Starting phenix.real_space_refine
on Wed Mar  4 03:21:45 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8ibz_35350/03_2026/8ibz_35350.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8ibz_35350/03_2026/8ibz_35350.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8ibz_35350/03_2026/8ibz_35350.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8ibz_35350/03_2026/8ibz_35350.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8ibz_35350/03_2026/8ibz_35350.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8ibz_35350/03_2026/8ibz_35350.map"
  }
  resolution = 3.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.069
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P     180      5.49       5
     S      33      5.16       5
     C    5747      2.51       5
     N    1936      2.21       5
     O    2376      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 10273
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 6419
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 817, 6419
          Classifications: {'peptide': 817}
          Link IDs: {'PTRANS': 40, 'TRANS': 776}
          Chain breaks: 2
          Unresolved non-hydrogen bonds: 28
          Unresolved non-hydrogen angles: 36
          Unresolved non-hydrogen dihedrals: 20
          Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 5, 'GLU:plan': 2}
          Unresolved non-hydrogen planarities: 26
    Chain: "E"
      Number of atoms: 3853
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 180, 3853
          Classifications: {'RNA': 180}
          Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 13, 'rna3p_pur': 84, 'rna3p_pyr': 68}
          Link IDs: {'rna2p': 27, 'rna3p': 152}
          Chain breaks: 3
    Chain: "C"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   5049  SG  CYS C 934      23.361  91.141  71.596  1.00 19.77           S
  ATOM   5075  SG  CYS C 938      21.307  94.372  71.712  1.00 27.76           S
  ATOM   5180  SG  CYS C 951      24.106  93.871  74.236  1.00 14.04           S

  Time building chain proxies: 2.30, per 1000 atoms: 0.22
  Number of scatterers: 10273
  At special positions: 0
  Unit cell: (114.745, 142.89, 123.405, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      33     16.00
     P     180     15.00
     O    2376      8.00
     N    1936      7.00
     C    5747      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.83
  Conformation dependent library (CDL) restraints added in 537.9 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN C1201 "
        pdb="ZN    ZN C1201 " - pdb=" NE2 HIS C 946 "
        pdb="ZN    ZN C1201 " - pdb=" SG  CYS C 938 "
        pdb="ZN    ZN C1201 " - pdb=" SG  CYS C 951 "
        pdb="ZN    ZN C1201 " - pdb=" SG  CYS C 934 "
      Number of angles added : 3


  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1512

  Finding SS restraints...
    Secondary structure from input PDB file:
      39 helices and 7 sheets defined
      55.8% alpha, 9.7% beta
      46 base pairs and 94 stacking pairs defined.
    Time for finding SS restraints: 1.09
  Creating SS restraints...
    Processing helix  chain 'C' and resid 260 through 283
    Processing helix  chain 'C' and resid 306 through 324
    Processing helix  chain 'C' and resid 324 through 335
    Processing helix  chain 'C' and resid 347 through 356
      Proline residue:  C 353  - end of helix
    Processing helix  chain 'C' and resid 365 through 374
    Processing helix  chain 'C' and resid 393 through 399
      removed outlier: 3.675A  pdb=" N   LYS C 397 " --> pdb=" O   VAL C 393 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 421 through 436
    Processing helix  chain 'C' and resid 439 through 444
      removed outlier: 3.649A  pdb=" N   GLN C 444 " --> pdb=" O   GLU C 440 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 458 through 460
      No H-bonds generated for 'chain 'C' and resid 458 through 460'
    Processing helix  chain 'C' and resid 469 through 487
      removed outlier: 3.662A  pdb=" N   ILE C 478 " --> pdb=" O   HIS C 474 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LEU C 479 " --> pdb=" O   PHE C 475 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 503 through 519
      removed outlier: 4.322A  pdb=" N   ALA C 507 " --> pdb=" O   LEU C 503 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 538 through 549
    Processing helix  chain 'C' and resid 552 through 565
    Processing helix  chain 'C' and resid 592 through 607
      removed outlier: 3.850A  pdb=" N   ASN C 598 " --> pdb=" O   PRO C 594 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL C 599 " --> pdb=" O   ILE C 595 " (cutoff:3.500A)
      removed outlier: 3.700A  pdb=" N   VAL C 600 " --> pdb=" O   LEU C 596 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 636 through 654
    Processing helix  chain 'C' and resid 719 through 730
    Processing helix  chain 'C' and resid 733 through 744
    Processing helix  chain 'C' and resid 745 through 750
    Processing helix  chain 'C' and resid 751 through 755
    Processing helix  chain 'C' and resid 759 through 779
      removed outlier: 3.806A  pdb=" N   LEU C 763 " --> pdb=" O   SER C 759 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 785 through 791
      removed outlier: 4.047A  pdb=" N   TYR C 789 " --> pdb=" O   PRO C 785 " (cutoff:3.500A)
      removed outlier: 3.998A  pdb=" N   HIS C 790 " --> pdb=" O   LYS C 786 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 802 through 817
      Proline residue:  C 808  - end of helix
      removed outlier: 4.394A  pdb=" N   GLY C 817 " --> pdb=" O   ARG C 813 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 818 through 821
    Processing helix  chain 'C' and resid 823 through 831
      removed outlier: 3.839A  pdb=" N   ARG C 827 " --> pdb=" O   TRP C 823 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   LYS C 831 " --> pdb=" O   ARG C 827 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 833 through 849
    Processing helix  chain 'C' and resid 861 through 871
    Processing helix  chain 'C' and resid 878 through 883
      removed outlier: 4.096A  pdb=" N   THR C 882 " --> pdb=" O   ARG C 879 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   ARG C 883 " --> pdb=" O   GLU C 880 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 884 through 889
      removed outlier: 3.615A  pdb=" N   THR C 888 " --> pdb=" O   PRO C 885 " (cutoff:3.500A)
      removed outlier: 3.853A  pdb=" N   LYS C 889 " --> pdb=" O   THR C 886 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 899 through 911
    Processing helix  chain 'C' and resid 918 through 922
      removed outlier: 3.513A  pdb=" N   SER C 921 " --> pdb=" O   ILE C 918 " (cutoff:3.500A)
      removed outlier: 3.996A  pdb=" N   ARG C 922 " --> pdb=" O   ARG C 919 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 918 through 922'
    Processing helix  chain 'C' and resid 928 through 932
    Processing helix  chain 'C' and resid 943 through 950
    Processing helix  chain 'C' and resid 951 through 953
      No H-bonds generated for 'chain 'C' and resid 951 through 953'
    Processing helix  chain 'C' and resid 954 through 976
    Processing helix  chain 'C' and resid 1018 through 1032
      removed outlier: 3.507A  pdb=" N   LEU C1022 " --> pdb=" O   SER C1018 " (cutoff:3.500A)
      removed outlier: 3.920A  pdb=" N   LYS C1029 " --> pdb=" O   GLU C1025 " (cutoff:3.500A)
      removed outlier: 4.314A  pdb=" N   TYR C1030 " --> pdb=" O   LYS C1026 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1035 through 1045
    Processing helix  chain 'C' and resid 1066 through 1076
    Processing helix  chain 'C' and resid 1080 through 1085
    Processing helix  chain 'C' and resid 1086 through 1105
      removed outlier: 3.711A  pdb=" N   MET C1105 " --> pdb=" O   ARG C1101 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 462 through 467
    Processing sheet with id=AA2, first strand: chain 'C' and resid 623 through 625
    Processing sheet with id=AA3, first strand: chain 'C' and resid 623 through 625
    Processing sheet with id=AA4, first strand: chain 'C' and resid 614 through 615
    Processing sheet with id=AA5, first strand: chain 'C' and resid 686 through 687
      removed outlier: 3.644A  pdb=" N   LYS C 690 " --> pdb=" O   ILE C 687 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 851 through 852
    Processing sheet with id=AA7, first strand: chain 'C' and resid 981 through 982
      removed outlier: 6.894A  pdb=" N   GLY C1005 " --> pdb=" O   ARG C1053 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   THR C1055 " --> pdb=" O   GLY C1005 " (cutoff:3.500A)
      removed outlier: 5.799A  pdb=" N   ILE C1007 " --> pdb=" O   THR C1055 " (cutoff:3.500A)
      removed outlier: 6.958A  pdb=" N   CYS C1057 " --> pdb=" O   ILE C1007 " (cutoff:3.500A)
      removed outlier: 6.479A  pdb=" N   ASP C1009 " --> pdb=" O   CYS C1057 " (cutoff:3.500A)
      removed outlier: 7.451A  pdb=" N   ILE C1059 " --> pdb=" O   ASP C1009 " (cutoff:3.500A)
      removed outlier: 6.232A  pdb=" N   GLN C1011 " --> pdb=" O   ILE C1059 " (cutoff:3.500A)

