Starting phenix.real_space_refine
on Sat Jan 18 13:14:47 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9gck_51231/01_2025/9gck_51231.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9gck_51231/01_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_51231/01_2025/9gck_51231.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9gck_51231/01_2025/9gck_51231.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9gck_51231/01_2025/9gck_51231.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9gck_51231/01_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-5571/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: 7.55, per 1000 atoms: 0.61
  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: 3.11
  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: 4.76
  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: 4.62

  Time building geometry restraints manager: 3.58 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:             1.930
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.510
  Check model and map are aligned:         0.090
  Set scattering table:                    0.120
  Process input model:                     33.360
  Find NCS groups from input model:        0.140
  Set up NCS constraints:                  0.060
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   39.010
-------------------------------------------------------------------------------
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= 0.922
  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 

*********************** 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  : 1.086 
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: 0.3207
  time to fit residues: 90.8247
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  : 1.326 
-------------------------------------------------------------------------------
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 = 0.103862 restraints weight = 53058.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.4545 r_free = 0.4545 target = 0.107267 restraints weight = 25169.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4558 r_free = 0.4558 target = 0.107660 restraints weight = 14469.126|
|-----------------------------------------------------------------------------|
r_work (final): 0.4488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5857
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= 0.265
  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 

*********************** 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  : 1.365 
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: 0.6036 (mtm) cc_final: 0.5353 (ttt)
REVERT: A  826 LEU cc_start: 0.8641 (mm) cc_final: 0.8172 (pp)
REVERT: A  833 PHE cc_start: 0.8750 (m-80) cc_final: 0.7932 (m-80)
REVERT: A  872 MET cc_start: 0.4839 (mtm) cc_final: 0.4171 (mtm)
REVERT: A 1018 LEU cc_start: 0.6108 (mp) cc_final: 0.5463 (tp)
REVERT: A 1069 VAL cc_start: 0.6915 (t) cc_final: 0.6617 (m)
REVERT: B  779 LYS cc_start: 0.8309 (mttt) cc_final: 0.8095 (mttm)
REVERT: B  871 LYS cc_start: 0.8350 (mttt) cc_final: 0.7951 (pttp)
REVERT: C  204 GLN cc_start: 0.8574 (mt0) cc_final: 0.8068 (mp10)
REVERT: C  235 MET cc_start: 0.3033 (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: 0.0387 (mmm) cc_final: -0.1672 (tpt)
REVERT: D  205 ASP cc_start: 0.8311 (OUTLIER) cc_final: 0.7958 (p0)
  outliers start: 23
  outliers final: 9
  residues processed: 163
  average time/residue: 0.2894
  time to fit residues: 65.8028
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  : 1.389 
-------------------------------------------------------------------------------
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:    0.9990
   chunk 32 optimal weight:    5.9990
   chunk 20 optimal weight:    0.9990
   chunk 63 optimal weight:    0.7980
   chunk 100 optimal weight:    5.9990
   chunk 103 optimal weight:    0.4980
   chunk 130 optimal weight:    9.9990
   chunk 37 optimal weight:    0.9980
   chunk 7 optimal weight:   10.0000
   chunk 3 optimal weight:    6.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
A 877 GLN
B 836 GLN
B 959 GLN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4740 r_free = 0.4740 target = 0.123573 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 58)----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.098499 restraints weight = 58240.196|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4339 r_free = 0.4339 target = 0.101063 restraints weight = 31849.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4379 r_free = 0.4379 target = 0.103184 restraints weight = 21011.800|
|-----------------------------------------------------------------------------|
r_work (final): 0.4317
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5974
moved from start:          0.3911

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= 0.229
  Angle     :  0.680   8.100  17632  Z= 0.377
  Chirality :  0.042   0.230   1957
  Planarity :  0.004   0.053   1931
  Dihedral  : 22.749  70.686   2485
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 13.75
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  2.28 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 11.35 %
    Favored  : 86.52 %
  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: -0.50 (0.23), residues: 1273
  helix: -0.07 (0.21), residues: 577
  sheet: -0.01 (0.61), residues: 65
  loop : -0.50 (0.25), residues: 631

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 830 
 HIS   0.010   0.001   HIS B 919 
 PHE   0.021   0.002   PHE B 839 
 TYR   0.029   0.002   TYR B1000 
 ARG   0.004   0.000   ARG A 983 

