O    1267      8.00
     N    1204      7.00
     C    4481      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: 0.61
  Conformation dependent library (CDL) restraints added in 454.8 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1638

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      51.8% alpha, 12.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.32
  Creating SS restraints...
    Processing helix  chain 'A' and resid 107 through 122
      removed outlier: 3.792A  pdb=" N   ARG A 115 " --> pdb=" O   LYS A 111 " (cutoff:3.500A)
      removed outlier: 3.937A  pdb=" N   GLU A 116 " --> pdb=" O   ILE A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 130
      removed outlier: 3.586A  pdb=" N   ASP A 129 " --> pdb=" O   VAL A 125 " (cutoff:3.500A)
      removed outlier: 3.607A  pdb=" N   MET A 130 " --> pdb=" O   CYS A 126 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 125 through 130'
    Processing helix  chain 'A' and resid 133 through 141
    Processing helix  chain 'A' and resid 144 through 146
      No H-bonds generated for 'chain 'A' and resid 144 through 146'
    Processing helix  chain 'A' and resid 147 through 155
    Processing helix  chain 'A' and resid 159 through 167
    Processing helix  chain 'A' and resid 178 through 184
    Processing helix  chain 'A' and resid 218 through 229
      removed outlier: 3.971A  pdb=" N   ALA A 222 " --> pdb=" O   GLU A 218 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   GLU A 223 " --> pdb=" O   GLN A 219 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 270 through 280
    Processing helix  chain 'A' and resid 290 through 295
    Processing helix  chain 'A' and resid 305 through 309
      removed outlier: 3.642A  pdb=" N   ARG A 309 " --> pdb=" O   SER A 306 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 328 through 330
      No H-bonds generated for 'chain 'A' and resid 328 through 330'
    Processing helix  chain 'A' and resid 394 through 396
      No H-bonds generated for 'chain 'A' and resid 394 through 396'
    Processing helix  chain 'A' and resid 488 through 500
      removed outlier: 3.560A  pdb=" N   SER A 499 " --> pdb=" O   HIS A 495 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 525 through 537
      removed outlier: 3.950A  pdb=" N   GLU A 529 " --> pdb=" O   GLU A 525 " (cutoff:3.500A)
      removed outlier: 3.608A  pdb=" N   LYS A 532 " --> pdb=" O   LYS A 528 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 544 through 554
      removed outlier: 3.723A  pdb=" N   HIS A 554 " --> pdb=" O   PHE A 550 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 554 through 559
      removed outlier: 3.668A  pdb=" N   VAL A 559 " --> pdb=" O   ARG A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 561 through 563
      No H-bonds generated for 'chain 'A' and resid 561 through 563'
    Processing helix  chain 'A' and resid 564 through 572
      removed outlier: 3.698A  pdb=" N   LEU A 570 " --> pdb=" O   PRO A 566 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 576 through 589
      removed outlier: 3.515A  pdb=" N   CYS A 585 " --> pdb=" O   ALA A 581 " (cutoff:3.500A)
      removed outlier: 3.585A  pdb=" N   LEU A 586 " --> pdb=" O   GLN A 582 " (cutoff:3.500A)
      removed outlier: 3.778A  pdb=" N   ASP A 589 " --> pdb=" O   CYS A 585 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 601
      removed outlier: 4.146A  pdb=" N   GLU A 600 " --> pdb=" O   GLU A 596 " (cutoff:3.500A)
      removed outlier: 4.041A  pdb=" N   LEU A 601 " --> pdb=" O   GLN A 597 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 623
      removed outlier: 3.501A  pdb=" N   ALA A 615 " --> pdb=" O   VAL A 611 " (cutoff:3.500A)
      removed outlier: 4.000A  pdb=" N   VAL A 616 " --> pdb=" O   ARG A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 624 through 638
      removed outlier: 4.942A  pdb=" N   ILE A 633 " --> pdb=" O   SER A 629 " (cutoff:3.500A)
      removed outlier: 5.484A  pdb=" N   GLN A 634 " --> pdb=" O   GLN A 630 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   GLN A 637 " --> pdb=" O   ILE A 633 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 658
      removed outlier: 3.700A  pdb=" N   ARG A 651 " --> pdb=" O   ASN A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 660 through 674
    Processing helix  chain 'A' and resid 680 through 695
      removed outlier: 3.886A  pdb=" N   ALA A 694 " --> pdb=" O   SER A 690 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 697 through 722
      removed outlier: 3.767A  pdb=" N   HIS A 701 " --> pdb=" O   MET A 697 " (cutoff:3.500A)
      removed outlier: 3.973A  pdb=" N   GLU A 722 " --> pdb=" O   ILE A 718 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 729 through 740
      removed outlier: 3.729A  pdb=" N   ARG A 740 " --> pdb=" O   VAL A 736 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 741 through 748
      removed outlier: 3.696A  pdb=" N   ALA A 747 " --> pdb=" O   ASP A 743 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 3.792A  pdb=" N   CYS A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 789 through 793
    Processing helix  chain 'A' and resid 807 through 827
    Processing helix  chain 'A' and resid 857 through 861
    Processing helix  chain 'A' and resid 875 through 884
