Starting phenix.real_space_refine
on Thu Jul 24 13:40:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7yg1_33804/07_2025/7yg1_33804_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7yg1_33804/07_2025/7yg1_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7yg1_33804/07_2025/7yg1_33804.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7yg1_33804/07_2025/7yg1_33804.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7yg1_33804/07_2025/7yg1_33804_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7yg1_33804/07_2025/7yg1_33804_neut.cif"
  }
  resolution = 3.77
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.023
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): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: {'TYR:plan': 1, 'ASN:plan1': 1}
          Unresolved non-hydrogen planarities: 10
  Time building chain proxies: 4.62, per 1000 atoms: 0.74
  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: 1.76
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

  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: 0.71
  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: 1.60

  Time building geometry restraints manager: 2.03 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:             2.020
  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:          0.260
  Check model and map are aligned:         0.050
  Set scattering table:                    0.070
  Process input model:                     19.320
  Find NCS groups from input model:        0.220
  Set up NCS constraints:                  0.030
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.980
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -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
 TRP   0.037   0.002   TRP B 939 
 HIS   0.003   0.001   HIS B 907 
 PHE   0.016   0.001   PHE B 665 
 TYR   0.023   0.002   TYR B 627 
 ARG   0.005   0.001   ARG A 719 

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

*********************** 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  : 0.722 
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: 0.8809 (m)
REVERT: A  785 MET cc_start: 0.5182 (mpp) cc_final: 0.4601 (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: 0.2143 (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: 0.4355 (mtt-85)
REVERT: B  712 VAL cc_start: 0.8947 (t) cc_final: 0.8406 (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: 0.2415
  time to fit residues: 60.1554
Evaluate side-chains
  151 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 146
  time to evaluate  : 0.664 
-------------------------------------------------------------------------------
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 64 optimal weight:    8.9990
   chunk 57 optimal weight:    5.9990
   chunk 31 optimal weight:    4.9990
   chunk 19 optimal weight:    8.9990
   chunk 38 optimal weight:    7.9990
   chunk 30 optimal weight:    7.9990
   chunk 59 optimal weight:    2.9990
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    0.8980
   chunk 44 optimal weight:    6.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    2.9788

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

Flipped N/Q/H residues before XYZ refinement:
** A 632 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 817 GLN
** A 956 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 999 GLN
A1014 ASN
** B 750 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 902 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4350 r_free = 0.4350 target = 0.137654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.114348 restraints weight = 20177.876|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.117438 restraints weight = 13352.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.119477 restraints weight = 10054.835|
|-----------------------------------------------------------------------------|
r_work (final): 0.4077
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6990
moved from start:          0.3542

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.051   6335  Z= 0.258
  Angle     :  0.897   9.788   8547  Z= 0.467
  Chirality :  0.053   0.178    942
  Planarity :  0.008   0.098   1098
  Dihedral  :  6.422  46.324    857
  Min Nonbonded Distance : 2.527

Molprobity Statistics.
  All-atom Clashscore : 27.65
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.92 %
    Favored  : 91.08 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 19.62 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.94 (0.28), residues: 762
  helix: -0.80 (0.29), residues: 289
  sheet: -1.63 (0.57), residues: 71
  loop : -3.00 (0.28), residues: 402

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.035   0.004   TRP A 939 
 HIS   0.005   0.001   HIS B 750 
 PHE   0.033   0.003   PHE A1018 
 TYR   0.027   0.003   TYR A 709 
 ARG   0.011   0.001   ARG B 703 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.06631 (  224)
  hydrogen bonds       : angle       6.92785 (  636)
  covalent geometry    : bond        0.00570 ( 6335)
  covalent geometry    : angle       0.89683 ( 8547)