*********************** 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
  155 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 130
  time to evaluate  : 1.125 
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  784 ARG cc_start: 0.8290 (ptp-110) cc_final: 0.8082 (ptp-170)
REVERT: A  803 MET cc_start: 0.5993 (mtm) cc_final: 0.5186 (ttp)
REVERT: A  826 LEU cc_start: 0.8604 (OUTLIER) cc_final: 0.8127 (pp)
REVERT: A  833 PHE cc_start: 0.8831 (m-80) cc_final: 0.8252 (m-80)
REVERT: A  949 GLN cc_start: 0.7420 (mp10) cc_final: 0.7043 (tp-100)
REVERT: A 1033 LEU cc_start: 0.7022 (mp) cc_final: 0.6592 (mt)
REVERT: A 1131 LYS cc_start: 0.7584 (mmmm) cc_final: 0.7130 (tmmt)
REVERT: B  871 LYS cc_start: 0.8350 (mttt) cc_final: 0.7823 (pttp)
REVERT: C  116 ILE cc_start: 0.7859 (mm) cc_final: 0.7572 (mm)
REVERT: C  204 GLN cc_start: 0.8301 (mt0) cc_final: 0.7861 (mp10)
REVERT: D  141 MET cc_start: 0.8135 (mtt) cc_final: 0.7836 (mmm)
REVERT: D  188 MET cc_start: -0.0509 (mmm) cc_final: -0.1735 (tpt)
  outliers start: 25
  outliers final: 14
  residues processed: 149
  average time/residue: 0.2634
  time to fit residues: 55.7165
Evaluate side-chains
  123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 108
  time to evaluate  : 1.333 
-------------------------------------------------------------------------------
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  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  836 GLN
Chi-restraints excluded: chain B residue  901 LEU
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  212 LEU
Chi-restraints excluded: chain D residue  165 LEU
Chi-restraints excluded: chain D residue  204 LEU
Chi-restraints excluded: chain D residue  297 SER
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:    4.9990
   chunk 47 optimal weight:    2.9990
   chunk 129 optimal weight:   10.0000
   chunk 83 optimal weight:    0.8980
   chunk 30 optimal weight:    9.9990
   chunk 4 optimal weight:    5.9990
   chunk 67 optimal weight:    4.9990
   chunk 130 optimal weight:    9.9990
   chunk 3 optimal weight:    8.9990
   chunk 72 optimal weight:    3.9990
   overall best weight:    3.5788

-------------------------------------------------------------------------------
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 946 HIS
B 959 GLN
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4634 r_free = 0.4634 target = 0.117131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.091516 restraints weight = 56743.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.4191 r_free = 0.4191 target = 0.093720 restraints weight = 33129.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4228 r_free = 0.4228 target = 0.095366 restraints weight = 22214.747|
|-----------------------------------------------------------------------------|
r_work (final): 0.4177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6224
moved from start:          0.4382

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.075  12749  Z= 0.386
  Angle     :  0.760   8.261  17632  Z= 0.411
  Chirality :  0.045   0.236   1957
  Planarity :  0.005   0.062   1931
  Dihedral  : 23.162  69.802   2485
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 20.50
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.77 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.74 %
    Favored  : 83.62 %
  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: -0.94 (0.23), residues: 1273
  helix: -0.54 (0.20), residues: 572
  sheet: -0.17 (0.58), residues: 78
  loop : -0.64 (0.25), residues: 623

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.046   0.003   TRP A 830 
 HIS   0.013   0.002   HIS B 919 
 PHE   0.036   0.003   PHE D 150 
 TYR   0.032   0.003   TYR B1000 
 ARG   0.006   0.001   ARG A1077 