    329 hydrogen bonds defined for protein.
    936 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      116 hydrogen bonds
      208 hydrogen bond angles
      0 basepair planarities
      46 basepair parallelities
      94 stacking parallelities
  Total time for adding SS restraints: 2.14

  Time building geometry restraints manager: 1.13 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 2312
        1.33 -     1.45: 3196
        1.45 -     1.57: 4946
        1.57 -     1.69: 356
        1.69 -     1.81: 47
  Bond restraints: 10857
  Sorted by residual:
  bond pdb=" CG  PRO C 822 "
       pdb=" CD  PRO C 822 "
    ideal  model  delta    sigma   weight residual
    1.503  1.571 -0.068 3.40e-02 8.65e+02 4.02e+00
  bond pdb=" C   SER C 821 "
       pdb=" N   PRO C 822 "
    ideal  model  delta    sigma   weight residual
    1.331  1.343 -0.011 7.90e-03 1.60e+04 2.03e+00
  bond pdb=" C3'   A E 179 "
       pdb=" O3'   A E 179 "
    ideal  model  delta    sigma   weight residual
    1.427  1.446 -0.019 1.50e-02 4.44e+03 1.58e+00
  bond pdb=" CB  GLU C 975 "
       pdb=" CG  GLU C 975 "
    ideal  model  delta    sigma   weight residual
    1.520  1.555 -0.035 3.00e-02 1.11e+03 1.40e+00
  bond pdb=" C3'   A E 181 "
       pdb=" O3'   A E 181 "
    ideal  model  delta    sigma   weight residual
    1.427  1.444 -0.017 1.50e-02 4.44e+03 1.23e+00
  ... (remaining 10852 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 15354
        2.26 -     4.52: 171
        4.52 -     6.78: 26
        6.78 -     9.04: 3
        9.04 -    11.30: 1
  Bond angle restraints: 15555
  Sorted by residual:
  angle pdb=" C3'   U E 114 "
        pdb=" O3'   U E 114 "
        pdb=" P     A E 115 "
      ideal   model   delta    sigma   weight residual
     120.20  125.61   -5.41 1.50e+00 4.44e-01 1.30e+01
  angle pdb=" C3'   A E 179 "
        pdb=" O3'   A E 179 "
        pdb=" P     A E 180 "
      ideal   model   delta    sigma   weight residual
     120.20  125.38   -5.18 1.50e+00 4.44e-01 1.19e+01
  angle pdb=" CA  PRO C 822 "
        pdb=" N   PRO C 822 "
        pdb=" CD  PRO C 822 "
      ideal   model   delta    sigma   weight residual
     112.00  107.33    4.67 1.40e+00 5.10e-01 1.11e+01
  angle pdb=" CA  LEU C 755 "
        pdb=" CB  LEU C 755 "
        pdb=" CG  LEU C 755 "
      ideal   model   delta    sigma   weight residual
     116.30  127.60  -11.30 3.50e+00 8.16e-02 1.04e+01
  angle pdb=" O3'   C E 186 "
        pdb=" C3'   C E 186 "
        pdb=" C2'   C E 186 "
      ideal   model   delta    sigma   weight residual
     109.50  114.08   -4.58 1.50e+00 4.44e-01 9.33e+00
  ... (remaining 15550 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.58: 6113
       35.58 -    71.17: 606
       71.17 -   106.75: 72
      106.75 -   142.33: 4
      142.33 -   177.91: 5
  Dihedral angle restraints: 6800
    sinusoidal: 4459
      harmonic: 2341
  Sorted by residual:
  dihedral pdb=" C4'   C E 186 "
           pdb=" C3'   C E 186 "
           pdb=" C2'   C E 186 "
           pdb=" C1'   C E 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -35.00   35.06  -70.06     1      8.00e+00 1.56e-02 9.88e+01
  dihedral pdb=" C5'   C E 186 "
           pdb=" C4'   C E 186 "
           pdb=" C3'   C E 186 "
           pdb=" O3'   C E 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
     147.00   80.84   66.16     1      8.00e+00 1.56e-02 8.94e+01
  dihedral pdb=" O4'   C E 186 "
           pdb=" C4'   C E 186 "
           pdb=" C3'   C E 186 "
           pdb=" C2'   C E 186 "
      ideal   model   delta sinusoidal    sigma   weight residual
      24.00  -34.97   58.97     1      8.00e+00 1.56e-02 7.27e+01
  ... (remaining 6797 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.060: 1676
       0.060 -    0.121: 183
       0.121 -    0.181: 15
       0.181 -    0.241: 3
       0.241 -    0.302: 1
  Chirality restraints: 1878
  Sorted by residual:
  chirality pdb=" C3'   C E 186 "
            pdb=" C4'   C E 186 "
            pdb=" O3'   C E 186 "
            pdb=" C2'   C E 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.44   -0.30 2.00e-01 2.50e+01 2.28e+00
  chirality pdb=" C2'   C E 186 "
            pdb=" C3'   C E 186 "
            pdb=" O2'   C E 186 "
            pdb=" C1'   C E 186 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.52   -2.74    0.22 2.00e-01 2.50e+01 1.24e+00
  chirality pdb=" C1'   C E  78 "
            pdb=" O4'   C E  78 "
            pdb=" C2'   C E  78 "
            pdb=" N1    C E  78 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.26    0.20 2.00e-01 2.50e+01 1.04e+00
  ... (remaining 1875 not shown)