*********************** 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
  181 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 143
  time to evaluate  : 0.711 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  673 ILE cc_start: 0.8778 (mm) cc_final: 0.8555 (mt)
REVERT: A  708 PHE cc_start: 0.7800 (m-80) cc_final: 0.7570 (m-80)
REVERT: A  711 ASP cc_start: 0.7896 (m-30) cc_final: 0.7512 (p0)
REVERT: A  931 ASN cc_start: 0.7321 (m-40) cc_final: 0.7003 (m-40)
REVERT: B  642 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7377 (mmp80)
REVERT: B  730 LEU cc_start: 0.7439 (OUTLIER) cc_final: 0.7109 (pp)
REVERT: B  785 MET cc_start: 0.7072 (pmm) cc_final: 0.6436 (mtt)
REVERT: B  955 ARG cc_start: 0.8935 (mtt-85) cc_final: 0.8438 (mtt90)
REVERT: B 1018 PHE cc_start: 0.8211 (t80) cc_final: 0.7765 (t80)
  outliers start: 38
  outliers final: 20
  residues processed: 173
  average time/residue: 0.2065
  time to fit residues: 45.7700
Evaluate side-chains
  141 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 119
  time to evaluate  : 0.752 
-------------------------------------------------------------------------------
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  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 1008 ILE
Chi-restraints excluded: chain A residue 1016 LEU
Chi-restraints excluded: chain B residue  629 VAL
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  642 ARG
Chi-restraints excluded: chain B residue  670 SER
Chi-restraints excluded: chain B residue  730 LEU
Chi-restraints excluded: chain B residue  738 LEU
Chi-restraints excluded: chain B residue  754 VAL
Chi-restraints excluded: chain B residue  766 ASP
Chi-restraints excluded: chain B residue  782 VAL
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  962 ILE
Chi-restraints excluded: chain B residue  976 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 36 optimal weight:   10.0000
   chunk 38 optimal weight:    0.9990
   chunk 54 optimal weight:    0.2980
   chunk 68 optimal weight:    5.9990
   chunk 16 optimal weight:    0.5980
   chunk 62 optimal weight:    0.6980
   chunk 34 optimal weight:    3.9990
   chunk 9 optimal weight:    5.9990
   chunk 57 optimal weight:    0.8980
   chunk 29 optimal weight:    5.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
A 999 GLN
B 684 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4384 r_free = 0.4384 target = 0.140192 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.116606 restraints weight = 19896.395|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4098 r_free = 0.4098 target = 0.119830 restraints weight = 12892.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4129 r_free = 0.4129 target = 0.122022 restraints weight = 9637.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.4122
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.4181

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052   6335  Z= 0.164
  Angle     :  0.799  11.445   8547  Z= 0.400
  Chirality :  0.049   0.169    942
  Planarity :  0.005   0.048   1098
  Dihedral  :  5.854  32.815    852
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 22.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.19 %
    Favored  : 90.81 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 20.35 %
    Favored  : 74.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.42 (0.29), residues: 762
  helix: -0.27 (0.31), residues: 288
  sheet: -2.22 (0.50), residues: 86
  loop : -2.58 (0.30), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP A 939 
 HIS   0.006   0.001   HIS B 750 
 PHE   0.020   0.002   PHE B 924 
 TYR   0.016   0.002   TYR B 621 
 ARG   0.005   0.001   ARG A1009 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05614 (  224)
  hydrogen bonds       : angle       6.38306 (  636)
  covalent geometry    : bond        0.00367 ( 6335)
  covalent geometry    : angle       0.79861 ( 8547)

*********************** 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
  178 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 146
  time to evaluate  : 1.334 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  699 TRP cc_start: 0.6796 (t60) cc_final: 0.6466 (t60)
REVERT: A  711 ASP cc_start: 0.8002 (m-30) cc_final: 0.7513 (p0)
REVERT: A  926 ASP cc_start: 0.8430 (m-30) cc_final: 0.7574 (p0)
REVERT: A  931 ASN cc_start: 0.7236 (m-40) cc_final: 0.6969 (m110)
REVERT: B  704 LYS cc_start: 0.8099 (tppt) cc_final: 0.7375 (ttpt)
REVERT: B  826 GLN cc_start: 0.6258 (OUTLIER) cc_final: 0.6054 (tm-30)
REVERT: B  856 TRP cc_start: 0.7390 (m100) cc_final: 0.6986 (m-90)
REVERT: B  886 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6351 (t80)
REVERT: B  955 ARG cc_start: 0.8931 (mtt-85) cc_final: 0.8485 (mtt90)
REVERT: B 1018 PHE cc_start: 0.8228 (t80) cc_final: 0.7968 (t80)
  outliers start: 32
  outliers final: 24
  residues processed: 167
  average time/residue: 0.1923
  time to fit residues: 43.1293
Evaluate side-chains
  155 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 129
  time to evaluate  : 1.031 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  642 ARG
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  821 ILE
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  911 PHE
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  782 VAL
Chi-restraints excluded: chain B residue  786 MET
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  826 GLN
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=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 24 optimal weight:    8.9990
   chunk 10 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 23 optimal weight:    6.9990
   chunk 50 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9980
   chunk 36 optimal weight:    1.9990
   chunk 27 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 66 optimal weight:    9.9990
   chunk 61 optimal weight:    0.0050
   overall best weight:    1.4000