      removed outlier: 3.503A  pdb=" N   LEU A 881 " --> pdb=" O   LEU A 877 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 889 through 911
      removed outlier: 3.524A  pdb=" N   ALA A 893 " --> pdb=" O   ILE A 889 " (cutoff:3.500A)
      removed outlier: 3.735A  pdb=" N   PHE A 897 " --> pdb=" O   ALA A 893 " (cutoff:3.500A)
      removed outlier: 3.621A  pdb=" N   ARG A 899 " --> pdb=" O   ASP A 895 " (cutoff:3.500A)
      removed outlier: 3.645A  pdb=" N   GLY A 903 " --> pdb=" O   ARG A 899 " (cutoff:3.500A)
      removed outlier: 4.420A  pdb=" N   TYR A 904 " --> pdb=" O   SER A 900 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 958 through 965
      removed outlier: 3.939A  pdb=" N   VAL A 963 " --> pdb=" O   ASP A 959 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 974 through 994
      removed outlier: 4.084A  pdb=" N   GLU A 978 " --> pdb=" O   THR A 974 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   ARG A 979 " --> pdb=" O   ARG A 975 " (cutoff:3.500A)
      removed outlier: 4.037A  pdb=" N   CYS A 984 " --> pdb=" O   PHE A 980 " (cutoff:3.500A)
      removed outlier: 3.572A  pdb=" N   TYR A 988 " --> pdb=" O   CYS A 984 " (cutoff:3.500A)
      removed outlier: 4.407A  pdb=" N   LEU A 989 " --> pdb=" O   TYR A 985 " (cutoff:3.500A)
      removed outlier: 4.475A  pdb=" N   ALA A 990 " --> pdb=" O   LYS A 986 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   ILE A 991 " --> pdb=" O   ALA A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 994 through 1001
      removed outlier: 3.801A  pdb=" N   PHE A 998 " --> pdb=" O   HIS A 994 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1004 through 1009
      removed outlier: 4.052A  pdb=" N   GLY A1007 " --> pdb=" O   MET A1004 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   GLY A1009 " --> pdb=" O   LEU A1006 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1010 through 1014
      removed outlier: 3.864A  pdb=" N   GLN A1014 " --> pdb=" O   PRO A1011 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1015 through 1018
    Processing helix  chain 'A' and resid 1019 through 1027
      removed outlier: 4.020A  pdb=" N   ARG A1023 " --> pdb=" O   ILE A1019 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1031 through 1047
      removed outlier: 3.628A  pdb=" N   LEU A1036 " --> pdb=" O   GLU A1032 " (cutoff:3.500A)
      removed outlier: 5.160A  pdb=" N   GLU A1037 " --> pdb=" O   GLN A1033 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   TYR A1038 " --> pdb=" O   GLU A1034 " (cutoff:3.500A)
      removed outlier: 3.718A  pdb=" N   PHE A1039 " --> pdb=" O   ALA A1035 " (cutoff:3.500A)
      removed outlier: 3.663A  pdb=" N   ASP A1045 " --> pdb=" O   LYS A1041 " (cutoff:3.500A)
      removed outlier: 3.654A  pdb=" N   ALA A1046 " --> pdb=" O   GLN A1042 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 205 through 212
      removed outlier: 3.555A  pdb=" N   ILE A 211 " --> pdb=" O   ILE A 190 " (cutoff:3.500A)
      removed outlier: 8.418A  pdb=" N   LEU A 285 " --> pdb=" O   ILE A 191 " (cutoff:3.500A)
      removed outlier: 5.823A  pdb=" N   VAL A 193 " --> pdb=" O   LEU A 285 " (cutoff:3.500A)
      removed outlier: 7.534A  pdb=" N   LEU A 287 " --> pdb=" O   VAL A 193 " (cutoff:3.500A)
      removed outlier: 7.014A  pdb=" N   TRP A 195 " --> pdb=" O   LEU A 287 " (cutoff:3.500A)
      removed outlier: 8.767A  pdb=" N   ALA A 289 " --> pdb=" O   TRP A 195 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 325 through 326
      removed outlier: 6.407A  pdb=" N   LYS A 325 " --> pdb=" O   LYS A 485 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'A' and resid 382 through 392
      removed outlier: 6.764A  pdb=" N   TRP A 383 " --> pdb=" O   CYS A 340 " (cutoff:3.500A)
      removed outlier: 7.218A  pdb=" N   CYS A 340 " --> pdb=" O   TRP A 383 " (cutoff:3.500A)
      removed outlier: 4.042A  pdb=" N   LEU A 334 " --> pdb=" O   TYR A 389 " (cutoff:3.500A)
      removed outlier: 7.147A  pdb=" N   GLU A 474 " --> pdb=" O   LEU A 339 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   ALA A 341 " --> pdb=" O   CYS A 472 " (cutoff:3.500A)
      removed outlier: 6.260A  pdb=" N   CYS A 472 " --> pdb=" O   ALA A 341 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 365 through 366
      removed outlier: 3.902A  pdb=" N   GLU A 365 " --> pdb=" O   HIS A 362 " (cutoff:3.500A)
      removed outlier: 6.573A  pdb=" N   LEU A 402 " --> pdb=" O   ASN A 426 " (cutoff:3.500A)
      removed outlier: 4.447A  pdb=" N   ASN A 426 " --> pdb=" O   LEU A 402 " (cutoff:3.500A)
      removed outlier: 6.439A  pdb=" N   LEU A 404 " --> pdb=" O   TRP A 424 " (cutoff:3.500A)
      removed outlier: 4.589A  pdb=" N   TRP A 424 " --> pdb=" O   LEU A 404 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   ILE A 406 " --> pdb=" O   LEU A 422 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 752 through 753
      removed outlier: 5.727A  pdb=" N   HIS A 759 " --> pdb=" O   SER A 753 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 770 through 771
      removed outlier: 3.514A  pdb=" N   GLY A 846 " --> pdb=" O   LYS A 802 " (cutoff:3.500A)
      removed outlier: 6.736A  pdb=" N   VAL A 845 " --> pdb=" O   ILE A 841 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 854 through 856
      removed outlier: 3.528A  pdb=" N   HIS A 855 " --> pdb=" O   VAL A 923 " (cutoff:3.500A)

