Starting phenix.real_space_refine
on Sat Dec 28 00:59:36 2024 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8gua_34271/12_2024/8gua_34271.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8gua_34271/12_2024/8gua_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8gua_34271/12_2024/8gua_34271.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8gua_34271/12_2024/8gua_34271.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8gua_34271/12_2024/8gua_34271.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8gua_34271/12_2024/8gua_34271.cif"
  }
  resolution = 2.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 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): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: 4.71, per 1000 atoms: 0.67
  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: 1.72
  Conformation dependent library (CDL) restraints added in 1.0 seconds
  

  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: 0.90
  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: 2.23

  Time building geometry restraints manager: 1.94 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:             0.900
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.250
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     20.020
  Find NCS groups from input model:        0.060
  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:11.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.960
-------------------------------------------------------------------------------
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= 0.421
  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 : 10.99
  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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.005   0.001   TRP A 783 
 HIS   0.003   0.001   HIS A 160 
 PHE   0.012   0.001   PHE A 960 
 TYR   0.024   0.001   TYR A 392 
 ARG   0.005   0.000   ARG A 382 

*********************** 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  : 0.793 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 103
  average time/residue: 1.2948
  time to fit residues: 140.7244
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  : 0.788 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    1.9990
   chunk 64 optimal weight:    1.9990
   chunk 35 optimal weight:    8.9990
   chunk 22 optimal weight:    1.9990
   chunk 43 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 66 optimal weight:    3.9990
   chunk 25 optimal weight:    0.0970
   chunk 40 optimal weight:    0.9990
   chunk 49 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6018
moved from start:          0.1489

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.065   7173  Z= 0.234
  Angle     :  0.635   6.741   9696  Z= 0.331
  Chirality :  0.043   0.217   1054
  Planarity :  0.006   0.100   1238
  Dihedral  :  5.441  35.925    943
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 9.71
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.29 %
    Favored  : 95.59 %
  Rotamer:
    Outliers :  1.53 %
    Allowed  : 10.71 %
    Favored  : 87.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.74 (0.29), residues: 839
  helix: -0.51 (0.25), residues: 389
  sheet:  0.36 (0.50), residues: 99
  loop : -0.51 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 669 
 HIS   0.007   0.001   HIS A 936 
 PHE   0.012   0.002   PHE A 666 
 TYR   0.020   0.002   TYR A 392 
 ARG   0.007   0.001   ARG A 382 

*********************** 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
  112 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 100
  time to evaluate  : 0.757 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.6404 (t0) cc_final: 0.6026 (t0)
REVERT: A  594 LYS cc_start: 0.6807 (mmtm) cc_final: 0.6262 (mmpt)
REVERT: A  599 MET cc_start: 0.6394 (mtp) cc_final: 0.5991 (mtm)
REVERT: A  682 GLN cc_start: 0.6699 (mp-120) cc_final: 0.5865 (mt0)
REVERT: A  717 ASP cc_start: 0.6401 (OUTLIER) cc_final: 0.6028 (m-30)
REVERT: A  979 ARG cc_start: 0.6133 (OUTLIER) cc_final: 0.5193 (mtt-85)
REVERT: A 1039 PHE cc_start: 0.4721 (t80) cc_final: 0.4412 (t80)
  outliers start: 12
  outliers final: 4
  residues processed: 107
  average time/residue: 1.3811
  time to fit residues: 156.2744
Evaluate side-chains
  89 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 83
  time to evaluate  : 0.798 
-------------------------------------------------------------------------------
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  979 ARG
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 42 optimal weight:    0.0570
   chunk 23 optimal weight:    0.9980
   chunk 64 optimal weight:    0.6980
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    2.9990
   chunk 77 optimal weight:    1.9990
   chunk 83 optimal weight:    0.5980
   chunk 68 optimal weight:    0.0670
   chunk 76 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 62 optimal weight:    1.9990
   overall best weight:    0.4636

