Starting phenix.real_space_refine
on Fri Jul  3 09:43:20 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7tre_26087/07_2026/7tre_26087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tre_26087/07_2026/7tre_26087.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7tre_26087/07_2026/7tre_26087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tre_26087/07_2026/7tre_26087.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7tre_26087/07_2026/7tre_26087.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7tre_26087/07_2026/7tre_26087.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tre_26087/07_2026/7tre_26087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tre_26087/07_2026/7tre_26087.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.004
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     224      5.49       5
     S      40      5.16       5
     C    7660      2.51       5
     N    2426      2.21       5
     O    3061      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 75 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 13411
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "B"
      Number of atoms: 4605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 4605
          Classifications: {'RNA': 217}
          Modifications used: {'rna2p_pur': 14, 'rna2p_pyr': 20, 'rna3p_pur': 86, 'rna3p_pyr': 97}
          Link IDs: {'rna2p': 34, 'rna3p': 182}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 7488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 934, 7488
          Classifications: {'peptide': 934}
          Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 147
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
    Chain: "C"
      Number of atoms: 1171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1171
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 9, 'TRANS': 142}
  Time building chain proxies: 2.56, per 1000 atoms: 0.19
  Number of scatterers: 13411
  At special positions: 0
  Unit cell: (140.8, 122.1, 108.9, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      40     16.00
     P     224     15.00
     O    3061      8.00
     N    2426      7.00
     C    7660      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 487.1 milliseconds
  

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2044

  Finding SS restraints...
    Secondary structure from input PDB file:
      48 helices and 8 sheets defined
      50.6% alpha, 14.7% beta
      61 base pairs and 96 stacking pairs defined.
    Time for finding SS restraints: 1.34
  Creating SS restraints...
    Processing helix  chain 'A' and resid 7 through 18
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 76 through 92
    Processing helix  chain 'A' and resid 95 through 99
      removed outlier: 3.542A  pdb=" N   PHE A  99 " --> pdb=" O   VAL A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 134
      removed outlier: 3.512A  pdb=" N   GLY A 133 " --> pdb=" O   ASP A 129 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 146 through 155
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.812A  pdb=" N   LEU A 178 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 331
      No H-bonds generated for 'chain 'A' and resid 329 through 331'
    Processing helix  chain 'A' and resid 353 through 366
      removed outlier: 3.730A  pdb=" N   ALA A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 402
      removed outlier: 3.943A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
      removed outlier: 3.551A  pdb=" N   GLN A 402 " --> pdb=" O   GLY A 398 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.828A  pdb=" N   LEU A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 453
    Processing helix  chain 'A' and resid 457 through 470
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.628A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.648A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 551
      removed outlier: 3.908A  pdb=" N   HIS A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
      removed outlier: 3.849A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 4.355A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.822A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.786A  pdb=" N   LYS A 594 " --> pdb=" O   ARG A 590 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 610
    Processing helix  chain 'A' and resid 652 through 672
      removed outlier: 3.664A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.836A  pdb=" N   LEU A 676 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY A 677 " --> pdb=" O   GLY A 674 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 673 through 677'
    Processing helix  chain 'A' and resid 682 through 699
      removed outlier: 3.876A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
      removed outlier: 3.756A  pdb=" N   ALA A 699 " --> pdb=" O   LEU A 695 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 772 through 784
    Processing helix  chain 'A' and resid 802 through 814
    Processing helix  chain 'A' and resid 837 through 854
    Processing helix  chain 'A' and resid 856 through 860
      removed outlier: 4.160A  pdb=" N   ASP A 860 " --> pdb=" O   ILE A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 890
      removed outlier: 3.605A  pdb=" N   GLY A 890 " --> pdb=" O   THR A 886 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.809A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 958
      removed outlier: 4.033A  pdb=" N   LEU A 958 " --> pdb=" O   ARG A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 982
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 993 through 1017
    Processing helix  chain 'A' and resid 1024 through 1027
    Processing helix  chain 'A' and resid 1028 through 1051
      removed outlier: 4.094A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1082
      removed outlier: 4.072A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.771A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.702A  pdb=" N   TRP A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.675A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.638A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 5.640A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.690A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.875A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   LEU A1107 " --> pdb=" O   LEU A1103 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1118
    Processing helix  chain 'C' and resid 98 through 104
      removed outlier: 3.865A  pdb=" N   LEU C 104 " --> pdb=" O   ARG C 100 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 158 through 164
    Processing helix  chain 'C' and resid 167 through 171
      removed outlier: 3.507A  pdb=" N   LYS C 170 " --> pdb=" O   TRP C 167 " (cutoff:3.500A)
      removed outlier: 4.454A  pdb=" N   GLU C 171 " --> pdb=" O   GLU C 168 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 167 through 171'
    Processing helix  chain 'C' and resid 223 through 226
    Processing helix  chain 'C' and resid 227 through 241
    Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 23
      removed outlier: 3.728A  pdb=" N   GLU A  20 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 6.401A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 6.192A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 8.072A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 8.337A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.962A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.973A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 20.101A  pdb=" N   SER A 797 " --> pdb=" O   CYS A 171 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 4.837A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.849A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 5.399A  pdb=" N   LEU A 798 " --> pdb=" O   TYR A 739 " (cutoff:3.500A)
      removed outlier: 5.644A  pdb=" N   TYR A 739 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
      removed outlier: 3.814A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102
    Processing sheet with id=AA3, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA4, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA5, first strand: chain 'A' and resid 598 through 600
      removed outlier: 4.566A  pdb=" N   GLN A 827 " --> pdb=" O   HIS A 816 " (cutoff:3.500A)
      removed outlier: 6.590A  pdb=" N   HIS A 816 " --> pdb=" O   GLN A 827 " (cutoff:3.500A)
      removed outlier: 6.914A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 8.379A  pdb=" N   ARG A 819 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 6.735A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 862 through 865
      removed outlier: 3.537A  pdb=" N   VAL A 904 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 4.160A  pdb=" N   ASP A 712 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
      removed outlier: 6.822A  pdb=" N   LYS A 902 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 927 through 930
    Processing sheet with id=AA8, first strand: chain 'C' and resid 114 through 120
      removed outlier: 7.126A  pdb=" N   LEU C 145 " --> pdb=" O   LEU C 118 " (cutoff:3.500A)
      removed outlier: 5.330A  pdb=" N   VAL C 120 " --> pdb=" O   THR C 143 " (cutoff:3.500A)
      removed outlier: 7.600A  pdb=" N   THR C 143 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 9.417A  pdb=" N   LEU C 204 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 6.769A  pdb=" N   ARG C 154 " --> pdb=" O   LEU C 204 " (cutoff:3.500A)
      removed outlier: 7.639A  pdb=" N   VAL C 206 " --> pdb=" O   ARG C 154 " (cutoff:3.500A)
      removed outlier: 6.342A  pdb=" N   LEU C 156 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 7.976A  pdb=" N   ARG C 208 " --> pdb=" O   LEU C 156 " (cutoff:3.500A)
      removed outlier: 6.135A  pdb=" N   ASP C 186 " --> pdb=" O   ASP C 207 " (cutoff:3.500A)
      removed outlier: 6.615A  pdb=" N   PHE C 209 " --> pdb=" O   LEU C 184 " (cutoff:3.500A)
      removed outlier: 6.561A  pdb=" N   LEU C 184 " --> pdb=" O   PHE C 209 " (cutoff:3.500A)
      removed outlier: 6.817A  pdb=" N   LEU C 211 " --> pdb=" O   LEU C 182 " (cutoff:3.500A)
      removed outlier: 6.824A  pdb=" N   LEU C 182 " --> pdb=" O   LEU C 211 " (cutoff:3.500A)
      removed outlier: 7.569A  pdb=" N   ARG C 180 " --> pdb=" O   PRO C 213 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ARG C 180 " --> pdb=" O   LEU C 117 " (cutoff:3.500A)

