Starting phenix.real_space_refine
on Tue Mar  3 14:46:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yg1_33804/03_2026/7yg1_33804_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yg1_33804/03_2026/7yg1_33804.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.77
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yg1_33804/03_2026/7yg1_33804_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yg1_33804/03_2026/7yg1_33804_neut.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yg1_33804/03_2026/7yg1_33804.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yg1_33804/03_2026/7yg1_33804.map"
  }
  resolution = 3.77
  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=   0.023
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      38      5.16       5
     C    3961      2.51       5
     N    1117      2.21       5
     O    1092      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 46 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6208
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 3109
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3109
          Classifications: {'peptide': 385}
          Link IDs: {'PTRANS': 18, 'TRANS': 366}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 3099
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 385, 3099
          Classifications: {'peptide': 385}
          Incomplete info: {'truncation_to_alanine': 2}
          Link IDs: {'PTRANS': 18, 'TRANS': 366}
          Chain breaks: 1
          Unresolved non-hydrogen bonds: 11
          Unresolved non-hydrogen angles: 15
          Unresolved non-hydrogen dihedrals: 10
          Planarities with less than four sites: {'ASN:plan1': 1, 'TYR:plan': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 1.42, per 1000 atoms: 0.23
  Number of scatterers: 6208
  At special positions: 0
  Unit cell: (77.404, 82.634, 107.738, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      38     16.00
     O    1092      8.00
     N    1117      7.00
     C    3961      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: 0.53
  Conformation dependent library (CDL) restraints added in 157.4 milliseconds
  

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1440

  Finding SS restraints...
    Secondary structure from input PDB file:
      33 helices and 2 sheets defined
      45.5% alpha, 6.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.19
  Creating SS restraints...
    Processing helix  chain 'A' and resid 620 through 631
      removed outlier: 3.878A  pdb=" N   ALA A 624 " --> pdb=" O   SER A 620 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 632 through 634
      No H-bonds generated for 'chain 'A' and resid 632 through 634'
    Processing helix  chain 'A' and resid 655 through 665
      removed outlier: 4.194A  pdb=" N   VAL A 659 " --> pdb=" O   ARG A 655 " (cutoff:3.500A)
      removed outlier: 4.008A  pdb=" N   PHE A 665 " --> pdb=" O   PHE A 661 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 686 through 703
      removed outlier: 4.686A  pdb=" N   GLN A 690 " --> pdb=" O   MET A 686 " (cutoff:3.500A)
      removed outlier: 4.691A  pdb=" N   LEU A 691 " --> pdb=" O   PRO A 687 " (cutoff:3.500A)
      removed outlier: 4.882A  pdb=" N   ILE A 692 " --> pdb=" O   GLU A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 716 through 726
      removed outlier: 3.518A  pdb=" N   LEU A 724 " --> pdb=" O   GLY A 720 " (cutoff:3.500A)
      removed outlier: 3.744A  pdb=" N   GLN A 726 " --> pdb=" O   GLN A 722 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 752 through 767
      removed outlier: 3.987A  pdb=" N   ASP A 756 " --> pdb=" O   ALA A 752 " (cutoff:3.500A)
      removed outlier: 3.696A  pdb=" N   LEU A 761 " --> pdb=" O   TYR A 757 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 825
      removed outlier: 5.315A  pdb=" N   PHE A 822 " --> pdb=" O   ALA A 818 " (cutoff:3.500A)
      removed outlier: 4.094A  pdb=" N   GLN A 823 " --> pdb=" O   THR A 819 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 840 through 844
      removed outlier: 3.507A  pdb=" N   THR A 843 " --> pdb=" O   GLY A 840 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 845 through 852
    Processing helix  chain 'A' and resid 854 through 858
      removed outlier: 3.792A  pdb=" N   LYS A 858 " --> pdb=" O   ARG A 855 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 875 through 884
      removed outlier: 3.743A  pdb=" N   SER A 884 " --> pdb=" O   ILE A 880 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 896 through 901
      removed outlier: 4.274A  pdb=" N   ASN A 900 " --> pdb=" O   PRO A 897 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   GLN A 901 " --> pdb=" O   ASP A 898 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 904 through 914
      removed outlier: 3.518A  pdb=" N   THR A 908 " --> pdb=" O   ARG A 904 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 921 through 923
      No H-bonds generated for 'chain 'A' and resid 921 through 923'
    Processing helix  chain 'A' and resid 924 through 934
    Processing helix  chain 'A' and resid 949 through 966
      removed outlier: 3.677A  pdb=" N   SER A 953 " --> pdb=" O   ASN A 949 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 986 through 998
      removed outlier: 4.378A  pdb=" N   SER A 998 " --> pdb=" O   LEU A 994 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 618 through 628
      removed outlier: 3.785A  pdb=" N   SER B 626 " --> pdb=" O   ASN B 622 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 655 through 665
      removed outlier: 3.749A  pdb=" N   VAL B 659 " --> pdb=" O   ARG B 655 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 687 through 703
    Processing helix  chain 'B' and resid 717 through 728
      removed outlier: 4.089A  pdb=" N   LEU B 724 " --> pdb=" O   GLY B 720 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   GLN B 726 " --> pdb=" O   GLN B 722 " (cutoff:3.500A)
      removed outlier: 3.830A  pdb=" N   ALA B 727 " --> pdb=" O   ILE B 723 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 730 through 734
    Processing helix  chain 'B' and resid 750 through 767
      removed outlier: 4.266A  pdb=" N   VAL B 754 " --> pdb=" O   HIS B 750 " (cutoff:3.500A)
      removed outlier: 3.749A  pdb=" N   LEU B 761 " --> pdb=" O   TYR B 757 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 812 through 820
    Processing helix  chain 'B' and resid 821 through 824
    Processing helix  chain 'B' and resid 841 through 852
      Proline residue:  B 847  - end of helix
    Processing helix  chain 'B' and resid 853 through 859
      removed outlier: 3.997A  pdb=" N   LYS B 858 " --> pdb=" O   ARG B 855 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 872 through 886
      removed outlier: 4.325A  pdb=" N   ALA B 878 " --> pdb=" O   GLN B 874 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 896 through 900
      removed outlier: 3.901A  pdb=" N   ILE B 899 " --> pdb=" O   LEU B 896 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 904 through 914
    Processing helix  chain 'B' and resid 924 through 935
    Processing helix  chain 'B' and resid 949 through 965
    Processing helix  chain 'B' and resid 986 through 998
    Processing sheet with id=AA1, first strand: chain 'A' and resid 711 through 713
      removed outlier: 4.337A  pdb=" N   GLY A 741 " --> pdb=" O   LEU A 648 " (cutoff:3.500A)
      removed outlier: 4.036A  pdb=" N   ARG A 775 " --> pdb=" O   VAL A1005 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 708 through 712
      removed outlier: 3.760A  pdb=" N   PHE B 708 " --> pdb=" O   MET B 672 " (cutoff:3.500A)
      removed outlier: 6.869A  pdb=" N   CYS B 645 " --> pdb=" O   ILE B 673 " (cutoff:3.500A)
      removed outlier: 7.618A  pdb=" N   GLY B 675 " --> pdb=" O   CYS B 645 " (cutoff:3.500A)
      removed outlier: 6.483A  pdb=" N   VAL B 647 " --> pdb=" O   GLY B 675 " (cutoff:3.500A)
      removed outlier: 7.643A  pdb=" N   VAL B 677 " --> pdb=" O   VAL B 647 " (cutoff:3.500A)
      removed outlier: 6.334A  pdb=" N   LEU B 646 " --> pdb=" O   VAL B 739 " (cutoff:3.500A)
      removed outlier: 4.468A  pdb=" N   MET B 774 " --> pdb=" O   VAL B 740 " (cutoff:3.500A)
      removed outlier: 5.423A  pdb=" N   ILE B 973 " --> pdb=" O   ILE B1006 " (cutoff:3.500A)
      removed outlier: 7.110A  pdb=" N   ILE B1008 " --> pdb=" O   ILE B 973 " (cutoff:3.500A)
      removed outlier: 6.500A  pdb=" N   ILE B 975 " --> pdb=" O   ILE B1008 " (cutoff:3.500A)