*********************** 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: 31
    poor density    : 107
  time to evaluate  : 1.373 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.6023 (mtm) cc_final: 0.5272 (ttp)
REVERT: A  826 LEU cc_start: 0.8735 (OUTLIER) cc_final: 0.8312 (pp)
REVERT: A  833 PHE cc_start: 0.9080 (m-80) cc_final: 0.8541 (m-80)
REVERT: A 1033 LEU cc_start: 0.7319 (mp) cc_final: 0.6808 (tp)
REVERT: A 1051 ILE cc_start: 0.7612 (mm) cc_final: 0.7383 (mm)
REVERT: A 1104 PHE cc_start: 0.7388 (m-80) cc_final: 0.6875 (m-80)
REVERT: B  740 MET cc_start: 0.4872 (mmm) cc_final: 0.3908 (mmt)
REVERT: B  871 LYS cc_start: 0.8660 (mttt) cc_final: 0.8124 (pttp)
REVERT: B  927 LEU cc_start: 0.5799 (OUTLIER) cc_final: 0.5548 (mt)
REVERT: C  204 GLN cc_start: 0.8807 (mt0) cc_final: 0.8250 (mp10)
REVERT: D  141 MET cc_start: 0.8180 (mtt) cc_final: 0.7853 (mpp)
REVERT: D  188 MET cc_start: -0.0094 (mmm) cc_final: -0.0612 (tpt)
  outliers start: 31
  outliers final: 20
  residues processed: 128
  average time/residue: 0.2692
  time to fit residues: 49.5076
Evaluate side-chains
  122 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 100
  time to evaluate  : 1.238 
-------------------------------------------------------------------------------
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  984 CYS
Chi-restraints excluded: chain A residue 1045 LEU
Chi-restraints excluded: chain A residue 1086 ILE
Chi-restraints excluded: chain A residue 1117 CYS
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  212 LEU
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  297 SER
Chi-restraints excluded: chain D residue  298 VAL
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:    4.9990
   chunk 3 optimal weight:    7.9990
   chunk 50 optimal weight:    1.9990
   chunk 81 optimal weight:    0.0670
   chunk 126 optimal weight:    0.8980
   chunk 120 optimal weight:   10.0000
   chunk 25 optimal weight:    0.9990
   chunk 130 optimal weight:   10.0000
   chunk 129 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   overall best weight:    1.3924

-------------------------------------------------------------------------------
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**
** B1008 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1017 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 = 0.4687 r_free = 0.4687 target = 0.120444 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.096157 restraints weight = 56214.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4286 r_free = 0.4286 target = 0.098767 restraints weight = 30876.405|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.4322 r_free = 0.4322 target = 0.100280 restraints weight = 20327.062|
|-----------------------------------------------------------------------------|
r_work (final): 0.4254
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6068
moved from start:          0.4821

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057  12749  Z= 0.242
  Angle     :  0.658   8.121  17632  Z= 0.360
  Chirality :  0.042   0.220   1957
  Planarity :  0.005   0.056   1931
  Dihedral  : 23.005  72.561   2482
  Min Nonbonded Distance : 2.549

Molprobity Statistics.
  All-atom Clashscore : 16.73
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.38 %
    Favored  : 96.54 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.82 %
    Favored  : 83.53 %
  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: -0.60 (0.23), residues: 1273
  helix: -0.17 (0.21), residues: 576
  sheet: -0.09 (0.62), residues: 72
  loop : -0.53 (0.26), residues: 625

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.058   0.002   TRP A 830 
 HIS   0.010   0.001   HIS B 919 
 PHE   0.029   0.002   PHE D 150 
 TYR   0.030   0.002   TYR B1000 
 ARG   0.008   0.000   ARG A 784 

