Starting phenix.real_space_refine
on Wed Jun 11 02:28:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gck_51231/06_2025/9gck_51231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gck_51231/06_2025/9gck_51231.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9gck_51231/06_2025/9gck_51231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gck_51231/06_2025/9gck_51231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gck_51231/06_2025/9gck_51231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gck_51231/06_2025/9gck_51231.cif"
  }
  resolution = 3.7
  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=   0.001
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P      90      5.49       5
     S      41      5.16       5
     C    7590      2.51       5
     N    2092      2.21       5
     O    2485      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 69 residue(s): 0.04s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 12298
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 3491
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 429, 3491
          Classifications: {'peptide': 429}
          Link IDs: {'PTRANS': 13, 'TRANS': 415}
    Chain: "B"
      Number of atoms: 2443
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 294, 2443
          Classifications: {'peptide': 294}
          Link IDs: {'PTRANS': 6, 'TRANS': 287}
    Chain: "C"
      Number of atoms: 1823
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 231, 1823
          Classifications: {'peptide': 231}
          Link IDs: {'PTRANS': 20, 'TRANS': 210}
    Chain: "D"
      Number of atoms: 2696
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 333, 2696
          Classifications: {'peptide': 333}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 309}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 1
          Unresolved non-hydrogen dihedrals: 1
    Chain: "E"
      Number of atoms: 900
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 900
          Classifications: {'DNA': 45}
          Link IDs: {'rna3p': 44}
    Chain: "F"
      Number of atoms: 945
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 45, 945
          Classifications: {'DNA': 45}
          Link IDs: {'rna3p': 44}
  Time building chain proxies: 7.92, per 1000 atoms: 0.64
  Number of scatterers: 12298
  At special positions: 0
  Unit cell: (89.598, 116.724, 160.29, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      41     16.00
     P      90     15.00
     O    2485      8.00
     N    2092      7.00
     C    7590      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: 3.35
  Conformation dependent library (CDL) restraints added in 1.5 seconds
  

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2460

  Finding SS restraints...
    Secondary structure from input PDB file:
      52 helices and 5 sheets defined
      50.4% alpha, 7.7% beta
      33 base pairs and 87 stacking pairs defined.
    Time for finding SS restraints: 4.55
  Creating SS restraints...
    Processing helix  chain 'A' and resid 739 through 758
      removed outlier: 4.211A  pdb=" N   GLN A 744 " --> pdb=" O   LYS A 740 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 761 through 766
    Processing helix  chain 'A' and resid 767 through 769
      No H-bonds generated for 'chain 'A' and resid 767 through 769'
    Processing helix  chain 'A' and resid 773 through 809
      removed outlier: 6.192A  pdb=" N   HIS A 790 " --> pdb=" O   VAL A 786 " (cutoff:3.500A)
      removed outlier: 7.957A  pdb=" N   SER A 791 " --> pdb=" O   ARG A 787 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   ARG A 794 " --> pdb=" O   HIS A 790 " (cutoff:3.500A)
      removed outlier: 4.508A  pdb=" N   ALA A 795 " --> pdb=" O   SER A 791 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 814 through 820
      removed outlier: 3.598A  pdb=" N   VAL A 818 " --> pdb=" O   SER A 814 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 822 through 838
    Processing helix  chain 'A' and resid 847 through 855
    Processing helix  chain 'A' and resid 874 through 885
    Processing helix  chain 'A' and resid 897 through 916
      removed outlier: 4.039A  pdb=" N   SER A 903 " --> pdb=" O   SER A 899 " (cutoff:3.500A)
      removed outlier: 4.378A  pdb=" N   TYR A 906 " --> pdb=" O   GLN A 902 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 923 through 927
      removed outlier: 4.146A  pdb=" N   GLU A 927 " --> pdb=" O   ARG A 923 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 923 through 927'
    Processing helix  chain 'A' and resid 933 through 947
    Processing helix  chain 'A' and resid 961 through 971
    Processing helix  chain 'A' and resid 972 through 991
      removed outlier: 3.882A  pdb=" N   PHE A 976 " --> pdb=" O   ASN A 972 " (cutoff:3.500A)
      removed outlier: 3.722A  pdb=" N   CYS A 984 " --> pdb=" O   PHE A 980 " (cutoff:3.500A)
      removed outlier: 4.688A  pdb=" N   LEU A 989 " --> pdb=" O   LYS A 985 " (cutoff:3.500A)
      removed outlier: 4.440A  pdb=" N   GLU A 991 " --> pdb=" O   ASN A 987 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1003 through 1016
      removed outlier: 4.557A  pdb=" N   ASP A1012 " --> pdb=" O   TRP A1008 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1041 through 1046
      removed outlier: 3.660A  pdb=" N   LEU A1045 " --> pdb=" O   ILE A1042 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1087 through 1105
      removed outlier: 4.265A  pdb=" N   PHE A1104 " --> pdb=" O   ASN A1100 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1109 through 1117
      removed outlier: 3.668A  pdb=" N   LEU A1113 " --> pdb=" O   THR A1109 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1122 through 1136
      removed outlier: 4.536A  pdb=" N   GLU A1128 " --> pdb=" O   HIS A1124 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   ILE A1129 " --> pdb=" O   GLU A1125 " (cutoff:3.500A)
      removed outlier: 3.609A  pdb=" N   TRP A1132 " --> pdb=" O   GLU A1128 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1143 through 1145
      No H-bonds generated for 'chain 'A' and resid 1143 through 1145'
    Processing helix  chain 'B' and resid 733 through 747
    Processing helix  chain 'B' and resid 752 through 765
      removed outlier: 3.502A  pdb=" N   VAL B 758 " --> pdb=" O   ASP B 754 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 765 through 770
    Processing helix  chain 'B' and resid 771 through 787
      removed outlier: 3.533A  pdb=" N   LEU B 787 " --> pdb=" O   LEU B 783 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 792 through 804
      removed outlier: 3.714A  pdb=" N   ASN B 804 " --> pdb=" O   ARG B 800 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 809 through 820
    Processing helix  chain 'B' and resid 823 through 825
      No H-bonds generated for 'chain 'B' and resid 823 through 825'
    Processing helix  chain 'B' and resid 826 through 832
      removed outlier: 3.785A  pdb=" N   LEU B 830 " --> pdb=" O   SER B 826 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 832 through 852
      removed outlier: 3.774A  pdb=" N   PHE B 838 " --> pdb=" O   ILE B 834 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 874 through 887
      removed outlier: 4.131A  pdb=" N   ILE B 880 " --> pdb=" O   TYR B 876 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 890 through 903
      removed outlier: 3.851A  pdb=" N   TYR B 897 " --> pdb=" O   SER B 893 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 908 through 924
      removed outlier: 3.774A  pdb=" N   ASN B 912 " --> pdb=" O   ASP B 908 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 930 through 953
      removed outlier: 3.507A  pdb=" N   HIS B 937 " --> pdb=" O   PHE B 933 " (cutoff:3.500A)
      removed outlier: 4.096A  pdb=" N   GLY B 938 " --> pdb=" O   GLN B 934 " (cutoff:3.500A)
      removed outlier: 3.666A  pdb=" N   TYR B 941 " --> pdb=" O   HIS B 937 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 954 through 957
    Processing helix  chain 'B' and resid 958 through 972
    Processing helix  chain 'B' and resid 974 through 988
      removed outlier: 3.749A  pdb=" N   TYR B 981 " --> pdb=" O   ILE B 977 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 992 through 1009
      removed outlier: 3.915A  pdb=" N   HIS B 997 " --> pdb=" O   LYS B 993 " (cutoff:3.500A)
      removed outlier: 3.939A  pdb=" N   ILE B1005 " --> pdb=" O   ASN B1001 " (cutoff:3.500A)
      removed outlier: 3.678A  pdb=" N   GLN B1008 " --> pdb=" O   ILE B1004 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 1011 through 1023
    Processing helix  chain 'C' and resid 48 through 59
      removed outlier: 4.066A  pdb=" N   LYS C  54 " --> pdb=" O   SER C  50 " (cutoff:3.500A)
      removed outlier: 3.951A  pdb=" N   CYS C  59 " --> pdb=" O   ALA C  55 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 60 through 71
      removed outlier: 4.176A  pdb=" N   LYS C  64 " --> pdb=" O   GLY C  60 " (cutoff:3.500A)
      removed outlier: 3.862A  pdb=" N   LYS C  66 " --> pdb=" O   ILE C  62 " (cutoff:3.500A)
      removed outlier: 4.105A  pdb=" N   PHE C  69 " --> pdb=" O   VAL C  65 " (cutoff:3.500A)
      removed outlier: 3.872A  pdb=" N   LYS C  70 " --> pdb=" O   LYS C  66 " (cutoff:3.500A)
      removed outlier: 3.673A  pdb=" N   GLU C  71 " --> pdb=" O   GLU C  67 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 124 through 129
    Processing helix  chain 'C' and resid 132 through 139
    Processing helix  chain 'C' and resid 173 through 183
    Processing helix  chain 'C' and resid 187 through 196
      removed outlier: 5.185A  pdb=" N   SER C 193 " --> pdb=" O   ASN C 189 " (cutoff:3.500A)
      removed outlier: 4.405A  pdb=" N   PHE C 194 " --> pdb=" O   ASN C 190 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 208 through 213
    Processing helix  chain 'D' and resid 14 through 18
    Processing helix  chain 'D' and resid 37 through 54
      removed outlier: 3.562A  pdb=" N   LEU D  54 " --> pdb=" O   TYR D  50 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 66 through 81
      removed outlier: 3.597A  pdb=" N   LEU D  70 " --> pdb=" O   PHE D  66 " (cutoff:3.500A)
      Proline residue:  D  75  - end of helix
      removed outlier: 3.813A  pdb=" N   LYS D  78 " --> pdb=" O   GLN D  74 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 88 through 91
    Processing helix  chain 'D' and resid 107 through 115
      removed outlier: 4.435A  pdb=" N   LYS D 113 " --> pdb=" O   GLU D 109 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   PHE D 114 " --> pdb=" O   ILE D 110 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 135 through 158
      Proline residue:  D 148  - end of helix
      removed outlier: 3.520A  pdb=" N   LYS D 156 " --> pdb=" O   GLU D 152 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 169 through 182
      removed outlier: 3.603A  pdb=" N   LEU D 176 " --> pdb=" O   SER D 172 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 351 through 354
    Processing sheet with id=AA1, first strand: chain 'A' and resid 858 through 860
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 858 through 860
    current: chain 'C' and resid 103 through 107
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 103 through 107
    current: chain 'C' and resid 147 through 162
  WARNING: can't find start of bonding for strands!
    previous: chain 'C' and resid 147 through 162
    current: chain 'D' and resid 328 through 331
      removed outlier: 4.396A  pdb=" N   LEU D 335 " --> pdb=" O   VAL D 432 " (cutoff:3.500A)
      removed outlier: 3.605A  pdb=" N   GLU D 337 " --> pdb=" O   SER D 430 " (cutoff:3.500A)
      removed outlier: 7.751A  pdb=" N   LYS D 424 " --> pdb=" O   LEU D 343 " (cutoff:3.500A)
      removed outlier: 10.844A  pdb=" N   GLY D 345 " --> pdb=" O   ARG D 422 " (cutoff:3.500A)
      removed outlier: 9.997A  pdb=" N   ARG D 422 " --> pdb=" O   GLY D 345 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 920 through 922
    Processing sheet with id=AA3, first strand: chain 'A' and resid 997 through 998
    Processing sheet with id=AA4, first strand: chain 'A' and resid 1139 through 1141
    Processing sheet with id=AA5, first strand: chain 'D' and resid 119 through 120
      removed outlier: 6.326A  pdb=" N   VAL D  84 " --> pdb=" O   SER D 120 " (cutoff:3.500A)
      removed outlier: 6.522A  pdb=" N   ALA D  61 " --> pdb=" O   TYR D  85 " (cutoff:3.500A)
      removed outlier: 7.170A  pdb=" N   LYS D 206 " --> pdb=" O   ASN D 241 " (cutoff:3.500A)
      removed outlier: 5.501A  pdb=" N   ASN D 241 " --> pdb=" O   LYS D 206 " (cutoff:3.500A)
      removed outlier: 7.459A  pdb=" N   GLU D 208 " --> pdb=" O   THR D 239 " (cutoff:3.500A)
      removed outlier: 6.249A  pdb=" N   THR D 239 " --> pdb=" O   GLU D 208 " (cutoff:3.500A)