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5991
moved from start:          0.1789

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   7173  Z= 0.188
  Angle     :  0.572   9.975   9696  Z= 0.295
  Chirality :  0.042   0.215   1054
  Planarity :  0.006   0.097   1238
  Dihedral  :  5.120  34.836    943
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 10.06
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.69 %
    Favored  : 96.19 %
  Rotamer:
    Outliers :  1.91 %
    Allowed  : 14.67 %
    Favored  : 83.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.47 (0.29), residues: 839
  helix: -0.20 (0.25), residues: 391
  sheet:  0.44 (0.49), residues: 98
  loop : -0.48 (0.35), residues: 350

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

*********************** 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
  103 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 0.765 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.7372 (OUTLIER) cc_final: 0.7147 (tttm)
REVERT: A  278 MET cc_start: 0.3624 (mmp) cc_final: 0.3280 (ttt)
REVERT: A  441 MET cc_start: 0.7390 (OUTLIER) cc_final: 0.7043 (ttt)
REVERT: A  594 LYS cc_start: 0.6806 (mmtm) cc_final: 0.6294 (mmpt)
REVERT: A  599 MET cc_start: 0.6435 (mtp) cc_final: 0.6063 (mtm)
REVERT: A  682 GLN cc_start: 0.6701 (mp-120) cc_final: 0.5778 (mt0)
REVERT: A  717 ASP cc_start: 0.6472 (OUTLIER) cc_final: 0.6265 (t0)
REVERT: A  820 MET cc_start: 0.7294 (mtt) cc_final: 0.6700 (mtt)
REVERT: A  832 ARG cc_start: 0.4770 (OUTLIER) cc_final: 0.4569 (tpt170)
REVERT: A  979 ARG cc_start: 0.6192 (OUTLIER) cc_final: 0.5198 (mtt-85)
REVERT: A  983 MET cc_start: 0.5390 (ttm) cc_final: 0.4357 (ptt)
  outliers start: 15
  outliers final: 4
  residues processed: 97
  average time/residue: 1.2326
  time to fit residues: 126.7690
Evaluate side-chains
  94 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 85
  time to evaluate  : 0.833 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  198 VAL
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 MET
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  979 ARG
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 76 optimal weight:    0.9990
   chunk 58 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9990
   chunk 8 optimal weight:    2.9990
   chunk 36 optimal weight:    7.9990
   chunk 51 optimal weight:    0.9990
   chunk 77 optimal weight:    0.0040
   chunk 82 optimal weight:    2.9990
   chunk 73 optimal weight:    2.9990
   chunk 22 optimal weight:    1.9990
   chunk 68 optimal weight:    1.9990
   overall best weight:    1.0000

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6078
moved from start:          0.2024

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= 0.263
  Angle     :  0.626   6.872   9696  Z= 0.321
  Chirality :  0.044   0.217   1054
  Planarity :  0.006   0.094   1238
  Dihedral  :  5.343  36.061    943
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 11.42
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.89 %
    Favored  : 94.99 %
  Rotamer:
    Outliers :  2.81 %
    Allowed  : 16.07 %
    Favored  : 81.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.29), residues: 839
  helix: -0.23 (0.25), residues: 390
  sheet:  0.16 (0.50), residues: 96
  loop : -0.54 (0.35), residues: 353

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 759 
 PHE   0.018   0.002   PHE A 666 
 TYR   0.017   0.002   TYR A 904 
 ARG   0.008   0.001   ARG A 382 