  Planarity restraints: 1322
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TRP C 701 "    0.021 2.00e-02 2.50e+03   1.84e-02 8.46e+00
        pdb=" CG  TRP C 701 "   -0.050 2.00e-02 2.50e+03
        pdb=" CD1 TRP C 701 "    0.021 2.00e-02 2.50e+03
        pdb=" CD2 TRP C 701 "    0.000 2.00e-02 2.50e+03
        pdb=" NE1 TRP C 701 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TRP C 701 "    0.000 2.00e-02 2.50e+03
        pdb=" CE3 TRP C 701 "    0.002 2.00e-02 2.50e+03
        pdb=" CZ2 TRP C 701 "    0.001 2.00e-02 2.50e+03
        pdb=" CZ3 TRP C 701 "    0.003 2.00e-02 2.50e+03
        pdb=" CH2 TRP C 701 "    0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E  78 "   -0.032 2.00e-02 2.50e+03   1.67e-02 6.30e+00
        pdb=" N1    C E  78 "    0.035 2.00e-02 2.50e+03
        pdb=" C2    C E  78 "   -0.004 2.00e-02 2.50e+03
        pdb=" O2    C E  78 "    0.006 2.00e-02 2.50e+03
        pdb=" N3    C E  78 "    0.004 2.00e-02 2.50e+03
        pdb=" C4    C E  78 "   -0.011 2.00e-02 2.50e+03
        pdb=" N4    C E  78 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    C E  78 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    C E  78 "    0.009 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   C E 117 "   -0.006 2.00e-02 2.50e+03   1.58e-02 5.62e+00
        pdb=" N1    C E 117 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    C E 117 "    0.039 2.00e-02 2.50e+03
        pdb=" O2    C E 117 "   -0.021 2.00e-02 2.50e+03
        pdb=" N3    C E 117 "   -0.006 2.00e-02 2.50e+03
        pdb=" C4    C E 117 "    0.008 2.00e-02 2.50e+03
        pdb=" N4    C E 117 "   -0.008 2.00e-02 2.50e+03
        pdb=" C5    C E 117 "   -0.003 2.00e-02 2.50e+03
        pdb=" C6    C E 117 "   -0.006 2.00e-02 2.50e+03
  ... (remaining 1319 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 932
        2.73 -     3.27: 9727
        3.27 -     3.82: 18691
        3.82 -     4.36: 21932
        4.36 -     4.90: 33764
  Nonbonded interactions: 85046
  Sorted by model distance:
  nonbonded pdb=" O   ALA C1091 "
            pdb=" OG  SER C1095 "
     model   vdw
     2.190 3.040
  nonbonded pdb=" O2    U E 109 "
            pdb=" O2'   G E 110 "
     model   vdw
     2.193 3.040
  nonbonded pdb=" O2'   U E 131 "
            pdb=" OP1   G E 132 "
     model   vdw
     2.214 3.040
  nonbonded pdb=" O2'   A E  79 "
            pdb=" O4'   A E  80 "
     model   vdw
     2.248 3.040
  nonbonded pdb=" O   LEU C 878 "
            pdb=" OG  SER C 881 "
     model   vdw
     2.254 3.040
  ... (remaining 85041 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.170
  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:             0.000
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     13.110
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.520
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.070
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7148
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      :  0.003   0.068  10861  Z= 0.152
  Angle     :  0.603  11.303  15558  Z= 0.308
  Chirality :  0.038   0.302   1878
  Planarity :  0.005   0.055   1322
  Dihedral  : 23.457 177.913   5288
  Min Nonbonded Distance : 2.190

Molprobity Statistics.
  All-atom Clashscore : 9.49
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.32 %
    Favored  : 95.56 %
  Rotamer:
    Outliers :  0.29 %
    Allowed  : 23.75 %
    Favored  : 75.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.68 (0.31), residues: 811
  helix:  1.83 (0.27), residues: 390
  sheet: -0.13 (0.66), residues: 62
  loop : -1.02 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 748 
 TYR   0.012   0.002   TYR C 703 
 PHE   0.015   0.002   PHE C 753 
 TRP   0.050   0.002   TRP C 701 
 HIS   0.005   0.001   HIS C 868 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 (10857)
  covalent geometry    : angle       0.60257 (15555)
  hydrogen bonds       : bond        0.14567 (  431)
  hydrogen bonds       : angle       5.30120 ( 1144)
  metal coordination   : bond        0.00247 (    4)
  metal coordination   : angle       1.24801 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 57
  time to evaluate  : 0.301 
Fit side-chains
  outliers start: 2
  outliers final: 1
  residues processed: 59
  average time/residue: 0.1227
  time to fit residues: 9.8826
Evaluate side-chains
  54 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 53
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue 1021 GLU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 49 optimal weight:    1.9990
   chunk 97 optimal weight:    7.9990
   chunk 53 optimal weight:    0.9980
   chunk 5 optimal weight:    0.6980
   chunk 33 optimal weight:    0.0030
   chunk 65 optimal weight:    0.0040
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.5980
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.4002

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

Flipped N/Q/H residues before XYZ refinement:
C 653 GLN
C 769 GLN
** C 946 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 = 0.4487 r_free = 0.4487 target = 0.185828 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.142021 restraints weight = 15621.380|
|-----------------------------------------------------------------------------|
r_work (start): 0.3932 rms_B_bonded: 2.43
r_work: 0.3504 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3504
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7767
moved from start:          0.0870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10861  Z= 0.115
  Angle     :  0.596   8.895  15558  Z= 0.295
  Chirality :  0.037   0.219   1878
  Planarity :  0.005   0.063   1322
  Dihedral  : 24.067 171.449   3723
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 7.78
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.82 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 23.01 %
    Favored  : 74.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.31), residues: 811
  helix:  2.04 (0.27), residues: 396
  sheet:  0.54 (0.71), residues: 56
  loop : -1.20 (0.34), residues: 359

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 814 
 TYR   0.009   0.001   TYR C 703 
 PHE   0.014   0.001   PHE C 749 
 TRP   0.019   0.001   TRP C 701 
 HIS   0.004   0.001   HIS C1096 