    431 hydrogen bonds defined for protein.
    1251 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      66 hydrogen bonds
      132 hydrogen bond angles
      0 basepair planarities
      33 basepair parallelities
      87 stacking parallelities
  Total time for adding SS restraints: 4.54

  Time building geometry restraints manager: 3.72 seconds

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

  Histogram of bond lengths:
        1.18 -     1.32: 1985
        1.32 -     1.46: 3902
        1.46 -     1.61: 6685
        1.61 -     1.75: 105
        1.75 -     1.89: 72
  Bond restraints: 12749
  Sorted by residual:
  bond pdb=" CA  SER A1076 "
       pdb=" CB  SER A1076 "
    ideal  model  delta    sigma   weight residual
    1.530  1.443  0.086 1.69e-02 3.50e+03 2.61e+01
  bond pdb=" C   VAL A1080 "
       pdb=" O   VAL A1080 "
    ideal  model  delta    sigma   weight residual
    1.238  1.182  0.056 1.10e-02 8.26e+03 2.59e+01
  bond pdb=" C   TYR B1000 "
       pdb=" O   TYR B1000 "
    ideal  model  delta    sigma   weight residual
    1.236  1.178  0.058 1.15e-02 7.56e+03 2.55e+01
  bond pdb=" N   VAL D 104 "
       pdb=" CA  VAL D 104 "
    ideal  model  delta    sigma   weight residual
    1.454  1.493 -0.039 7.70e-03 1.69e+04 2.54e+01
  bond pdb=" C   ASN B 964 "
       pdb=" O   ASN B 964 "
    ideal  model  delta    sigma   weight residual
    1.237  1.180  0.057 1.16e-02 7.43e+03 2.40e+01
  ... (remaining 12744 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.31: 13894
        2.31 -     4.62: 3344
        4.62 -     6.93: 367
        6.93 -     9.24: 21
        9.24 -    11.55: 6
  Bond angle restraints: 17632
  Sorted by residual:
  angle pdb=" CA  PHE B 933 "
        pdb=" CB  PHE B 933 "
        pdb=" CG  PHE B 933 "
      ideal   model   delta    sigma   weight residual
     113.80  124.03  -10.23 1.00e+00 1.00e+00 1.05e+02
  angle pdb=" C4'  DT E  30 "
        pdb=" C3'  DT E  30 "
        pdb=" O3'  DT E  30 "
      ideal   model   delta    sigma   weight residual
     110.00   99.28   10.72 1.50e+00 4.44e-01 5.11e+01
  angle pdb=" CA  ASN B 964 "
        pdb=" CB  ASN B 964 "
        pdb=" CG  ASN B 964 "
      ideal   model   delta    sigma   weight residual
     112.60  105.87    6.73 1.00e+00 1.00e+00 4.53e+01
  angle pdb=" C   LEU C 140 "
        pdb=" N   LYS C 141 "
        pdb=" CA  LYS C 141 "
      ideal   model   delta    sigma   weight residual
     120.38  129.13   -8.75 1.37e+00 5.33e-01 4.08e+01
  angle pdb=" C   ASN C  44 "
        pdb=" CA  ASN C  44 "
        pdb=" CB  ASN C  44 "
      ideal   model   delta    sigma   weight residual
     112.07  121.26   -9.19 1.48e+00 4.57e-01 3.85e+01
  ... (remaining 17627 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.93: 6066
       17.93 -    35.86: 963
       35.86 -    53.79: 355
       53.79 -    71.72: 198
       71.72 -    89.65: 10
  Dihedral angle restraints: 7592
    sinusoidal: 3794
      harmonic: 3798
  Sorted by residual:
  dihedral pdb=" CA  LEU D 343 "
           pdb=" C   LEU D 343 "
           pdb=" N   VAL D 344 "
           pdb=" CA  VAL D 344 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  147.73   32.27     0      5.00e+00 4.00e-02 4.17e+01
  dihedral pdb=" CA  ARG C  35 "
           pdb=" C   ARG C  35 "
           pdb=" N   ILE C  36 "
           pdb=" CA  ILE C  36 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -148.21  -31.79     0      5.00e+00 4.00e-02 4.04e+01
  dihedral pdb=" CA  TYR C 242 "
           pdb=" C   TYR C 242 "
           pdb=" N   LYS C 243 "
           pdb=" CA  LYS C 243 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  148.55   31.45     0      5.00e+00 4.00e-02 3.96e+01
  ... (remaining 7589 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.128: 1610
       0.128 -    0.255: 250
       0.255 -    0.383: 43
       0.383 -    0.510: 52
       0.510 -    0.638: 2
  Chirality restraints: 1957
  Sorted by residual:
  chirality pdb=" P    DA F   1 "
            pdb=" OP1  DA F   1 "
            pdb=" OP2  DA F   1 "
            pdb=" O5'  DA F   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.98   -0.64 2.00e-01 2.50e+01 1.02e+01
  chirality pdb=" P    DT E   1 "
            pdb=" OP1  DT E   1 "
            pdb=" OP2  DT E   1 "
            pdb=" O5'  DT E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.97   -0.62 2.00e-01 2.50e+01 9.67e+00
  chirality pdb=" P    DT E  28 "
            pdb=" OP1  DT E  28 "
            pdb=" OP2  DT E  28 "
            pdb=" O5'  DT E  28 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.35   -2.85   -0.50 2.00e-01 2.50e+01 6.29e+00
  ... (remaining 1954 not shown)