*********************** 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
  117 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 95
  time to evaluate  : 0.754 
Fit side-chains
REVERT: A  264 LYS cc_start: 0.7435 (OUTLIER) cc_final: 0.7162 (tttm)
REVERT: A  278 MET cc_start: 0.4027 (mmp) cc_final: 0.3514 (ttt)
REVERT: A  374 GLN cc_start: 0.7776 (mp10) cc_final: 0.7474 (mp10)
REVERT: A  441 MET cc_start: 0.7404 (OUTLIER) cc_final: 0.6980 (ttt)
REVERT: A  594 LYS cc_start: 0.6901 (mmtm) cc_final: 0.6377 (mmpt)
REVERT: A  599 MET cc_start: 0.6572 (mtp) cc_final: 0.6221 (mtm)
REVERT: A  682 GLN cc_start: 0.6705 (mp-120) cc_final: 0.5768 (mt0)
REVERT: A  717 ASP cc_start: 0.6507 (OUTLIER) cc_final: 0.6298 (t0)
REVERT: A  832 ARG cc_start: 0.4859 (OUTLIER) cc_final: 0.4589 (tpt170)
REVERT: A  979 ARG cc_start: 0.6297 (OUTLIER) cc_final: 0.5270 (mtt-85)
  outliers start: 22
  outliers final: 5
  residues processed: 104
  average time/residue: 1.1775
  time to fit residues: 129.7531
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 88
  time to evaluate  : 0.789 
-------------------------------------------------------------------------------
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  441 MET
Chi-restraints excluded: chain A residue  461 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  717 ASP
Chi-restraints excluded: chain A residue  802 LYS
Chi-restraints excluded: chain A residue  832 ARG
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 46 optimal weight:    1.9990
   chunk 1 optimal weight:    1.9990
   chunk 61 optimal weight:    0.9980
   chunk 33 optimal weight:    6.9990
   chunk 70 optimal weight:    0.0040
   chunk 56 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   chunk 73 optimal weight:    0.9990
   chunk 20 optimal weight:    5.9990
   chunk 27 optimal weight:    0.9990
   overall best weight:    0.7998

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6067
moved from start:          0.2140

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= 0.229
  Angle     :  0.604   6.778   9696  Z= 0.311
  Chirality :  0.043   0.217   1054
  Planarity :  0.006   0.092   1238
  Dihedral  :  5.312  36.313    943
  Min Nonbonded Distance : 2.501

Molprobity Statistics.
  All-atom Clashscore : 10.63
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.65 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  2.93 %
    Allowed  : 16.45 %
    Favored  : 80.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.53 (0.29), residues: 839
  helix: -0.13 (0.26), residues: 391
  sheet:  0.03 (0.49), residues: 96
  loop : -0.53 (0.35), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.016   0.002   PHE A 909 
 TYR   0.014   0.002   TYR A 691 
 ARG   0.006   0.000   ARG A 382 

*********************** 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
  114 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.766 
Fit side-chains
   revert: symmetry clash
REVERT: A  264 LYS cc_start: 0.7425 (OUTLIER) cc_final: 0.7165 (tttm)
REVERT: A  267 LEU cc_start: 0.6891 (tp) cc_final: 0.6687 (tp)
REVERT: A  278 MET cc_start: 0.4267 (mmp) cc_final: 0.3734 (mtt)
REVERT: A  374 GLN cc_start: 0.7813 (mp10) cc_final: 0.7533 (mp10)
REVERT: A  441 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.7034 (ttt)
REVERT: A  594 LYS cc_start: 0.6902 (mmtm) cc_final: 0.6382 (mmpt)
REVERT: A  599 MET cc_start: 0.6565 (mtp) cc_final: 0.5958 (mtm)
REVERT: A  682 GLN cc_start: 0.6704 (mp-120) cc_final: 0.5765 (mt0)
REVERT: A  717 ASP cc_start: 0.6533 (OUTLIER) cc_final: 0.6331 (t0)
REVERT: A  832 ARG cc_start: 0.5077 (OUTLIER) cc_final: 0.4836 (tpt170)
REVERT: A  979 ARG cc_start: 0.6321 (OUTLIER) cc_final: 0.5284 (mtt-85)
REVERT: A  983 MET cc_start: 0.5519 (ttm) cc_final: 0.4417 (ptt)
  outliers start: 23
  outliers final: 6
  residues processed: 102
  average time/residue: 1.1298
  time to fit residues: 122.4519
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  : 0.794 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  264 LYS
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 MET
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  717 ASP
Chi-restraints excluded: chain A residue  832 ARG
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 73 optimal weight:    0.7980
   chunk 16 optimal weight:    3.9990
   chunk 48 optimal weight:    0.9980
   chunk 20 optimal weight:    5.9990
   chunk 82 optimal weight:    0.1980
   chunk 68 optimal weight:    0.3980
   chunk 38 optimal weight:    0.9990
   chunk 6 optimal weight:    1.9990
   chunk 27 optimal weight:    0.7980
   chunk 43 optimal weight:    2.9990
   chunk 79 optimal weight:    0.5980
   overall best weight:    0.5580