*********************** 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
  140 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 109
  time to evaluate  : 1.232 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  790 HIS cc_start: 0.4929 (m-70) cc_final: 0.4707 (m-70)
REVERT: A  803 MET cc_start: 0.5888 (mtm) cc_final: 0.4997 (ptm)
REVERT: A  826 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8265 (pp)
REVERT: A  827 LEU cc_start: 0.8461 (mt) cc_final: 0.7899 (mt)
REVERT: A  833 PHE cc_start: 0.9012 (m-80) cc_final: 0.8747 (m-80)
REVERT: A 1033 LEU cc_start: 0.7290 (mp) cc_final: 0.6982 (mp)
REVERT: A 1051 ILE cc_start: 0.7470 (mm) cc_final: 0.7214 (mm)
REVERT: A 1104 PHE cc_start: 0.7102 (m-80) cc_final: 0.6546 (m-80)
REVERT: A 1135 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7677 (mt-10)
REVERT: B  779 LYS cc_start: 0.8292 (mttm) cc_final: 0.8019 (mtpp)
REVERT: B  871 LYS cc_start: 0.8617 (mttt) cc_final: 0.8111 (pttp)
REVERT: B  927 LEU cc_start: 0.5763 (OUTLIER) cc_final: 0.5544 (mt)
REVERT: C  204 GLN cc_start: 0.8598 (mt0) cc_final: 0.8051 (mp10)
REVERT: D  141 MET cc_start: 0.8223 (mtt) cc_final: 0.7965 (mpp)
REVERT: D  178 MET cc_start: 0.7310 (mmm) cc_final: 0.5987 (mmt)
REVERT: D  188 MET cc_start: 0.0365 (mmm) cc_final: -0.0106 (tpt)
REVERT: D  310 GLU cc_start: 0.7695 (mt-10) cc_final: 0.7286 (tp30)
  outliers start: 31
  outliers final: 18
  residues processed: 131
  average time/residue: 0.2370
  time to fit residues: 45.9732
Evaluate side-chains
  123 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 103
  time to evaluate  : 1.361 
-------------------------------------------------------------------------------
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 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  985 VAL
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 D residue  120 SER
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:    8.9990
   chunk 62 optimal weight:    5.9990
   chunk 35 optimal weight:    0.0670
   chunk 101 optimal weight:    5.9990
   chunk 118 optimal weight:    8.9990
   chunk 26 optimal weight:    0.8980
   chunk 121 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 3 optimal weight:   10.0000
   chunk 97 optimal weight:   10.0000
   chunk 24 optimal weight:    1.9990
   overall best weight:    1.1522

-------------------------------------------------------------------------------
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 946 HIS
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4711 r_free = 0.4711 target = 0.121692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.097508 restraints weight = 56906.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.4319 r_free = 0.4319 target = 0.100237 restraints weight = 30272.396|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.4355 r_free = 0.4355 target = 0.101928 restraints weight = 20054.015|
|-----------------------------------------------------------------------------|
r_work (final): 0.4287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6008
moved from start:          0.5243

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= 0.217
  Angle     :  0.626   7.447  17632  Z= 0.342
  Chirality :  0.041   0.199   1957
  Planarity :  0.004   0.058   1931
  Dihedral  : 22.833  71.396   2482
  Min Nonbonded Distance : 2.510

Molprobity Statistics.
  All-atom Clashscore : 15.43
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.53 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.22 %
    Allowed  : 15.10 %
    Favored  : 82.68 %
  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: -0.35 (0.23), residues: 1273
  helix:  0.13 (0.21), residues: 576
  sheet: -0.17 (0.63), residues: 69
  loop : -0.48 (0.26), residues: 628

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.036   0.002   TRP A 830 
 HIS   0.009   0.001   HIS B 919 
 PHE   0.024   0.002   PHE D 150 
 TYR   0.027   0.002   TYR B1000 
 ARG   0.006   0.000   ARG A 784 

*********************** 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
  146 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 120
  time to evaluate  : 1.394 
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  790 HIS cc_start: 0.5112 (m-70) cc_final: 0.4390 (m170)
REVERT: A  803 MET cc_start: 0.5783 (mtm) cc_final: 0.4863 (ptm)
REVERT: A  826 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8241 (pp)
REVERT: A  827 LEU cc_start: 0.8424 (mt) cc_final: 0.7876 (mt)
REVERT: A  833 PHE cc_start: 0.8998 (m-80) cc_final: 0.8745 (m-80)
REVERT: A 1026 MET cc_start: 0.7550 (pmm) cc_final: 0.6817 (pmm)
REVERT: A 1033 LEU cc_start: 0.7086 (mp) cc_final: 0.6778 (mp)
REVERT: A 1104 PHE cc_start: 0.7103 (m-80) cc_final: 0.6582 (m-80)
REVERT: A 1131 LYS cc_start: 0.7689 (mmmm) cc_final: 0.7078 (tmmt)
REVERT: A 1135 GLU cc_start: 0.7998 (mm-30) cc_final: 0.7629 (mt-10)
REVERT: B  871 LYS cc_start: 0.8606 (mttt) cc_final: 0.8118 (pttp)
REVERT: C   36 ILE cc_start: 0.7671 (mm) cc_final: 0.7455 (mm)
REVERT: C  204 GLN cc_start: 0.8511 (mt0) cc_final: 0.8020 (mp10)
REVERT: D  188 MET cc_start: 0.0220 (mmm) cc_final: -0.1250 (tpt)
REVERT: D  310 GLU cc_start: 0.7665 (mt-10) cc_final: 0.7249 (tt0)
  outliers start: 26
  outliers final: 18
  residues processed: 136
  average time/residue: 0.2686
  time to fit residues: 53.2918
Evaluate side-chains
  127 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 108
  time to evaluate  : 1.306 
-------------------------------------------------------------------------------
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 1012 ASP
Chi-restraints excluded: chain A residue 1043 ARG
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  970 HIS
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 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:    0.7980
   chunk 74 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 6 optimal weight:    7.9990
   chunk 101 optimal weight:    7.9990
   chunk 40 optimal weight:    0.9990
   chunk 123 optimal weight:    7.9990
   chunk 33 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 104 optimal weight:    5.9990
   chunk 115 optimal weight:    6.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
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 946 HIS
** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4649 r_free = 0.4649 target = 0.118189 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4176 r_free = 0.4176 target = 0.092364 restraints weight = 56296.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4226 r_free = 0.4226 target = 0.094710 restraints weight = 31440.573|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.4262 r_free = 0.4262 target = 0.096365 restraints weight = 21242.643|
|-----------------------------------------------------------------------------|
r_work (final): 0.4201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6209
moved from start:          0.5521