  Planarity restraints: 1931
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 943 "    0.126 2.00e-02 2.50e+03   7.04e-02 9.91e+01
        pdb=" CG  TYR B 943 "   -0.055 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 943 "   -0.029 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 943 "   -0.056 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 943 "   -0.048 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 943 "   -0.025 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 943 "   -0.027 2.00e-02 2.50e+03
        pdb=" OH  TYR B 943 "    0.114 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 886 "    0.095 2.00e-02 2.50e+03   4.88e-02 4.76e+01
        pdb=" CG  TYR B 886 "   -0.059 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 886 "   -0.037 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 886 "   -0.047 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 886 "   -0.003 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 886 "    0.007 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 886 "   -0.008 2.00e-02 2.50e+03
        pdb=" OH  TYR B 886 "    0.052 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B 963 "   -0.094 2.00e-02 2.50e+03   4.85e-02 4.70e+01
        pdb=" CG  TYR B 963 "    0.076 2.00e-02 2.50e+03
        pdb=" CD1 TYR B 963 "    0.028 2.00e-02 2.50e+03
        pdb=" CD2 TYR B 963 "    0.025 2.00e-02 2.50e+03
        pdb=" CE1 TYR B 963 "    0.012 2.00e-02 2.50e+03
        pdb=" CE2 TYR B 963 "    0.015 2.00e-02 2.50e+03
        pdb=" CZ  TYR B 963 "   -0.016 2.00e-02 2.50e+03
        pdb=" OH  TYR B 963 "   -0.046 2.00e-02 2.50e+03
  ... (remaining 1928 not shown)

  Histogram of nonbonded interaction distances:
        1.95 -     2.54: 33
        2.54 -     3.13: 9360
        3.13 -     3.72: 20085
        3.72 -     4.31: 30106
        4.31 -     4.90: 45890
  Nonbonded interactions: 105474
  Sorted by model distance:
  nonbonded pdb=" NZ  LYS B 811 "
            pdb=" O   SER C 197 "
     model   vdw
     1.954 3.120
  nonbonded pdb=" OG  SER C  38 "
            pdb=" OE2 GLU D 347 "
     model   vdw
     2.265 3.040
  nonbonded pdb=" OH  TYR B 879 "
            pdb=" O   PRO C 228 "
     model   vdw
     2.276 3.040
  nonbonded pdb=" NE2 GLN B 814 "
            pdb=" O   GLN C 226 "
     model   vdw
     2.280 3.120
  nonbonded pdb=" OD1 ASN A1054 "
            pdb=" NZ  LYS B 947 "
     model   vdw
     2.286 3.120
  ... (remaining 105469 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=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:             2.710
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.010
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.580
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     34.660
  Find NCS groups from input model:        0.150
  Set up NCS constraints:                  0.050
  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:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.510
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6969
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      :  0.015   0.091  12749  Z= 1.033
  Angle     :  1.892  11.545  17632  Z= 1.274
  Chirality :  0.122   0.638   1957
  Planarity :  0.010   0.153   1931
  Dihedral  : 21.024  89.645   5132
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 10.65
  Ramachandran Plot:
    Outliers :  0.24 %
    Allowed  :  5.03 %
    Favored  : 94.74 %
  Rotamer:
    Outliers :  0.77 %
    Allowed  :  3.33 %
    Favored  : 95.90 %
  Cbeta Deviations :  0.33 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.49 %

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: -2.69 (0.21), residues: 1273
  helix: -2.43 (0.16), residues: 547
  sheet: -0.46 (0.56), residues: 64
  loop : -1.23 (0.23), residues: 662

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.012   TRP A1153 
 HIS   0.027   0.005   HIS A1151 
 PHE   0.055   0.009   PHE D 350 
 TYR   0.126   0.014   TYR B 943 
 ARG   0.028   0.002   ARG A 923 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.19361 (  497)
  hydrogen bonds       : angle       8.39377 ( 1383)
  covalent geometry    : bond        0.01457 (12749)
  covalent geometry    : angle       1.89227 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  212 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 203
  time to evaluate  : 1.332 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6571 (mtm) cc_final: 0.5509 (ttp)
REVERT: A 1033 LEU cc_start: 0.8015 (mp) cc_final: 0.7518 (tp)
REVERT: A 1040 PHE cc_start: 0.6134 (t80) cc_final: 0.5763 (t80)
REVERT: A 1045 LEU cc_start: 0.6994 (OUTLIER) cc_final: 0.6537 (tt)
REVERT: A 1068 LYS cc_start: 0.9081 (mptt) cc_final: 0.8732 (tmtt)
REVERT: A 1069 VAL cc_start: 0.7888 (t) cc_final: 0.7647 (t)
REVERT: A 1097 MET cc_start: 0.9627 (ttp) cc_final: 0.9303 (tmm)
REVERT: B  740 MET cc_start: 0.6936 (mmp) cc_final: 0.6433 (mmt)
REVERT: B  777 MET cc_start: 0.5755 (ttm) cc_final: 0.5471 (ttt)
REVERT: B  793 GLU cc_start: 0.8960 (mt-10) cc_final: 0.8652 (tm-30)
REVERT: B  870 ASN cc_start: 0.9605 (m-40) cc_final: 0.9337 (t0)
REVERT: B  871 LYS cc_start: 0.8782 (mttt) cc_final: 0.8354 (ptmm)
REVERT: B  910 MET cc_start: 0.7625 (mmm) cc_final: 0.7204 (mmm)
REVERT: C   79 HIS cc_start: 0.8358 (m-70) cc_final: 0.7978 (m90)
REVERT: C  116 ILE cc_start: 0.8724 (mt) cc_final: 0.8512 (mm)
REVERT: C  204 GLN cc_start: 0.9396 (mt0) cc_final: 0.9107 (mm-40)
REVERT: C  233 LEU cc_start: 0.8461 (mt) cc_final: 0.8212 (mt)
REVERT: D   55 ASP cc_start: 0.8666 (m-30) cc_final: 0.8384 (m-30)
REVERT: D  141 MET cc_start: 0.8862 (mmm) cc_final: 0.8579 (mtt)
REVERT: D  204 LEU cc_start: 0.6800 (tp) cc_final: 0.6393 (tp)
REVERT: D  239 THR cc_start: 0.2250 (p) cc_final: 0.1807 (p)
REVERT: D  323 GLU cc_start: 0.8586 (pm20) cc_final: 0.8254 (mp0)
  outliers start: 9
  outliers final: 3
  residues processed: 211
  average time/residue: 0.3172
  time to fit residues: 89.7363
Evaluate side-chains
  134 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 130
  time to evaluate  : 1.338 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  816 ARG
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1128 GLU
Chi-restraints excluded: chain B residue  836 GLN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 113 optimal weight:   20.0000
   chunk 102 optimal weight:    4.9990
   chunk 56 optimal weight:    0.9990
   chunk 34 optimal weight:    3.9990
   chunk 69 optimal weight:    0.9980
   chunk 54 optimal weight:   10.0000
   chunk 105 optimal weight:    5.9990
   chunk 40 optimal weight:    0.8980
   chunk 64 optimal weight:    0.9980
   chunk 78 optimal weight:    0.4980
   chunk 122 optimal weight:    6.9990
   overall best weight:    0.8782