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4376 r_free = 0.4376 target = 0.139370 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.117315 restraints weight = 19455.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.120404 restraints weight = 12355.270|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4135 r_free = 0.4135 target = 0.122616 restraints weight = 9056.138|
|-----------------------------------------------------------------------------|
r_work (final): 0.4105
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6952
moved from start:          0.4885

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6335  Z= 0.164
  Angle     :  0.788  13.562   8547  Z= 0.393
  Chirality :  0.050   0.196    942
  Planarity :  0.005   0.037   1098
  Dihedral  :  5.555  19.346    848
  Min Nonbonded Distance : 2.525

Molprobity Statistics.
  All-atom Clashscore : 21.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.53 %
    Favored  : 91.47 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 22.57 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.07 (0.30), residues: 762
  helix: -0.22 (0.31), residues: 297
  sheet: -1.51 (0.54), residues: 77
  loop : -2.34 (0.31), residues: 388

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 939 
 HIS   0.006   0.001   HIS B 750 
 PHE   0.025   0.002   PHE B 924 
 TYR   0.016   0.002   TYR B 621 
 ARG   0.006   0.001   ARG B 904 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05093 (  224)
  hydrogen bonds       : angle       6.09248 (  636)
  covalent geometry    : bond        0.00374 ( 6335)
  covalent geometry    : angle       0.78822 ( 8547)

*********************** 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
  176 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 135
  time to evaluate  : 0.962 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  699 TRP cc_start: 0.6893 (t60) cc_final: 0.6623 (t60)
REVERT: A  710 SER cc_start: 0.9045 (t) cc_final: 0.8823 (m)
REVERT: A  711 ASP cc_start: 0.8094 (m-30) cc_final: 0.7646 (p0)
REVERT: A  776 MET cc_start: 0.4717 (pmm) cc_final: 0.4143 (pmm)
REVERT: A  785 MET cc_start: 0.5299 (mpp) cc_final: 0.4862 (mpp)
REVERT: A  926 ASP cc_start: 0.8405 (m-30) cc_final: 0.7564 (p0)
REVERT: A 1018 PHE cc_start: 0.6541 (OUTLIER) cc_final: 0.6287 (m-80)
REVERT: B  826 GLN cc_start: 0.6280 (OUTLIER) cc_final: 0.6000 (tm-30)
REVERT: B  856 TRP cc_start: 0.7502 (m100) cc_final: 0.7147 (m100)
REVERT: B  886 PHE cc_start: 0.7171 (OUTLIER) cc_final: 0.6616 (t80)
REVERT: B  933 MET cc_start: 0.7932 (ppp) cc_final: 0.7525 (ppp)
REVERT: B  955 ARG cc_start: 0.8959 (mtt-85) cc_final: 0.8557 (mtm-85)
REVERT: B  984 LYS cc_start: 0.7108 (mmtt) cc_final: 0.6796 (mmtp)
REVERT: B 1018 PHE cc_start: 0.8431 (t80) cc_final: 0.8205 (t80)
  outliers start: 41
  outliers final: 29
  residues processed: 161
  average time/residue: 0.2270
  time to fit residues: 49.1872
Evaluate side-chains
  158 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.786 
-------------------------------------------------------------------------------
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  821 ILE
Chi-restraints excluded: chain A residue  833 ILE
Chi-restraints excluded: chain A residue  836 LEU
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  911 PHE
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain A residue 1018 PHE
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  786 MET
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  826 GLN
Chi-restraints excluded: chain B residue  833 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 1005 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 2 optimal weight:    0.5980
   chunk 39 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 5 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0060
   chunk 67 optimal weight:    8.9990
   chunk 56 optimal weight:    9.9990
   chunk 53 optimal weight:    2.9990
   chunk 40 optimal weight:    0.4980
   chunk 15 optimal weight:    4.9990
   chunk 71 optimal weight:    0.6980
   overall best weight:    0.3794

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

Flipped N/Q/H residues before XYZ refinement:
A 640 ASN
A 931 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4402 r_free = 0.4402 target = 0.141496 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.119771 restraints weight = 19075.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4141 r_free = 0.4141 target = 0.123062 restraints weight = 11920.014|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.125326 restraints weight = 8597.361|
|-----------------------------------------------------------------------------|
r_work (final): 0.4152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6873
moved from start:          0.5225