    410 hydrogen bonds defined for protein.
    1173 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      166 hydrogen bonds
      316 hydrogen bond angles
      0 basepair planarities
      61 basepair parallelities
      96 stacking parallelities
  Total time for adding SS restraints: 3.19

  Time building geometry restraints manager: 1.50 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: 2319
        1.33 -     1.45: 4595
        1.45 -     1.57: 6752
        1.57 -     1.69: 444
        1.69 -     1.81: 51
  Bond restraints: 14161
  Sorted by residual:
  bond pdb=" C3'  DG D  18 "
       pdb=" O3'  DG D  18 "
    ideal  model  delta    sigma   weight residual
    1.435  1.389  0.046 1.30e-02 5.92e+03 1.26e+01
  bond pdb=" C3'  DT D  13 "
       pdb=" C2'  DT D  13 "
    ideal  model  delta    sigma   weight residual
    1.516  1.542 -0.026 8.00e-03 1.56e+04 1.03e+01
  bond pdb=" C3'  DA D  15 "
       pdb=" O3'  DA D  15 "
    ideal  model  delta    sigma   weight residual
    1.435  1.399  0.036 1.30e-02 5.92e+03 7.73e+00
  bond pdb=" N   VAL A 127 "
       pdb=" CA  VAL A 127 "
    ideal  model  delta    sigma   weight residual
    1.461  1.493 -0.032 1.17e-02 7.31e+03 7.41e+00
  bond pdb=" C4'  DG D  18 "
       pdb=" C3'  DG D  18 "
    ideal  model  delta    sigma   weight residual
    1.529  1.502  0.027 1.00e-02 1.00e+04 7.36e+00
  ... (remaining 14156 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 19411
        1.73 -     3.47: 756
        3.47 -     5.20: 80
        5.20 -     6.93: 14
        6.93 -     8.66: 5
  Bond angle restraints: 20266
  Sorted by residual:
  angle pdb=" O4'  DG D  18 "
        pdb=" C4'  DG D  18 "
        pdb=" C3'  DG D  18 "
      ideal   model   delta    sigma   weight residual
     106.00  102.84    3.16 6.00e-01 2.78e+00 2.78e+01
  angle pdb=" N3   DT D  14 "
        pdb=" C4   DT D  14 "
        pdb=" O4   DT D  14 "
      ideal   model   delta    sigma   weight residual
     119.90  122.40   -2.50 6.00e-01 2.78e+00 1.74e+01
  angle pdb=" N3   DT D  13 "
        pdb=" C4   DT D  13 "
        pdb=" O4   DT D  13 "
      ideal   model   delta    sigma   weight residual
     119.90  122.32   -2.42 6.00e-01 2.78e+00 1.63e+01
  angle pdb=" N3   DT D  12 "
        pdb=" C4   DT D  12 "
        pdb=" O4   DT D  12 "
      ideal   model   delta    sigma   weight residual
     119.90  122.31   -2.41 6.00e-01 2.78e+00 1.61e+01
  angle pdb=" O4   DT D  14 "
        pdb=" C4   DT D  14 "
        pdb=" C5   DT D  14 "
      ideal   model   delta    sigma   weight residual
     124.90  122.31    2.59 7.00e-01 2.04e+00 1.37e+01
  ... (remaining 20261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.50: 7699
       35.50 -    70.99: 294
       70.99 -   106.49: 24
      106.49 -   141.98: 5
      141.98 -   177.48: 3
  Dihedral angle restraints: 8025
    sinusoidal: 4871
      harmonic: 3154
  Sorted by residual:
  dihedral pdb=" O4'   U B  43 "
           pdb=" C1'   U B  43 "
           pdb=" N1    U B  43 "
           pdb=" C2    U B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   54.52  177.48     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B 133 "
           pdb=" C1'   U B 133 "
           pdb=" N1    U B 133 "
           pdb=" C2    U B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   59.89  172.11     1      1.70e+01 3.46e-03 6.61e+01
  dihedral pdb=" O4'   U B 291 "
           pdb=" C1'   U B 291 "
           pdb=" N1    U B 291 "
           pdb=" C2    U B 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   41.00 -169.00     1      1.70e+01 3.46e-03 6.58e+01
  ... (remaining 8022 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 2009
       0.054 -    0.109: 368
       0.109 -    0.163: 67
       0.163 -    0.217: 17
       0.217 -    0.271: 8
  Chirality restraints: 2469
  Sorted by residual:
  chirality pdb=" P     G B  63 "
            pdb=" OP1   G B  63 "
            pdb=" OP2   G B  63 "
            pdb=" O5'   G B  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.68   -0.27 2.00e-01 2.50e+01 1.84e+00
  chirality pdb=" C3'   A B  62 "
            pdb=" C4'   A B  62 "
            pdb=" O3'   A B  62 "
            pdb=" C2'   A B  62 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.74    0.26 2.00e-01 2.50e+01 1.74e+00
  chirality pdb=" C3'   A B  55 "
            pdb=" C4'   A B  55 "
            pdb=" O3'   A B  55 "
            pdb=" C2'   A B  55 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.72    0.24 2.00e-01 2.50e+01 1.45e+00
  ... (remaining 2466 not shown)