Details of bonding type rmsd
  covalent geometry    : bond        0.00226 (10857)
  covalent geometry    : angle       0.59511 (15555)
  hydrogen bonds       : bond        0.06331 (  431)
  hydrogen bonds       : angle       3.63514 ( 1144)
  metal coordination   : bond        0.01171 (    4)
  metal coordination   : angle       1.67295 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 60
  time to evaluate  : 0.314 
Fit side-chains
REVERT: C  401 PHE cc_start: 0.7330 (t80) cc_final: 0.7098 (t80)
REVERT: C  704 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6473 (pp)
REVERT: C 1072 GLU cc_start: 0.7859 (OUTLIER) cc_final: 0.7535 (mt-10)
REVERT: C 1105 MET cc_start: 0.7450 (ppp) cc_final: 0.6844 (ppp)
  outliers start: 18
  outliers final: 8
  residues processed: 76
  average time/residue: 0.1205
  time to fit residues: 12.6482
Evaluate side-chains
  63 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 53
  time to evaluate  : 0.315 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  410 ASP
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  704 LEU
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  861 VAL
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1072 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 1 optimal weight:    5.9990
   chunk 80 optimal weight:    2.9990
   chunk 75 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 0 optimal weight:   20.0000
   chunk 84 optimal weight:    7.9990
   chunk 81 optimal weight:   20.0000
   chunk 40 optimal weight:    1.9990
   chunk 42 optimal weight:    3.9990
   chunk 12 optimal weight:    2.9990
   chunk 82 optimal weight:   30.0000
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
C 493 GLN
** C 946 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 963 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4422 r_free = 0.4422 target = 0.180013 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3925 r_free = 0.3925 target = 0.136727 restraints weight = 15682.803|
|-----------------------------------------------------------------------------|
r_work (start): 0.3877 rms_B_bonded: 3.06
r_work: 0.3351 rms_B_bonded: 4.22 restraints_weight: 0.5000
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7949
moved from start:          0.1216

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.070  10861  Z= 0.261
  Angle     :  0.691   9.301  15558  Z= 0.348
  Chirality :  0.042   0.211   1878
  Planarity :  0.006   0.068   1322
  Dihedral  : 24.049 170.324   3720
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 8.69
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.29 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  4.57 %
    Allowed  : 23.30 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.20 (0.30), residues: 811
  helix:  1.42 (0.27), residues: 404
  sheet:  0.04 (0.67), residues: 57
  loop : -1.43 (0.34), residues: 350

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 549 
 TYR   0.022   0.003   TYR C 703 
 PHE   0.023   0.003   PHE C 749 
 TRP   0.034   0.002   TRP C 701 
 HIS   0.006   0.002   HIS C 868 

Details of bonding type rmsd
  covalent geometry    : bond        0.00601 (10857)
  covalent geometry    : angle       0.68911 (15555)
  hydrogen bonds       : bond        0.06263 (  431)
  hydrogen bonds       : angle       3.94392 ( 1144)
  metal coordination   : bond        0.00685 (    4)
  metal coordination   : angle       3.30228 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 56
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: C  548 LEU cc_start: 0.8112 (tp) cc_final: 0.7884 (tp)
REVERT: C  814 ARG cc_start: 0.7738 (ttt180) cc_final: 0.7147 (ttt180)
REVERT: C  883 ARG cc_start: 0.7846 (OUTLIER) cc_final: 0.7496 (ptm160)
REVERT: C 1072 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7715 (mt-10)
REVERT: C 1105 MET cc_start: 0.7583 (ppp) cc_final: 0.6901 (ppp)
  outliers start: 31
  outliers final: 19
  residues processed: 81
  average time/residue: 0.1045
  time to fit residues: 12.0855
Evaluate side-chains
  75 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 54
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 CYS
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  513 LEU
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  656 LEU
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  714 VAL
Chi-restraints excluded: chain C residue  761 ASP
Chi-restraints excluded: chain C residue  850 SER
Chi-restraints excluded: chain C residue  861 VAL
Chi-restraints excluded: chain C residue  883 ARG
Chi-restraints excluded: chain C residue  988 THR
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1052 VAL
Chi-restraints excluded: chain C residue 1072 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 11 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   chunk 90 optimal weight:    8.9990
   chunk 74 optimal weight:    0.3980
   chunk 64 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 82 optimal weight:   40.0000
   chunk 23 optimal weight:    0.9990
   chunk 29 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.2788

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

Flipped N/Q/H residues before XYZ refinement:
** C 946 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 = 0.4448 r_free = 0.4448 target = 0.182488 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3945 r_free = 0.3945 target = 0.138252 restraints weight = 15644.920|
|-----------------------------------------------------------------------------|
r_work (start): 0.3897 rms_B_bonded: 2.65
r_work: 0.3422 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7868
moved from start:          0.1358

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037  10861  Z= 0.144
  Angle     :  0.584   8.780  15558  Z= 0.293
  Chirality :  0.037   0.211   1878
  Planarity :  0.005   0.065   1322
  Dihedral  : 23.942 170.478   3720
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.82 %
    Favored  : 96.05 %
  Rotamer:
    Outliers :  4.28 %
    Allowed  : 23.75 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.46 (0.31), residues: 811
  helix:  1.67 (0.27), residues: 408
  sheet: -0.08 (0.67), residues: 56
  loop : -1.34 (0.34), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 987 
 TYR   0.018   0.002   TYR C 703 
 PHE   0.017   0.002   PHE C 749 
 TRP   0.027   0.001   TRP C 701 
 HIS   0.003   0.001   HIS C1096 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 (10857)
  covalent geometry    : angle       0.58304 (15555)
  hydrogen bonds       : bond        0.05200 (  431)
  hydrogen bonds       : angle       3.60092 ( 1144)
  metal coordination   : bond        0.00734 (    4)
  metal coordination   : angle       1.91155 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 60
  time to evaluate  : 0.288 
Fit side-chains
REVERT: C  410 ASP cc_start: 0.6609 (OUTLIER) cc_final: 0.5870 (p0)
REVERT: C  435 ARG cc_start: 0.7040 (ttp-170) cc_final: 0.6682 (ttp-170)
REVERT: C  548 LEU cc_start: 0.8083 (tp) cc_final: 0.7828 (tp)
REVERT: C  551 MET cc_start: 0.7500 (OUTLIER) cc_final: 0.6975 (mtt)
REVERT: C  776 GLN cc_start: 0.8089 (OUTLIER) cc_final: 0.7761 (tt0)
REVERT: C  814 ARG cc_start: 0.7667 (ttt180) cc_final: 0.7004 (ttt180)
REVERT: C  883 ARG cc_start: 0.7677 (OUTLIER) cc_final: 0.7341 (ptm160)
REVERT: C  950 GLN cc_start: 0.8266 (OUTLIER) cc_final: 0.7265 (pp30)
REVERT: C  987 ARG cc_start: 0.6647 (OUTLIER) cc_final: 0.3866 (mmp-170)
REVERT: C 1026 LYS cc_start: 0.8133 (mmtt) cc_final: 0.7841 (mmmt)
REVERT: C 1072 GLU cc_start: 0.7972 (OUTLIER) cc_final: 0.7687 (mt-10)
REVERT: C 1105 MET cc_start: 0.7604 (ppp) cc_final: 0.7076 (ppp)
  outliers start: 29
  outliers final: 15
  residues processed: 84
  average time/residue: 0.1105
  time to fit residues: 12.8233
Evaluate side-chains
  77 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 55
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 CYS
Chi-restraints excluded: chain C residue  410 ASP
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  513 LEU
Chi-restraints excluded: chain C residue  551 MET
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  714 VAL
Chi-restraints excluded: chain C residue  757 ASN
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  803 VAL
Chi-restraints excluded: chain C residue  861 VAL
Chi-restraints excluded: chain C residue  883 ARG
Chi-restraints excluded: chain C residue  950 GLN
Chi-restraints excluded: chain C residue  987 ARG
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1072 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 1 optimal weight:    6.9990
   chunk 73 optimal weight:    0.9980
   chunk 85 optimal weight:   20.0000
   chunk 69 optimal weight:    4.9990
   chunk 15 optimal weight:    0.0170
   chunk 29 optimal weight:    3.9990
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9980
   chunk 91 optimal weight:   10.0000
   chunk 60 optimal weight:    1.9990
   overall best weight:    0.9220