    279 hydrogen bonds defined for protein.
    801 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.39

  Time building geometry restraints manager: 0.83 seconds

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

  Histogram of bond lengths:
        1.18 -     1.30: 1160
        1.30 -     1.43: 1820
        1.43 -     1.56: 4092
        1.56 -     1.68: 7
        1.68 -     1.81: 94
  Bond restraints: 7173
  Sorted by residual:
  bond pdb=" C9  1LT A1101 "
       pdb=" S   1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.738  1.530  0.208 2.00e-02 2.50e+03 1.08e+02
  bond pdb=" C2  1LT A1101 "
       pdb=" S   1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.734  1.533  0.201 2.00e-02 2.50e+03 1.01e+02
  bond pdb=" N   1LT A1101 "
       pdb=" C1  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.368  1.568 -0.200 2.00e-02 2.50e+03 1.00e+02
  bond pdb=" C5  1LT A1101 "
       pdb=" C6  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.525  1.350  0.175 2.00e-02 2.50e+03 7.62e+01
  bond pdb=" N   1LT A1101 "
       pdb=" C2  1LT A1101 "
    ideal  model  delta    sigma   weight residual
    1.291  1.415 -0.124 2.00e-02 2.50e+03 3.84e+01
  ... (remaining 7168 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.84: 9656
        3.84 -     7.67: 34
        7.67 -    11.50: 2
       11.50 -    15.34: 2
       15.34 -    19.17: 2
  Bond angle restraints: 9696
  Sorted by residual:
  angle pdb=" N1  1LT A1101 "
        pdb=" C2  1LT A1101 "
        pdb=" S   1LT A1101 "
      ideal   model   delta    sigma   weight residual
     118.47  137.64  -19.17 3.00e+00 1.11e-01 4.09e+01
  angle pdb=" C   TRP A 446 "
        pdb=" N   PRO A 447 "
        pdb=" CA  PRO A 447 "
      ideal   model   delta    sigma   weight residual
     120.03  113.74    6.29 9.90e-01 1.02e+00 4.04e+01
  angle pdb=" C2  1LT A1101 "
        pdb=" S   1LT A1101 "
        pdb=" C9  1LT A1101 "
      ideal   model   delta    sigma   weight residual
      88.90  107.66  -18.76 3.00e+00 1.11e-01 3.91e+01
  angle pdb=" N   1LT A1101 "
        pdb=" C2  1LT A1101 "
        pdb=" N1  1LT A1101 "
      ideal   model   delta    sigma   weight residual
     126.74  114.29   12.45 3.00e+00 1.11e-01 1.72e+01
  angle pdb=" N   PRO A 449 "
        pdb=" CA  PRO A 449 "
        pdb=" C   PRO A 449 "
      ideal   model   delta    sigma   weight residual
     112.47  120.27   -7.80 2.06e+00 2.36e-01 1.43e+01
  ... (remaining 9691 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.85: 3868
       17.85 -    35.69: 408
       35.69 -    53.54: 71
       53.54 -    71.39: 15
       71.39 -    89.24: 7
  Dihedral angle restraints: 4369
    sinusoidal: 1851
      harmonic: 2518
  Sorted by residual:
  dihedral pdb=" C   PHE A 937 "
           pdb=" N   PHE A 937 "
           pdb=" CA  PHE A 937 "
           pdb=" CB  PHE A 937 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -131.55    8.95     0      2.50e+00 1.60e-01 1.28e+01
  dihedral pdb=" N   PHE A 937 "
           pdb=" C   PHE A 937 "
           pdb=" CA  PHE A 937 "
           pdb=" CB  PHE A 937 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  130.99   -8.19     0      2.50e+00 1.60e-01 1.07e+01
  dihedral pdb=" CA  PRO A 539 "
           pdb=" C   PRO A 539 "
           pdb=" N   LEU A 540 "
           pdb=" CA  LEU A 540 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  163.70   16.30     0      5.00e+00 4.00e-02 1.06e+01
  ... (remaining 4366 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.069: 966
       0.069 -    0.139: 82
       0.139 -    0.208: 2
       0.208 -    0.278: 2
       0.278 -    0.347: 2
  Chirality restraints: 1054
  Sorted by residual:
  chirality pdb=" CA  PRO A 449 "
            pdb=" N   PRO A 449 "
            pdb=" C   PRO A 449 "
            pdb=" CB  PRO A 449 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    2.37    0.35 2.00e-01 2.50e+01 3.02e+00
  chirality pdb=" CA  PHE A 937 "
            pdb=" N   PHE A 937 "
            pdb=" C   PHE A 937 "
            pdb=" CB  PHE A 937 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.19    0.32 2.00e-01 2.50e+01 2.63e+00
  chirality pdb=" CA  LEU A 938 "
            pdb=" N   LEU A 938 "
            pdb=" C   LEU A 938 "
            pdb=" CB  LEU A 938 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.27    0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 1051 not shown)

  Planarity restraints: 1238
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A 448 "   -0.069 5.00e-02 4.00e+02   1.03e-01 1.70e+01
        pdb=" N   PRO A 449 "    0.178 5.00e-02 4.00e+02
        pdb=" CA  PRO A 449 "   -0.056 5.00e-02 4.00e+02
        pdb=" CD  PRO A 449 "   -0.054 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 159 "    0.017 2.00e-02 2.50e+03   3.66e-02 1.34e+01
        pdb=" C   PRO A 159 "   -0.063 2.00e-02 2.50e+03
        pdb=" O   PRO A 159 "    0.025 2.00e-02 2.50e+03
        pdb=" N   HIS A 160 "    0.022 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  MET A 858 "   -0.011 2.00e-02 2.50e+03   2.15e-02 4.60e+00
        pdb=" C   MET A 858 "    0.037 2.00e-02 2.50e+03
        pdb=" O   MET A 858 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLN A 859 "   -0.013 2.00e-02 2.50e+03
  ... (remaining 1235 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1076
        2.76 -     3.29: 6880
        3.29 -     3.83: 11606
        3.83 -     4.36: 14524
        4.36 -     4.90: 23807
  Nonbonded interactions: 57893
  Sorted by model distance:
  nonbonded pdb=" OG  SER A 900 "
            pdb=" O   LEU A 929 "
     model   vdw
     2.224 3.040
  nonbonded pdb=" OH  TYR A 584 "
            pdb=" OD1 ASP A 608 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" O   GLU A 722 "
            pdb=" NE2 GLN A 731 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" NH1 ARG A 808 "
            pdb=" O   SER A1008 "
     model   vdw
     2.248 3.120
  nonbonded pdb=" NE2 GLN A 825 "
            pdb=" O   LEU A 831 "
     model   vdw
     2.251 3.120
  ... (remaining 57888 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.50 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     8.680
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:9.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5968
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      :  0.007   0.208   7173  Z= 0.347
  Angle     :  0.695  19.175   9696  Z= 0.345
  Chirality :  0.044   0.347   1054
  Planarity :  0.005   0.103   1238
  Dihedral  : 15.036  89.236   2731
  Min Nonbonded Distance : 2.224