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6038
moved from start:          0.2277

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= 0.200
  Angle     :  0.573   6.813   9696  Z= 0.295
  Chirality :  0.042   0.217   1054
  Planarity :  0.006   0.090   1238
  Dihedral  :  5.170  35.287    943
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 10.70
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.05 %
    Favored  : 95.83 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 17.98 %
    Favored  : 78.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.38 (0.29), residues: 839
  helix:  0.05 (0.26), residues: 392
  sheet:  0.06 (0.49), residues: 96
  loop : -0.51 (0.35), residues: 351

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 665 
 PHE   0.015   0.002   PHE A 960 
 TYR   0.014   0.001   TYR A 392 
 ARG   0.009   0.000   ARG A 777 

*********************** 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
  115 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 90
  time to evaluate  : 0.760 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 ASP cc_start: 0.6282 (t0) cc_final: 0.5875 (t0)
REVERT: A  278 MET cc_start: 0.4299 (mmp) cc_final: 0.3725 (mtt)
REVERT: A  374 GLN cc_start: 0.7769 (mp10) cc_final: 0.7503 (mp10)
REVERT: A  594 LYS cc_start: 0.6902 (mmtm) cc_final: 0.6384 (mmpt)
REVERT: A  599 MET cc_start: 0.6523 (mtp) cc_final: 0.6137 (mtm)
REVERT: A  682 GLN cc_start: 0.6696 (mp-120) cc_final: 0.5823 (mt0)
REVERT: A  832 ARG cc_start: 0.5306 (OUTLIER) cc_final: 0.5057 (tpt170)
REVERT: A  979 ARG cc_start: 0.6326 (OUTLIER) cc_final: 0.5280 (mtt-85)
REVERT: A  983 MET cc_start: 0.5474 (mtm) cc_final: 0.4417 (ptt)
  outliers start: 25
  outliers final: 6
  residues processed: 107
  average time/residue: 1.1266
  time to fit residues: 128.4043
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  : 0.789 
-------------------------------------------------------------------------------
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  461 VAL
Chi-restraints excluded: chain A residue  484 VAL
Chi-restraints excluded: chain A residue  553 SER
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  979 ARG
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 9 optimal weight:    2.9990
   chunk 46 optimal weight:    2.9990
   chunk 60 optimal weight:    0.8980
   chunk 69 optimal weight:    2.9990
   chunk 45 optimal weight:    1.9990
   chunk 81 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 49 optimal weight:    1.9990
   chunk 37 optimal weight:    1.9990
   chunk 50 optimal weight:    0.0050
   chunk 32 optimal weight:    3.9990
   overall best weight:    1.1198

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6106
moved from start:          0.2395

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= 0.278
  Angle     :  0.646   8.140   9696  Z= 0.332
  Chirality :  0.044   0.219   1054
  Planarity :  0.006   0.089   1238
  Dihedral  :  5.481  38.493    943
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.35
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.01 %
    Favored  : 94.87 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 19.26 %
    Favored  : 78.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.64 (0.28), residues: 839
  helix: -0.16 (0.26), residues: 391
  sheet: -0.11 (0.48), residues: 96
  loop : -0.66 (0.34), residues: 352