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

Flipped N/Q/H residues before XYZ refinement:
** C 946 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 = 0.4461 r_free = 0.4461 target = 0.183690 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3965 r_free = 0.3965 target = 0.140017 restraints weight = 15880.752|
|-----------------------------------------------------------------------------|
r_work (start): 0.3921 rms_B_bonded: 2.85
r_work: 0.3422 rms_B_bonded: 4.25 restraints_weight: 0.5000
r_work (final): 0.3422
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7864
moved from start:          0.1584

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10861  Z= 0.125
  Angle     :  0.556   8.654  15558  Z= 0.279
  Chirality :  0.036   0.200   1878
  Planarity :  0.005   0.060   1322
  Dihedral  : 23.747 170.070   3720
  Min Nonbonded Distance : 2.506

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  5.06 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  5.16 %
    Allowed  : 23.60 %
    Favored  : 71.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.63 (0.31), residues: 811
  helix:  1.85 (0.27), residues: 409
  sheet: -0.15 (0.67), residues: 56
  loop : -1.30 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 748 
 TYR   0.046   0.002   TYR C 703 
 PHE   0.015   0.001   PHE C 749 
 TRP   0.026   0.001   TRP C 701 
 HIS   0.004   0.001   HIS C 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (10857)
  covalent geometry    : angle       0.55546 (15555)
  hydrogen bonds       : bond        0.04781 (  431)
  hydrogen bonds       : angle       3.42709 ( 1144)
  metal coordination   : bond        0.00742 (    4)
  metal coordination   : angle       1.50176 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 35
    poor density    : 56
  time to evaluate  : 0.303 
Fit side-chains
REVERT: C  435 ARG cc_start: 0.6988 (ttp-170) cc_final: 0.6622 (ttp-170)
REVERT: C  548 LEU cc_start: 0.8186 (tp) cc_final: 0.7935 (tp)
REVERT: C  551 MET cc_start: 0.7591 (OUTLIER) cc_final: 0.7123 (mtt)
REVERT: C  776 GLN cc_start: 0.8120 (OUTLIER) cc_final: 0.7788 (tt0)
REVERT: C  814 ARG cc_start: 0.7611 (ttt180) cc_final: 0.6812 (ttt180)
REVERT: C  950 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7314 (pp30)
REVERT: C 1026 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7884 (mmmt)
REVERT: C 1072 GLU cc_start: 0.7960 (OUTLIER) cc_final: 0.7668 (mt-10)
REVERT: C 1080 ARG cc_start: 0.7763 (mpp-170) cc_final: 0.7501 (mtt180)
REVERT: C 1105 MET cc_start: 0.7696 (ppp) cc_final: 0.7167 (ppp)
  outliers start: 35
  outliers final: 19
  residues processed: 86
  average time/residue: 0.1026
  time to fit residues: 12.5441
Evaluate side-chains
  79 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 56
  time to evaluate  : 0.276 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 CYS
Chi-restraints excluded: chain C residue  410 ASP
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  513 LEU
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  551 MET
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  711 SER
Chi-restraints excluded: chain C residue  714 VAL
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  861 VAL
Chi-restraints excluded: chain C residue  950 GLN
Chi-restraints excluded: chain C residue  960 LEU
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1021 GLU
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1072 GLU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    0.7980
   chunk 57 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    0.8980
   chunk 81 optimal weight:   20.0000
   chunk 66 optimal weight:    4.9990
   chunk 87 optimal weight:    5.9990
   chunk 73 optimal weight:    1.9990
   chunk 74 optimal weight:    0.9980
   chunk 36 optimal weight:    0.7980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
** C 946 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 = 0.4468 r_free = 0.4468 target = 0.184360 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3972 r_free = 0.3972 target = 0.140355 restraints weight = 15955.754|
|-----------------------------------------------------------------------------|
r_work (start): 0.3924 rms_B_bonded: 2.74
r_work: 0.3442 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3442
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1799

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032  10861  Z= 0.117
  Angle     :  0.546   8.627  15558  Z= 0.273
  Chirality :  0.036   0.194   1878
  Planarity :  0.004   0.057   1322
  Dihedral  : 23.605 169.964   3720
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.33 %
    Favored  : 96.55 %
  Rotamer:
    Outliers :  5.60 %
    Allowed  : 22.42 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.72 (0.31), residues: 811
  helix:  1.93 (0.27), residues: 409
  sheet: -0.04 (0.66), residues: 56
  loop : -1.28 (0.34), residues: 346