Molprobity Statistics.
  All-atom Clashscore : 11.06
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  3.81 %
    Favored  : 95.95 %
  Rotamer:
    Outliers :  0.13 %
    Allowed  :  0.77 %
    Favored  : 99.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.79 (0.29), residues: 839
  helix: -0.84 (0.27), residues: 363
  sheet:  0.24 (0.51), residues: 98
  loop : -0.20 (0.35), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 382 
 TYR   0.024   0.001   TYR A 392 
 PHE   0.012   0.001   PHE A 960 
 TRP   0.005   0.001   TRP A 783 
 HIS   0.003   0.001   HIS A 160 

Details of bonding type rmsd
  covalent geometry    : bond        0.00686 ( 7173)
  covalent geometry    : angle       0.69461 ( 9696)
  hydrogen bonds       : bond        0.27639 (  279)
  hydrogen bonds       : angle       8.36492 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 103
  time to evaluate  : 0.335 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 0.5802
  time to fit residues: 63.1028
Evaluate side-chains
  78 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.8980
   chunk 61 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 74 optimal weight:    0.8980
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
A 643 GLN
** A 796 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 = 0.4543 r_free = 0.4543 target = 0.227643 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4320 r_free = 0.4320 target = 0.202535 restraints weight = 6471.277|
|-----------------------------------------------------------------------------|
r_work (start): 0.4328 rms_B_bonded: 1.16
r_work: 0.4123 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3986 rms_B_bonded: 4.49 restraints_weight: 0.2500
r_work (final): 0.3986
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3960
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3960 r_free = 0.3960    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3958 r_free = 0.3958    target_work(ls_wunit_k1) = 0.165         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3958
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6360
moved from start:          0.1561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   7173  Z= 0.165
  Angle     :  0.641   6.581   9696  Z= 0.333
  Chirality :  0.044   0.228   1054
  Planarity :  0.006   0.101   1238
  Dihedral  :  5.446  35.711    943
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.56
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.65 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 10.33 %
    Favored  : 87.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.78 (0.29), residues: 839
  helix: -0.54 (0.25), residues: 391
  sheet:  0.33 (0.50), residues: 99
  loop : -0.54 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 382 
 TYR   0.021   0.002   TYR A 392 
 PHE   0.013   0.002   PHE A 937 
 TRP   0.008   0.001   TRP A 669 
 HIS   0.006   0.001   HIS A 936 

Details of bonding type rmsd
  covalent geometry    : bond        0.00387 ( 7173)
  covalent geometry    : angle       0.64082 ( 9696)
  hydrogen bonds       : bond        0.05258 (  279)
  hydrogen bonds       : angle       5.50888 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 0.280 
Fit side-chains
   revert: symmetry clash
REVERT: A  594 LYS cc_start: 0.7034 (mmtm) cc_final: 0.6380 (mmpt)
REVERT: A  599 MET cc_start: 0.6845 (mtp) cc_final: 0.6439 (mtm)
REVERT: A  682 GLN cc_start: 0.6991 (mp-120) cc_final: 0.6016 (mt0)
REVERT: A  717 ASP cc_start: 0.6967 (OUTLIER) cc_final: 0.6616 (m-30)
REVERT: A  979 ARG cc_start: 0.6663 (OUTLIER) cc_final: 0.5499 (mtt-85)
REVERT: A 1039 PHE cc_start: 0.4837 (t80) cc_final: 0.4545 (t80)
  outliers start: 14
  outliers final: 5
  residues processed: 107
  average time/residue: 0.5892
  time to fit residues: 66.6065
Evaluate side-chains
  91 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  857 ILE
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 11 optimal weight:    3.9990
   chunk 36 optimal weight:    6.9990
   chunk 64 optimal weight:    0.5980
   chunk 48 optimal weight:    0.8980
   chunk 7 optimal weight:    5.9990
   chunk 80 optimal weight:    0.6980
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    1.9990
   chunk 59 optimal weight:    0.6980
   chunk 75 optimal weight:    0.5980
   chunk 72 optimal weight:    0.6980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4552 r_free = 0.4552 target = 0.228469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4283 r_free = 0.4283 target = 0.198702 restraints weight = 6393.717|
|-----------------------------------------------------------------------------|
r_work (start): 0.4272 rms_B_bonded: 1.42
r_work: 0.4078 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4078
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4063
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4063 r_free = 0.4063    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.35   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4063 r_free = 0.4063    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4063
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6254
moved from start:          0.1887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7173  Z= 0.139
  Angle     :  0.587  10.151   9696  Z= 0.303
  Chirality :  0.043   0.220   1054
  Planarity :  0.006   0.097   1238
  Dihedral  :  5.199  34.732    943
  Min Nonbonded Distance : 2.500