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.072  12749  Z= 0.307
  Angle     :  0.684   8.881  17632  Z= 0.368
  Chirality :  0.043   0.203   1957
  Planarity :  0.005   0.063   1931
  Dihedral  : 22.891  77.526   2482
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 19.71
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  4.63 %
    Favored  : 95.29 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 16.98 %
    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: -0.49 (0.24), residues: 1273
  helix: -0.03 (0.21), residues: 578
  sheet: -0.47 (0.57), residues: 79
  loop : -0.47 (0.26), residues: 616

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP D  93 
 HIS   0.008   0.001   HIS B 919 
 PHE   0.032   0.003   PHE D 150 
 TYR   0.030   0.002   TYR B1000 
 ARG   0.006   0.001   ARG C  35 

*********************** 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
  136 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 111
  time to evaluate  : 1.304 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  803 MET cc_start: 0.5785 (mtm) cc_final: 0.5230 (ptm)
REVERT: A  826 LEU cc_start: 0.8772 (OUTLIER) cc_final: 0.8382 (pp)
REVERT: A  827 LEU cc_start: 0.8547 (mt) cc_final: 0.8031 (mt)
REVERT: A  833 PHE cc_start: 0.9194 (m-80) cc_final: 0.8909 (m-80)
REVERT: A 1026 MET cc_start: 0.7574 (pmm) cc_final: 0.6909 (pmm)
REVERT: A 1104 PHE cc_start: 0.7041 (m-80) cc_final: 0.6606 (m-80)
REVERT: A 1135 GLU cc_start: 0.7990 (mm-30) cc_final: 0.7705 (mt-10)
REVERT: B  774 ARG cc_start: 0.8112 (mmp-170) cc_final: 0.7700 (mmp80)
REVERT: B  779 LYS cc_start: 0.8262 (mttm) cc_final: 0.8044 (mtpp)
REVERT: B  871 LYS cc_start: 0.8714 (mttt) cc_final: 0.8261 (pttp)
REVERT: C  204 GLN cc_start: 0.8757 (mt0) cc_final: 0.8220 (mp10)
REVERT: D  141 MET cc_start: 0.7052 (mmt) cc_final: 0.6683 (mpp)
REVERT: D  188 MET cc_start: 0.0046 (mmm) cc_final: -0.1250 (tpt)
REVERT: D  310 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7393 (tt0)
  outliers start: 25
  outliers final: 22
  residues processed: 128
  average time/residue: 0.2576
  time to fit residues: 47.7600
Evaluate side-chains
  128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 105
  time to evaluate  : 1.236 
-------------------------------------------------------------------------------
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 1012 ASP
Chi-restraints excluded: chain A residue 1043 ARG
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  970 HIS
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  120 SER
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:    2.9990
   chunk 99 optimal weight:    0.7980
   chunk 132 optimal weight:   10.0000
   chunk 111 optimal weight:    5.9990
   chunk 11 optimal weight:    2.9990
   chunk 101 optimal weight:   10.0000
   chunk 112 optimal weight:    6.9990
   chunk 126 optimal weight:    6.9990
   chunk 9 optimal weight:    6.9990
   chunk 106 optimal weight:    9.9990
   chunk 14 optimal weight:    5.9990
   overall best weight:    3.7588