  Planarity restraints: 1759
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 216 "    0.035 5.00e-02 4.00e+02   5.36e-02 4.59e+00
        pdb=" N   PRO C 217 "   -0.093 5.00e-02 4.00e+02
        pdb=" CA  PRO C 217 "    0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO C 217 "    0.030 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   A B 167 "    0.027 2.00e-02 2.50e+03   1.26e-02 4.35e+00
        pdb=" N9    A B 167 "   -0.030 2.00e-02 2.50e+03
        pdb=" C8    A B 167 "   -0.004 2.00e-02 2.50e+03
        pdb=" N7    A B 167 "    0.003 2.00e-02 2.50e+03
        pdb=" C5    A B 167 "    0.002 2.00e-02 2.50e+03
        pdb=" C6    A B 167 "    0.005 2.00e-02 2.50e+03
        pdb=" N6    A B 167 "    0.004 2.00e-02 2.50e+03
        pdb=" N1    A B 167 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    A B 167 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    A B 167 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    A B 167 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B 310 "    0.027 2.00e-02 2.50e+03   1.19e-02 4.23e+00
        pdb=" N9    G B 310 "   -0.029 2.00e-02 2.50e+03
        pdb=" C8    G B 310 "   -0.002 2.00e-02 2.50e+03
        pdb=" N7    G B 310 "    0.002 2.00e-02 2.50e+03
        pdb=" C5    G B 310 "    0.000 2.00e-02 2.50e+03
        pdb=" C6    G B 310 "    0.003 2.00e-02 2.50e+03
        pdb=" O6    G B 310 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G B 310 "    0.002 2.00e-02 2.50e+03
        pdb=" C2    G B 310 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B 310 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    G B 310 "   -0.004 2.00e-02 2.50e+03
        pdb=" C4    G B 310 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 1756 not shown)

  Histogram of nonbonded interaction distances:
        2.19 -     2.73: 1175
        2.73 -     3.27: 12061
        3.27 -     3.82: 22665
        3.82 -     4.36: 26991
        4.36 -     4.90: 41781
  Nonbonded interactions: 104673
  Sorted by model distance:
  nonbonded pdb=" O2'   A B 175 "
            pdb=" OP1   A B 176 "
     model   vdw
     2.188 3.040
  nonbonded pdb=" O   LEU A1079 "
            pdb=" OG1 THR A1083 "
     model   vdw
     2.200 3.040
  nonbonded pdb=" O2'   U B 314 "
            pdb=" OE2 GLU A 538 "
     model   vdw
     2.203 3.040
  nonbonded pdb=" O2'   A B  48 "
            pdb=" OP2   A B  49 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" N1    G B  93 "
            pdb=" O6    G B 121 "
     model   vdw
     2.253 3.120
  ... (remaining 104668 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.040
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.220
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   16.780
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
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      :  0.006   0.066  14161  Z= 0.303
  Angle     :  0.771   8.664  20266  Z= 0.431
  Chirality :  0.048   0.271   2469
  Planarity :  0.005   0.054   1759
  Dihedral  : 16.757 177.475   5981
  Min Nonbonded Distance : 2.188