    224 hydrogen bonds defined for protein.
    636 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: 0.83

  Time building geometry restraints manager: 0.70 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2041
        1.34 -     1.46: 1079
        1.46 -     1.58: 3153
        1.58 -     1.69: 0
        1.69 -     1.81: 62
  Bond restraints: 6335
  Sorted by residual:
  bond pdb=" CA  TYR B 621 "
       pdb=" C   TYR B 621 "
    ideal  model  delta    sigma   weight residual
    1.524  1.478  0.046 1.28e-02 6.10e+03 1.30e+01
  bond pdb=" CA  HIS A 750 "
       pdb=" C   HIS A 750 "
    ideal  model  delta    sigma   weight residual
    1.524  1.484  0.040 1.26e-02 6.30e+03 9.84e+00
  bond pdb=" N   PRO A 751 "
       pdb=" CD  PRO A 751 "
    ideal  model  delta    sigma   weight residual
    1.473  1.514 -0.041 1.40e-02 5.10e+03 8.61e+00
  bond pdb=" N   HIS A 750 "
       pdb=" CA  HIS A 750 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.41e-02 5.03e+03 8.05e+00
  bond pdb=" N   ILE A 880 "
       pdb=" CA  ILE A 880 "
    ideal  model  delta    sigma   weight residual
    1.459  1.496 -0.036 1.30e-02 5.92e+03 7.81e+00
  ... (remaining 6330 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.53: 8181
        2.53 -     5.05: 297
        5.05 -     7.58: 54
        7.58 -    10.11: 14
       10.11 -    12.63: 1
  Bond angle restraints: 8547
  Sorted by residual:
  angle pdb=" N   LEU A 836 "
        pdb=" CA  LEU A 836 "
        pdb=" C   LEU A 836 "
      ideal   model   delta    sigma   weight residual
     113.97  101.34   12.63 1.28e+00 6.10e-01 9.74e+01
  angle pdb=" N   ALA A 878 "
        pdb=" CA  ALA A 878 "
        pdb=" C   ALA A 878 "
      ideal   model   delta    sigma   weight residual
     111.28  102.13    9.15 1.09e+00 8.42e-01 7.04e+01
  angle pdb=" N   ASP B 943 "
        pdb=" CA  ASP B 943 "
        pdb=" C   ASP B 943 "
      ideal   model   delta    sigma   weight residual
     112.87  103.14    9.73 1.20e+00 6.94e-01 6.57e+01
  angle pdb=" N   LEU B 780 "
        pdb=" CA  LEU B 780 "
        pdb=" C   LEU B 780 "
      ideal   model   delta    sigma   weight residual
     111.07  103.10    7.97 1.07e+00 8.73e-01 5.55e+01
  angle pdb=" C   LEU A1016 "
        pdb=" CA  LEU A1016 "
        pdb=" CB  LEU A1016 "
      ideal   model   delta    sigma   weight residual
     111.89  101.99    9.90 1.42e+00 4.96e-01 4.86e+01
  ... (remaining 8542 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.59: 3441
       17.59 -    35.18: 357
       35.18 -    52.76: 54
       52.76 -    70.35: 8
       70.35 -    87.94: 5
  Dihedral angle restraints: 3865
    sinusoidal: 1638
      harmonic: 2227
  Sorted by residual:
  dihedral pdb=" N   ILE A 880 "
           pdb=" C   ILE A 880 "
           pdb=" CA  ILE A 880 "
           pdb=" CB  ILE A 880 "
      ideal   model   delta  harmonic     sigma   weight residual
     123.40  135.03  -11.63     0      2.50e+00 1.60e-01 2.16e+01
  dihedral pdb=" C   ILE A 880 "
           pdb=" N   ILE A 880 "
           pdb=" CA  ILE A 880 "
           pdb=" CB  ILE A 880 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -132.69   10.69     0      2.50e+00 1.60e-01 1.83e+01
  dihedral pdb=" CA  VAL B 629 "
           pdb=" C   VAL B 629 "
           pdb=" N   GLY B 630 "
           pdb=" CA  GLY B 630 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.40   20.60     0      5.00e+00 4.00e-02 1.70e+01
  ... (remaining 3862 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.085: 832
       0.085 -    0.169: 92
       0.169 -    0.254: 13
       0.254 -    0.338: 3
       0.338 -    0.423: 2
  Chirality restraints: 942
  Sorted by residual:
  chirality pdb=" CA  LYS A 784 "
            pdb=" N   LYS A 784 "
            pdb=" C   LYS A 784 "
            pdb=" CB  LYS A 784 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.09    0.42 2.00e-01 2.50e+01 4.47e+00
  chirality pdb=" CA  HIS A 750 "
            pdb=" N   HIS A 750 "
            pdb=" C   HIS A 750 "
            pdb=" CB  HIS A 750 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.13    0.38 2.00e-01 2.50e+01 3.57e+00
  chirality pdb=" CA  ILE A 880 "
            pdb=" N   ILE A 880 "
            pdb=" C   ILE A 880 "
            pdb=" CB  ILE A 880 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.10    0.33 2.00e-01 2.50e+01 2.70e+00
  ... (remaining 939 not shown)