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 386 
 HIS   0.004   0.001   HIS A 759 
 PHE   0.018   0.002   PHE A 666 
 TYR   0.018   0.002   TYR A 691 
 ARG   0.011   0.001   ARG A 777 

*********************** 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
  113 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 94
  time to evaluate  : 0.863 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6437 (t0) cc_final: 0.6008 (t0)
REVERT: A  374 GLN cc_start: 0.7849 (mp10) cc_final: 0.7577 (mp10)
REVERT: A  441 MET cc_start: 0.7427 (OUTLIER) cc_final: 0.6990 (ttt)
REVERT: A  594 LYS cc_start: 0.6951 (mmtm) cc_final: 0.6432 (mmpt)
REVERT: A  682 GLN cc_start: 0.6738 (mp-120) cc_final: 0.5837 (mt0)
REVERT: A  697 MET cc_start: 0.6130 (ttp) cc_final: 0.5905 (ttm)
REVERT: A  821 GLU cc_start: 0.6799 (pp20) cc_final: 0.6537 (tm-30)
REVERT: A  832 ARG cc_start: 0.5635 (OUTLIER) cc_final: 0.5165 (tpt170)
REVERT: A  979 ARG cc_start: 0.6241 (OUTLIER) cc_final: 0.5125 (mtt-85)
REVERT: A 1040 MET cc_start: 0.7398 (OUTLIER) cc_final: 0.5679 (mpt)
  outliers start: 19
  outliers final: 9
  residues processed: 105
  average time/residue: 1.0603
  time to fit residues: 118.9555
Evaluate side-chains
  102 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.806 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
Chi-restraints excluded: chain A residue  402 LEU
Chi-restraints excluded: chain A residue  438 SER
Chi-restraints excluded: chain A residue  441 MET
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  788 ILE
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  832 ARG
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1022 ILE
Chi-restraints excluded: chain A residue 1040 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 24 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 15 optimal weight:    0.9980
   chunk 52 optimal weight:    0.7980
   chunk 55 optimal weight:    0.8980
   chunk 40 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 64 optimal weight:    0.5980
   chunk 74 optimal weight:    2.9990
   chunk 78 optimal weight:    0.9990
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 637 GLN
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6082
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      :  0.004   0.061   7173  Z= 0.239
  Angle     :  0.622   8.986   9696  Z= 0.319
  Chirality :  0.043   0.231   1054
  Planarity :  0.006   0.084   1238
  Dihedral  :  5.428  38.402    943
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.53 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 20.28 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.58 (0.29), residues: 839
  helix: -0.08 (0.26), residues: 394
  sheet: -0.05 (0.48), residues: 95
  loop : -0.67 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 783 
 HIS   0.005   0.001   HIS A 665 
 PHE   0.017   0.002   PHE A 909 
 TYR   0.015   0.002   TYR A 691 
 ARG   0.013   0.001   ARG A 777 

*********************** 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
  107 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 88
  time to evaluate  : 0.758 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6369 (t0) cc_final: 0.5972 (t0)
REVERT: A  374 GLN cc_start: 0.7800 (mp10) cc_final: 0.7542 (mp10)
REVERT: A  594 LYS cc_start: 0.6929 (mmtm) cc_final: 0.6391 (mmpt)
REVERT: A  682 GLN cc_start: 0.6701 (mp-120) cc_final: 0.5781 (mt0)
REVERT: A  697 MET cc_start: 0.6089 (ttp) cc_final: 0.5882 (ttm)
REVERT: A  979 ARG cc_start: 0.6230 (OUTLIER) cc_final: 0.5146 (mtt-85)
REVERT: A  983 MET cc_start: 0.5502 (mtm) cc_final: 0.4457 (ptt)
REVERT: A 1040 MET cc_start: 0.7417 (OUTLIER) cc_final: 0.5696 (mpt)
  outliers start: 19
  outliers final: 9
  residues processed: 100
  average time/residue: 0.9558
  time to fit residues: 102.0605
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  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
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  788 ILE
Chi-restraints excluded: chain A residue  793 LEU
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1040 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 71 optimal weight:    2.9990
   chunk 76 optimal weight:    0.9980
   chunk 78 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9990
   chunk 59 optimal weight:    0.7980
   chunk 23 optimal weight:    5.9990
   chunk 68 optimal weight:    0.0870
   chunk 72 optimal weight:    0.6980
   chunk 50 optimal weight:    0.9990
   chunk 80 optimal weight:    0.6980
   overall best weight:    0.6558