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 748 
 TYR   0.025   0.002   TYR C 703 
 PHE   0.015   0.002   PHE C 749 
 TRP   0.023   0.001   TRP C 701 
 HIS   0.003   0.001   HIS C1096 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 (10857)
  covalent geometry    : angle       0.54525 (15555)
  hydrogen bonds       : bond        0.04590 (  431)
  hydrogen bonds       : angle       3.35415 ( 1144)
  metal coordination   : bond        0.00631 (    4)
  metal coordination   : angle       1.42413 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 38
    poor density    : 63
  time to evaluate  : 0.297 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  483 LEU cc_start: 0.8362 (mt) cc_final: 0.8068 (mm)
REVERT: C  548 LEU cc_start: 0.8185 (tp) cc_final: 0.7923 (tp)
REVERT: C  551 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7136 (mtt)
REVERT: C  758 ILE cc_start: 0.6374 (OUTLIER) cc_final: 0.6142 (tt)
REVERT: C  776 GLN cc_start: 0.8101 (OUTLIER) cc_final: 0.7769 (tt0)
REVERT: C  883 ARG cc_start: 0.7655 (OUTLIER) cc_final: 0.7315 (ptm160)
REVERT: C  950 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.7308 (pp30)
REVERT: C 1026 LYS cc_start: 0.8135 (mmtt) cc_final: 0.7875 (mmmt)
REVERT: C 1072 GLU cc_start: 0.7918 (OUTLIER) cc_final: 0.7560 (mt-10)
REVERT: C 1105 MET cc_start: 0.7639 (ppp) cc_final: 0.7191 (ppp)
  outliers start: 38
  outliers final: 24
  residues processed: 93
  average time/residue: 0.1042
  time to fit residues: 13.4581
Evaluate side-chains
  88 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 58
  time to evaluate  : 0.290 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 CYS
Chi-restraints excluded: chain C residue  349 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  410 ASP
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  513 LEU
Chi-restraints excluded: chain C residue  551 MET
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  711 SER
Chi-restraints excluded: chain C residue  714 VAL
Chi-restraints excluded: chain C residue  757 ASN
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  765 MET
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  855 THR
Chi-restraints excluded: chain C residue  861 VAL
Chi-restraints excluded: chain C residue  883 ARG
Chi-restraints excluded: chain C residue  950 GLN
Chi-restraints excluded: chain C residue  960 LEU
Chi-restraints excluded: chain C residue  982 LEU
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1021 GLU
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1072 GLU
Chi-restraints excluded: chain C residue 1083 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 48 optimal weight:    0.4980
   chunk 34 optimal weight:    0.9980
   chunk 9 optimal weight:    8.9990
   chunk 0 optimal weight:   20.0000
   chunk 89 optimal weight:   10.0000
   chunk 44 optimal weight:    7.9990
   chunk 97 optimal weight:    8.9990
   chunk 86 optimal weight:   10.0000
   chunk 32 optimal weight:    6.9990
   chunk 80 optimal weight:    4.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    2.8384

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

Flipped N/Q/H residues before XYZ refinement:
C 870 HIS
** C 946 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 = 0.4421 r_free = 0.4421 target = 0.180028 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3909 r_free = 0.3909 target = 0.135706 restraints weight = 15686.336|
|-----------------------------------------------------------------------------|
r_work (start): 0.3863 rms_B_bonded: 2.88
r_work: 0.3355 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3355
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7946
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.082  10861  Z= 0.253
  Angle     :  0.659   8.895  15558  Z= 0.333
  Chirality :  0.041   0.189   1878
  Planarity :  0.005   0.059   1322
  Dihedral  : 23.707 169.191   3720
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.38
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  6.29 %
    Favored  : 93.59 %
  Rotamer:
    Outliers :  5.75 %
    Allowed  : 21.83 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.24 (0.30), residues: 811
  helix:  1.52 (0.27), residues: 406
  sheet: -0.42 (0.64), residues: 56
  loop : -1.44 (0.33), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 748 
 TYR   0.027   0.003   TYR C 703 
 PHE   0.022   0.003   PHE C 749 
 TRP   0.032   0.002   TRP C 701 
 HIS   0.005   0.001   HIS C 868 

Details of bonding type rmsd
  covalent geometry    : bond        0.00583 (10857)
  covalent geometry    : angle       0.65763 (15555)
  hydrogen bonds       : bond        0.05461 (  431)
  hydrogen bonds       : angle       3.79969 ( 1144)
  metal coordination   : bond        0.00572 (    4)
  metal coordination   : angle       2.97620 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  97 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 39
    poor density    : 58
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: C  337 CYS cc_start: 0.6694 (OUTLIER) cc_final: 0.6279 (m)
REVERT: C  410 ASP cc_start: 0.6888 (OUTLIER) cc_final: 0.6454 (p0)
REVERT: C  435 ARG cc_start: 0.7151 (ttp-170) cc_final: 0.6782 (ttp-170)
REVERT: C  758 ILE cc_start: 0.7129 (OUTLIER) cc_final: 0.6907 (tp)
REVERT: C  776 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7872 (tt0)
REVERT: C  883 ARG cc_start: 0.7810 (OUTLIER) cc_final: 0.7461 (ptm160)
REVERT: C  950 GLN cc_start: 0.8337 (OUTLIER) cc_final: 0.7359 (pp30)
REVERT: C 1026 LYS cc_start: 0.8190 (mmtt) cc_final: 0.7889 (mmmt)
  outliers start: 39
  outliers final: 27
  residues processed: 86
  average time/residue: 0.0983
  time to fit residues: 12.1377
Evaluate side-chains
  90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 57
  time to evaluate  : 0.293 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 CYS
Chi-restraints excluded: chain C residue  349 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  410 ASP
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  513 LEU
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  654 MET
Chi-restraints excluded: chain C residue  656 LEU
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  711 SER
Chi-restraints excluded: chain C residue  714 VAL
Chi-restraints excluded: chain C residue  757 ASN
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  761 ASP
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  803 VAL
Chi-restraints excluded: chain C residue  855 THR
Chi-restraints excluded: chain C residue  861 VAL
Chi-restraints excluded: chain C residue  883 ARG
Chi-restraints excluded: chain C residue  950 GLN
Chi-restraints excluded: chain C residue  960 LEU
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1021 GLU
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1072 GLU
Chi-restraints excluded: chain C residue 1083 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 23 optimal weight:    1.9990
   chunk 33 optimal weight:    0.6980
   chunk 87 optimal weight:    5.9990
   chunk 27 optimal weight:    6.9990
   chunk 1 optimal weight:    5.9990
   chunk 95 optimal weight:   30.0000
   chunk 90 optimal weight:    6.9990
   chunk 41 optimal weight:    0.0970
   chunk 61 optimal weight:    0.9990
   chunk 10 optimal weight:    9.9990
   chunk 69 optimal weight:    3.9990
   overall best weight:    1.5584

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

Flipped N/Q/H residues before XYZ refinement:
** C 946 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 = 0.4440 r_free = 0.4440 target = 0.181736 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3924 r_free = 0.3924 target = 0.136741 restraints weight = 15724.714|
|-----------------------------------------------------------------------------|
r_work (start): 0.3879 rms_B_bonded: 2.75
r_work: 0.3395 rms_B_bonded: 4.10 restraints_weight: 0.5000
r_work (final): 0.3395
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7901
moved from start:          0.2059