  Planarity restraints: 1098
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B1002 "    0.039 5.00e-02 4.00e+02   5.87e-02 5.51e+00
        pdb=" N   PRO B1003 "   -0.102 5.00e-02 4.00e+02
        pdb=" CA  PRO B1003 "    0.030 5.00e-02 4.00e+02
        pdb=" CD  PRO B1003 "    0.032 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP B 939 "   -0.014 2.00e-02 2.50e+03   1.37e-02 4.66e+00
        pdb=" CG  TRP B 939 "    0.037 2.00e-02 2.50e+03
        pdb=" CD1 TRP B 939 "   -0.018 2.00e-02 2.50e+03
        pdb=" CD2 TRP B 939 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP B 939 "    0.000 2.00e-02 2.50e+03
        pdb=" CE2 TRP B 939 "   -0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP B 939 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP B 939 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP B 939 "   -0.005 2.00e-02 2.50e+03
        pdb=" CH2 TRP B 939 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ARG B 655 "    0.033 5.00e-02 4.00e+02   4.91e-02 3.86e+00
        pdb=" N   PRO B 656 "   -0.085 5.00e-02 4.00e+02
        pdb=" CA  PRO B 656 "    0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B 656 "    0.028 5.00e-02 4.00e+02
  ... (remaining 1095 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1506
        2.76 -     3.30: 6961
        3.30 -     3.83: 10805
        3.83 -     4.37: 13336
        4.37 -     4.90: 19879
  Nonbonded interactions: 52487
  Sorted by model distance:
  nonbonded pdb=" OE2 GLU B 755 "
            pdb=" OG  SER B 987 "
     model   vdw
     2.230 3.040
  nonbonded pdb=" O   ASN B 768 "
            pdb=" ND2 ASN B1011 "
     model   vdw
     2.256 3.120
  nonbonded pdb=" NH2 ARG B 667 "
            pdb=" O   LYS B 704 "
     model   vdw
     2.298 3.120
  nonbonded pdb=" O   ALA B 878 "
            pdb=" OG  SER B 881 "
     model   vdw
     2.310 3.040
  nonbonded pdb=" OE1 GLN B 722 "
            pdb=" NE2 GLN B 726 "
     model   vdw
     2.311 3.120
  ... (remaining 52482 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
Found NCS groups:
ncs_group {
  reference = (chain 'A' and (resid 617 through 959 or (resid 960 and (name N or name CA or na \ 
me C or name O or name CB )) or resid 961 through 989 or (resid 990 and (name N  \ 
or name CA or name C or name O or name CB )) or resid 991 through 1020))
  selection = chain 'B'
}

Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.050
  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:          0.100
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.770
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.150
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6615
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.052   6335  Z= 0.323
  Angle     :  1.151  12.634   8547  Z= 0.753
  Chirality :  0.059   0.423    942
  Planarity :  0.005   0.059   1098
  Dihedral  : 14.003  87.938   2425
  Min Nonbonded Distance : 2.230

Molprobity Statistics.
  All-atom Clashscore : 42.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 14.04 %
    Favored  : 85.96 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 17.85 %
    Favored  : 80.83 %
  Cbeta Deviations :  0.14 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -3.77 (0.27), residues: 762
  helix: -1.54 (0.29), residues: 281
  sheet: -1.64 (0.56), residues: 71
  loop : -3.53 (0.26), residues: 410

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 719 
 TYR   0.023   0.002   TYR B 627 
 PHE   0.016   0.001   PHE B 665 
 TRP   0.037   0.002   TRP B 939 
 HIS   0.003   0.001   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00470 ( 6335)
  covalent geometry    : angle       1.15119 ( 8547)
  hydrogen bonds       : bond        0.24371 (  224)
  hydrogen bonds       : angle       9.36897 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 198
  time to evaluate  : 0.222 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  671 LEU cc_start: 0.6959 (tp) cc_final: 0.6590 (tp)
REVERT: A  710 SER cc_start: 0.9087 (t) cc_final: 0.8808 (m)
REVERT: A  785 MET cc_start: 0.5182 (mpp) cc_final: 0.4600 (mpp)
REVERT: A  843 THR cc_start: 0.7276 (p) cc_final: 0.7020 (p)
REVERT: A  909 LYS cc_start: 0.5995 (tmtt) cc_final: 0.5785 (tptp)
REVERT: A  914 MET cc_start: 0.2879 (ttt) cc_final: 0.2141 (ttt)
REVERT: A  926 ASP cc_start: 0.8195 (m-30) cc_final: 0.7658 (p0)
REVERT: A  931 ASN cc_start: 0.6945 (m-40) cc_final: 0.6738 (m110)
REVERT: A  991 MET cc_start: 0.7301 (tmm) cc_final: 0.6140 (mmm)
REVERT: B  621 TYR cc_start: 0.7661 (t80) cc_final: 0.6541 (t80)
REVERT: B  642 ARG cc_start: 0.7114 (OUTLIER) cc_final: 0.6740 (mmp80)
REVERT: B  655 ARG cc_start: 0.4581 (mtt180) cc_final: 0.4356 (mtt-85)
REVERT: B  712 VAL cc_start: 0.8947 (t) cc_final: 0.8407 (t)
REVERT: B  782 VAL cc_start: 0.7480 (OUTLIER) cc_final: 0.7085 (p)
REVERT: B  839 ASP cc_start: 0.4554 (t0) cc_final: 0.3829 (p0)
REVERT: B  939 TRP cc_start: 0.7722 (p90) cc_final: 0.6834 (m-10)
REVERT: B  955 ARG cc_start: 0.8935 (mtt-85) cc_final: 0.8497 (mtt90)
  outliers start: 9
  outliers final: 3
  residues processed: 203
  average time/residue: 0.0975
  time to fit residues: 24.6965
Evaluate side-chains
  152 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 147
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  622 ASN
Chi-restraints excluded: chain A residue  686 MET
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    4.9990
   chunk 53 optimal weight:    1.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    0.3980
   chunk 65 optimal weight:    8.9990
   chunk 62 optimal weight:    8.9990
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    0.9980
   chunk 61 optimal weight:    6.9990
   chunk 45 optimal weight:    0.4980
   chunk 74 optimal weight:    2.9990
   overall best weight:    0.9782