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

Flipped N/Q/H residues before XYZ refinement:
A 987 ASN
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D  57 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4898 r_free = 0.4898 target = 0.126429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4469 r_free = 0.4469 target = 0.103859 restraints weight = 53058.376|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4544 r_free = 0.4544 target = 0.107240 restraints weight = 25169.565|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4557 r_free = 0.4557 target = 0.107644 restraints weight = 14474.505|
|-----------------------------------------------------------------------------|
r_work (final): 0.4487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5859
moved from start:          0.2967

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.052  12749  Z= 0.188
  Angle     :  0.766   8.100  17632  Z= 0.426
  Chirality :  0.045   0.237   1957
  Planarity :  0.005   0.051   1931
  Dihedral  : 22.831  79.223   2494
  Min Nonbonded Distance : 2.424

Molprobity Statistics.
  All-atom Clashscore : 12.70
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.59 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  :  8.79 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.02 (0.22), residues: 1273
  helix: -0.59 (0.20), residues: 569
  sheet: -0.16 (0.53), residues: 85
  loop : -0.69 (0.25), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.025   0.002   TRP A 800 
 HIS   0.010   0.001   HIS B 919 
 PHE   0.034   0.002   PHE B 839 
 TYR   0.034   0.002   TYR B1000 
 ARG   0.007   0.001   ARG C 177 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05692 (  497)
  hydrogen bonds       : angle       5.39234 ( 1383)
  covalent geometry    : bond        0.00421 (12749)
  covalent geometry    : angle       0.76588 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  172 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 149
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6035 (mtm) cc_final: 0.5351 (ttt)
REVERT: A  826 LEU cc_start: 0.8641 (mm) cc_final: 0.8172 (pp)
REVERT: A  833 PHE cc_start: 0.8749 (m-80) cc_final: 0.7931 (m-80)
REVERT: A  872 MET cc_start: 0.4836 (mtm) cc_final: 0.4170 (mtm)
REVERT: A 1018 LEU cc_start: 0.6113 (mp) cc_final: 0.5464 (tp)
REVERT: A 1069 VAL cc_start: 0.6915 (t) cc_final: 0.6618 (m)
REVERT: B  779 LYS cc_start: 0.8308 (mttt) cc_final: 0.8095 (mttm)
REVERT: B  871 LYS cc_start: 0.8350 (mttt) cc_final: 0.7951 (pttp)
REVERT: C   79 HIS cc_start: 0.7373 (m-70) cc_final: 0.7172 (m90)
REVERT: C  204 GLN cc_start: 0.8575 (mt0) cc_final: 0.8068 (mp10)
REVERT: C  235 MET cc_start: 0.3032 (mmm) cc_final: 0.2812 (mmm)
REVERT: C  241 LEU cc_start: 0.8990 (tp) cc_final: 0.8789 (mt)
REVERT: D  158 TYR cc_start: 0.6110 (m-80) cc_final: 0.5303 (m-80)
REVERT: D  188 MET cc_start: 0.0388 (mmm) cc_final: -0.1671 (tpt)
REVERT: D  205 ASP cc_start: 0.8310 (OUTLIER) cc_final: 0.7959 (p0)
  outliers start: 23
  outliers final: 9
  residues processed: 163
  average time/residue: 0.2812
  time to fit residues: 64.5540
Evaluate side-chains
  120 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 110
  time to evaluate  : 1.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  781 TRP
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain B residue  836 GLN
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  205 ASP
Chi-restraints excluded: chain D residue  297 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 4 optimal weight:    7.9990
   chunk 50 optimal weight:    0.9980
   chunk 32 optimal weight:    6.9990
   chunk 20 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 100 optimal weight:   10.0000
   chunk 103 optimal weight:   30.0000
   chunk 130 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 7 optimal weight:    8.9990
   chunk 3 optimal weight:    6.9990
   overall best weight:    3.1386

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

Flipped N/Q/H residues before XYZ refinement:
A 877 GLN
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 836 GLN
B 946 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4645 r_free = 0.4645 target = 0.117741 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4158 r_free = 0.4158 target = 0.092044 restraints weight = 56541.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4215 r_free = 0.4215 target = 0.094641 restraints weight = 31460.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.4251 r_free = 0.4251 target = 0.096314 restraints weight = 21129.879|
|-----------------------------------------------------------------------------|
r_work (final): 0.4203
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6186
moved from start:          0.3881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.079  12749  Z= 0.247
  Angle     :  0.772   7.835  17632  Z= 0.422
  Chirality :  0.045   0.225   1957
  Planarity :  0.005   0.063   1931
  Dihedral  : 23.113  66.849   2485
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 20.04
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.14 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 11.77 %
    Favored  : 85.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.08 %

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: -1.01 (0.23), residues: 1273
  helix: -0.59 (0.20), residues: 573
  sheet: -0.17 (0.55), residues: 82
  loop : -0.68 (0.25), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 830 
 HIS   0.013   0.002   HIS B 919 
 PHE   0.025   0.002   PHE B 839 
 TYR   0.034   0.003   TYR B1000 
 ARG   0.006   0.001   ARG A 983 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05981 (  497)
  hydrogen bonds       : angle       5.50129 ( 1383)
  covalent geometry    : bond        0.00565 (12749)
  covalent geometry    : angle       0.77193 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  153 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 119
  time to evaluate  : 1.344 
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  803 MET cc_start: 0.6070 (mtm) cc_final: 0.5146 (ttp)
REVERT: A  826 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8244 (pp)
REVERT: A  833 PHE cc_start: 0.8971 (m-80) cc_final: 0.8434 (m-80)
REVERT: A 1033 LEU cc_start: 0.7305 (mp) cc_final: 0.6988 (mt)
REVERT: B  779 LYS cc_start: 0.8374 (mttt) cc_final: 0.8154 (mttm)
REVERT: B  871 LYS cc_start: 0.8548 (mttt) cc_final: 0.8066 (pttp)
REVERT: C   79 HIS cc_start: 0.7614 (m-70) cc_final: 0.7348 (m90)
REVERT: C  116 ILE cc_start: 0.7917 (mm) cc_final: 0.7707 (mm)
REVERT: C  204 GLN cc_start: 0.8804 (mt0) cc_final: 0.8307 (mp10)
REVERT: D  141 MET cc_start: 0.8181 (mtt) cc_final: 0.7735 (mmm)
REVERT: D  158 TYR cc_start: 0.7023 (m-80) cc_final: 0.6552 (m-80)
REVERT: D  188 MET cc_start: -0.0286 (mmm) cc_final: -0.1649 (tpt)
REVERT: D  252 GLU cc_start: 0.7774 (tt0) cc_final: 0.7514 (pt0)
  outliers start: 34
  outliers final: 20
  residues processed: 140
  average time/residue: 0.2683
  time to fit residues: 53.9077
Evaluate side-chains
  123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 102
  time to evaluate  : 1.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  781 TRP
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain D residue  204 LEU
Chi-restraints excluded: chain D residue  297 SER
Chi-restraints excluded: chain D residue  310 GLU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 122 optimal weight:    5.9990
   chunk 43 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 129 optimal weight:   10.0000
   chunk 83 optimal weight:    6.9990
   chunk 30 optimal weight:    0.1980
   chunk 4 optimal weight:    4.9990
   chunk 67 optimal weight:    4.9990
   chunk 130 optimal weight:    9.9990
   chunk 3 optimal weight:   10.0000
   chunk 72 optimal weight:    0.9980
   overall best weight:    2.2184