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= 0.139
  Angle     :  0.765  10.068   8547  Z= 0.374
  Chirality :  0.049   0.196    942
  Planarity :  0.005   0.069   1098
  Dihedral  :  5.448  19.897    848
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 19.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.48 %
    Favored  : 92.52 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 24.78 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.89 (0.31), residues: 762
  helix: -0.03 (0.32), residues: 299
  sheet: -1.78 (0.50), residues: 92
  loop : -2.17 (0.32), residues: 371

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 939 
 HIS   0.005   0.001   HIS B 750 
 PHE   0.021   0.002   PHE B 924 
 TYR   0.011   0.001   TYR A 621 
 ARG   0.013   0.001   ARG A1009 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04663 (  224)
  hydrogen bonds       : angle       5.90728 (  636)
  covalent geometry    : bond        0.00312 ( 6335)
  covalent geometry    : angle       0.76457 ( 8547)

*********************** 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
  182 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 145
  time to evaluate  : 0.804 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  698 LYS cc_start: 0.9023 (mmtm) cc_final: 0.8733 (mmtm)
REVERT: A  711 ASP cc_start: 0.8124 (m-30) cc_final: 0.7518 (p0)
REVERT: A  785 MET cc_start: 0.5500 (mpp) cc_final: 0.5173 (mpp)
REVERT: A  926 ASP cc_start: 0.8422 (m-30) cc_final: 0.7588 (p0)
REVERT: B  826 GLN cc_start: 0.6348 (OUTLIER) cc_final: 0.5815 (tm-30)
REVERT: B  856 TRP cc_start: 0.7306 (m100) cc_final: 0.7058 (m100)
REVERT: B  886 PHE cc_start: 0.7100 (OUTLIER) cc_final: 0.6560 (t80)
REVERT: B  933 MET cc_start: 0.7861 (ppp) cc_final: 0.7440 (ppp)
REVERT: B  954 LEU cc_start: 0.8429 (mm) cc_final: 0.8200 (mm)
REVERT: B  955 ARG cc_start: 0.8862 (mtt-85) cc_final: 0.8504 (mtm-85)
REVERT: B  977 LEU cc_start: 0.7398 (OUTLIER) cc_final: 0.6992 (tt)
REVERT: B  984 LYS cc_start: 0.7041 (mmtt) cc_final: 0.6747 (mmtp)
  outliers start: 37
  outliers final: 27
  residues processed: 168
  average time/residue: 0.2002
  time to fit residues: 44.5251
Evaluate side-chains
  161 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 131
  time to evaluate  : 0.701 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  677 VAL
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  821 ILE
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  844 LEU
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  782 VAL
Chi-restraints excluded: chain B residue  786 MET
Chi-restraints excluded: chain B residue  821 ILE
Chi-restraints excluded: chain B residue  826 GLN
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  977 LEU
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 52 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 69 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0970
   chunk 51 optimal weight:    7.9990
   chunk 31 optimal weight:    9.9990
   chunk 23 optimal weight:    3.9990
   chunk 72 optimal weight:    0.4980
   chunk 49 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 65 optimal weight:    3.9990
   overall best weight:    2.3184

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.135598 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.114556 restraints weight = 19727.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4062 r_free = 0.4062 target = 0.117632 restraints weight = 12343.041|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4094 r_free = 0.4094 target = 0.119716 restraints weight = 8954.247|
|-----------------------------------------------------------------------------|
r_work (final): 0.4066
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7029
moved from start:          0.5726

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.067   6335  Z= 0.199
  Angle     :  0.840  18.230   8547  Z= 0.410
  Chirality :  0.051   0.209    942
  Planarity :  0.005   0.048   1098
  Dihedral  :  5.556  21.199    848
  Min Nonbonded Distance : 2.515

Molprobity Statistics.
  All-atom Clashscore : 24.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.84 %
    Favored  : 90.16 %
  Rotamer:
    Outliers :  6.05 %
    Allowed  : 25.37 %
    Favored  : 68.58 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.00 (0.31), residues: 762
  helix: -0.06 (0.31), residues: 301
  sheet: -2.29 (0.49), residues: 96
  loop : -2.16 (0.32), residues: 365