Molprobity Statistics.
  All-atom Clashscore : 7.45
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.42 %
    Favored  : 93.58 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  :  0.64 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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: -0.75 (0.25), residues: 1074
  helix:  0.82 (0.24), residues: 477
  sheet: -1.09 (0.38), residues: 131
  loop : -1.73 (0.28), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A1011 
 TYR   0.018   0.002   TYR A 122 
 PHE   0.026   0.003   PHE A 331 
 TRP   0.028   0.002   TRP C 167 
 HIS   0.008   0.002   HIS A 592 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00613 /  0.30 (14161)
  covalent geometry    : angle       0.77094 /  0.43 (20266)
  hydrogen bonds       : bond        0.12603 /  7.53 (  576)
  hydrogen bonds       : angle       5.11481 /  3.28 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  186 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 185
  time to evaluate  : 0.315 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  769 LEU cc_start: 0.7756 (pt) cc_final: 0.7493 (pt)
REVERT: A  849 MET cc_start: 0.8015 (ttp) cc_final: 0.7571 (ttp)
  outliers start: 1
  outliers final: 0
  residues processed: 185
  average time/residue: 0.1598
  time to fit residues: 38.7625
Evaluate side-chains
  80 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 80
  time to evaluate  : 0.329 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 98 optimal weight:    0.8980
   chunk 107 optimal weight:    0.0870
   chunk 10 optimal weight:   30.0000
   chunk 66 optimal weight:    1.9990
   chunk 124 optimal weight:   30.0000
   chunk 103 optimal weight:    0.6980
   chunk 77 optimal weight:    6.9990
   chunk 122 optimal weight:    5.9990
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   overall best weight:    0.9160

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 748 GLN
A 770 GLN
A 779 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4117 r_free = 0.4117 target = 0.145633 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.093626 restraints weight = 27829.167|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.096411 restraints weight = 13803.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.098095 restraints weight = 9797.714|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.098815 restraints weight = 8291.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.099366 restraints weight = 7709.583|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8045
moved from start:          0.1870

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14161  Z= 0.142
  Angle     :  0.655  11.791  20266  Z= 0.322
  Chirality :  0.037   0.330   2469
  Planarity :  0.005   0.052   1759
  Dihedral  : 16.168 178.586   3882
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.47 %
    Favored  : 95.53 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  :  9.26 %
    Favored  : 89.89 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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: -0.21 (0.26), residues: 1074
  helix:  1.27 (0.24), residues: 478
  sheet: -0.87 (0.39), residues: 135
  loop : -1.44 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.018   0.001   ARG C 113 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.022   0.002   PHE A 919 
 TRP   0.031   0.003   TRP A  60 
 HIS   0.010   0.002   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00303 /  0.14 (14161)
  covalent geometry    : angle       0.65545 /  0.32 (20266)
  hydrogen bonds       : bond        0.05017 /  3.02 (  576)
  hydrogen bonds       : angle       4.35614 /  2.72 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 94
  time to evaluate  : 0.238 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  849 MET cc_start: 0.8677 (ttp) cc_final: 0.8256 (ttp)
REVERT: A 1054 MET cc_start: 0.7638 (tpp) cc_final: 0.7099 (ttt)
REVERT: C  175 ARG cc_start: 0.8475 (tpm170) cc_final: 0.8046 (tpt170)
  outliers start: 8
  outliers final: 5
  residues processed: 99
  average time/residue: 0.1189
  time to fit residues: 16.6997
Evaluate side-chains
  74 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 69
  time to evaluate  : 0.428 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    9.9990
   chunk 18 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 81 optimal weight:    4.9990
   chunk 128 optimal weight:    6.9990
   chunk 91 optimal weight:    4.9990
   chunk 87 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   chunk 94 optimal weight:    0.7980
   chunk 112 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    2.5588

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 384 GLN
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4048 r_free = 0.4048 target = 0.140218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.089841 restraints weight = 27811.858|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.090386 restraints weight = 15557.082|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.090752 restraints weight = 11987.639|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.090961 restraints weight = 10773.911|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.091035 restraints weight = 10410.596|
|-----------------------------------------------------------------------------|
r_work (final): 0.3235
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8224
moved from start:          0.2743

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047  14161  Z= 0.212
  Angle     :  0.650   9.179  20266  Z= 0.329
  Chirality :  0.038   0.195   2469
  Planarity :  0.005   0.047   1759
  Dihedral  : 16.027 178.370   3882
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 6.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.75 %
    Favored  : 95.25 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 11.70 %
    Favored  : 86.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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: -0.25 (0.26), residues: 1074
  helix:  1.15 (0.24), residues: 483
  sheet: -0.91 (0.39), residues: 130
  loop : -1.36 (0.29), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG C 100 
 TYR   0.019   0.002   TYR A 176 
 PHE   0.025   0.002   PHE A 331 
 TRP   0.067   0.003   TRP A  60 
 HIS   0.007   0.002   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00468 /  0.21 (14161)
  covalent geometry    : angle       0.65004 /  0.33 (20266)
  hydrogen bonds       : bond        0.05540 /  3.30 (  576)
  hydrogen bonds       : angle       4.26843 /  2.68 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.382 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LYS cc_start: 0.8332 (mtpp) cc_final: 0.7810 (tmtt)
REVERT: A   85 LEU cc_start: 0.9233 (mt) cc_final: 0.9027 (pp)
REVERT: A  362 GLU cc_start: 0.8176 (tp30) cc_final: 0.7964 (tt0)
REVERT: A  849 MET cc_start: 0.8693 (ttp) cc_final: 0.8422 (ttp)
REVERT: A 1054 MET cc_start: 0.7581 (tpp) cc_final: 0.7116 (ttt)
REVERT: C  122 GLN cc_start: 0.7547 (mm-40) cc_final: 0.7088 (tt0)
  outliers start: 17
  outliers final: 11
  residues processed: 91
  average time/residue: 0.1219
  time to fit residues: 15.9295
Evaluate side-chains
  80 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 69
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1092 LEU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  183 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 117 optimal weight:    0.9980
   chunk 7 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 32 optimal weight:    9.9990
   chunk 23 optimal weight:    7.9990
   chunk 69 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 76 optimal weight:    7.9990
   chunk 24 optimal weight:    9.9990
   chunk 128 optimal weight:    1.9990
   overall best weight:    3.1986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 GLN
A 779 HIS
A 794 GLN
** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4024 r_free = 0.4024 target = 0.138407 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.087514 restraints weight = 27965.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3252 r_free = 0.3252 target = 0.088334 restraints weight = 16042.494|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3255 r_free = 0.3255 target = 0.088704 restraints weight = 12243.308|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.088863 restraints weight = 11462.667|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3258 r_free = 0.3258 target = 0.088910 restraints weight = 11122.908|
|-----------------------------------------------------------------------------|
r_work (final): 0.3205
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3270