-------------------------------------------------------------------------------
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

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6060
moved from start:          0.2526

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= 0.216
  Angle     :  0.608   9.452   9696  Z= 0.310
  Chirality :  0.043   0.233   1054
  Planarity :  0.006   0.081   1238
  Dihedral  :  5.357  37.298    943
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.77 %
    Favored  : 95.11 %
  Rotamer:
    Outliers :  2.04 %
    Allowed  : 21.05 %
    Favored  : 76.91 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.29), residues: 839
  helix:  0.07 (0.26), residues: 394
  sheet:  0.04 (0.48), residues: 95
  loop : -0.64 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 554 
 PHE   0.016   0.002   PHE A 909 
 TYR   0.014   0.002   TYR A 432 
 ARG   0.014   0.001   ARG A 777 

*********************** 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: 16
    poor density    : 88
  time to evaluate  : 0.837 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6430 (t0) cc_final: 0.6019 (t0)
REVERT: A  278 MET cc_start: 0.4519 (mmp) cc_final: 0.3383 (ttm)
REVERT: A  374 GLN cc_start: 0.7774 (mp10) cc_final: 0.7523 (mp10)
REVERT: A  594 LYS cc_start: 0.6924 (mmtm) cc_final: 0.6381 (mmpt)
REVERT: A  682 GLN cc_start: 0.6693 (mp-120) cc_final: 0.5777 (mt0)
REVERT: A  697 MET cc_start: 0.6075 (ttp) cc_final: 0.5780 (tpp)
REVERT: A  979 ARG cc_start: 0.6220 (OUTLIER) cc_final: 0.5137 (mtt-85)
REVERT: A  983 MET cc_start: 0.5474 (mtm) cc_final: 0.4445 (ptt)
REVERT: A 1040 MET cc_start: 0.7392 (OUTLIER) cc_final: 0.5684 (mpt)
  outliers start: 16
  outliers final: 10
  residues processed: 98
  average time/residue: 0.9307
  time to fit residues: 97.2537
Evaluate side-chains
  96 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.792 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
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  681 SER
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1040 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 38 optimal weight:    0.7980
   chunk 56 optimal weight:    2.9990
   chunk 84 optimal weight:    0.8980
   chunk 77 optimal weight:    4.9990
   chunk 67 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0670
   chunk 52 optimal weight:    0.4980
   chunk 41 optimal weight:    0.7980
   chunk 53 optimal weight:    0.5980
   chunk 71 optimal weight:    3.9990
   overall best weight:    0.5518

-------------------------------------------------------------------------------
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**
A 677 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6042
moved from start:          0.2579

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= 0.205
  Angle     :  0.606   9.868   9696  Z= 0.308
  Chirality :  0.043   0.233   1054
  Planarity :  0.005   0.079   1238
  Dihedral  :  5.309  36.042    943
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 11.77
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.41 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.66 %
    Allowed  : 21.94 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.30 (0.29), residues: 839
  helix:  0.20 (0.26), residues: 394
  sheet:  0.10 (0.48), residues: 95
  loop : -0.61 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 669 
 HIS   0.003   0.001   HIS A 554 
 PHE   0.016   0.002   PHE A 960 
 TYR   0.015   0.001   TYR A 432 
 ARG   0.014   0.001   ARG A 777 