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053  10861  Z= 0.160
  Angle     :  0.586   8.646  15558  Z= 0.295
  Chirality :  0.038   0.193   1878
  Planarity :  0.005   0.056   1322
  Dihedral  : 23.653 169.647   3720
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 8.48
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.19 %
    Favored  : 95.68 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 23.01 %
    Favored  : 72.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.45 (0.31), residues: 811
  helix:  1.71 (0.27), residues: 408
  sheet: -0.31 (0.66), residues: 56
  loop : -1.37 (0.33), residues: 347

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 748 
 TYR   0.026   0.002   TYR C 703 
 PHE   0.019   0.002   PHE C 749 
 TRP   0.027   0.002   TRP C 701 
 HIS   0.004   0.001   HIS C 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00361 (10857)
  covalent geometry    : angle       0.58527 (15555)
  hydrogen bonds       : bond        0.04795 (  431)
  hydrogen bonds       : angle       3.57085 ( 1144)
  metal coordination   : bond        0.00533 (    4)
  metal coordination   : angle       1.90038 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 62
  time to evaluate  : 0.280 
Fit side-chains
REVERT: C  337 CYS cc_start: 0.6849 (OUTLIER) cc_final: 0.6524 (m)
REVERT: C  548 LEU cc_start: 0.8217 (tp) cc_final: 0.7977 (tp)
REVERT: C  551 MET cc_start: 0.7348 (OUTLIER) cc_final: 0.6974 (mtt)
REVERT: C  704 LEU cc_start: 0.7100 (OUTLIER) cc_final: 0.6495 (pp)
REVERT: C  758 ILE cc_start: 0.6833 (OUTLIER) cc_final: 0.6589 (tp)
REVERT: C  776 GLN cc_start: 0.8085 (OUTLIER) cc_final: 0.7767 (tt0)
REVERT: C  814 ARG cc_start: 0.7617 (ttt180) cc_final: 0.7001 (ttt180)
REVERT: C  883 ARG cc_start: 0.7672 (OUTLIER) cc_final: 0.7360 (ptm160)
REVERT: C  950 GLN cc_start: 0.8318 (OUTLIER) cc_final: 0.7333 (pp30)
REVERT: C 1026 LYS cc_start: 0.8173 (mmtt) cc_final: 0.7944 (mmmm)
REVERT: C 1072 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.7681 (mt-10)
REVERT: C 1105 MET cc_start: 0.7658 (ppp) cc_final: 0.7357 (ppp)
  outliers start: 33
  outliers final: 25
  residues processed: 88
  average time/residue: 0.0972
  time to fit residues: 12.1267
Evaluate side-chains
  90 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 33
    poor density    : 57
  time to evaluate  : 0.237 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 CYS
Chi-restraints excluded: chain C residue  349 THR
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  410 ASP
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  513 LEU
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  551 MET
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  654 MET
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  704 LEU
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  714 VAL
Chi-restraints excluded: chain C residue  757 ASN
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  803 VAL
Chi-restraints excluded: chain C residue  855 THR
Chi-restraints excluded: chain C residue  861 VAL
Chi-restraints excluded: chain C residue  883 ARG
Chi-restraints excluded: chain C residue  950 GLN
Chi-restraints excluded: chain C residue  960 LEU
Chi-restraints excluded: chain C residue  986 LEU
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1021 GLU
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1072 GLU
Chi-restraints excluded: chain C residue 1083 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 40 optimal weight:    4.9990
   chunk 66 optimal weight:    2.9990
   chunk 91 optimal weight:    9.9990
   chunk 28 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 16 optimal weight:    0.3980
   chunk 49 optimal weight:    1.9990
   chunk 11 optimal weight:    0.2980
   chunk 46 optimal weight:    0.8980
   chunk 74 optimal weight:    6.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** C 946 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 = 0.4471 r_free = 0.4471 target = 0.184572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3976 r_free = 0.3976 target = 0.140898 restraints weight = 15731.961|
|-----------------------------------------------------------------------------|
r_work (start): 0.3931 rms_B_bonded: 2.80
r_work: 0.3445 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3445
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7831
moved from start:          0.2196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030  10861  Z= 0.109
  Angle     :  0.541   8.469  15558  Z= 0.271
  Chirality :  0.035   0.195   1878
  Planarity :  0.004   0.054   1322
  Dihedral  : 23.470 169.439   3720
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 7.30
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.44 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  4.42 %
    Allowed  : 23.60 %
    Favored  : 71.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.78 (0.31), residues: 811
  helix:  2.02 (0.27), residues: 407
  sheet: -0.07 (0.67), residues: 56
  loop : -1.27 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG C 748 
 TYR   0.019   0.001   TYR C 703 
 PHE   0.017   0.002   PHE C 749 
 TRP   0.023   0.001   TRP C 701 
 HIS   0.004   0.001   HIS C1096 

Details of bonding type rmsd
  covalent geometry    : bond        0.00232 (10857)
  covalent geometry    : angle       0.54088 (15555)
  hydrogen bonds       : bond        0.04400 (  431)
  hydrogen bonds       : angle       3.35286 ( 1144)
  metal coordination   : bond        0.00931 (    4)
  metal coordination   : angle       1.26489 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 57
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: C  548 LEU cc_start: 0.8238 (tp) cc_final: 0.8036 (tp)
REVERT: C  704 LEU cc_start: 0.6936 (OUTLIER) cc_final: 0.6432 (pp)
REVERT: C  758 ILE cc_start: 0.6229 (OUTLIER) cc_final: 0.6009 (tt)
REVERT: C  767 ASP cc_start: 0.8229 (OUTLIER) cc_final: 0.7992 (m-30)
REVERT: C  776 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7679 (tt0)
REVERT: C  883 ARG cc_start: 0.7603 (OUTLIER) cc_final: 0.7302 (ptm160)
REVERT: C  950 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.7339 (pp30)
REVERT: C 1080 ARG cc_start: 0.7553 (mpp-170) cc_final: 0.7212 (mtt180)
REVERT: C 1105 MET cc_start: 0.7596 (ppp) cc_final: 0.7075 (ppp)
  outliers start: 30
  outliers final: 19
  residues processed: 81
  average time/residue: 0.0991
  time to fit residues: 11.4940
Evaluate side-chains
  81 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 56
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 CYS
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  410 ASP
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  503 LEU
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  704 LEU
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  714 VAL
Chi-restraints excluded: chain C residue  757 ASN
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  767 ASP
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  803 VAL
Chi-restraints excluded: chain C residue  855 THR
Chi-restraints excluded: chain C residue  883 ARG
Chi-restraints excluded: chain C residue  950 GLN
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1083 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 98 optimal weight:    6.9990
   chunk 90 optimal weight:    8.9990
   chunk 70 optimal weight:    0.7980
   chunk 38 optimal weight:    0.1980
   chunk 55 optimal weight:    0.8980
   chunk 44 optimal weight:    0.9990
   chunk 82 optimal weight:   40.0000
   chunk 23 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   chunk 40 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** C 946 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 = 0.4468 r_free = 0.4468 target = 0.184304 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.140606 restraints weight = 15563.603|
|-----------------------------------------------------------------------------|
r_work (start): 0.3928 rms_B_bonded: 2.82
r_work: 0.3434 rms_B_bonded: 4.13 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7848
moved from start:          0.2306

