Starting phenix.real_space_refine
on Wed Mar  4 12:00:13 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7tre_26087/03_2026/7tre_26087.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7tre_26087/03_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_26087/03_2026/7tre_26087.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7tre_26087/03_2026/7tre_26087.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7tre_26087/03_2026/7tre_26087.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7tre_26087/03_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-5986/lib/python3.9/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: 3.06, per 1000 atoms: 0.23
  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: 1.08
  Conformation dependent library (CDL) restraints added in 254.4 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: 1.84
  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: 3.42

  Time building geometry restraints manager: 1.44 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=" 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=" N   HIS A 609 "
       pdb=" CA  HIS A 609 "
    ideal  model  delta    sigma   weight residual
    1.456  1.491 -0.034 1.31e-02 5.83e+03 6.84e+00
  bond pdb=" N   SER A 134 "
       pdb=" CA  SER A 134 "
    ideal  model  delta    sigma   weight residual
    1.456  1.488 -0.031 1.22e-02 6.72e+03 6.50e+00
  bond pdb=" N   ARG A 610 "
       pdb=" CA  ARG A 610 "
    ideal  model  delta    sigma   weight residual
    1.456  1.489 -0.034 1.32e-02 5.74e+03 6.48e+00
  bond pdb=" N   LEU A 131 "
       pdb=" CA  LEU A 131 "
    ideal  model  delta    sigma   weight residual
    1.459  1.490 -0.030 1.21e-02 6.83e+03 6.34e+00
  ... (remaining 14156 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.73: 19428
        1.73 -     3.47: 739
        3.47 -     5.20: 80
        5.20 -     6.93: 14
        6.93 -     8.66: 5
  Bond angle restraints: 20266
  Sorted by residual:
  angle pdb=" C4'   A B  62 "
        pdb=" C3'   A B  62 "
        pdb=" O3'   A B  62 "
      ideal   model   delta    sigma   weight residual
     113.00  107.88    5.12 1.50e+00 4.44e-01 1.17e+01
  angle pdb=" O3'   A B  55 "
        pdb=" C3'   A B  55 "
        pdb=" C2'   A B  55 "
      ideal   model   delta    sigma   weight residual
     113.70  109.21    4.49 1.50e+00 4.44e-01 8.95e+00
  angle pdb=" CA  VAL A 127 "
        pdb=" C   VAL A 127 "
        pdb=" O   VAL A 127 "
      ideal   model   delta    sigma   weight residual
     121.17  118.09    3.08 1.06e+00 8.90e-01 8.46e+00
  angle pdb=" O   GLY A 135 "
        pdb=" C   GLY A 135 "
        pdb=" N   ALA A 136 "
      ideal   model   delta    sigma   weight residual
     122.19  124.95   -2.76 9.70e-01 1.06e+00 8.10e+00
  angle pdb=" O3'   G B  71 "
        pdb=" C3'   G B  71 "
        pdb=" C2'   G B  71 "
      ideal   model   delta    sigma   weight residual
     113.70  117.95   -4.25 1.50e+00 4.44e-01 8.01e+00
  ... (remaining 20261 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.50: 8136
       35.50 -    70.99: 644
       70.99 -   106.49: 95
      106.49 -   141.98: 5
      141.98 -   177.48: 3
  Dihedral angle restraints: 8883
    sinusoidal: 5729
      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 8880 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.054: 2011
       0.054 -    0.109: 371
       0.109 -    0.163: 62
       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:             1.380
  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:          0.190
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     14.870
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:1.380
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.990
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
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= 0.287
  Angle     :  0.767   8.664  20266  Z= 0.418
  Chirality :  0.048   0.271   2469
  Planarity :  0.005   0.054   1759
  Dihedral  : 21.804 177.475   6839
  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
  covalent geometry    : bond        0.00610 (14161)
  covalent geometry    : angle       0.76703 (20266)
  hydrogen bonds       : bond        0.12603 (  576)
  hydrogen bonds       : angle       5.11481 ( 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  : 0.266 
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: 0.1664
  time to fit residues: 39.6370
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  : 0.364 
-------------------------------------------------------------------------------
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...