Molprobity Statistics.
  All-atom Clashscore : 10.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.17 %
    Favored  : 95.71 %
  Rotamer:
    Outliers :  2.17 %
    Allowed  : 14.67 %
    Favored  : 83.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.59 (0.29), residues: 839
  helix: -0.32 (0.25), residues: 392
  sheet:  0.36 (0.50), residues: 98
  loop : -0.50 (0.35), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 382 
 TYR   0.016   0.002   TYR A 392 
 PHE   0.012   0.002   PHE A 937 
 TRP   0.009   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 7173)
  covalent geometry    : angle       0.58683 ( 9696)
  hydrogen bonds       : bond        0.04528 (  279)
  hydrogen bonds       : angle       5.05046 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 91
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: A  278 MET cc_start: 0.3993 (mmp) cc_final: 0.3533 (ttt)
REVERT: A  594 LYS cc_start: 0.7007 (mmtm) cc_final: 0.6423 (mmpt)
REVERT: A  599 MET cc_start: 0.6840 (mtp) cc_final: 0.6380 (mtm)
REVERT: A  682 GLN cc_start: 0.6967 (mp-120) cc_final: 0.5962 (mt0)
REVERT: A  717 ASP cc_start: 0.6862 (OUTLIER) cc_final: 0.6618 (t0)
REVERT: A  979 ARG cc_start: 0.6587 (OUTLIER) cc_final: 0.5427 (mtt-85)
  outliers start: 17
  outliers final: 5
  residues processed: 100
  average time/residue: 0.5604
  time to fit residues: 59.6187
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 88
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  340 CYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 34 optimal weight:    0.8980
   chunk 20 optimal weight:    5.9990
   chunk 4 optimal weight:    0.6980
   chunk 9 optimal weight:    0.7980
   chunk 48 optimal weight:    0.5980
   chunk 31 optimal weight:    5.9990
   chunk 8 optimal weight:    0.8980
   chunk 26 optimal weight:    4.9990
   chunk 49 optimal weight:    0.5980
   overall best weight:    0.7180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4539 r_free = 0.4539 target = 0.226700 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4291 r_free = 0.4291 target = 0.199049 restraints weight = 6514.936|
|-----------------------------------------------------------------------------|
r_work (start): 0.4297 rms_B_bonded: 1.43
r_work: 0.4114 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3977 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3977
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3955
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3955 r_free = 0.3955    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3955
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6352
moved from start:          0.2086

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7173  Z= 0.142
  Angle     :  0.580   6.355   9696  Z= 0.299
  Chirality :  0.043   0.217   1054
  Planarity :  0.006   0.094   1238
  Dihedral  :  5.196  35.606    943
  Min Nonbonded Distance : 2.485

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.89 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 16.07 %
    Favored  : 81.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.47 (0.29), residues: 839
  helix: -0.14 (0.25), residues: 391
  sheet:  0.25 (0.50), residues: 96
  loop : -0.49 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 382 
 TYR   0.016   0.002   TYR A 392 
 PHE   0.014   0.002   PHE A 909 
 TRP   0.008   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 7173)
  covalent geometry    : angle       0.58006 ( 9696)
  hydrogen bonds       : bond        0.04141 (  279)
  hydrogen bonds       : angle       4.87234 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 93
  time to evaluate  : 0.306 
Fit side-chains
   revert: symmetry clash
REVERT: A  278 MET cc_start: 0.4399 (mmp) cc_final: 0.3634 (mtt)
REVERT: A  374 GLN cc_start: 0.7912 (mp10) cc_final: 0.7642 (mp10)
REVERT: A  594 LYS cc_start: 0.7129 (mmtm) cc_final: 0.6470 (mmpt)
REVERT: A  599 MET cc_start: 0.6973 (mtp) cc_final: 0.6573 (mtm)
REVERT: A  682 GLN cc_start: 0.6985 (mp-120) cc_final: 0.5936 (mt0)
REVERT: A  697 MET cc_start: 0.7054 (ttp) cc_final: 0.6610 (tpp)
REVERT: A  717 ASP cc_start: 0.6941 (OUTLIER) cc_final: 0.6698 (t0)
REVERT: A  832 ARG cc_start: 0.5494 (OUTLIER) cc_final: 0.5283 (mmt90)
REVERT: A  979 ARG cc_start: 0.6769 (OUTLIER) cc_final: 0.5490 (mtt-85)
REVERT: A  983 MET cc_start: 0.5745 (ttm) cc_final: 0.4465 (ptt)
  outliers start: 21
  outliers final: 6
  residues processed: 103
  average time/residue: 0.5663
  time to fit residues: 61.7968
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 89
  time to evaluate  : 0.300 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  547 GLU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  833 MET
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 51 optimal weight:    0.4980
   chunk 45 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 80 optimal weight:    0.4980
   chunk 28 optimal weight:    0.8980
   chunk 1 optimal weight:    0.2980
   chunk 60 optimal weight:    0.0670
   chunk 43 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   chunk 47 optimal weight:    0.4980
   chunk 73 optimal weight:    0.1980
   overall best weight:    0.3118

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4561 r_free = 0.4561 target = 0.229776 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4296 r_free = 0.4296 target = 0.200212 restraints weight = 6424.674|
|-----------------------------------------------------------------------------|
r_work (start): 0.4295 rms_B_bonded: 1.43
r_work: 0.4095 rms_B_bonded: 3.20 restraints_weight: 0.5000
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4069
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4069 r_free = 0.4069    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4069 r_free = 0.4069    target_work(ls_wunit_k1) = 0.176         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4069
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6215
moved from start:          0.2209

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7173  Z= 0.112
  Angle     :  0.540   6.891   9696  Z= 0.278
  Chirality :  0.041   0.217   1054
  Planarity :  0.005   0.091   1238
  Dihedral  :  4.985  34.651    943
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.81 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 17.35 %
    Favored  : 79.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.19 (0.29), residues: 839
  helix:  0.17 (0.26), residues: 392
  sheet:  0.27 (0.50), residues: 96
  loop : -0.42 (0.36), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 382 
 TYR   0.013   0.001   TYR A 432 
 PHE   0.014   0.001   PHE A 909 
 TRP   0.010   0.001   TRP A 669 
 HIS   0.004   0.000   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00264 ( 7173)
  covalent geometry    : angle       0.53989 ( 9696)
  hydrogen bonds       : bond        0.03519 (  279)
  hydrogen bonds       : angle       4.57553 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 91
  time to evaluate  : 0.295 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.6849 (t70) cc_final: 0.6556 (t70)
REVERT: A  278 MET cc_start: 0.4303 (mmp) cc_final: 0.3570 (mtt)
REVERT: A  540 LEU cc_start: 0.6905 (OUTLIER) cc_final: 0.6680 (mt)
REVERT: A  599 MET cc_start: 0.6732 (mtp) cc_final: 0.6173 (mtm)
REVERT: A  682 GLN cc_start: 0.6905 (mp-120) cc_final: 0.5904 (mt0)
REVERT: A  717 ASP cc_start: 0.6901 (OUTLIER) cc_final: 0.6689 (t0)
REVERT: A  979 ARG cc_start: 0.6637 (OUTLIER) cc_final: 0.5640 (mtt-85)
REVERT: A  983 MET cc_start: 0.5498 (ttm) cc_final: 0.4379 (ptt)
  outliers start: 22
  outliers final: 6
  residues processed: 104
  average time/residue: 0.5251
  time to fit residues: 58.1864
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 86
  time to evaluate  : 0.283 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 75 optimal weight:    0.6980
   chunk 11 optimal weight:    1.9990
   chunk 7 optimal weight:    0.7980
   chunk 47 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0570
   chunk 45 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 65 optimal weight:    0.9980
   chunk 63 optimal weight:    0.0870
   chunk 25 optimal weight:    0.0070
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.3294