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 939 
 HIS   0.004   0.001   HIS B 750 
 PHE   0.022   0.002   PHE B 924 
 TYR   0.011   0.002   TYR B 621 
 ARG   0.009   0.001   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04779 (  224)
  hydrogen bonds       : angle       6.00093 (  636)
  covalent geometry    : bond        0.00449 ( 6335)
  covalent geometry    : angle       0.84040 ( 8547)

*********************** 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
  179 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 138
  time to evaluate  : 0.889 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  711 ASP cc_start: 0.8177 (m-30) cc_final: 0.7884 (p0)
REVERT: A  774 MET cc_start: 0.7804 (OUTLIER) cc_final: 0.6973 (tmm)
REVERT: A  785 MET cc_start: 0.5627 (mpp) cc_final: 0.5302 (mpp)
REVERT: A  926 ASP cc_start: 0.8429 (m-30) cc_final: 0.7624 (p0)
REVERT: B  774 MET cc_start: 0.6636 (tmm) cc_final: 0.6242 (tmm)
REVERT: B  886 PHE cc_start: 0.7182 (OUTLIER) cc_final: 0.6782 (t80)
REVERT: B  933 MET cc_start: 0.7757 (ppp) cc_final: 0.7388 (ppp)
REVERT: B  955 ARG cc_start: 0.8920 (mtt-85) cc_final: 0.8472 (mtm-85)
REVERT: B  977 LEU cc_start: 0.7607 (OUTLIER) cc_final: 0.7206 (tt)
  outliers start: 41
  outliers final: 31
  residues processed: 163
  average time/residue: 0.2032
  time to fit residues: 43.3167
Evaluate side-chains
  160 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 126
  time to evaluate  : 0.746 
-------------------------------------------------------------------------------
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  754 VAL
Chi-restraints excluded: chain A residue  761 LEU
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  836 LEU
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  911 PHE
Chi-restraints excluded: chain A residue  940 LYS
Chi-restraints excluded: chain A residue 1008 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  740 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  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  977 LEU
Chi-restraints excluded: chain B residue  997 LEU
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 49 optimal weight:    0.0980
   chunk 34 optimal weight:    1.9990
   chunk 17 optimal weight:    0.5980
   chunk 66 optimal weight:    1.9990
   chunk 27 optimal weight:    6.9990
   chunk 7 optimal weight:    0.9980
   chunk 22 optimal weight:    4.9990
   chunk 14 optimal weight:    0.6980
   chunk 25 optimal weight:    8.9990
   chunk 41 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   overall best weight:    0.6780

-------------------------------------------------------------------------------
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 = 0.138261 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.116873 restraints weight = 19466.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.120047 restraints weight = 12018.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4131 r_free = 0.4131 target = 0.122230 restraints weight = 8644.717|
|-----------------------------------------------------------------------------|
r_work (final): 0.4088
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6958
moved from start:          0.5959

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= 0.145
  Angle     :  0.799  12.694   8547  Z= 0.385
  Chirality :  0.050   0.201    942
  Planarity :  0.004   0.042   1098
  Dihedral  :  5.508  20.856    848
  Min Nonbonded Distance : 2.551

Molprobity Statistics.
  All-atom Clashscore : 20.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.27 %
    Favored  : 91.73 %
  Rotamer:
    Outliers :  5.46 %
    Allowed  : 27.58 %
    Favored  : 66.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.78 (0.31), residues: 762
  helix:  0.02 (0.31), residues: 302
  sheet: -1.54 (0.54), residues: 86
  loop : -2.15 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.037   0.003   TRP A 939 
 HIS   0.017   0.001   HIS A 682 
 PHE   0.019   0.002   PHE B 924 
 TYR   0.011   0.001   TYR B 621 
 ARG   0.009   0.001   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04601 (  224)
  hydrogen bonds       : angle       5.85421 (  636)
  covalent geometry    : bond        0.00327 ( 6335)
  covalent geometry    : angle       0.79860 ( 8547)