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

Flipped N/Q/H residues before XYZ refinement:
A 972 ASN
A1000 GLN
A1114 GLN
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B1011 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4707 r_free = 0.4707 target = 0.117732 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4232 r_free = 0.4232 target = 0.093960 restraints weight = 55134.709|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4312 r_free = 0.4312 target = 0.097139 restraints weight = 30469.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4327 r_free = 0.4327 target = 0.097598 restraints weight = 16910.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.4251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6202
moved from start:          0.5956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.078  12749  Z= 0.394
  Angle     :  0.765  10.307  17632  Z= 0.410
  Chirality :  0.045   0.202   1957
  Planarity :  0.005   0.066   1931
  Dihedral  : 22.996  76.305   2482
  Min Nonbonded Distance : 2.459

Molprobity Statistics.
  All-atom Clashscore : 24.66
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.66 %
    Favored  : 94.27 %
  Rotamer:
    Outliers :  2.99 %
    Allowed  : 16.64 %
    Favored  : 80.38 %
  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: -0.99 (0.23), residues: 1273
  helix: -0.53 (0.20), residues: 574
  sheet: -0.85 (0.54), residues: 80
  loop : -0.61 (0.26), residues: 619

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.064   0.004   TRP A 830 
 HIS   0.012   0.002   HIS B 919 
 PHE   0.032   0.003   PHE C 166 
 TYR   0.031   0.003   TYR B1000 
 ARG   0.006   0.001   ARG A 784 

*********************** 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
  134 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 99
  time to evaluate  : 1.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  752 VAL cc_start: 0.7912 (t) cc_final: 0.7689 (t)
REVERT: A  803 MET cc_start: 0.5904 (mtm) cc_final: 0.4891 (ttp)
REVERT: A  826 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8453 (pp)
REVERT: A  827 LEU cc_start: 0.8621 (mt) cc_final: 0.8100 (mt)
REVERT: A  833 PHE cc_start: 0.9211 (m-80) cc_final: 0.8793 (m-80)
REVERT: A 1104 PHE cc_start: 0.7132 (m-80) cc_final: 0.6844 (m-80)
REVERT: A 1135 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7846 (mt-10)
REVERT: B  770 GLN cc_start: 0.8432 (pp30) cc_final: 0.8100 (pm20)
REVERT: B  871 LYS cc_start: 0.8804 (mttt) cc_final: 0.8478 (pttp)
REVERT: C  204 GLN cc_start: 0.8926 (mt0) cc_final: 0.8357 (mp10)
REVERT: D  137 GLN cc_start: 0.6948 (mp10) cc_final: 0.6721 (mp10)
REVERT: D  141 MET cc_start: 0.7317 (mmt) cc_final: 0.6833 (mpp)
REVERT: D  188 MET cc_start: 0.0329 (mmm) cc_final: -0.0895 (tpt)
  outliers start: 35
  outliers final: 23
  residues processed: 125
  average time/residue: 0.2423
  time to fit residues: 44.9968
Evaluate side-chains
  118 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 94
  time to evaluate  : 1.235 
-------------------------------------------------------------------------------
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  886 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 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  914 LEU
Chi-restraints excluded: chain B residue  915 MET
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  212 LEU
Chi-restraints excluded: chain C residue  227 LEU
Chi-restraints excluded: chain D residue  120 SER
Chi-restraints excluded: chain D residue  298 VAL
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:    0.8980
   chunk 36 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 92 optimal weight:    3.9990
   chunk 93 optimal weight:    2.9990
   chunk 7 optimal weight:    5.9990
   chunk 126 optimal weight:    1.9990
   chunk 94 optimal weight:    7.9990
   chunk 21 optimal weight:    4.9990
   chunk 113 optimal weight:    2.9990
   chunk 39 optimal weight:    0.6980
   overall best weight:    1.0782

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

Flipped N/Q/H residues before XYZ refinement:
** A1114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 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 = 0.4774 r_free = 0.4774 target = 0.121894 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4315 r_free = 0.4315 target = 0.097154 restraints weight = 55751.479|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.099954 restraints weight = 28252.126|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4416 r_free = 0.4416 target = 0.101683 restraints weight = 17999.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.4356
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6104
moved from start:          0.6132