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

Flipped N/Q/H residues before XYZ refinement:
A 817 GLN
** A 900 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 999 GLN
A1014 ASN
B 762 HIS

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4415 r_free = 0.4415 target = 0.143126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4092 r_free = 0.4092 target = 0.119505 restraints weight = 20271.400|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.122902 restraints weight = 13150.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4171 r_free = 0.4171 target = 0.125218 restraints weight = 9735.148|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4193 r_free = 0.4193 target = 0.126837 restraints weight = 7885.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.128014 restraints weight = 6771.822|
|-----------------------------------------------------------------------------|
r_work (final): 0.4197
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6766
moved from start:          0.2982

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050   6335  Z= 0.184
  Angle     :  0.834  10.468   8547  Z= 0.426
  Chirality :  0.050   0.165    942
  Planarity :  0.007   0.107   1098
  Dihedral  :  6.104  47.215    857
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 24.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 18.44 %
    Favored  : 76.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.88 (0.28), residues: 762
  helix: -0.73 (0.29), residues: 295
  sheet: -1.51 (0.58), residues: 72
  loop : -3.04 (0.27), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 642 
 TYR   0.025   0.002   TYR B 621 
 PHE   0.018   0.002   PHE A1018 
 TRP   0.031   0.003   TRP A 939 
 HIS   0.003   0.001   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00408 ( 6335)
  covalent geometry    : angle       0.83395 ( 8547)
  hydrogen bonds       : bond        0.06820 (  224)
  hydrogen bonds       : angle       6.97727 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  192 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 157
  time to evaluate  : 0.236 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  710 SER cc_start: 0.9080 (t) cc_final: 0.8595 (p)
REVERT: A  711 ASP cc_start: 0.7858 (m-30) cc_final: 0.7277 (p0)
REVERT: A  843 THR cc_start: 0.7208 (p) cc_final: 0.6781 (p)
REVERT: A  926 ASP cc_start: 0.8246 (m-30) cc_final: 0.7626 (p0)
REVERT: A  931 ASN cc_start: 0.7200 (m-40) cc_final: 0.6891 (m110)
REVERT: B  785 MET cc_start: 0.7005 (pmm) cc_final: 0.6364 (mtt)
REVERT: B  856 TRP cc_start: 0.7298 (m100) cc_final: 0.6954 (m-90)
REVERT: B  939 TRP cc_start: 0.7584 (p90) cc_final: 0.6660 (m-10)
REVERT: B  955 ARG cc_start: 0.8834 (mtt-85) cc_final: 0.8447 (mtt90)
  outliers start: 35
  outliers final: 17
  residues processed: 182
  average time/residue: 0.0801
  time to fit residues: 19.1617
Evaluate side-chains
  156 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 139
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ARG
Chi-restraints excluded: chain A residue  740 VAL
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain A residue 1005 VAL
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  946 ILE
Chi-restraints excluded: chain B residue  962 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 54 optimal weight:    5.9990
   chunk 31 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 12 optimal weight:    0.9990
   chunk 42 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 37 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9980
   chunk 57 optimal weight:   10.0000
   overall best weight:    1.3586

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

Flipped N/Q/H residues before XYZ refinement:
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
B 684 GLN
B 762 HIS
B 902 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.140805 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.117580 restraints weight = 20073.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.120849 restraints weight = 12968.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4146 r_free = 0.4146 target = 0.123064 restraints weight = 9652.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4168 r_free = 0.4168 target = 0.124590 restraints weight = 7847.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4183 r_free = 0.4183 target = 0.125672 restraints weight = 6759.154|
|-----------------------------------------------------------------------------|
r_work (final): 0.4173
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6832
moved from start:          0.3839

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062   6335  Z= 0.175
  Angle     :  0.804  10.963   8547  Z= 0.404
  Chirality :  0.050   0.171    942
  Planarity :  0.005   0.037   1098
  Dihedral  :  5.567  19.376    848
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 24.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 19.17 %
    Favored  : 75.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.41 (0.29), residues: 762
  helix: -0.50 (0.30), residues: 291
  sheet: -1.61 (0.55), residues: 76
  loop : -2.53 (0.29), residues: 395

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG B 732 
 TYR   0.014   0.002   TYR A 709 
 PHE   0.024   0.002   PHE B 661 
 TRP   0.032   0.003   TRP A 939 
 HIS   0.004   0.001   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00393 ( 6335)
  covalent geometry    : angle       0.80435 ( 8547)
  hydrogen bonds       : bond        0.05577 (  224)
  hydrogen bonds       : angle       6.52022 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  181 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 145
  time to evaluate  : 0.274 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 LYS cc_start: 0.8887 (mmtm) cc_final: 0.8632 (mmtm)
REVERT: A  710 SER cc_start: 0.9095 (t) cc_final: 0.8621 (p)
REVERT: A  711 ASP cc_start: 0.7952 (m-30) cc_final: 0.7435 (p0)
REVERT: A  774 MET cc_start: 0.6735 (OUTLIER) cc_final: 0.5673 (tmm)
REVERT: A  931 ASN cc_start: 0.7380 (m-40) cc_final: 0.7010 (m110)
REVERT: A  933 MET cc_start: 0.8758 (ptt) cc_final: 0.8540 (ptp)
REVERT: B  837 PHE cc_start: 0.6261 (OUTLIER) cc_final: 0.5917 (m-80)
REVERT: B  850 LEU cc_start: 0.8958 (tp) cc_final: 0.8730 (tp)
REVERT: B  856 TRP cc_start: 0.7401 (m100) cc_final: 0.6987 (m100)
REVERT: B  886 PHE cc_start: 0.6792 (OUTLIER) cc_final: 0.6340 (t80)
REVERT: B  933 MET cc_start: 0.7920 (ppp) cc_final: 0.7719 (ppp)
REVERT: B  955 ARG cc_start: 0.8860 (mtt-85) cc_final: 0.8425 (mtm-85)
  outliers start: 36
  outliers final: 20
  residues processed: 165
  average time/residue: 0.0775
  time to fit residues: 17.1071
Evaluate side-chains
  155 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 132
  time to evaluate  : 0.220 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ARG
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  786 MET
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  837 PHE
Chi-restraints excluded: chain B residue  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  976 THR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 14 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 59 optimal weight:    0.6980
   chunk 49 optimal weight:    0.5980
   chunk 24 optimal weight:    1.9990
   chunk 48 optimal weight:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 13 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   chunk 6 optimal weight:   10.0000
   chunk 8 optimal weight:    7.9990
   overall best weight:    0.8384