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

Flipped N/Q/H residues before XYZ refinement:
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4668 r_free = 0.4668 target = 0.119266 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4187 r_free = 0.4187 target = 0.094194 restraints weight = 56649.266|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4243 r_free = 0.4243 target = 0.096783 restraints weight = 31527.778|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4281 r_free = 0.4281 target = 0.098497 restraints weight = 20772.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.4224
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6130
moved from start:          0.4408

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066  12749  Z= 0.196
  Angle     :  0.696   7.356  17632  Z= 0.379
  Chirality :  0.043   0.241   1957
  Planarity :  0.005   0.058   1931
  Dihedral  : 23.113  70.714   2482
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 17.95
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.30 %
    Favored  : 96.62 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 13.23 %
    Favored  : 84.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.23), residues: 1273
  helix: -0.43 (0.20), residues: 580
  sheet: -0.39 (0.57), residues: 82
  loop : -0.66 (0.26), residues: 611

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP D  93 
 HIS   0.011   0.001   HIS B 919 
 PHE   0.024   0.002   PHE C 249 
 TYR   0.023   0.002   TYR B1000 
 ARG   0.007   0.001   ARG A 784 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04984 (  497)
  hydrogen bonds       : angle       5.24470 ( 1383)
  covalent geometry    : bond        0.00445 (12749)
  covalent geometry    : angle       0.69645 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 1.231 
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  803 MET cc_start: 0.6121 (mtm) cc_final: 0.5504 (ttt)
REVERT: A  826 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8263 (pp)
REVERT: A  833 PHE cc_start: 0.9042 (m-80) cc_final: 0.8059 (m-80)
REVERT: A  872 MET cc_start: 0.5271 (mtm) cc_final: 0.5064 (ttm)
REVERT: A 1033 LEU cc_start: 0.7353 (mp) cc_final: 0.6829 (tp)
REVERT: A 1104 PHE cc_start: 0.7290 (m-80) cc_final: 0.6791 (m-80)
REVERT: A 1135 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7735 (mt-10)
REVERT: B  740 MET cc_start: 0.4922 (mmm) cc_final: 0.4099 (mmt)
REVERT: B  779 LYS cc_start: 0.8311 (mttt) cc_final: 0.8080 (tttm)
REVERT: B  871 LYS cc_start: 0.8578 (mttt) cc_final: 0.8092 (pttp)
REVERT: B  927 LEU cc_start: 0.5617 (OUTLIER) cc_final: 0.5233 (mt)
REVERT: C   79 HIS cc_start: 0.7532 (m-70) cc_final: 0.7213 (m90)
REVERT: C  204 GLN cc_start: 0.8740 (mt0) cc_final: 0.8218 (mp10)
REVERT: D  141 MET cc_start: 0.8104 (mtt) cc_final: 0.7772 (mpp)
REVERT: D  158 TYR cc_start: 0.7056 (m-80) cc_final: 0.6712 (m-80)
REVERT: D  188 MET cc_start: -0.0168 (mmm) cc_final: -0.0670 (tpt)
REVERT: D  310 GLU cc_start: 0.7297 (mt-10) cc_final: 0.6843 (tp30)
  outliers start: 29
  outliers final: 16
  residues processed: 131
  average time/residue: 0.2367
  time to fit residues: 45.5309
Evaluate side-chains
  116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 98
  time to evaluate  : 1.241 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  863 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1012 ASP
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain D residue  190 LEU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 3 optimal weight:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 81 optimal weight:    3.9990
   chunk 126 optimal weight:    0.4980
   chunk 120 optimal weight:    6.9990
   chunk 25 optimal weight:    1.9990
   chunk 130 optimal weight:    9.9990
   chunk 129 optimal weight:   10.0000
   chunk 43 optimal weight:    8.9990
   overall best weight:    2.6988

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

Flipped N/Q/H residues before XYZ refinement:
A1000 GLN
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1017 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4644 r_free = 0.4644 target = 0.117951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4159 r_free = 0.4159 target = 0.093025 restraints weight = 56557.957|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.095610 restraints weight = 31103.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4255 r_free = 0.4255 target = 0.097282 restraints weight = 20587.942|
|-----------------------------------------------------------------------------|
r_work (final): 0.4195
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6173
moved from start:          0.4912

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  12749  Z= 0.218
  Angle     :  0.717   8.160  17632  Z= 0.386
  Chirality :  0.043   0.237   1957
  Planarity :  0.005   0.060   1931
  Dihedral  : 23.203  71.577   2482
  Min Nonbonded Distance : 2.555

Molprobity Statistics.
  All-atom Clashscore : 19.58
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.01 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 14.93 %
    Favored  : 82.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.23), residues: 1273
  helix: -0.34 (0.21), residues: 572
  sheet: -0.29 (0.61), residues: 71
  loop : -0.65 (0.25), residues: 630

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.043   0.002   TRP A 830 
 HIS   0.011   0.002   HIS B 919 
 PHE   0.018   0.002   PHE C 249 
 TYR   0.027   0.002   TYR B 945 
 ARG   0.005   0.001   ARG A1039 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05302 (  497)
  hydrogen bonds       : angle       5.38283 ( 1383)
  covalent geometry    : bond        0.00495 (12749)
  covalent geometry    : angle       0.71669 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 107
  time to evaluate  : 1.243 
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  784 ARG cc_start: 0.7827 (ptt90) cc_final: 0.7361 (ptt90)
REVERT: A  788 MET cc_start: 0.7321 (ppp) cc_final: 0.5858 (tpp)
REVERT: A  803 MET cc_start: 0.6156 (mtm) cc_final: 0.5450 (ptm)
REVERT: A  826 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8349 (pp)
REVERT: A  833 PHE cc_start: 0.9117 (m-80) cc_final: 0.8843 (m-80)
REVERT: A 1021 MET cc_start: 0.5172 (OUTLIER) cc_final: 0.4857 (mtm)
REVERT: A 1104 PHE cc_start: 0.7158 (m-80) cc_final: 0.6784 (m-80)
REVERT: A 1135 GLU cc_start: 0.8085 (mm-30) cc_final: 0.7801 (mt-10)
REVERT: B  777 MET cc_start: 0.5892 (ttp) cc_final: 0.5590 (ttp)
REVERT: B  779 LYS cc_start: 0.8322 (mttt) cc_final: 0.8100 (mttm)
REVERT: B  871 LYS cc_start: 0.8712 (mttt) cc_final: 0.8236 (pttp)
REVERT: B  927 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5665 (mt)
REVERT: C   79 HIS cc_start: 0.7617 (m-70) cc_final: 0.7328 (m90)
REVERT: C  204 GLN cc_start: 0.8817 (mt0) cc_final: 0.8276 (mp10)
REVERT: D   93 TRP cc_start: 0.6901 (t60) cc_final: 0.6657 (t60)
REVERT: D  141 MET cc_start: 0.7983 (mtt) cc_final: 0.7648 (mpp)
REVERT: D  158 TYR cc_start: 0.7050 (m-80) cc_final: 0.6714 (m-80)
REVERT: D  178 MET cc_start: 0.7196 (mmm) cc_final: 0.6679 (mmt)
REVERT: D  188 MET cc_start: 0.0488 (mmm) cc_final: 0.0056 (tpt)
REVERT: D  310 GLU cc_start: 0.7549 (mt-10) cc_final: 0.7079 (tp30)
  outliers start: 35
  outliers final: 21
  residues processed: 131
  average time/residue: 0.2464
  time to fit residues: 47.0330
Evaluate side-chains
  125 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 101
  time to evaluate  : 1.350 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1000 GLN
Chi-restraints excluded: chain A residue 1012 ASP
Chi-restraints excluded: chain A residue 1021 MET
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1069 VAL
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain D residue  298 VAL
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 62 optimal weight:    0.7980
   chunk 35 optimal weight:    0.4980
   chunk 101 optimal weight:    5.9990
   chunk 118 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 121 optimal weight:    0.9980
   chunk 19 optimal weight:    0.8980
   chunk 3 optimal weight:   10.0000
   chunk 97 optimal weight:   20.0000
   chunk 24 optimal weight:    0.9980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A1114 GLN
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B1017 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4703 r_free = 0.4703 target = 0.121215 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.095902 restraints weight = 57193.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4292 r_free = 0.4292 target = 0.098613 restraints weight = 31478.305|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.4335 r_free = 0.4335 target = 0.100507 restraints weight = 20768.254|
|-----------------------------------------------------------------------------|
r_work (final): 0.4273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6061
moved from start:          0.5259