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  12749  Z= 0.232
  Angle     :  0.680  10.638  17632  Z= 0.366
  Chirality :  0.043   0.328   1957
  Planarity :  0.005   0.062   1931
  Dihedral  : 22.727  75.763   2482
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 18.45
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.85 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  1.71 %
    Allowed  : 17.66 %
    Favored  : 80.63 %
  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: -0.53 (0.24), residues: 1273
  helix: -0.12 (0.21), residues: 577
  sheet: -0.80 (0.54), residues: 81
  loop : -0.36 (0.27), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.049   0.002   TRP A 830 
 HIS   0.009   0.001   HIS B 919 
 PHE   0.027   0.002   PHE C 166 
 TYR   0.033   0.002   TYR D 140 
 ARG   0.006   0.000   ARG A 784 

*********************** 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
  128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 108
  time to evaluate  : 1.255 
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: 0.7934 (t) cc_final: 0.7695 (t)
REVERT: A  803 MET cc_start: 0.6017 (mtm) cc_final: 0.5376 (ptm)
REVERT: A  826 LEU cc_start: 0.8730 (OUTLIER) cc_final: 0.8361 (pp)
REVERT: A  827 LEU cc_start: 0.8600 (mt) cc_final: 0.7935 (mt)
REVERT: A  833 PHE cc_start: 0.9279 (m-80) cc_final: 0.9013 (m-80)
REVERT: A 1104 PHE cc_start: 0.7082 (m-80) cc_final: 0.6640 (m-80)
REVERT: A 1135 GLU cc_start: 0.8027 (mm-30) cc_final: 0.7747 (mt-10)
REVERT: B  770 GLN cc_start: 0.8346 (pp30) cc_final: 0.8039 (pm20)
REVERT: B  774 ARG cc_start: 0.8203 (mmp-170) cc_final: 0.7893 (mmp80)
REVERT: B  871 LYS cc_start: 0.8838 (mttt) cc_final: 0.8455 (pttp)
REVERT: C  204 GLN cc_start: 0.8742 (mt0) cc_final: 0.8167 (mp10)
REVERT: D    1 MET cc_start: 0.4611 (ppp) cc_final: 0.4355 (tpt)
REVERT: D  141 MET cc_start: 0.7517 (mmt) cc_final: 0.7113 (mpp)
REVERT: D  188 MET cc_start: -0.0368 (mmm) cc_final: -0.1104 (tpt)
  outliers start: 20
  outliers final: 14
  residues processed: 123
  average time/residue: 0.2275
  time to fit residues: 42.3633
Evaluate side-chains
  117 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 102
  time to evaluate  : 1.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 LEU
Chi-restraints excluded: chain A residue  963 LEU
Chi-restraints excluded: chain A residue 1012 ASP
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 1017 HIS
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  120 SER
Chi-restraints excluded: chain D residue  139 MET
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:    4.9990
   chunk 28 optimal weight:    0.8980
   chunk 123 optimal weight:    6.9990
   chunk 79 optimal weight:    0.9990
   chunk 114 optimal weight:    3.9990
   chunk 80 optimal weight:    0.9990
   chunk 68 optimal weight:    0.6980
   chunk 76 optimal weight:    8.9990
   chunk 115 optimal weight:   10.0000
   chunk 38 optimal weight:    0.0670
   chunk 1 optimal weight:    8.9990
   overall best weight:    0.7322

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

Flipped N/Q/H residues before XYZ refinement:
A1114 GLN
** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** C  86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  11 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 = 0.4791 r_free = 0.4791 target = 0.123251 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.4353 r_free = 0.4353 target = 0.098921 restraints weight = 55877.244|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4419 r_free = 0.4419 target = 0.101987 restraints weight = 28422.467|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4456 r_free = 0.4456 target = 0.103797 restraints weight = 18151.179|
|-----------------------------------------------------------------------------|
r_work (final): 0.4405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6027
moved from start:          0.6434

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= 0.207
  Angle     :  0.669  13.083  17632  Z= 0.358
  Chirality :  0.042   0.276   1957
  Planarity :  0.005   0.063   1931
  Dihedral  : 22.479  73.560   2482
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 16.56
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  3.61 %
    Favored  : 96.31 %
  Rotamer:
    Outliers :  1.11 %
    Allowed  : 18.34 %
    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: -0.26 (0.24), residues: 1273
  helix:  0.15 (0.21), residues: 576
  sheet: -0.59 (0.53), residues: 89
  loop : -0.28 (0.28), residues: 608