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  10861  Z= 0.115
  Angle     :  0.539   8.556  15558  Z= 0.271
  Chirality :  0.035   0.195   1878
  Planarity :  0.004   0.054   1322
  Dihedral  : 23.392 169.184   3720
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  3.45 %
    Favored  : 96.42 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 23.89 %
    Favored  : 72.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.31), residues: 811
  helix:  2.10 (0.27), residues: 407
  sheet: -0.06 (0.66), residues: 56
  loop : -1.27 (0.34), residues: 348

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 748 
 TYR   0.021   0.002   TYR C 703 
 PHE   0.015   0.001   PHE C 749 
 TRP   0.024   0.001   TRP C 701 
 HIS   0.004   0.001   HIS C 423 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 (10857)
  covalent geometry    : angle       0.53861 (15555)
  hydrogen bonds       : bond        0.04366 (  431)
  hydrogen bonds       : angle       3.34177 ( 1144)
  metal coordination   : bond        0.00866 (    4)
  metal coordination   : angle       1.67224 (    3)

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

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

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1622 Ramachandran restraints generated.
    811 Oldfield, 0 Emsley, 811 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 59
  time to evaluate  : 0.187 
Fit side-chains
   revert: symmetry clash
REVERT: C  483 LEU cc_start: 0.8224 (OUTLIER) cc_final: 0.8023 (mp)
REVERT: C  704 LEU cc_start: 0.7041 (OUTLIER) cc_final: 0.6569 (pp)
REVERT: C  758 ILE cc_start: 0.6342 (OUTLIER) cc_final: 0.6112 (tt)
REVERT: C  767 ASP cc_start: 0.8243 (OUTLIER) cc_final: 0.7991 (m-30)
REVERT: C  776 GLN cc_start: 0.8133 (OUTLIER) cc_final: 0.7676 (tt0)
REVERT: C  883 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7335 (ptm160)
REVERT: C  950 GLN cc_start: 0.8314 (OUTLIER) cc_final: 0.7297 (pp30)
REVERT: C 1080 ARG cc_start: 0.7572 (mpp-170) cc_final: 0.7236 (mtt180)
REVERT: C 1105 MET cc_start: 0.7606 (ppp) cc_final: 0.6901 (ppp)
  outliers start: 26
  outliers final: 19
  residues processed: 82
  average time/residue: 0.0935
  time to fit residues: 10.8021
Evaluate side-chains
  82 residues out of total 687 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 56
  time to evaluate  : 0.197 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  337 CYS
Chi-restraints excluded: chain C residue  387 LEU
Chi-restraints excluded: chain C residue  410 ASP
Chi-restraints excluded: chain C residue  450 VAL
Chi-restraints excluded: chain C residue  483 LEU
Chi-restraints excluded: chain C residue  528 LEU
Chi-restraints excluded: chain C residue  649 CYS
Chi-restraints excluded: chain C residue  658 LEU
Chi-restraints excluded: chain C residue  677 HIS
Chi-restraints excluded: chain C residue  701 TRP
Chi-restraints excluded: chain C residue  704 LEU
Chi-restraints excluded: chain C residue  706 VAL
Chi-restraints excluded: chain C residue  714 VAL
Chi-restraints excluded: chain C residue  758 ILE
Chi-restraints excluded: chain C residue  767 ASP
Chi-restraints excluded: chain C residue  776 GLN
Chi-restraints excluded: chain C residue  784 VAL
Chi-restraints excluded: chain C residue  803 VAL
Chi-restraints excluded: chain C residue  855 THR
Chi-restraints excluded: chain C residue  883 ARG
Chi-restraints excluded: chain C residue  950 GLN
Chi-restraints excluded: chain C residue 1004 VAL
Chi-restraints excluded: chain C residue 1013 VAL
Chi-restraints excluded: chain C residue 1021 GLU
Chi-restraints excluded: chain C residue 1046 LEU
Chi-restraints excluded: chain C residue 1083 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 99
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0870
   chunk 86 optimal weight:   10.0000
   chunk 43 optimal weight:    3.9990
   chunk 94 optimal weight:   10.0000
   chunk 60 optimal weight:    0.4980
   chunk 37 optimal weight:    0.8980
   chunk 30 optimal weight:    0.7980
   chunk 36 optimal weight:    0.2980
   chunk 57 optimal weight:    0.7980
   chunk 84 optimal weight:    7.9990
   overall best weight:    0.4958

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

Flipped N/Q/H residues before XYZ refinement:
** C 946 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 = 0.4479 r_free = 0.4479 target = 0.185345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.141838 restraints weight = 15569.231|
|-----------------------------------------------------------------------------|
r_work (start): 0.3944 rms_B_bonded: 2.52
r_work: 0.3488 rms_B_bonded: 3.88 restraints_weight: 0.5000
r_work (final): 0.3488
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7787
moved from start:          0.2450

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031  10861  Z= 0.100
  Angle     :  0.532  10.707  15558  Z= 0.264
  Chirality :  0.035   0.196   1878
  Planarity :  0.004   0.053   1322
  Dihedral  : 23.350 169.322   3720
  Min Nonbonded Distance : 2.404

Molprobity Statistics.
  All-atom Clashscore : 7.94
  Ramachandran Plot:
    Outliers :  0.12 %
    Allowed  :  4.07 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  3.24 %
    Allowed  : 24.34 %
    Favored  : 72.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.95 (0.31), residues: 811
  helix:  2.22 (0.27), residues: 406
  sheet:  0.06 (0.66), residues: 56
  loop : -1.27 (0.34), residues: 349

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 748 
 TYR   0.016   0.001   TYR C 703 
 PHE   0.014   0.001   PHE C 749 
 TRP   0.022   0.001   TRP C 701 
 HIS   0.004   0.001   HIS C 910 

Details of bonding type rmsd
  covalent geometry    : bond        0.00208 (10857)
  covalent geometry    : angle       0.53188 (15555)
  hydrogen bonds       : bond        0.04251 (  431)
  hydrogen bonds       : angle       3.27112 ( 1144)
  metal coordination   : bond        0.01032 (    4)
  metal coordination   : angle       1.43637 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2810.00 seconds
wall clock time: 48 minutes 40.01 seconds (2920.01 seconds total)