Flipped N/Q/H residues before XYZ refinement:
A 748 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 = 0.4111 r_free = 0.4111 target = 0.145125 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.092638 restraints weight = 27949.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.095424 restraints weight = 14433.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 49)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.097073 restraints weight = 10361.276|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.097880 restraints weight = 8882.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3417 r_free = 0.3417 target = 0.098185 restraints weight = 8256.019|
|-----------------------------------------------------------------------------|
r_work (final): 0.3367
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7914
moved from start:          0.2188

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.052  14161  Z= 0.131
  Angle     :  0.619  11.584  20266  Z= 0.304
  Chirality :  0.035   0.231   2469
  Planarity :  0.005   0.049   1759
  Dihedral  : 23.055 179.752   4740
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.82 %
    Favored  : 96.18 %
  Rotamer:
    Outliers :  1.06 %
    Allowed  :  9.15 %
    Favored  : 89.79 %
  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: -0.05 (0.26), residues: 1074
  helix:  1.42 (0.24), residues: 479
  sheet: -0.84 (0.38), residues: 128
  loop : -1.34 (0.29), residues: 467

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 113 
 TYR   0.011   0.001   TYR A 168 
 PHE   0.019   0.002   PHE A 159 
 TRP   0.033   0.003   TRP A  60 
 HIS   0.007   0.001   HIS A 779 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 (14161)
  covalent geometry    : angle       0.61855 (20266)
  hydrogen bonds       : bond        0.04498 (  576)
  hydrogen bonds       : angle       4.19891 ( 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
  108 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 98
  time to evaluate  : 0.264 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  166 CYS cc_start: 0.7683 (m) cc_final: 0.6807 (m)
REVERT: A  781 GLN cc_start: 0.8504 (pt0) cc_final: 0.7957 (pt0)
REVERT: A  849 MET cc_start: 0.8654 (ttp) cc_final: 0.8166 (ttp)
REVERT: A 1054 MET cc_start: 0.7666 (tpp) cc_final: 0.7155 (ttt)
REVERT: C   98 TRP cc_start: 0.8477 (OUTLIER) cc_final: 0.7731 (p-90)
REVERT: C  122 GLN cc_start: 0.7481 (mm-40) cc_final: 0.6976 (tt0)
  outliers start: 10
  outliers final: 6
  residues processed: 104
  average time/residue: 0.1077
  time to fit residues: 16.4791
Evaluate side-chains
  84 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 77
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
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
Chi-restraints excluded: chain C residue   98 TRP
Chi-restraints excluded: chain C residue  158 THR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 115 optimal weight:    5.9990
   chunk 18 optimal weight:   10.0000
   chunk 82 optimal weight:    4.9990
   chunk 81 optimal weight:    2.9990
   chunk 128 optimal weight:    4.9990
   chunk 91 optimal weight:    0.9990
   chunk 87 optimal weight:    3.9990
   chunk 69 optimal weight:    0.7980
   chunk 94 optimal weight:    0.6980
   chunk 112 optimal weight:    2.9990
   chunk 52 optimal weight:    0.8980
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 770 GLN
** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4079 r_free = 0.4079 target = 0.142509 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3277 r_free = 0.3277 target = 0.089438 restraints weight = 27759.780|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.092121 restraints weight = 14500.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.093664 restraints weight = 10521.995|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 53)----------------|
| r_work = 0.3360 r_free = 0.3360 target = 0.094518 restraints weight = 9042.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3365 r_free = 0.3365 target = 0.094864 restraints weight = 8395.784|
|-----------------------------------------------------------------------------|
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7993
moved from start:          0.2995

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= 0.135
  Angle     :  0.555   7.380  20266  Z= 0.279
  Chirality :  0.034   0.193   2469
  Planarity :  0.005   0.046   1759
  Dihedral  : 22.813 179.164   4740
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 5.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 11.38 %
    Favored  : 87.34 %
  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:  0.22 (0.26), residues: 1074
  helix:  1.68 (0.24), residues: 483
  sheet: -0.77 (0.39), residues: 123
  loop : -1.27 (0.29), residues: 468

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 100 
 TYR   0.018   0.001   TYR A 176 
 PHE   0.018   0.002   PHE A 331 
 TRP   0.039   0.002   TRP A  60 
 HIS   0.006   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (14161)
  covalent geometry    : angle       0.55497 (20266)
  hydrogen bonds       : bond        0.04445 (  576)
  hydrogen bonds       : angle       3.94651 ( 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
  96 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 84
  time to evaluate  : 0.366 
Fit side-chains
   revert: symmetry clash
REVERT: A   78 LYS cc_start: 0.8379 (mtpp) cc_final: 0.7852 (tmtt)
REVERT: A   85 LEU cc_start: 0.9255 (mt) cc_final: 0.9022 (pp)
REVERT: A  794 GLN cc_start: 0.7809 (OUTLIER) cc_final: 0.7586 (mm110)
REVERT: A  849 MET cc_start: 0.8591 (ttp) cc_final: 0.8147 (ttp)
REVERT: A 1054 MET cc_start: 0.7411 (tpp) cc_final: 0.7041 (ttt)
REVERT: C  122 GLN cc_start: 0.7580 (mm-40) cc_final: 0.7118 (tt0)
  outliers start: 12
  outliers final: 6
  residues processed: 92
  average time/residue: 0.1221
  time to fit residues: 16.3341
Evaluate side-chains
  77 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 70
  time to evaluate  : 0.371 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   15 ARG
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  794 GLN
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
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:   30.0000
   chunk 7 optimal weight:    7.9990
   chunk 5 optimal weight:   20.0000
   chunk 18 optimal weight:   10.0000
   chunk 32 optimal weight:   10.0000
   chunk 23 optimal weight:    9.9990
   chunk 69 optimal weight:    5.9990
   chunk 37 optimal weight:    0.9990
   chunk 76 optimal weight:    0.9990
   chunk 24 optimal weight:   10.0000
   chunk 128 optimal weight:    6.9990
   overall best weight:    4.5990