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

Flipped N/Q/H residues before XYZ refinement:
A 575 ASN
A 637 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4564 r_free = 0.4564 target = 0.230250 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.4305 r_free = 0.4305 target = 0.200890 restraints weight = 6487.863|
|-----------------------------------------------------------------------------|
r_work (start): 0.4305 rms_B_bonded: 1.41
r_work: 0.4109 rms_B_bonded: 3.15 restraints_weight: 0.5000
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4093
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4093 r_free = 0.4093    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4093 r_free = 0.4093    target_work(ls_wunit_k1) = 0.178         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4093
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6200
moved from start:          0.2380

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7173  Z= 0.110
  Angle     :  0.548   7.197   9696  Z= 0.281
  Chirality :  0.041   0.217   1054
  Planarity :  0.005   0.089   1238
  Dihedral  :  4.918  34.750    943
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 9.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.05 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 18.11 %
    Favored  : 79.21 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.06 (0.29), residues: 839
  helix:  0.33 (0.26), residues: 391
  sheet:  0.40 (0.50), residues: 95
  loop : -0.44 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 832 
 TYR   0.013   0.001   TYR A 432 
 PHE   0.016   0.001   PHE A 960 
 TRP   0.007   0.001   TRP A 669 
 HIS   0.004   0.000   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 7173)
  covalent geometry    : angle       0.54772 ( 9696)
  hydrogen bonds       : bond        0.03342 (  279)
  hydrogen bonds       : angle       4.45927 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 91
  time to evaluate  : 0.349 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.6714 (t70) cc_final: 0.6422 (t70)
REVERT: A  540 LEU cc_start: 0.6918 (OUTLIER) cc_final: 0.6693 (mt)
REVERT: A  599 MET cc_start: 0.6765 (mtp) cc_final: 0.6404 (mtm)
REVERT: A  661 GLN cc_start: 0.6255 (OUTLIER) cc_final: 0.6029 (mt0)
REVERT: A  682 GLN cc_start: 0.6929 (mp-120) cc_final: 0.5829 (mt0)
REVERT: A  717 ASP cc_start: 0.6890 (OUTLIER) cc_final: 0.6687 (t0)
REVERT: A  820 MET cc_start: 0.7269 (mtt) cc_final: 0.6776 (mtt)
REVERT: A  821 GLU cc_start: 0.6981 (pp20) cc_final: 0.6752 (tm-30)
REVERT: A  979 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5616 (mtt-85)
REVERT: A  983 MET cc_start: 0.5441 (ttm) cc_final: 0.4378 (ptt)
REVERT: A 1004 MET cc_start: 0.6844 (OUTLIER) cc_final: 0.5926 (mmm)
  outliers start: 21
  outliers final: 6
  residues processed: 104
  average time/residue: 0.5129
  time to fit residues: 56.8618
Evaluate side-chains
  95 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 84
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  661 GLN
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1004 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 79 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 7 optimal weight:    0.9990
   chunk 10 optimal weight:    0.4980
   chunk 32 optimal weight:    3.9990
   chunk 67 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 59 optimal weight:    0.5980
   chunk 68 optimal weight:    1.9990
   chunk 70 optimal weight:    0.0000
   chunk 37 optimal weight:    0.9990
   overall best weight:    0.4984

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

Flipped N/Q/H residues before XYZ refinement:
A 374 GLN
A 637 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.229168 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.199822 restraints weight = 6428.545|
|-----------------------------------------------------------------------------|
r_work (start): 0.4295 rms_B_bonded: 1.40
r_work: 0.4105 rms_B_bonded: 3.05 restraints_weight: 0.5000
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4087
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4087 r_free = 0.4087    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.33   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4087 r_free = 0.4087    target_work(ls_wunit_k1) = 0.177         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4087
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6211
moved from start:          0.2435

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   7173  Z= 0.122
  Angle     :  0.564   8.215   9696  Z= 0.288
  Chirality :  0.042   0.217   1054
  Planarity :  0.005   0.087   1238
  Dihedral  :  4.955  35.074    943
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 10.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.29 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  2.68 %
    Allowed  : 19.64 %
    Favored  : 77.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.02 (0.29), residues: 839
  helix:  0.39 (0.26), residues: 391
  sheet:  0.45 (0.50), residues: 95
  loop : -0.48 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 832 
 TYR   0.017   0.001   TYR A 904 
 PHE   0.015   0.001   PHE A 909 
 TRP   0.006   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 7173)
  covalent geometry    : angle       0.56361 ( 9696)
  hydrogen bonds       : bond        0.03446 (  279)
  hydrogen bonds       : angle       4.46361 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 83
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: A  138 ASP cc_start: 0.6647 (t70) cc_final: 0.6327 (t70)
REVERT: A  278 MET cc_start: 0.4373 (mmp) cc_final: 0.3136 (ttm)
REVERT: A  540 LEU cc_start: 0.6943 (OUTLIER) cc_final: 0.6716 (mt)
REVERT: A  599 MET cc_start: 0.6881 (mtp) cc_final: 0.6523 (mtm)
REVERT: A  661 GLN cc_start: 0.6293 (OUTLIER) cc_final: 0.6049 (mt0)
REVERT: A  682 GLN cc_start: 0.6863 (mp-120) cc_final: 0.5821 (mt0)
REVERT: A  820 MET cc_start: 0.7169 (mtt) cc_final: 0.6688 (mtt)
REVERT: A  979 ARG cc_start: 0.6617 (OUTLIER) cc_final: 0.5607 (mtt-85)
REVERT: A  983 MET cc_start: 0.5416 (ttm) cc_final: 0.4393 (ptt)
  outliers start: 21
  outliers final: 7
  residues processed: 97
  average time/residue: 0.4706
  time to fit residues: 49.0375
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 79
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  540 LEU
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  661 GLN
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 26 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 64 optimal weight:    0.5980
   chunk 75 optimal weight:    0.5980
   chunk 2 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 47 optimal weight:    0.6980
   chunk 65 optimal weight:    0.0870
   chunk 40 optimal weight:    2.9990
   overall best weight:    0.5958