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049  12749  Z= 0.148
  Angle     :  0.639   7.329  17632  Z= 0.348
  Chirality :  0.041   0.202   1957
  Planarity :  0.004   0.057   1931
  Dihedral  : 22.966  72.673   2482
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 15.93
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.06 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 16.98 %
    Favored  : 81.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.43 (0.23), residues: 1273
  helix:  0.03 (0.21), residues: 577
  sheet: -0.37 (0.61), residues: 72
  loop : -0.45 (0.26), residues: 624

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.062   0.002   TRP A 830 
 HIS   0.009   0.001   HIS B 919 
 PHE   0.027   0.002   PHE C 166 
 TYR   0.023   0.002   TYR B 943 
 ARG   0.008   0.000   ARG A1043 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04228 (  497)
  hydrogen bonds       : angle       5.02252 ( 1383)
  covalent geometry    : bond        0.00336 (12749)
  covalent geometry    : angle       0.63941 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 119
  time to evaluate  : 1.556 
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  752 VAL cc_start: 0.7903 (t) cc_final: 0.7645 (t)
REVERT: A  788 MET cc_start: 0.7383 (ppp) cc_final: 0.6574 (ppp)
REVERT: A  803 MET cc_start: 0.5967 (mtm) cc_final: 0.5039 (ptm)
REVERT: A  826 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8297 (pp)
REVERT: A  827 LEU cc_start: 0.8537 (mt) cc_final: 0.8023 (mt)
REVERT: A  833 PHE cc_start: 0.9067 (m-80) cc_final: 0.8805 (m-80)
REVERT: A 1026 MET cc_start: 0.7572 (pmm) cc_final: 0.7072 (pmm)
REVERT: A 1104 PHE cc_start: 0.7019 (m-80) cc_final: 0.6611 (m-80)
REVERT: A 1131 LYS cc_start: 0.7700 (mmmm) cc_final: 0.7167 (tmmt)
REVERT: A 1135 GLU cc_start: 0.7927 (mm-30) cc_final: 0.7640 (mt-10)
REVERT: B  779 LYS cc_start: 0.8180 (mttt) cc_final: 0.7874 (mttm)
REVERT: B  871 LYS cc_start: 0.8699 (mttt) cc_final: 0.8216 (pttp)
REVERT: B  927 LEU cc_start: 0.5748 (OUTLIER) cc_final: 0.5445 (mt)
REVERT: C   79 HIS cc_start: 0.7374 (m-70) cc_final: 0.7118 (m90)
REVERT: C  204 GLN cc_start: 0.8584 (mt0) cc_final: 0.8093 (mp10)
REVERT: D   93 TRP cc_start: 0.6896 (t60) cc_final: 0.6689 (t60)
REVERT: D  141 MET cc_start: 0.7939 (mtt) cc_final: 0.7647 (mpp)
REVERT: D  188 MET cc_start: -0.0149 (mmm) cc_final: -0.1483 (tpt)
REVERT: D  310 GLU cc_start: 0.7607 (mt-10) cc_final: 0.7210 (tt0)
  outliers start: 21
  outliers final: 14
  residues processed: 132
  average time/residue: 0.2922
  time to fit residues: 55.2382
Evaluate side-chains
  118 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 1.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain B residue  970 HIS
Chi-restraints excluded: chain B residue 1017 HIS
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 57 optimal weight:    0.0870
   chunk 74 optimal weight:    9.9990
   chunk 11 optimal weight:    0.9990
   chunk 6 optimal weight:   10.0000
   chunk 101 optimal weight:    0.0770
   chunk 40 optimal weight:    2.9990
   chunk 123 optimal weight:    6.9990
   chunk 33 optimal weight:    0.2980
   chunk 81 optimal weight:    4.9990
   chunk 104 optimal weight:    0.5980
   chunk 115 optimal weight:    0.8980
   overall best weight:    0.3916

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

Flipped N/Q/H residues before XYZ refinement:
B1017 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4719 r_free = 0.4719 target = 0.122327 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.4270 r_free = 0.4270 target = 0.097596 restraints weight = 56847.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.100231 restraints weight = 31977.881|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.102033 restraints weight = 21125.152|
|-----------------------------------------------------------------------------|
r_work (final): 0.4310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5993
moved from start:          0.5599

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051  12749  Z= 0.140
  Angle     :  0.633  10.140  17632  Z= 0.343
  Chirality :  0.041   0.205   1957
  Planarity :  0.004   0.059   1931
  Dihedral  : 22.792  71.591   2482
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 15.77
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.06 %
    Favored  : 96.86 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 17.06 %
    Favored  : 81.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.20 (0.24), residues: 1273
  helix:  0.28 (0.21), residues: 576
  sheet: -0.48 (0.59), residues: 79
  loop : -0.36 (0.26), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.002   TRP A 830 
 HIS   0.018   0.002   HIS B1017 
 PHE   0.033   0.002   PHE D 150 
 TYR   0.024   0.002   TYR B 943 
 ARG   0.008   0.000   ARG C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04065 (  497)
  hydrogen bonds       : angle       4.87953 ( 1383)
  covalent geometry    : bond        0.00315 (12749)
  covalent geometry    : angle       0.63291 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 108
  time to evaluate  : 1.241 
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  788 MET cc_start: 0.7531 (ppp) cc_final: 0.5651 (tpp)
REVERT: A  790 HIS cc_start: 0.4792 (m-70) cc_final: 0.4191 (m170)
REVERT: A  803 MET cc_start: 0.5872 (mtm) cc_final: 0.4967 (ptm)
REVERT: A  826 LEU cc_start: 0.8614 (OUTLIER) cc_final: 0.8228 (pp)
REVERT: A  827 LEU cc_start: 0.8481 (mt) cc_final: 0.7980 (mt)
REVERT: A  833 PHE cc_start: 0.8987 (m-80) cc_final: 0.8744 (m-80)
REVERT: A 1026 MET cc_start: 0.7538 (pmm) cc_final: 0.6610 (pmm)
REVERT: A 1104 PHE cc_start: 0.6993 (m-80) cc_final: 0.6601 (m-80)
REVERT: A 1131 LYS cc_start: 0.7632 (mmmm) cc_final: 0.7054 (tmmt)
REVERT: A 1135 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7541 (mt-10)
REVERT: B  779 LYS cc_start: 0.8163 (mttt) cc_final: 0.7881 (mttm)
REVERT: B  871 LYS cc_start: 0.8665 (mttt) cc_final: 0.8178 (pttp)
REVERT: B  927 LEU cc_start: 0.5803 (OUTLIER) cc_final: 0.5521 (mt)
REVERT: C   79 HIS cc_start: 0.7444 (m-70) cc_final: 0.7114 (m90)
REVERT: C  204 GLN cc_start: 0.8471 (mt0) cc_final: 0.7946 (mp10)
REVERT: D  141 MET cc_start: 0.7909 (mtt) cc_final: 0.7621 (mpp)
REVERT: D  188 MET cc_start: -0.0072 (mmm) cc_final: -0.1466 (tpt)
REVERT: D  310 GLU cc_start: 0.7680 (mt-10) cc_final: 0.7322 (tt0)
  outliers start: 21
  outliers final: 14
  residues processed: 121
  average time/residue: 0.3620
  time to fit residues: 64.7430
Evaluate side-chains
  116 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 100
  time to evaluate  : 1.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  802 LEU
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   58 MET
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 38 optimal weight:    4.9990
   chunk 99 optimal weight:    0.9990
   chunk 132 optimal weight:   10.0000
   chunk 111 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 101 optimal weight:    8.9990
   chunk 112 optimal weight:    7.9990
   chunk 126 optimal weight:    0.6980
   chunk 9 optimal weight:    7.9990
   chunk 106 optimal weight:    7.9990
   chunk 14 optimal weight:    3.9990
   overall best weight:    2.9388