********************** 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
  100 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 87
  time to evaluate  : 0.785 
Fit side-chains
REVERT: A  133 ASP cc_start: 0.6419 (t0) cc_final: 0.6008 (t0)
REVERT: A  138 ASP cc_start: 0.6352 (t70) cc_final: 0.6040 (t70)
REVERT: A  374 GLN cc_start: 0.7741 (mp10) cc_final: 0.7492 (mp10)
REVERT: A  594 LYS cc_start: 0.6918 (mmtm) cc_final: 0.6337 (mmpt)
REVERT: A  637 GLN cc_start: 0.7302 (OUTLIER) cc_final: 0.6787 (mp-120)
REVERT: A  682 GLN cc_start: 0.6665 (mp-120) cc_final: 0.5759 (mt0)
REVERT: A  697 MET cc_start: 0.6165 (ttp) cc_final: 0.5878 (tpp)
REVERT: A  979 ARG cc_start: 0.6222 (OUTLIER) cc_final: 0.5131 (mtt-85)
REVERT: A  983 MET cc_start: 0.5422 (mtm) cc_final: 0.4416 (ptt)
REVERT: A 1033 GLN cc_start: 0.5383 (mp10) cc_final: 0.4819 (mm-40)
REVERT: A 1040 MET cc_start: 0.7384 (OUTLIER) cc_final: 0.5690 (mpt)
  outliers start: 13
  outliers final: 10
  residues processed: 95
  average time/residue: 1.0757
  time to fit residues: 109.2881
Evaluate side-chains
  98 residues out of total 784 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 85
  time to evaluate  : 0.784 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  295 SER
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  637 GLN
Chi-restraints excluded: chain A residue  681 SER
Chi-restraints excluded: chain A residue  788 ILE
Chi-restraints excluded: chain A residue  896 LEU
Chi-restraints excluded: chain A residue  979 ARG
Chi-restraints excluded: chain A residue 1040 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 85
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 62 optimal weight:    0.9990
   chunk 9 optimal weight:    0.8980
   chunk 18 optimal weight:    0.7980
   chunk 67 optimal weight:    0.7980
   chunk 28 optimal weight:    0.1980
   chunk 69 optimal weight:    6.9990
   chunk 8 optimal weight:    0.7980
   chunk 12 optimal weight:    0.5980
   chunk 59 optimal weight:    3.9990
   chunk 3 optimal weight:    0.0670
   overall best weight:    0.4918

-------------------------------------------------------------------------------
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
** A 661 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 677 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.227751 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.200644 restraints weight = 6399.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.4306 rms_B_bonded: 1.31
r_work: 0.4129 rms_B_bonded: 2.54 restraints_weight: 0.5000
r_work: 0.3989 rms_B_bonded: 4.34 restraints_weight: 0.2500
r_work (final): 0.3989
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3970
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3970 r_free = 0.3970    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3968 r_free = 0.3968    target_work(ls_wunit_k1) = 0.166         |
| occupancies: max = 1.00  min = 0.39   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
r_final: 0.3968
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6340
moved from start:          0.2611

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= 0.198
  Angle     :  0.611  10.998   9696  Z= 0.309
  Chirality :  0.043   0.231   1054
  Planarity :  0.005   0.078   1238
  Dihedral  :  5.276  35.130    943
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.70
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.41 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 21.94 %
    Favored  : 76.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 2.50 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.24 (0.29), residues: 839
  helix:  0.26 (0.26), residues: 394
  sheet:  0.16 (0.49), residues: 95
  loop : -0.60 (0.35), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 669 
 HIS   0.004   0.001   HIS A 665 
 PHE   0.016   0.002   PHE A 909 
 TYR   0.015   0.001   TYR A 432 
 ARG   0.014   0.001   ARG A 777 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2762.36 seconds
wall clock time: 52 minutes 32.05 seconds (3152.05 seconds total)