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

Flipped N/Q/H residues before XYZ refinement:
A 701 ASN
A 999 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.141698 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.119440 restraints weight = 19145.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.4140 r_free = 0.4140 target = 0.122642 restraints weight = 12202.866|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4172 r_free = 0.4172 target = 0.124859 restraints weight = 8976.805|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4195 r_free = 0.4195 target = 0.126387 restraints weight = 7205.603|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4208 r_free = 0.4208 target = 0.127360 restraints weight = 6144.612|
|-----------------------------------------------------------------------------|
r_work (final): 0.4200
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6811
moved from start:          0.4432

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6335  Z= 0.156
  Angle     :  0.785  13.091   8547  Z= 0.390
  Chirality :  0.049   0.168    942
  Planarity :  0.005   0.060   1098
  Dihedral  :  5.466  19.084    848
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 20.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.40 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 23.01 %
    Favored  : 72.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.29 (0.29), residues: 762
  helix: -0.35 (0.31), residues: 291
  sheet: -2.03 (0.50), residues: 85
  loop : -2.37 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG B 732 
 TYR   0.014   0.002   TYR A 621 
 PHE   0.019   0.003   PHE B 661 
 TRP   0.037   0.003   TRP A 939 
 HIS   0.004   0.001   HIS A 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00358 ( 6335)
  covalent geometry    : angle       0.78527 ( 8547)
  hydrogen bonds       : bond        0.05108 (  224)
  hydrogen bonds       : angle       6.26345 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 138
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 LYS cc_start: 0.8940 (mmtm) cc_final: 0.8635 (mmtm)
REVERT: A  710 SER cc_start: 0.9070 (t) cc_final: 0.8485 (p)
REVERT: A  711 ASP cc_start: 0.8085 (m-30) cc_final: 0.7530 (p0)
REVERT: A  926 ASP cc_start: 0.8359 (m-30) cc_final: 0.7527 (p0)
REVERT: A  931 ASN cc_start: 0.7332 (m-40) cc_final: 0.7115 (m110)
REVERT: A  933 MET cc_start: 0.8800 (ptt) cc_final: 0.8580 (ptp)
REVERT: B  785 MET cc_start: 0.7162 (pmm) cc_final: 0.6524 (mmt)
REVERT: B  856 TRP cc_start: 0.7344 (m100) cc_final: 0.6905 (m-90)
REVERT: B  886 PHE cc_start: 0.6790 (OUTLIER) cc_final: 0.6264 (t80)
REVERT: B  955 ARG cc_start: 0.8838 (mtt-85) cc_final: 0.8473 (mtm-85)
  outliers start: 30
  outliers final: 24
  residues processed: 155
  average time/residue: 0.0720
  time to fit residues: 14.9430
Evaluate side-chains
  155 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 0.251 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ARG
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  786 MET
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue 1005 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 65 optimal weight:    7.9990
   chunk 70 optimal weight:    1.9990
   chunk 34 optimal weight:    2.9990
   chunk 9 optimal weight:    5.9990
   chunk 73 optimal weight:    0.1980
   chunk 11 optimal weight:    0.9990
   chunk 18 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9980
   chunk 66 optimal weight:    0.2980
   chunk 21 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 640 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4404 r_free = 0.4404 target = 0.141675 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.120036 restraints weight = 19951.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4142 r_free = 0.4142 target = 0.123168 restraints weight = 12779.448|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.125314 restraints weight = 9435.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.4196 r_free = 0.4196 target = 0.126786 restraints weight = 7621.165|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4213 r_free = 0.4213 target = 0.127919 restraints weight = 6526.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.4190
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6814
moved from start:          0.4826

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.056   6335  Z= 0.146
  Angle     :  0.765   9.551   8547  Z= 0.376
  Chirality :  0.049   0.191    942
  Planarity :  0.004   0.042   1098
  Dihedral  :  5.347  18.766    848
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 19.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 24.04 %
    Favored  : 71.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.07 (0.30), residues: 762
  helix: -0.30 (0.31), residues: 301
  sheet: -1.86 (0.50), residues: 91
  loop : -2.18 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A1009 
 TYR   0.009   0.001   TYR A 621 
 PHE   0.017   0.002   PHE B 661 
 TRP   0.024   0.002   TRP B 835 
 HIS   0.003   0.001   HIS B 637 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6335)
  covalent geometry    : angle       0.76464 ( 8547)
  hydrogen bonds       : bond        0.04715 (  224)
  hydrogen bonds       : angle       6.06005 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  168 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 137
  time to evaluate  : 0.175 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 LYS cc_start: 0.8915 (mmtm) cc_final: 0.8654 (mmtm)
REVERT: A  711 ASP cc_start: 0.8074 (m-30) cc_final: 0.7520 (p0)
REVERT: A  785 MET cc_start: 0.5182 (mpp) cc_final: 0.4749 (mpp)
REVERT: A  926 ASP cc_start: 0.8257 (m-30) cc_final: 0.7484 (p0)
REVERT: A  933 MET cc_start: 0.8777 (ptt) cc_final: 0.8567 (ptp)
REVERT: B  820 THR cc_start: 0.7951 (p) cc_final: 0.7712 (p)
REVERT: B  856 TRP cc_start: 0.7167 (m100) cc_final: 0.6941 (m100)
REVERT: B  886 PHE cc_start: 0.6760 (OUTLIER) cc_final: 0.6161 (t80)
REVERT: B  933 MET cc_start: 0.7858 (ppp) cc_final: 0.7412 (ppp)
REVERT: B  955 ARG cc_start: 0.8795 (mtt-85) cc_final: 0.8448 (mtm-85)
REVERT: B  984 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6769 (mmtp)
  outliers start: 31
  outliers final: 25
  residues processed: 157
  average time/residue: 0.0677
  time to fit residues: 14.2519
Evaluate side-chains
  152 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 126
  time to evaluate  : 0.252 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  634 VAL
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  786 MET
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue 1005 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 7 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 63 optimal weight:    3.9990
   chunk 67 optimal weight:    0.9990
   chunk 29 optimal weight:    5.9990
   chunk 3 optimal weight:    5.9990
   chunk 71 optimal weight:    5.9990
   chunk 74 optimal weight:    2.9990
   chunk 15 optimal weight:    5.9990
   chunk 12 optimal weight:    2.9990
   overall best weight:    1.5388