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.048  14161  Z= 0.246
  Angle     :  0.649  10.681  20266  Z= 0.329
  Chirality :  0.038   0.198   2469
  Planarity :  0.005   0.079   1759
  Dihedral  : 16.059 179.062   3882
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 6.31
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.13 %
    Allowed  : 14.04 %
    Favored  : 83.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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: -0.36 (0.26), residues: 1074
  helix:  0.98 (0.24), residues: 485
  sheet: -0.92 (0.40), residues: 123
  loop : -1.35 (0.29), residues: 466

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG C 100 
 TYR   0.013   0.002   TYR A 176 
 PHE   0.023   0.002   PHE A  47 
 TRP   0.050   0.003   TRP A  60 
 HIS   0.019   0.002   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.25 (14161)
  covalent geometry    : angle       0.64861 /  0.33 (20266)
  hydrogen bonds       : bond        0.05381 /  3.23 (  576)
  hydrogen bonds       : angle       4.32354 /  2.72 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LEU cc_start: 0.9225 (mt) cc_final: 0.9021 (pp)
REVERT: A 1023 GLN cc_start: 0.8838 (OUTLIER) cc_final: 0.8604 (mt0)
REVERT: A 1054 MET cc_start: 0.7587 (tpp) cc_final: 0.7184 (ttt)
REVERT: C  122 GLN cc_start: 0.7603 (mm-40) cc_final: 0.7194 (tt0)
  outliers start: 20
  outliers final: 12
  residues processed: 95
  average time/residue: 0.1299
  time to fit residues: 17.4386
Evaluate side-chains
  89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.362 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue  726 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  780 LEU
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  813 MET
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 3 optimal weight:   30.0000
   chunk 87 optimal weight:    2.9990
   chunk 74 optimal weight:    4.9990
   chunk 127 optimal weight:    0.8980
   chunk 11 optimal weight:   30.0000
   chunk 29 optimal weight:    0.9990
   chunk 14 optimal weight:   10.9990
   chunk 31 optimal weight:    7.9990
   chunk 109 optimal weight:    0.7980
   chunk 82 optimal weight:    0.9990
   chunk 124 optimal weight:   10.0000
   overall best weight:    1.3386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  73 GLN
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.139949 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.089749 restraints weight = 27793.150|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.090309 restraints weight = 15612.585|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.090706 restraints weight = 11948.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3297 r_free = 0.3297 target = 0.090927 restraints weight = 10847.251|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.091242 restraints weight = 10534.709|
|-----------------------------------------------------------------------------|
r_work (final): 0.3244
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.3454

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14161  Z= 0.135
  Angle     :  0.567  11.211  20266  Z= 0.284
  Chirality :  0.034   0.202   2469
  Planarity :  0.004   0.044   1759
  Dihedral  : 15.922 179.654   3882
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.72 %
    Favored  : 96.28 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 15.96 %
    Favored  : 82.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.07 (0.26), residues: 1074
  helix:  1.38 (0.24), residues: 485
  sheet: -0.64 (0.40), residues: 130
  loop : -1.21 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 100 
 TYR   0.010   0.001   TYR A 168 
 PHE   0.024   0.002   PHE A  47 
 TRP   0.052   0.003   TRP C  98 
 HIS   0.009   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00299 /  0.14 (14161)
  covalent geometry    : angle       0.56692 /  0.28 (20266)
  hydrogen bonds       : bond        0.04464 /  2.67 (  576)
  hydrogen bonds       : angle       4.01176 /  2.51 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 0.391 
Fit side-chains
   revert: symmetry clash
REVERT: A   85 LEU cc_start: 0.9241 (mt) cc_final: 0.9034 (pp)
REVERT: A  362 GLU cc_start: 0.8268 (tp30) cc_final: 0.7963 (tt0)
REVERT: A 1023 GLN cc_start: 0.8773 (OUTLIER) cc_final: 0.8474 (mt0)
REVERT: A 1054 MET cc_start: 0.7486 (tpp) cc_final: 0.7254 (ttt)
REVERT: C  122 GLN cc_start: 0.7601 (mm-40) cc_final: 0.7185 (tt0)
REVERT: C  220 ARG cc_start: 0.7940 (ttp80) cc_final: 0.7452 (ttp80)
  outliers start: 19
  outliers final: 15
  residues processed: 91
  average time/residue: 0.1264
  time to fit residues: 16.5052
Evaluate side-chains
  90 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 74
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  236 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 88 optimal weight:    4.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    8.9990
   chunk 18 optimal weight:   10.0000
   chunk 62 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 128 optimal weight:    7.9990
   chunk 36 optimal weight:    0.0570
   chunk 23 optimal weight:   10.0000
   chunk 103 optimal weight:    0.9980
   chunk 85 optimal weight:    0.7980
   overall best weight:    1.1100