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4543 r_free = 0.4543 target = 0.227714 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.4277 r_free = 0.4277 target = 0.197740 restraints weight = 6463.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.4283 rms_B_bonded: 1.43
r_work: 0.4088 rms_B_bonded: 3.13 restraints_weight: 0.5000
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4068
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4068 r_free = 0.4068    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4068 r_free = 0.4068    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4068
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6241
moved from start:          0.2495

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   7173  Z= 0.129
  Angle     :  0.570   8.564   9696  Z= 0.293
  Chirality :  0.042   0.229   1054
  Planarity :  0.005   0.081   1238
  Dihedral  :  5.018  35.048    943
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.77 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 20.28 %
    Favored  : 77.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.06 (0.29), residues: 839
  helix:  0.39 (0.27), residues: 393
  sheet:  0.46 (0.50), residues: 95
  loop : -0.54 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 832 
 TYR   0.014   0.002   TYR A 432 
 PHE   0.016   0.002   PHE A 909 
 TRP   0.006   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 7173)
  covalent geometry    : angle       0.56995 ( 9696)
  hydrogen bonds       : bond        0.03509 (  279)
  hydrogen bonds       : angle       4.48767 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  106 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 92
  time to evaluate  : 0.288 
Fit side-chains
REVERT: A  138 ASP cc_start: 0.6640 (t70) cc_final: 0.6324 (t70)
REVERT: A  599 MET cc_start: 0.6903 (mtp) cc_final: 0.6703 (mtp)
REVERT: A  661 GLN cc_start: 0.6297 (OUTLIER) cc_final: 0.6072 (mt0)
REVERT: A  682 GLN cc_start: 0.6877 (mp-120) cc_final: 0.5815 (mt0)
REVERT: A  709 MET cc_start: 0.7091 (mmt) cc_final: 0.6883 (mmt)
REVERT: A  820 MET cc_start: 0.7219 (mtt) cc_final: 0.6716 (mtt)
REVERT: A  979 ARG cc_start: 0.6618 (OUTLIER) cc_final: 0.5629 (mtt-85)
REVERT: A  983 MET cc_start: 0.5482 (ttm) cc_final: 0.4438 (ptt)
  outliers start: 14
  outliers final: 6
  residues processed: 103
  average time/residue: 0.5213
  time to fit residues: 57.1277
Evaluate side-chains
  93 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 85
  time to evaluate  : 0.279 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  661 GLN
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 47 optimal weight:    0.6980
   chunk 53 optimal weight:    0.2980
   chunk 79 optimal weight:    3.9990
   chunk 32 optimal weight:    3.9990
   chunk 37 optimal weight:    0.6980
   chunk 17 optimal weight:    3.9990
   chunk 52 optimal weight:    0.6980
   chunk 60 optimal weight:    3.9990
   chunk 77 optimal weight:    0.5980
   chunk 84 optimal weight:    1.9990
   chunk 54 optimal weight:    0.6980
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4550 r_free = 0.4550 target = 0.228219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.4287 r_free = 0.4287 target = 0.198544 restraints weight = 6479.408|
|-----------------------------------------------------------------------------|
r_work (start): 0.4283 rms_B_bonded: 1.41
r_work: 0.4090 rms_B_bonded: 3.10 restraints_weight: 0.5000
r_work (final): 0.4090
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.4072
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.4072 r_free = 0.4072    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.34   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.4072 r_free = 0.4072    target_work(ls_wunit_k1) = 0.175         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.4072
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6242
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7173  Z= 0.133
  Angle     :  0.592   9.942   9696  Z= 0.303
  Chirality :  0.042   0.230   1054
  Planarity :  0.006   0.082   1238
  Dihedral  :  5.085  35.021    943
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.53 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 21.05 %
    Favored  : 77.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.07 (0.29), residues: 839
  helix:  0.39 (0.27), residues: 393
  sheet:  0.45 (0.50), residues: 95
  loop : -0.55 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 777 
 TYR   0.015   0.002   TYR A 904 
 PHE   0.016   0.002   PHE A 909 
 TRP   0.006   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00324 ( 7173)
  covalent geometry    : angle       0.59208 ( 9696)
  hydrogen bonds       : bond        0.03492 (  279)
  hydrogen bonds       : angle       4.50647 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  104 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 91
  time to evaluate  : 0.308 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6418 (t0) cc_final: 0.5917 (t0)
REVERT: A  138 ASP cc_start: 0.6633 (t70) cc_final: 0.6328 (t70)
REVERT: A  278 MET cc_start: 0.4229 (mmp) cc_final: 0.3109 (ttm)
REVERT: A  382 ARG cc_start: 0.7437 (tpt90) cc_final: 0.7236 (tpt90)
REVERT: A  637 GLN cc_start: 0.7564 (OUTLIER) cc_final: 0.7040 (mp-120)
REVERT: A  661 GLN cc_start: 0.6275 (OUTLIER) cc_final: 0.6056 (mt0)
REVERT: A  682 GLN cc_start: 0.6888 (mp-120) cc_final: 0.5851 (mt0)
REVERT: A  820 MET cc_start: 0.7107 (mtt) cc_final: 0.6663 (mtt)
REVERT: A  979 ARG cc_start: 0.6606 (OUTLIER) cc_final: 0.5591 (mtt-85)
REVERT: A  983 MET cc_start: 0.5470 (ttm) cc_final: 0.4446 (ptt)
REVERT: A 1033 GLN cc_start: 0.5240 (mp10) cc_final: 0.4690 (mm-40)
  outliers start: 13
  outliers final: 8
  residues processed: 100
  average time/residue: 0.5475
  time to fit residues: 58.2048
Evaluate side-chains
  100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 89
  time to evaluate  : 0.287 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  661 GLN
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 10 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9980
   chunk 44 optimal weight:    0.6980
   chunk 26 optimal weight:    4.9990
   chunk 81 optimal weight:    3.9990
   chunk 77 optimal weight:    0.0980
   chunk 16 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 54 optimal weight:    2.9990
   chunk 50 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4529 r_free = 0.4529 target = 0.225590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4303 r_free = 0.4303 target = 0.199666 restraints weight = 6461.433|
|-----------------------------------------------------------------------------|
r_work (start): 0.4305 rms_B_bonded: 1.21
r_work: 0.4107 rms_B_bonded: 2.60 restraints_weight: 0.5000
r_work: 0.3971 rms_B_bonded: 4.39 restraints_weight: 0.2500
r_work (final): 0.3971
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3949
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3949 r_free = 0.3949    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.36   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3949 r_free = 0.3949    target_work(ls_wunit_k1) = 0.164         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3949
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6378
moved from start:          0.2574