-------------------------------------------------------------------------------
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 = 0.4364 r_free = 0.4364 target = 0.138702 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4052 r_free = 0.4052 target = 0.117121 restraints weight = 19761.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.120125 restraints weight = 12762.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.122184 restraints weight = 9453.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4150 r_free = 0.4150 target = 0.123554 restraints weight = 7631.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4165 r_free = 0.4165 target = 0.124604 restraints weight = 6571.562|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6897
moved from start:          0.5274

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.058   6335  Z= 0.162
  Angle     :  0.779  10.812   8547  Z= 0.386
  Chirality :  0.050   0.232    942
  Planarity :  0.005   0.096   1098
  Dihedral  :  5.408  18.793    848
  Min Nonbonded Distance : 2.528

Molprobity Statistics.
  All-atom Clashscore : 20.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  6.19 %
    Allowed  : 24.04 %
    Favored  : 69.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -2.02 (0.30), residues: 762
  helix: -0.14 (0.31), residues: 298
  sheet: -2.07 (0.49), residues: 95
  loop : -2.17 (0.32), residues: 369

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 642 
 TYR   0.009   0.002   TYR B 621 
 PHE   0.018   0.002   PHE B 661 
 TRP   0.041   0.003   TRP A 939 
 HIS   0.004   0.001   HIS B 907 

Details of bonding type rmsd
  covalent geometry    : bond        0.00368 ( 6335)
  covalent geometry    : angle       0.77945 ( 8547)
  hydrogen bonds       : bond        0.04691 (  224)
  hydrogen bonds       : angle       5.98778 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  182 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 140
  time to evaluate  : 0.267 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 LYS cc_start: 0.8943 (mmtm) cc_final: 0.8688 (mmtm)
REVERT: A  711 ASP cc_start: 0.8051 (m-30) cc_final: 0.7688 (p0)
REVERT: A  774 MET cc_start: 0.7546 (OUTLIER) cc_final: 0.7292 (tpt)
REVERT: A  785 MET cc_start: 0.5237 (mpp) cc_final: 0.4794 (mpp)
REVERT: A  926 ASP cc_start: 0.8330 (m-30) cc_final: 0.7530 (p0)
REVERT: A  933 MET cc_start: 0.8786 (ptt) cc_final: 0.8582 (ptp)
REVERT: B  698 LYS cc_start: 0.9096 (tptt) cc_final: 0.8836 (pttt)
REVERT: B  886 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6338 (t80)
REVERT: B  933 MET cc_start: 0.7756 (ppp) cc_final: 0.7365 (ppp)
REVERT: B  955 ARG cc_start: 0.8817 (mtt-85) cc_final: 0.8369 (mtm-85)
REVERT: B  984 LYS cc_start: 0.7050 (mmtt) cc_final: 0.6747 (mmtp)
  outliers start: 42
  outliers final: 30
  residues processed: 166
  average time/residue: 0.0730
  time to fit residues: 16.4327
Evaluate side-chains
  160 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 128
  time to evaluate  : 0.167 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  833 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  895 ILE
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  634 VAL
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  766 ASP
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  786 MET
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  833 ILE
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  976 THR
Chi-restraints excluded: chain B residue 1005 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 25 optimal weight:    8.9990
   chunk 20 optimal weight:    0.6980
   chunk 71 optimal weight:    1.9990
   chunk 47 optimal weight:    0.9990
   chunk 16 optimal weight:    5.9990
   chunk 49 optimal weight:    0.4980
   chunk 36 optimal weight:    0.6980
   chunk 39 optimal weight:    1.9990
   chunk 35 optimal weight:    0.8980
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 644 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 682 HIS
A 931 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.141515 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.117025 restraints weight = 21033.315|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.120071 restraints weight = 14662.635|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.122201 restraints weight = 11356.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.123708 restraints weight = 9471.870|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 20)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.124422 restraints weight = 8288.960|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6914
moved from start:          0.5620

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.062   6335  Z= 0.140
  Angle     :  0.798   9.987   8547  Z= 0.387
  Chirality :  0.052   0.244    942
  Planarity :  0.004   0.046   1098
  Dihedral  :  5.331  19.475    848
  Min Nonbonded Distance : 2.444

Molprobity Statistics.
  All-atom Clashscore : 20.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 26.11 %
    Favored  : 68.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.81 (0.31), residues: 762
  helix: -0.01 (0.32), residues: 302
  sheet: -1.79 (0.51), residues: 95
  loop : -2.08 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 642 
 TYR   0.008   0.001   TYR A 709 
 PHE   0.016   0.002   PHE A 837 
 TRP   0.040   0.003   TRP A 939 
 HIS   0.004   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6335)
  covalent geometry    : angle       0.79813 ( 8547)
  hydrogen bonds       : bond        0.04553 (  224)
  hydrogen bonds       : angle       5.84742 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  169 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 135
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  711 ASP cc_start: 0.8091 (m-30) cc_final: 0.7684 (p0)
REVERT: A  785 MET cc_start: 0.5673 (mpp) cc_final: 0.5316 (mpp)
REVERT: A  926 ASP cc_start: 0.8284 (m-30) cc_final: 0.7490 (p0)
REVERT: A  933 MET cc_start: 0.8745 (ptt) cc_final: 0.8543 (ptp)
REVERT: A  982 LYS cc_start: 0.8021 (tppt) cc_final: 0.7817 (tppt)
REVERT: B  886 PHE cc_start: 0.6975 (OUTLIER) cc_final: 0.6485 (t80)
REVERT: B  933 MET cc_start: 0.7825 (ppp) cc_final: 0.7427 (ppp)
REVERT: B  955 ARG cc_start: 0.8917 (mtt-85) cc_final: 0.8556 (mtm-85)
  outliers start: 34
  outliers final: 28
  residues processed: 156
  average time/residue: 0.0815
  time to fit residues: 16.8560
Evaluate side-chains
  154 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 125
  time to evaluate  : 0.235 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  772 CYS
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  634 VAL
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  769 TYR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  833 ILE
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue 1005 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 16 optimal weight:    4.9990
   chunk 38 optimal weight:    4.9990
   chunk 74 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 48 optimal weight:    0.0270
   chunk 14 optimal weight:    4.9990
   chunk 12 optimal weight:    0.7980
   chunk 49 optimal weight:    0.8980
   chunk 58 optimal weight:    0.4980
   chunk 33 optimal weight:    5.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6438