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

Flipped N/Q/H residues before XYZ refinement:
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4650 r_free = 0.4650 target = 0.118541 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.4174 r_free = 0.4174 target = 0.093320 restraints weight = 58004.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4233 r_free = 0.4233 target = 0.095938 restraints weight = 32286.272|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4272 r_free = 0.4272 target = 0.097642 restraints weight = 21942.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.4210
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6192
moved from start:          0.5745

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.071  12749  Z= 0.216
  Angle     :  0.695  13.752  17632  Z= 0.371
  Chirality :  0.043   0.210   1957
  Planarity :  0.005   0.066   1931
  Dihedral  : 22.858  72.451   2482
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 19.67
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.08 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.96 %
    Allowed  : 17.15 %
    Favored  : 80.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.46 (0.24), residues: 1273
  helix:  0.04 (0.21), residues: 584
  sheet: -0.41 (0.60), residues: 67
  loop : -0.51 (0.26), residues: 622

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.055   0.003   TRP D  93 
 HIS   0.011   0.002   HIS B 970 
 PHE   0.026   0.003   PHE C 166 
 TYR   0.026   0.002   TYR B1000 
 ARG   0.006   0.001   ARG C  35 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.05042 (  497)
  hydrogen bonds       : angle       5.14013 ( 1383)
  covalent geometry    : bond        0.00496 (12749)
  covalent geometry    : angle       0.69515 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 101
  time to evaluate  : 1.355 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  788 MET cc_start: 0.7558 (ppp) cc_final: 0.5726 (tpp)
REVERT: A  790 HIS cc_start: 0.4940 (m-70) cc_final: 0.4154 (m170)
REVERT: A  803 MET cc_start: 0.5829 (mtm) cc_final: 0.5196 (ptm)
REVERT: A  826 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8380 (pp)
REVERT: A  827 LEU cc_start: 0.8641 (mt) cc_final: 0.8140 (mt)
REVERT: A  833 PHE cc_start: 0.9212 (m-80) cc_final: 0.8932 (m-80)
REVERT: A 1026 MET cc_start: 0.7556 (pmm) cc_final: 0.6731 (pmm)
REVERT: A 1104 PHE cc_start: 0.7170 (m-80) cc_final: 0.6757 (m-80)
REVERT: A 1135 GLU cc_start: 0.7959 (mm-30) cc_final: 0.7681 (mt-10)
REVERT: B  779 LYS cc_start: 0.8220 (mttt) cc_final: 0.7957 (mttm)
REVERT: B  871 LYS cc_start: 0.8776 (mttt) cc_final: 0.8348 (pttp)
REVERT: B  927 LEU cc_start: 0.6226 (OUTLIER) cc_final: 0.5998 (mt)
REVERT: C   79 HIS cc_start: 0.7528 (m-70) cc_final: 0.7232 (m90)
REVERT: C  204 GLN cc_start: 0.8787 (mt0) cc_final: 0.8244 (mp10)
REVERT: D   93 TRP cc_start: 0.6371 (t60) cc_final: 0.6044 (t60)
REVERT: D  188 MET cc_start: 0.0222 (mmm) cc_final: -0.1352 (tpt)
REVERT: D  310 GLU cc_start: 0.7647 (mt-10) cc_final: 0.7248 (tt0)
  outliers start: 23
  outliers final: 18
  residues processed: 118
  average time/residue: 0.2381
  time to fit residues: 42.8558
Evaluate side-chains
  115 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 1.137 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue  984 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  802 LEU
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain B residue  915 MET
Chi-restraints excluded: chain B residue  927 LEU
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 22 optimal weight:    2.9990
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    0.0030
   chunk 92 optimal weight:    0.9980
   chunk 93 optimal weight:    2.9990
   chunk 7 optimal weight:    0.2980
   chunk 126 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 21 optimal weight:    0.0370
   chunk 113 optimal weight:   10.0000
   chunk 39 optimal weight:    0.6980
   overall best weight:    0.3668

-------------------------------------------------------------------------------
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 = 0.4826 r_free = 0.4826 target = 0.125045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.4396 r_free = 0.4396 target = 0.100798 restraints weight = 55670.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4460 r_free = 0.4460 target = 0.103803 restraints weight = 28525.475|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.4498 r_free = 0.4498 target = 0.105748 restraints weight = 18186.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.4444
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5951
moved from start:          0.6089

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  12749  Z= 0.139
  Angle     :  0.638  12.708  17632  Z= 0.344
  Chirality :  0.041   0.192   1957
  Planarity :  0.004   0.062   1931
  Dihedral  : 22.564  73.298   2482
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 14.76
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.14 %
    Favored  : 96.78 %
  Rotamer:
    Outliers :  1.62 %
    Allowed  : 17.83 %
    Favored  : 80.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.15 (0.24), residues: 1273
  helix:  0.33 (0.21), residues: 583
  sheet: -0.52 (0.60), residues: 72
  loop : -0.34 (0.27), residues: 618