*********************** 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
  172 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 135
  time to evaluate  : 1.416 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  711 ASP cc_start: 0.8222 (m-30) cc_final: 0.7785 (p0)
REVERT: A  785 MET cc_start: 0.5648 (mpp) cc_final: 0.5363 (mpp)
REVERT: A  849 LEU cc_start: 0.7878 (mm) cc_final: 0.7609 (mm)
REVERT: A  926 ASP cc_start: 0.8348 (m-30) cc_final: 0.7502 (p0)
REVERT: B  774 MET cc_start: 0.6519 (tmm) cc_final: 0.6317 (tmm)
REVERT: B  886 PHE cc_start: 0.7041 (OUTLIER) cc_final: 0.6648 (t80)
REVERT: B  933 MET cc_start: 0.7722 (ppp) cc_final: 0.7355 (ppp)
REVERT: B  955 ARG cc_start: 0.8899 (mtt-85) cc_final: 0.8525 (mtm-85)
REVERT: B  977 LEU cc_start: 0.7653 (OUTLIER) cc_final: 0.7272 (tt)
  outliers start: 37
  outliers final: 29
  residues processed: 157
  average time/residue: 0.2216
  time to fit residues: 47.1656
Evaluate side-chains
  159 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 128
  time to evaluate  : 0.712 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  637 HIS
Chi-restraints excluded: chain A residue  677 VAL
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  754 VAL
Chi-restraints excluded: chain A residue  761 LEU
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  836 LEU
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  946 ILE
Chi-restraints excluded: chain A residue  985 CYS
Chi-restraints excluded: chain B residue  631 LEU
Chi-restraints excluded: chain B residue  634 VAL
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  821 ILE
Chi-restraints excluded: chain B residue  833 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  977 LEU
Chi-restraints excluded: chain B residue  997 LEU
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 71 optimal weight:    1.9990
   chunk 20 optimal weight:    7.9990
   chunk 1 optimal weight:    0.8980
   chunk 70 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    3.9990
   chunk 66 optimal weight:    0.0570
   chunk 39 optimal weight:    5.9990
   chunk 65 optimal weight:    0.4980
   chunk 4 optimal weight:    2.9990
   chunk 40 optimal weight:    7.9990
   overall best weight:    0.8700

-------------------------------------------------------------------------------
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 = 0.4334 r_free = 0.4334 target = 0.136872 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4023 r_free = 0.4023 target = 0.115484 restraints weight = 19759.153|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.118641 restraints weight = 12609.863|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.120813 restraints weight = 9196.858|
|-----------------------------------------------------------------------------|
r_work (final): 0.4089
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6956
moved from start:          0.6167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6335  Z= 0.141
  Angle     :  0.796  13.661   8547  Z= 0.384
  Chirality :  0.050   0.230    942
  Planarity :  0.004   0.046   1098
  Dihedral  :  5.443  21.572    848
  Min Nonbonded Distance : 2.584

Molprobity Statistics.
  All-atom Clashscore : 20.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.06 %
    Favored  : 90.94 %
  Rotamer:
    Outliers :  5.01 %
    Allowed  : 28.32 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.68 (0.31), residues: 762
  helix:  0.10 (0.32), residues: 302
  sheet: -1.36 (0.55), residues: 86
  loop : -2.12 (0.32), residues: 374

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.038   0.003   TRP A 939 
 HIS   0.004   0.001   HIS B 750 
 PHE   0.020   0.002   PHE B 924 
 TYR   0.014   0.001   TYR B 621 
 ARG   0.009   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04568 (  224)
  hydrogen bonds       : angle       5.81701 (  636)
  covalent geometry    : bond        0.00322 ( 6335)
  covalent geometry    : angle       0.79598 ( 8547)

*********************** 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
  168 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 134
  time to evaluate  : 0.782 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  711 ASP cc_start: 0.8132 (m-30) cc_final: 0.7751 (p0)
REVERT: A  774 MET cc_start: 0.7980 (tmm) cc_final: 0.6840 (tmm)
REVERT: A  785 MET cc_start: 0.5790 (mpp) cc_final: 0.5496 (mpp)
REVERT: A  926 ASP cc_start: 0.8331 (m-30) cc_final: 0.7537 (p0)
REVERT: B  886 PHE cc_start: 0.6791 (OUTLIER) cc_final: 0.6413 (t80)
REVERT: B  933 MET cc_start: 0.7737 (ppp) cc_final: 0.7370 (ppp)
  outliers start: 34
  outliers final: 31
  residues processed: 157
  average time/residue: 0.1818
  time to fit residues: 37.4697
Evaluate side-chains
  158 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 32
    poor density    : 126
  time to evaluate  : 0.734 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  637 HIS
Chi-restraints excluded: chain A residue  677 VAL
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  761 LEU
Chi-restraints excluded: chain A residue  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  834 TYR
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  946 ILE
Chi-restraints excluded: chain A residue  985 CYS
Chi-restraints excluded: chain A residue 1016 LEU
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  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  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  972 LEU
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  997 LEU
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 24 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 41 optimal weight:    0.0040
   chunk 13 optimal weight:    0.5980
   chunk 5 optimal weight:    1.9990
   chunk 74 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   chunk 49 optimal weight:    0.9980
   chunk 6 optimal weight:    1.9990
   chunk 48 optimal weight:    0.8980
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5992