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

Flipped N/Q/H residues before XYZ refinement:
** B 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.140265 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.118752 restraints weight = 19634.269|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4124 r_free = 0.4124 target = 0.122102 restraints weight = 12186.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.124369 restraints weight = 8727.821|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.4182 r_free = 0.4182 target = 0.125957 restraints weight = 6873.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4197 r_free = 0.4197 target = 0.127047 restraints weight = 5773.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.4181
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6831
moved from start:          0.5892

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6335  Z= 0.138
  Angle     :  0.809  19.041   8547  Z= 0.385
  Chirality :  0.051   0.237    942
  Planarity :  0.005   0.095   1098
  Dihedral  :  5.328  19.616    848
  Min Nonbonded Distance : 2.512

Molprobity Statistics.
  All-atom Clashscore : 19.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 25.81 %
    Favored  : 68.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.70 (0.31), residues: 762
  helix:  0.06 (0.32), residues: 301
  sheet: -1.27 (0.55), residues: 85
  loop : -2.12 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 887 
 TYR   0.010   0.001   TYR B 621 
 PHE   0.016   0.002   PHE B 661 
 TRP   0.040   0.003   TRP A 939 
 HIS   0.005   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 6335)
  covalent geometry    : angle       0.80938 ( 8547)
  hydrogen bonds       : bond        0.04318 (  224)
  hydrogen bonds       : angle       5.74507 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  163 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 127
  time to evaluate  : 0.252 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8613 (mmtm)
REVERT: A  711 ASP cc_start: 0.8174 (m-30) cc_final: 0.7710 (p0)
REVERT: A  774 MET cc_start: 0.7423 (OUTLIER) cc_final: 0.6404 (tmm)
REVERT: A  785 MET cc_start: 0.5657 (mpp) cc_final: 0.5331 (mpp)
REVERT: A  849 LEU cc_start: 0.8007 (mm) cc_final: 0.7799 (mm)
REVERT: A  926 ASP cc_start: 0.8240 (m-30) cc_final: 0.7463 (p0)
REVERT: A  991 MET cc_start: 0.7061 (tpt) cc_final: 0.6646 (mmm)
REVERT: B  774 MET cc_start: 0.6579 (tmm) cc_final: 0.6311 (tmm)
REVERT: B  873 ASP cc_start: 0.6421 (m-30) cc_final: 0.5234 (t0)
REVERT: B  886 PHE cc_start: 0.6773 (OUTLIER) cc_final: 0.6295 (t80)
REVERT: B  933 MET cc_start: 0.7722 (ppp) cc_final: 0.7324 (ppp)
  outliers start: 36
  outliers final: 29
  residues processed: 149
  average time/residue: 0.0738
  time to fit residues: 14.9828
Evaluate side-chains
  152 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 121
  time to evaluate  : 0.238 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  634 VAL
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  769 TYR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  833 ILE
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue 1005 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 42 optimal weight:    0.8980
   chunk 65 optimal weight:    6.9990
   chunk 53 optimal weight:    5.9990
   chunk 62 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0670
   chunk 72 optimal weight:    0.0070
   chunk 0 optimal weight:    8.9990
   chunk 67 optimal weight:    5.9990
   chunk 59 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 33 optimal weight:   10.0000
   overall best weight:    0.5536

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

Flipped N/Q/H residues before XYZ refinement:
** B 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 902 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.140453 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.118943 restraints weight = 19873.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.122079 restraints weight = 12591.974|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4148 r_free = 0.4148 target = 0.124231 restraints weight = 9204.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.4169 r_free = 0.4169 target = 0.125641 restraints weight = 7379.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.126748 restraints weight = 6334.321|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6816
moved from start:          0.6123

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.061   6335  Z= 0.135
  Angle     :  0.800  12.976   8547  Z= 0.383
  Chirality :  0.051   0.240    942
  Planarity :  0.005   0.058   1098
  Dihedral  :  5.258  19.690    848
  Min Nonbonded Distance : 2.521

Molprobity Statistics.
  All-atom Clashscore : 18.88
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.87 %
    Favored  : 91.99 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 27.29 %
    Favored  : 68.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.64 (0.31), residues: 762
  helix:  0.11 (0.32), residues: 301
  sheet: -1.18 (0.56), residues: 85
  loop : -2.11 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.000   ARG A 642 
 TYR   0.009   0.001   TYR B 621 
 PHE   0.014   0.002   PHE B 661 
 TRP   0.021   0.002   TRP B 856 
 HIS   0.004   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 6335)
  covalent geometry    : angle       0.79957 ( 8547)
  hydrogen bonds       : bond        0.04269 (  224)
  hydrogen bonds       : angle       5.69255 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  157 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 128
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 LYS cc_start: 0.8924 (mmtm) cc_final: 0.8575 (mmtm)
REVERT: A  711 ASP cc_start: 0.8150 (m-30) cc_final: 0.7736 (p0)
REVERT: A  774 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6970 (tpp)
REVERT: A  785 MET cc_start: 0.5619 (mpp) cc_final: 0.5301 (mpp)
REVERT: A  926 ASP cc_start: 0.8219 (m-30) cc_final: 0.7505 (p0)
REVERT: A  991 MET cc_start: 0.7006 (tpt) cc_final: 0.6632 (mmm)
REVERT: A 1009 ARG cc_start: 0.7160 (tpt170) cc_final: 0.6608 (tpt170)
REVERT: B  820 THR cc_start: 0.7970 (p) cc_final: 0.7729 (p)
REVERT: B  873 ASP cc_start: 0.6360 (m-30) cc_final: 0.5062 (t0)
REVERT: B  886 PHE cc_start: 0.6667 (OUTLIER) cc_final: 0.6177 (t80)
REVERT: B  933 MET cc_start: 0.7702 (ppp) cc_final: 0.7291 (ppp)
  outliers start: 29
  outliers final: 27
  residues processed: 146
  average time/residue: 0.0687
  time to fit residues: 13.6807
Evaluate side-chains
  151 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 122
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  973 ILE
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  634 VAL
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  769 TYR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  833 ILE
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  997 LEU
Chi-restraints excluded: chain B residue 1005 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    7.9990
   chunk 52 optimal weight:    3.9990
   chunk 44 optimal weight:    0.0370
   chunk 6 optimal weight:    0.0570
   chunk 7 optimal weight:    1.9990
   chunk 25 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 0 optimal weight:    8.9990
   chunk 60 optimal weight:    8.9990
   chunk 72 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   overall best weight:    0.9580