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.045   0.002   TRP A 830 
 HIS   0.011   0.002   HIS B 970 
 PHE   0.033   0.002   PHE D 231 
 TYR   0.025   0.002   TYR B1000 
 ARG   0.007   0.000   ARG A 784 

********************** 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
  128 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 115
  time to evaluate  : 1.352 
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  752 VAL cc_start: 0.7963 (t) cc_final: 0.7708 (t)
REVERT: A  826 LEU cc_start: 0.8687 (OUTLIER) cc_final: 0.8322 (pp)
REVERT: A  827 LEU cc_start: 0.8557 (mt) cc_final: 0.7890 (mt)
REVERT: A  833 PHE cc_start: 0.9249 (m-80) cc_final: 0.8774 (m-80)
REVERT: A  849 GLU cc_start: 0.8396 (mp0) cc_final: 0.8143 (pm20)
REVERT: A 1090 ILE cc_start: 0.6804 (mm) cc_final: 0.6392 (mm)
REVERT: A 1104 PHE cc_start: 0.7019 (m-80) cc_final: 0.6610 (m-80)
REVERT: A 1131 LYS cc_start: 0.7734 (mmmm) cc_final: 0.7192 (tmmt)
REVERT: A 1135 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7622 (mt-10)
REVERT: B  770 GLN cc_start: 0.8327 (pp30) cc_final: 0.8046 (pm20)
REVERT: B  774 ARG cc_start: 0.8080 (mmp-170) cc_final: 0.7844 (mmp80)
REVERT: B  779 LYS cc_start: 0.8005 (mtpp) cc_final: 0.7238 (ttpp)
REVERT: B  871 LYS cc_start: 0.8732 (mttt) cc_final: 0.8399 (pttp)
REVERT: C  204 GLN cc_start: 0.8519 (mt0) cc_final: 0.7995 (mp10)
REVERT: D    1 MET cc_start: 0.4783 (ppp) cc_final: 0.4505 (tpt)
REVERT: D  188 MET cc_start: -0.0565 (mmm) cc_final: -0.1437 (tpt)
  outliers start: 13
  outliers final: 11
  residues processed: 123
  average time/residue: 0.2366
  time to fit residues: 43.4802
Evaluate side-chains
  113 residues out of total 1173 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 1.432 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  826 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 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 D residue  139 MET
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:    3.9990
   chunk 125 optimal weight:    8.9990
   chunk 103 optimal weight:   10.0000
   chunk 116 optimal weight:   10.0000
   chunk 79 optimal weight:    1.9990
   chunk 7 optimal weight:    1.9990
   chunk 9 optimal weight:    5.9990
   chunk 13 optimal weight:    9.9990
   chunk 35 optimal weight:    6.9990
   chunk 128 optimal weight:    8.9990
   chunk 52 optimal weight:    3.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 972 ASN
A1000 GLN
** A1151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 896 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 970 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4714 r_free = 0.4714 target = 0.117932 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.093485 restraints weight = 55564.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.4301 r_free = 0.4301 target = 0.096477 restraints weight = 31352.234|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.4313 r_free = 0.4313 target = 0.096964 restraints weight = 17452.350|
|-----------------------------------------------------------------------------|
r_work (final): 0.4238
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6233
moved from start:          0.6548

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= 0.384
  Angle     :  0.776  12.393  17632  Z= 0.410
  Chirality :  0.046   0.304   1957
  Planarity :  0.005   0.068   1931
  Dihedral  : 22.724  74.055   2482
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 23.40
  Ramachandran Plot:
    Outliers :  0.08 %
    Allowed  :  5.03 %
    Favored  : 94.89 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.66 %
    Favored  : 80.29 %
  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: -0.75 (0.24), residues: 1273
  helix: -0.28 (0.21), residues: 577
  sheet: -0.92 (0.54), residues: 81
  loop : -0.51 (0.27), residues: 615

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.068   0.003   TRP A 830 
 HIS   0.009   0.002   HIS B 919 
 PHE   0.032   0.003   PHE D 231 
 TYR   0.044   0.003   TYR A 848 
 ARG   0.007   0.001   ARG D 330 
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4887.53 seconds
wall clock time: 88 minutes 12.31 seconds (5292.31 seconds total)