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

Flipped N/Q/H residues before XYZ refinement:
B 762 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.138064 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.116991 restraints weight = 19424.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.4090 r_free = 0.4090 target = 0.120105 restraints weight = 12187.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.122292 restraints weight = 8794.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.4100
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6926
moved from start:          0.6337

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= 0.137
  Angle     :  0.803  13.521   8547  Z= 0.386
  Chirality :  0.051   0.214    942
  Planarity :  0.004   0.045   1098
  Dihedral  :  5.386  21.767    848
  Min Nonbonded Distance : 2.564

Molprobity Statistics.
  All-atom Clashscore : 20.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.87 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 28.91 %
    Favored  : 65.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.73 (0.31), residues: 762
  helix:  0.19 (0.32), residues: 299
  sheet: -1.90 (0.50), residues: 95
  loop : -2.11 (0.32), residues: 368

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP B 856 
 HIS   0.004   0.001   HIS B 750 
 PHE   0.019   0.002   PHE B 924 
 TYR   0.012   0.001   TYR B 621 
 ARG   0.008   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04477 (  224)
  hydrogen bonds       : angle       5.73364 (  636)
  covalent geometry    : bond        0.00312 ( 6335)
  covalent geometry    : angle       0.80269 ( 8547)

*********************** 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
  169 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 134
  time to evaluate  : 0.755 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  711 ASP cc_start: 0.8228 (m-30) cc_final: 0.7741 (p0)
REVERT: A  774 MET cc_start: 0.7879 (tmm) cc_final: 0.6597 (tmm)
REVERT: A  785 MET cc_start: 0.5770 (mpp) cc_final: 0.5504 (mpp)
REVERT: A  926 ASP cc_start: 0.8345 (m-30) cc_final: 0.7587 (p0)
REVERT: B  704 LYS cc_start: 0.8145 (tppt) cc_final: 0.7561 (tppt)
REVERT: B  886 PHE cc_start: 0.6895 (OUTLIER) cc_final: 0.6499 (t80)
REVERT: B  933 MET cc_start: 0.7711 (ppp) cc_final: 0.7341 (ppp)
  outliers start: 35
  outliers final: 32
  residues processed: 156
  average time/residue: 0.2373
  time to fit residues: 50.0792
Evaluate side-chains
  160 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 127
  time to evaluate  : 1.444 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  637 HIS
Chi-restraints excluded: chain A residue  677 VAL
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  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  834 TYR
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  946 ILE
Chi-restraints excluded: chain A residue  985 CYS
Chi-restraints excluded: chain A residue 1016 LEU
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  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  740 VAL
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  886 PHE
Chi-restraints excluded: chain B residue  911 PHE
Chi-restraints excluded: chain B residue  972 LEU
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  997 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 51 optimal weight:    0.7980
   chunk 73 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0010
   chunk 3 optimal weight:    0.1980
   chunk 63 optimal weight:   10.0000
   chunk 36 optimal weight:    8.9990
   chunk 29 optimal weight:   20.0000
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.1980
   chunk 35 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   overall best weight:    0.4388

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

Flipped N/Q/H residues before XYZ refinement:
A 676 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4363 r_free = 0.4363 target = 0.138952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.117768 restraints weight = 19490.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.120955 restraints weight = 12184.061|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4133 r_free = 0.4133 target = 0.123180 restraints weight = 8769.181|
|-----------------------------------------------------------------------------|
r_work (final): 0.4109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6915
moved from start:          0.6541

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   6335  Z= 0.136
  Angle     :  0.811  13.339   8547  Z= 0.388
  Chirality :  0.053   0.420    942
  Planarity :  0.004   0.048   1098
  Dihedral  :  5.387  22.071    848
  Min Nonbonded Distance : 2.570

Molprobity Statistics.
  All-atom Clashscore : 18.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.14 %
    Favored  : 91.86 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 29.94 %
    Favored  : 65.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.70 (0.31), residues: 762
  helix:  0.27 (0.32), residues: 297
  sheet: -1.90 (0.51), residues: 95
  loop : -2.12 (0.32), residues: 370