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

Flipped N/Q/H residues before XYZ refinement:
** B 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4364 r_free = 0.4364 target = 0.139409 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4057 r_free = 0.4057 target = 0.118103 restraints weight = 19635.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4103 r_free = 0.4103 target = 0.121196 restraints weight = 12435.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4137 r_free = 0.4137 target = 0.123422 restraints weight = 9064.371|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.124920 restraints weight = 7210.868|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.4175 r_free = 0.4175 target = 0.126007 restraints weight = 6127.850|
|-----------------------------------------------------------------------------|
r_work (final): 0.4170
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6850
moved from start:          0.6268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.064   6335  Z= 0.139
  Angle     :  0.798  13.082   8547  Z= 0.385
  Chirality :  0.051   0.242    942
  Planarity :  0.005   0.064   1098
  Dihedral  :  5.306  19.484    848
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 19.28
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.27 %
    Favored  : 91.60 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 27.29 %
    Favored  : 68.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.62 (0.31), residues: 762
  helix:  0.18 (0.32), residues: 301
  sheet: -1.27 (0.56), residues: 85
  loop : -2.12 (0.31), residues: 376

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 642 
 TYR   0.010   0.001   TYR B 621 
 PHE   0.014   0.002   PHE B 661 
 TRP   0.024   0.002   TRP B 856 
 HIS   0.004   0.001   HIS B 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 6335)
  covalent geometry    : angle       0.79837 ( 8547)
  hydrogen bonds       : bond        0.04204 (  224)
  hydrogen bonds       : angle       5.63513 (  636)

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

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

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1524 Ramachandran restraints generated.
    762 Oldfield, 0 Emsley, 762 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 129
  time to evaluate  : 0.254 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 LYS cc_start: 0.8976 (mmtm) cc_final: 0.8597 (mmtm)
REVERT: A  711 ASP cc_start: 0.8230 (m-30) cc_final: 0.7770 (p0)
REVERT: A  774 MET cc_start: 0.7402 (OUTLIER) cc_final: 0.6299 (tmm)
REVERT: A  785 MET cc_start: 0.5577 (mpp) cc_final: 0.5275 (mpp)
REVERT: A  926 ASP cc_start: 0.8189 (m-30) cc_final: 0.7509 (p0)
REVERT: A  991 MET cc_start: 0.7137 (tpt) cc_final: 0.6763 (mmm)
REVERT: A 1009 ARG cc_start: 0.7226 (tpt170) cc_final: 0.6828 (tpt170)
REVERT: B  873 ASP cc_start: 0.6163 (m-30) cc_final: 0.4997 (t0)
REVERT: B  886 PHE cc_start: 0.6838 (OUTLIER) cc_final: 0.6346 (t80)
REVERT: B  933 MET cc_start: 0.7703 (ppp) cc_final: 0.7277 (ppp)
  outliers start: 31
  outliers final: 29
  residues processed: 149
  average time/residue: 0.0644
  time to fit residues: 13.4002
Evaluate side-chains
  157 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 126
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 VAL
Chi-restraints excluded: chain A residue  682 HIS
Chi-restraints excluded: chain A residue  700 LEU
Chi-restraints excluded: chain A residue  710 SER
Chi-restraints excluded: chain A residue  717 LEU
Chi-restraints excluded: chain A residue  738 LEU
Chi-restraints excluded: chain A residue  754 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  774 MET
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  634 VAL
Chi-restraints excluded: chain B residue  641 TYR
Chi-restraints excluded: chain B residue  671 LEU
Chi-restraints excluded: chain B residue  677 VAL
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  739 VAL
Chi-restraints excluded: chain B residue  769 TYR
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  833 ILE
Chi-restraints excluded: chain B residue  845 LEU
Chi-restraints excluded: chain B residue  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  997 LEU
Chi-restraints excluded: chain B residue 1005 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 32 optimal weight:    0.8980
   chunk 36 optimal weight:    2.9990
   chunk 8 optimal weight:    0.0970
   chunk 61 optimal weight:   20.0000
   chunk 52 optimal weight:    2.9990
   chunk 73 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 39 optimal weight:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 1 optimal weight:    0.9990
   chunk 64 optimal weight:    0.9990
   overall best weight:    0.7982

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

Flipped N/Q/H residues before XYZ refinement:
** B 762 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 902 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4394 r_free = 0.4394 target = 0.141183 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4096 r_free = 0.4096 target = 0.120525 restraints weight = 19562.619|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.4144 r_free = 0.4144 target = 0.123817 restraints weight = 12130.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.4177 r_free = 0.4177 target = 0.126018 restraints weight = 8657.301|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4201 r_free = 0.4201 target = 0.127607 restraints weight = 6815.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.128719 restraints weight = 5695.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.4205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6824
moved from start:          0.6504

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6335  Z= 0.133
  Angle     :  0.789  12.835   8547  Z= 0.380
  Chirality :  0.050   0.250    942
  Planarity :  0.004   0.052   1098
  Dihedral  :  5.215  19.267    848
  Min Nonbonded Distance : 2.518

Molprobity Statistics.
  All-atom Clashscore : 19.28
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  8.14 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 27.73 %
    Favored  : 67.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.51 (0.31), residues: 762
  helix:  0.32 (0.32), residues: 299
  sheet: -1.21 (0.55), residues: 85
  loop : -2.10 (0.31), residues: 378

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 642 
 TYR   0.008   0.001   TYR B 621 
 PHE   0.013   0.002   PHE B 661 
 TRP   0.014   0.002   TRP B 835 
 HIS   0.003   0.001   HIS A 762 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6335)
  covalent geometry    : angle       0.78864 ( 8547)
  hydrogen bonds       : bond        0.04063 (  224)
  hydrogen bonds       : angle       5.53552 (  636)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1261.56 seconds
wall clock time: 22 minutes 26.25 seconds (1346.25 seconds total)