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A 830 
 HIS   0.008   0.001   HIS B 919 
 PHE   0.029   0.002   PHE C 166 
 TYR   0.023   0.002   TYR B 943 
 ARG   0.014   0.000   ARG A 748 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04045 (  497)
  hydrogen bonds       : angle       4.88776 ( 1383)
  covalent geometry    : bond        0.00309 (12749)
  covalent geometry    : angle       0.63838 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  124 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 105
  time to evaluate  : 1.210 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  752 VAL cc_start: 0.7865 (t) cc_final: 0.7588 (t)
REVERT: A  788 MET cc_start: 0.7567 (ppp) cc_final: 0.5736 (tpp)
REVERT: A  790 HIS cc_start: 0.4992 (m-70) cc_final: 0.4258 (m170)
REVERT: A  826 LEU cc_start: 0.8583 (OUTLIER) cc_final: 0.8250 (pp)
REVERT: A  827 LEU cc_start: 0.8484 (mt) cc_final: 0.7977 (mt)
REVERT: A 1021 MET cc_start: 0.7014 (pmm) cc_final: 0.6456 (pmm)
REVERT: A 1026 MET cc_start: 0.7516 (pmm) cc_final: 0.6659 (pmm)
REVERT: A 1104 PHE cc_start: 0.6927 (m-80) cc_final: 0.6533 (m-80)
REVERT: A 1131 LYS cc_start: 0.7579 (mmmm) cc_final: 0.6972 (tmmt)
REVERT: A 1135 GLU cc_start: 0.7881 (mm-30) cc_final: 0.7562 (mt-10)
REVERT: B  871 LYS cc_start: 0.8656 (mttt) cc_final: 0.8270 (pttp)
REVERT: C  204 GLN cc_start: 0.8436 (mt0) cc_final: 0.7955 (mp10)
REVERT: D   93 TRP cc_start: 0.6279 (t60) cc_final: 0.5989 (t60)
REVERT: D  141 MET cc_start: 0.6766 (mmt) cc_final: 0.6421 (mpp)
REVERT: D  188 MET cc_start: 0.0093 (mmm) cc_final: -0.1404 (tpt)
REVERT: D  310 GLU cc_start: 0.7683 (mt-10) cc_final: 0.7301 (tt0)
REVERT: D  323 GLU cc_start: 0.7022 (mm-30) cc_final: 0.6590 (mm-30)
  outliers start: 19
  outliers final: 13
  residues processed: 119
  average time/residue: 0.2383
  time to fit residues: 42.5532
Evaluate side-chains
  113 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 99
  time to evaluate  : 1.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 119 optimal weight:    7.9990
   chunk 28 optimal weight:    0.9980
   chunk 123 optimal weight:    0.9980
   chunk 79 optimal weight:    0.8980
   chunk 114 optimal weight:   20.0000
   chunk 80 optimal weight:    5.9990
   chunk 68 optimal weight:    0.8980
   chunk 76 optimal weight:    4.9990
   chunk 115 optimal weight:    7.9990
   chunk 38 optimal weight:    0.4980
   chunk 1 optimal weight:    8.9990
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4822 r_free = 0.4822 target = 0.124705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 71)----------------|
| r_work = 0.4395 r_free = 0.4395 target = 0.100507 restraints weight = 56171.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.4459 r_free = 0.4459 target = 0.103541 restraints weight = 28684.160|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.4494 r_free = 0.4494 target = 0.105542 restraints weight = 18307.940|
|-----------------------------------------------------------------------------|
r_work (final): 0.4429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5966
moved from start:          0.6266

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  12749  Z= 0.141
  Angle     :  0.640  11.865  17632  Z= 0.344
  Chirality :  0.042   0.204   1957
  Planarity :  0.004   0.065   1931
  Dihedral  : 22.516  72.788   2482
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 15.72
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.61 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.45 %
    Allowed  : 18.34 %
    Favored  : 80.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.09 (0.24), residues: 1273
  helix:  0.44 (0.21), residues: 583
  sheet: -0.75 (0.57), residues: 78
  loop : -0.34 (0.27), residues: 612

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.052   0.002   TRP A 830 
 HIS   0.008   0.001   HIS B 919 
 PHE   0.029   0.002   PHE C 166 
 TYR   0.022   0.002   TYR B 943 
 ARG   0.005   0.000   ARG A1039 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04274 (  497)
  hydrogen bonds       : angle       4.87306 ( 1383)
  covalent geometry    : bond        0.00319 (12749)
  covalent geometry    : angle       0.63959 (17632)

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

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

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2546 Ramachandran restraints generated.
    1273 Oldfield, 0 Emsley, 1273 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 1.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  752 VAL cc_start: 0.7817 (t) cc_final: 0.7552 (t)
REVERT: A  788 MET cc_start: 0.7595 (ppp) cc_final: 0.5725 (tpp)
REVERT: A  790 HIS cc_start: 0.5045 (m-70) cc_final: 0.4527 (m170)
REVERT: A  826 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8267 (pp)
REVERT: A  827 LEU cc_start: 0.8490 (mt) cc_final: 0.7864 (mt)
REVERT: A  940 VAL cc_start: 0.8092 (m) cc_final: 0.7870 (p)
REVERT: A  984 CYS cc_start: 0.8024 (t) cc_final: 0.7733 (p)
REVERT: A 1021 MET cc_start: 0.6756 (pmm) cc_final: 0.6174 (pmm)
REVERT: A 1026 MET cc_start: 0.7507 (pmm) cc_final: 0.6681 (pmm)
REVERT: A 1104 PHE cc_start: 0.7051 (m-80) cc_final: 0.6617 (m-80)
REVERT: A 1131 LYS cc_start: 0.7595 (mmmm) cc_final: 0.6998 (tmmt)
REVERT: A 1135 GLU cc_start: 0.7839 (mm-30) cc_final: 0.7527 (mt-10)
REVERT: B  774 ARG cc_start: 0.8097 (mmp-170) cc_final: 0.7814 (mmp80)
REVERT: B  871 LYS cc_start: 0.8690 (mttt) cc_final: 0.8299 (pttp)
REVERT: C  204 GLN cc_start: 0.8494 (mt0) cc_final: 0.8006 (mp10)
REVERT: D   93 TRP cc_start: 0.6224 (t60) cc_final: 0.5987 (t60)
REVERT: D  141 MET cc_start: 0.6676 (mmt) cc_final: 0.6316 (mpp)
REVERT: D  188 MET cc_start: 0.0167 (mmm) cc_final: -0.1365 (tpt)
REVERT: D  310 GLU cc_start: 0.7718 (mt-10) cc_final: 0.7314 (tt0)
  outliers start: 17
  outliers final: 14
  residues processed: 112
  average time/residue: 0.2441
  time to fit residues: 40.6281
Evaluate side-chains
  113 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 98
  time to evaluate  : 1.280 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  886 THR
Chi-restraints excluded: chain A residue  921 THR
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1120 VAL
Chi-restraints excluded: chain A residue 1149 VAL
Chi-restraints excluded: chain B residue  861 ILE
Chi-restraints excluded: chain B residue  866 VAL
Chi-restraints excluded: chain B residue  911 VAL
Chi-restraints excluded: chain C residue   56 ILE
Chi-restraints excluded: chain C residue   72 HIS
Chi-restraints excluded: chain C residue  212 LEU
Chi-restraints excluded: chain D residue   49 HIS
Chi-restraints excluded: chain D residue  429 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 135
   random chunks:
   chunk 37 optimal weight:    8.9990
   chunk 125 optimal weight:    8.9990
   chunk 103 optimal weight:    7.9990
   chunk 116 optimal weight:    1.9990
   chunk 79 optimal weight:    0.7980
   chunk 7 optimal weight:    5.9990
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 35 optimal weight:    0.7980
   chunk 128 optimal weight:    8.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    2.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4760 r_free = 0.4760 target = 0.121752 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4306 r_free = 0.4306 target = 0.097222 restraints weight = 57756.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4365 r_free = 0.4365 target = 0.099736 restraints weight = 30244.065|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 54)----------------|
| r_work = 0.4401 r_free = 0.4401 target = 0.101473 restraints weight = 19712.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6117
moved from start:          0.6360

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.062  12749  Z= 0.181
  Angle     :  0.684  12.634  17632  Z= 0.362
  Chirality :  0.043   0.255   1957
  Planarity :  0.005   0.067   1931
  Dihedral  : 22.565  73.684   2482
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 18.78
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.08 %
    Favored  : 95.84 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 19.03 %
    Favored  : 79.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 3.23 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.25 (0.24), residues: 1273
  helix:  0.24 (0.21), residues: 585
  sheet: -0.72 (0.60), residues: 72
  loop : -0.37 (0.27), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.056   0.003   TRP A 830 
 HIS   0.010   0.001   HIS B 919 
 PHE   0.021   0.002   PHE B 739 
 TYR   0.024   0.002   TYR B1000 
 ARG   0.005   0.000   ARG A1039 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04770 (  497)
  hydrogen bonds       : angle       5.04029 ( 1383)
  covalent geometry    : bond        0.00415 (12749)
  covalent geometry    : angle       0.68410 (17632)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 5751.16 seconds
wall clock time: 101 minutes 28.44 seconds (6088.44 seconds total)