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.031   0.002   TRP B 835 
 HIS   0.004   0.001   HIS B 750 
 PHE   0.019   0.002   PHE B 924 
 TYR   0.013   0.001   TYR B 621 
 ARG   0.008   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04401 (  224)
  hydrogen bonds       : angle       5.73154 (  636)
  covalent geometry    : bond        0.00306 ( 6335)
  covalent geometry    : angle       0.81061 ( 8547)

********************** 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
  162 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 131
  time to evaluate  : 1.483 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  711 ASP cc_start: 0.8272 (m-30) cc_final: 0.7683 (p0)
REVERT: A  774 MET cc_start: 0.7869 (tmm) cc_final: 0.6723 (tmm)
REVERT: A  785 MET cc_start: 0.5767 (mpp) cc_final: 0.5506 (mpp)
REVERT: A  926 ASP cc_start: 0.8279 (m-30) cc_final: 0.7587 (p0)
REVERT: A  991 MET cc_start: 0.7427 (tpt) cc_final: 0.6890 (tpt)
REVERT: B  704 LYS cc_start: 0.8071 (tppt) cc_final: 0.7459 (tppt)
REVERT: B  766 ASP cc_start: 0.8490 (m-30) cc_final: 0.8213 (t0)
REVERT: B  873 ASP cc_start: 0.6268 (m-30) cc_final: 0.4996 (t0)
REVERT: B  886 PHE cc_start: 0.6924 (OUTLIER) cc_final: 0.6492 (t80)
REVERT: B  933 MET cc_start: 0.7689 (ppp) cc_final: 0.7310 (ppp)
REVERT: B  984 LYS cc_start: 0.7013 (mmtt) cc_final: 0.6681 (mmtp)
  outliers start: 31
  outliers final: 29
  residues processed: 154
  average time/residue: 0.2781
  time to fit residues: 59.2156
Evaluate side-chains
  158 residues out of total 680 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 128
  time to evaluate  : 2.645 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  637 HIS
Chi-restraints excluded: chain A residue  677 VAL
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  778 GLU
Chi-restraints excluded: chain A residue  821 ILE
Chi-restraints excluded: chain A residue  834 TYR
Chi-restraints excluded: chain A residue  836 LEU
Chi-restraints excluded: chain A residue  891 HIS
Chi-restraints excluded: chain A residue  907 HIS
Chi-restraints excluded: chain A residue  946 ILE
Chi-restraints excluded: chain A residue  985 CYS
Chi-restraints excluded: chain A residue 1016 LEU
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  670 SER
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  740 VAL
Chi-restraints excluded: chain B residue  782 VAL
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  972 LEU
Chi-restraints excluded: chain B residue  975 ILE
Chi-restraints excluded: chain B residue  997 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 21 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 33 optimal weight:   10.0000
   chunk 43 optimal weight:    0.8980
   chunk 22 optimal weight:    7.9990
   chunk 55 optimal weight:    6.9990
   chunk 59 optimal weight:    1.9990
   chunk 35 optimal weight:    0.7980
   chunk 61 optimal weight:    4.9990
   chunk 41 optimal weight:    0.9990
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.8782

-------------------------------------------------------------------------------
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 = 0.4371 r_free = 0.4371 target = 0.139093 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.118040 restraints weight = 19732.527|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4113 r_free = 0.4113 target = 0.121258 restraints weight = 12170.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4145 r_free = 0.4145 target = 0.123401 restraints weight = 8710.250|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6948
moved from start:          0.6689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.060   6335  Z= 0.137
  Angle     :  0.802  12.889   8547  Z= 0.385
  Chirality :  0.052   0.353    942
  Planarity :  0.004   0.051   1098
  Dihedral  :  5.320  21.688    848
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 19.84
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  7.74 %
    Favored  : 92.13 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 30.24 %
    Favored  : 64.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.57 (0.31), residues: 762
  helix:  0.29 (0.32), residues: 299
  sheet: -1.38 (0.56), residues: 83
  loop : -2.11 (0.31), residues: 380

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.033   0.002   TRP B 835 
 HIS   0.004   0.001   HIS B 750 
 PHE   0.020   0.002   PHE B 924 
 TYR   0.013   0.002   TYR B 627 
 ARG   0.008   0.000   ARG A 642 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04327 (  224)
  hydrogen bonds       : angle       5.69869 (  636)
  covalent geometry    : bond        0.00315 ( 6335)
  covalent geometry    : angle       0.80187 ( 8547)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3364.58 seconds
wall clock time: 62 minutes 29.07 seconds (3749.07 seconds total)