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 779 HIS
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS
C 185 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.140237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3237 r_free = 0.3237 target = 0.086980 restraints weight = 27904.719|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.089644 restraints weight = 14636.674|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 55)----------------|
| r_work = 0.3307 r_free = 0.3307 target = 0.091197 restraints weight = 10683.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3318 r_free = 0.3318 target = 0.091936 restraints weight = 9194.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3326 r_free = 0.3326 target = 0.092393 restraints weight = 8583.767|
|-----------------------------------------------------------------------------|
r_work (final): 0.3273
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8202
moved from start:          0.3586

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040  14161  Z= 0.123
  Angle     :  0.546   7.645  20266  Z= 0.275
  Chirality :  0.034   0.202   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 15.818 178.946   3882
  Min Nonbonded Distance : 2.429

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 15.74 %
    Favored  : 81.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.20 (0.26), residues: 1074
  helix:  1.55 (0.25), residues: 483
  sheet: -0.49 (0.40), residues: 129
  loop : -1.22 (0.30), residues: 462

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 657 
 TYR   0.008   0.001   TYR A 168 
 PHE   0.025   0.002   PHE A  47 
 TRP   0.023   0.002   TRP C  98 
 HIS   0.010   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00266 /  0.12 (14161)
  covalent geometry    : angle       0.54621 /  0.27 (20266)
  hydrogen bonds       : bond        0.04273 /  2.57 (  576)
  hydrogen bonds       : angle       3.97995 /  2.49 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 78
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7862 (ptp-110)
REVERT: A   60 TRP cc_start: 0.6504 (t-100) cc_final: 0.6098 (t-100)
REVERT: A   85 LEU cc_start: 0.9270 (mt) cc_final: 0.9031 (pp)
REVERT: A  362 GLU cc_start: 0.8252 (tp30) cc_final: 0.7904 (tt0)
REVERT: A 1023 GLN cc_start: 0.8735 (OUTLIER) cc_final: 0.8442 (mt0)
REVERT: C  101 GLU cc_start: 0.8549 (OUTLIER) cc_final: 0.8254 (tm-30)
REVERT: C  122 GLN cc_start: 0.7506 (mm-40) cc_final: 0.7176 (tt0)
REVERT: C  220 ARG cc_start: 0.7832 (ttp80) cc_final: 0.7340 (ttp80)
  outliers start: 25
  outliers final: 16
  residues processed: 92
  average time/residue: 0.1156
  time to fit residues: 15.3657
Evaluate side-chains
  94 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.232 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue   22 LEU
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  185 GLN
Chi-restraints excluded: chain C residue  236 ASP
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 30 optimal weight:    9.9990
   chunk 74 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 83 optimal weight:    1.9990
   chunk 113 optimal weight:    3.9990
   chunk 121 optimal weight:    5.9990
   chunk 96 optimal weight:    1.9990
   chunk 17 optimal weight:   20.0000
   chunk 42 optimal weight:    2.9990
   chunk 80 optimal weight:    7.9990
   chunk 54 optimal weight:    0.1980
   overall best weight:    1.8388

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 779 HIS
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 151 HIS
C 185 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.139435 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.089474 restraints weight = 27705.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3271 r_free = 0.3271 target = 0.089218 restraints weight = 16134.006|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.089587 restraints weight = 13295.917|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.089814 restraints weight = 11983.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.089874 restraints weight = 11456.119|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.3708

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043  14161  Z= 0.158
  Angle     :  0.562   7.631  20266  Z= 0.281
  Chirality :  0.035   0.203   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 15.785 178.699   3882
  Min Nonbonded Distance : 2.208

Molprobity Statistics.
  All-atom Clashscore : 5.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.55 %
    Allowed  : 16.06 %
    Favored  : 81.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.17 (0.26), residues: 1074
  helix:  1.49 (0.25), residues: 485
  sheet: -0.56 (0.40), residues: 130
  loop : -1.19 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 657 
 TYR   0.008   0.001   TYR A 168 
 PHE   0.025   0.002   PHE A  47 
 TRP   0.016   0.002   TRP C  98 
 HIS   0.009   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00353 /  0.16 (14161)
  covalent geometry    : angle       0.56196 /  0.28 (20266)
  hydrogen bonds       : bond        0.04441 /  2.67 (  576)
  hydrogen bonds       : angle       3.98254 /  2.48 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 74
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8343 (OUTLIER) cc_final: 0.8099 (ptm160)
REVERT: A   60 TRP cc_start: 0.6554 (t-100) cc_final: 0.5943 (t-100)
REVERT: A   85 LEU cc_start: 0.9262 (mt) cc_final: 0.9039 (pp)
REVERT: A 1023 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8451 (mt0)
REVERT: C  101 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8309 (tm-30)
REVERT: C  122 GLN cc_start: 0.7567 (mm-40) cc_final: 0.7214 (tt0)
REVERT: C  220 ARG cc_start: 0.7907 (ttp80) cc_final: 0.7435 (ttp80)
  outliers start: 24
  outliers final: 15
  residues processed: 89
  average time/residue: 0.1271
  time to fit residues: 15.8724
Evaluate side-chains
  91 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   10 VAL
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  161 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  767 THR
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  185 GLN
Chi-restraints excluded: chain C residue  189 VAL
Chi-restraints excluded: chain C residue  236 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 41 optimal weight:    0.0030
   chunk 124 optimal weight:    9.9990
   chunk 100 optimal weight:    0.8980
   chunk 116 optimal weight:    2.9990
   chunk 51 optimal weight:    1.9990
   chunk 109 optimal weight:    0.3980
   chunk 66 optimal weight:    0.0040
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.9980
   chunk 25 optimal weight:    7.9990
   overall best weight:    0.4602