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   7173  Z= 0.161
  Angle     :  0.634   9.621   9696  Z= 0.324
  Chirality :  0.044   0.232   1054
  Planarity :  0.006   0.077   1238
  Dihedral  :  5.256  35.213    943
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 11.20
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.89 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 21.05 %
    Favored  : 77.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.22 (0.29), residues: 839
  helix:  0.28 (0.26), residues: 392
  sheet:  0.30 (0.49), residues: 95
  loop : -0.63 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 777 
 TYR   0.015   0.002   TYR A 691 
 PHE   0.018   0.002   PHE A 960 
 TRP   0.008   0.001   TRP A 783 
 HIS   0.003   0.001   HIS A 554 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 7173)
  covalent geometry    : angle       0.63355 ( 9696)
  hydrogen bonds       : bond        0.03792 (  279)
  hydrogen bonds       : angle       4.63947 (  801)

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

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

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1678 Ramachandran restraints generated.
    839 Oldfield, 0 Emsley, 839 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6538 (t0) cc_final: 0.6002 (t0)
REVERT: A  138 ASP cc_start: 0.6768 (t70) cc_final: 0.6461 (t70)
REVERT: A  374 GLN cc_start: 0.7884 (mp10) cc_final: 0.7635 (mp10)
REVERT: A  382 ARG cc_start: 0.7537 (tpt90) cc_final: 0.7315 (tpt90)
REVERT: A  570 LEU cc_start: 0.7652 (mm) cc_final: 0.7449 (mt)
REVERT: A  637 GLN cc_start: 0.7601 (OUTLIER) cc_final: 0.7196 (mp-120)
REVERT: A  682 GLN cc_start: 0.7006 (mp-120) cc_final: 0.5964 (mt0)
REVERT: A  820 MET cc_start: 0.7219 (mtt) cc_final: 0.6750 (mtt)
REVERT: A  821 GLU cc_start: 0.6935 (OUTLIER) cc_final: 0.6172 (tt0)
REVERT: A  979 ARG cc_start: 0.6725 (OUTLIER) cc_final: 0.5719 (mtt-85)
REVERT: A  983 MET cc_start: 0.5688 (ttm) cc_final: 0.4555 (ptt)
REVERT: A 1033 GLN cc_start: 0.5314 (mp10) cc_final: 0.4767 (mm-40)
  outliers start: 12
  outliers final: 8
  residues processed: 95
  average time/residue: 0.5534
  time to fit residues: 55.6827
Evaluate side-chains
  96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 85
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  404 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  612 ARG
Chi-restraints excluded: chain A residue  637 GLN
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  821 GLU
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 45 optimal weight:    1.9990
   chunk 27 optimal weight:    0.6980
   chunk 53 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 1 optimal weight:    0.2980
   chunk 11 optimal weight:    0.5980
   chunk 13 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   chunk 32 optimal weight:    1.9990
   chunk 83 optimal weight:    0.0870
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN
** A 661 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 = 0.4544 r_free = 0.4544 target = 0.227606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.201788 restraints weight = 6437.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.4320 rms_B_bonded: 1.24
r_work: 0.4131 rms_B_bonded: 2.55 restraints_weight: 0.5000
r_work: 0.3995 rms_B_bonded: 4.37 restraints_weight: 0.2500
r_work (final): 0.3995
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3983
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3983 r_free = 0.3983    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.40   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3983 r_free = 0.3983    target_work(ls_wunit_k1) = 0.167         |
| occupancies: max = 1.00  min = 0.38   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3983
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6339
moved from start:          0.2616

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   7173  Z= 0.131
  Angle     :  0.606  10.595   9696  Z= 0.308
  Chirality :  0.042   0.230   1054
  Planarity :  0.005   0.075   1238
  Dihedral  :  5.165  35.116    943
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.29 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 21.43 %
    Favored  : 77.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    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: -0.10 (0.29), residues: 839
  helix:  0.40 (0.27), residues: 393
  sheet:  0.32 (0.50), residues: 95
  loop : -0.60 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A 777 
 TYR   0.015   0.001   TYR A 432 
 PHE   0.017   0.002   PHE A 909 
 TRP   0.013   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 7173)
  covalent geometry    : angle       0.60571 ( 9696)
  hydrogen bonds       : bond        0.03565 (  279)
  hydrogen bonds       : angle       4.57954 (  801)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2818.82 seconds
wall clock time: 48 minutes 59.46 seconds (2939.46 seconds total)