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 736 GLN
A 779 HIS
A1051 ASN
C 151 HIS
C 185 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.141067 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3264 r_free = 0.3264 target = 0.088288 restraints weight = 27438.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3308 r_free = 0.3308 target = 0.090974 restraints weight = 14389.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.092543 restraints weight = 10488.516|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.093370 restraints weight = 9018.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.093593 restraints weight = 8391.407|
|-----------------------------------------------------------------------------|
r_work (final): 0.3296
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8187
moved from start:          0.3812

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039  14161  Z= 0.099
  Angle     :  0.532   7.808  20266  Z= 0.266
  Chirality :  0.033   0.204   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 15.684 178.136   3882
  Min Nonbonded Distance : 2.270

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 16.38 %
    Favored  : 81.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.33 (0.27), residues: 1074
  helix:  1.68 (0.25), residues: 484
  sheet: -0.47 (0.41), residues: 129
  loop : -1.18 (0.30), residues: 461

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 657 
 TYR   0.008   0.001   TYR A 168 
 PHE   0.026   0.001   PHE A  47 
 TRP   0.016   0.002   TRP A 137 
 HIS   0.007   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00205 /  0.10 (14161)
  covalent geometry    : angle       0.53172 /  0.27 (20266)
  hydrogen bonds       : bond        0.03961 /  2.39 (  576)
  hydrogen bonds       : angle       3.85266 /  2.37 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 78
  time to evaluate  : 0.285 
Fit side-chains
   revert: symmetry clash
REVERT: A   15 ARG cc_start: 0.8390 (OUTLIER) cc_final: 0.8180 (ptm160)
REVERT: A   60 TRP cc_start: 0.6730 (t-100) cc_final: 0.6234 (t-100)
REVERT: A   85 LEU cc_start: 0.9275 (mt) cc_final: 0.9038 (pp)
REVERT: A  362 GLU cc_start: 0.8191 (tp30) cc_final: 0.7934 (tt0)
REVERT: A 1023 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8341 (mt0)
REVERT: C   98 TRP cc_start: 0.8509 (p-90) cc_final: 0.8279 (p-90)
REVERT: C  101 GLU cc_start: 0.8570 (OUTLIER) cc_final: 0.8266 (tm-30)
REVERT: C  122 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7206 (tt0)
REVERT: C  168 GLU cc_start: 0.7652 (pm20) cc_final: 0.7331 (pm20)
REVERT: C  220 ARG cc_start: 0.7858 (ttp80) cc_final: 0.7372 (ttp80)
  outliers start: 22
  outliers final: 10
  residues processed: 92
  average time/residue: 0.1075
  time to fit residues: 14.2258
Evaluate side-chains
  86 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.265 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  185 GLN
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 34 optimal weight:    5.9990
   chunk 106 optimal weight:    4.9990
   chunk 61 optimal weight:    0.9980
   chunk 98 optimal weight:    0.5980
   chunk 2 optimal weight:    9.9990
   chunk 12 optimal weight:   10.0000
   chunk 59 optimal weight:    3.9990
   chunk 8 optimal weight:    7.9990
   chunk 73 optimal weight:    1.9990
   chunk 67 optimal weight:    1.9990
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.7186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 752 HIS
A 779 HIS
C 151 HIS
C 185 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.139839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.089295 restraints weight = 27904.954|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3278 r_free = 0.3278 target = 0.089740 restraints weight = 16684.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.090173 restraints weight = 12654.154|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 24)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.090377 restraints weight = 11652.011|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.090396 restraints weight = 11134.639|
|-----------------------------------------------------------------------------|
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8259
moved from start:          0.3915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  14161  Z= 0.150
  Angle     :  0.550   7.725  20266  Z= 0.275
  Chirality :  0.034   0.204   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 15.652 178.092   3882
  Min Nonbonded Distance : 2.255

Molprobity Statistics.
  All-atom Clashscore : 5.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 16.91 %
    Favored  : 81.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.27 (0.27), residues: 1074
  helix:  1.60 (0.25), residues: 486
  sheet: -0.55 (0.41), residues: 129
  loop : -1.18 (0.30), residues: 459

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 865 
 TYR   0.007   0.001   TYR A 894 
 PHE   0.026   0.002   PHE A  47 
 TRP   0.017   0.002   TRP A 137 
 HIS   0.019   0.001   HIS A 779 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00335 /  0.15 (14161)
  covalent geometry    : angle       0.54953 /  0.27 (20266)
  hydrogen bonds       : bond        0.04286 /  2.58 (  576)
  hydrogen bonds       : angle       3.90284 /  2.42 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.420 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 TRP cc_start: 0.6759 (t-100) cc_final: 0.6272 (t-100)
REVERT: A   85 LEU cc_start: 0.9272 (mt) cc_final: 0.9042 (pp)
REVERT: A  362 GLU cc_start: 0.8198 (tp30) cc_final: 0.7894 (tt0)
REVERT: A 1023 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8413 (mt0)
REVERT: C  101 GLU cc_start: 0.8639 (OUTLIER) cc_final: 0.8325 (tm-30)
REVERT: C  122 GLN cc_start: 0.7597 (mm-40) cc_final: 0.7244 (tt0)
REVERT: C  220 ARG cc_start: 0.7902 (ttp80) cc_final: 0.7445 (ttp80)
  outliers start: 15
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1207
  time to fit residues: 14.4820
Evaluate side-chains
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  779 HIS
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  185 GLN
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 6 optimal weight:   10.0000
   chunk 39 optimal weight:    0.9990
   chunk 117 optimal weight:   30.0000
   chunk 112 optimal weight:    0.9980
   chunk 13 optimal weight:    6.9990
   chunk 113 optimal weight:    3.9990
   chunk 124 optimal weight:   20.0000
   chunk 77 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 78 optimal weight:    0.0980
   chunk 18 optimal weight:   10.0000
   overall best weight:    1.8186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 779 HIS
** C 151 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C 185 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.139509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3286 r_free = 0.3286 target = 0.089012 restraints weight = 27824.806|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.089453 restraints weight = 16686.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3274 r_free = 0.3274 target = 0.089706 restraints weight = 12627.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.090472 restraints weight = 11727.502|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.090359 restraints weight = 10864.969|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8262
moved from start:          0.4002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  14161  Z= 0.156
  Angle     :  0.557   8.881  20266  Z= 0.279
  Chirality :  0.035   0.363   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 15.647 177.971   3882
  Min Nonbonded Distance : 2.354

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 17.77 %
    Favored  : 80.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.23 (0.27), residues: 1074
  helix:  1.56 (0.25), residues: 486
  sheet: -0.60 (0.41), residues: 135
  loop : -1.17 (0.30), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG C 100 
 TYR   0.007   0.001   TYR A 168 
 PHE   0.027   0.002   PHE A  47 
 TRP   0.019   0.002   TRP A 137 
 HIS   0.008   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.16 (14161)
  covalent geometry    : angle       0.55741 /  0.28 (20266)
  hydrogen bonds       : bond        0.04384 /  2.64 (  576)
  hydrogen bonds       : angle       3.92645 /  2.43 ( 1489)

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

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

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2148 Ramachandran restraints generated.
    1074 Oldfield, 0 Emsley, 1074 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   60 TRP cc_start: 0.6778 (t-100) cc_final: 0.6091 (t-100)
REVERT: A   85 LEU cc_start: 0.9283 (mt) cc_final: 0.9052 (pp)
REVERT: A  362 GLU cc_start: 0.8221 (tp30) cc_final: 0.7912 (tt0)
REVERT: A 1023 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8447 (mt0)
REVERT: C   98 TRP cc_start: 0.8521 (p-90) cc_final: 0.8226 (p-90)
REVERT: C  101 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8288 (tm-30)
REVERT: C  122 GLN cc_start: 0.7573 (mm-40) cc_final: 0.7221 (tt0)
REVERT: C  168 GLU cc_start: 0.7739 (pm20) cc_final: 0.7367 (pm20)
REVERT: C  220 ARG cc_start: 0.7916 (ttp80) cc_final: 0.7459 (ttp80)
  outliers start: 14
  outliers final: 10
  residues processed: 84
  average time/residue: 0.1302
  time to fit residues: 15.6034
Evaluate side-chains
  87 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  141 LEU
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  940 LEU
Chi-restraints excluded: chain A residue  997 VAL
Chi-restraints excluded: chain A residue 1023 GLN
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain C residue   95 LEU
Chi-restraints excluded: chain C residue  101 GLU
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 90 optimal weight:    0.0670
   chunk 60 optimal weight:    1.9990
   chunk 17 optimal weight:   10.0000
   chunk 59 optimal weight:    0.6980
   chunk 31 optimal weight:    5.9990
   chunk 25 optimal weight:    2.9990
   chunk 79 optimal weight:    0.0980
   chunk 116 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 66 optimal weight:    0.9980
   chunk 65 optimal weight:    3.9990
   overall best weight:    0.7720

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 779 HIS
C 151 HIS
C 185 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.140951 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.090676 restraints weight = 27758.192|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.091505 restraints weight = 15784.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.091828 restraints weight = 11998.362|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.092112 restraints weight = 11098.138|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.092168 restraints weight = 10604.955|
|-----------------------------------------------------------------------------|
r_work (final): 0.3261
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8223
moved from start:          0.4111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.042  14161  Z= 0.107
  Angle     :  0.527   8.711  20266  Z= 0.263
  Chirality :  0.033   0.220   2469
  Planarity :  0.004   0.045   1759
  Dihedral  : 15.559 177.769   3882
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.70 %
    Allowed  : 17.66 %
    Favored  : 80.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.56 %
    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:  0.40 (0.27), residues: 1074
  helix:  1.74 (0.25), residues: 483
  sheet: -0.46 (0.41), residues: 135
  loop : -1.14 (0.30), residues: 456

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG C 100 
 TYR   0.009   0.001   TYR A 168 
 PHE   0.026   0.001   PHE A  47 
 TRP   0.018   0.002   TRP A 137 
 HIS   0.008   0.001   HIS C 241 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00230 /  0.11 (14161)
  covalent geometry    : angle       0.52680 /  0.26 (20266)
  hydrogen bonds       : bond        0.03954 /  2.39 (  576)
  hydrogen bonds       : angle       3.83876 /  2.36 ( 1489)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2014.53 seconds
wall clock time: 35 minutes 32.09 seconds (2132.09 seconds total)