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 340 GLN
A 384 GLN
** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 816 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3978 r_free = 0.3978 target = 0.135052 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.085710 restraints weight = 28156.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3197 r_free = 0.3197 target = 0.084775 restraints weight = 16237.560|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 23)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.085176 restraints weight = 13509.433|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.085470 restraints weight = 12345.496|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.085616 restraints weight = 11830.486|
|-----------------------------------------------------------------------------|
r_work (final): 0.3151
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.056  14161  Z= 0.358
  Angle     :  0.770  12.416  20266  Z= 0.386
  Chirality :  0.043   0.209   2469
  Planarity :  0.006   0.049   1759
  Dihedral  : 23.012 179.006   4740
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 7.73
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.21 %
    Favored  : 94.79 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 15.64 %
    Favored  : 82.13 %
  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 (0.25), residues: 1074
  helix:  0.81 (0.23), residues: 485
  sheet: -0.57 (0.41), residues: 131
  loop : -1.33 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.001   ARG A 132 
 TYR   0.014   0.002   TYR A1089 
 PHE   0.034   0.003   PHE A 331 
 TRP   0.022   0.002   TRP A 137 
 HIS   0.009   0.002   HIS A 816 

Details of bonding type rmsd
  covalent geometry    : bond        0.00809 (14161)
  covalent geometry    : angle       0.76968 (20266)
  hydrogen bonds       : bond        0.06808 (  576)
  hydrogen bonds       : angle       4.56189 ( 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
  93 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 72
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
REVERT: A   60 TRP cc_start: 0.6749 (t-100) cc_final: 0.6534 (t-100)
REVERT: A  794 GLN cc_start: 0.8049 (OUTLIER) cc_final: 0.7797 (mm110)
REVERT: A  811 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8404 (mpp80)
REVERT: A 1054 MET cc_start: 0.7662 (tpp) cc_final: 0.7288 (ttt)
REVERT: C   98 TRP cc_start: 0.8677 (p-90) cc_final: 0.8362 (p-90)
  outliers start: 21
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1189
  time to fit residues: 15.3989
Evaluate side-chains
  81 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 64
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
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  726 THR
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  794 GLN
Chi-restraints excluded: chain A residue  811 ARG
Chi-restraints excluded: chain A residue  997 VAL
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   95 LEU
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  236 ASP
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:    0.9980
   chunk 74 optimal weight:    0.7980
   chunk 127 optimal weight:    8.9990
   chunk 11 optimal weight:   30.0000
   chunk 29 optimal weight:    4.9990
   chunk 14 optimal weight:   10.9990
   chunk 31 optimal weight:    5.9990
   chunk 109 optimal weight:    0.9980
   chunk 82 optimal weight:    0.7980
   chunk 124 optimal weight:    5.9990
   overall best weight:    1.7182

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

Flipped N/Q/H residues before XYZ refinement:
** A  73 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 752 HIS
A 775 GLN
** A 781 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 816 HIS
** A1051 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4022 r_free = 0.4022 target = 0.138295 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.088750 restraints weight = 27930.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.088565 restraints weight = 15956.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.088889 restraints weight = 13343.884|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3269 r_free = 0.3269 target = 0.089117 restraints weight = 11845.435|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.089169 restraints weight = 11374.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3209
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8126
moved from start:          0.4175

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= 0.147
  Angle     :  0.579  12.076  20266  Z= 0.287
  Chirality :  0.035   0.211   2469
  Planarity :  0.004   0.041   1759
  Dihedral  : 22.888 177.899   4740
  Min Nonbonded Distance : 2.433

Molprobity Statistics.
  All-atom Clashscore : 6.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.19 %
    Favored  : 95.81 %
  Rotamer:
    Outliers :  2.02 %
    Allowed  : 17.23 %
    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:  0.08 (0.26), residues: 1074
  helix:  1.38 (0.24), residues: 485
  sheet: -0.45 (0.41), residues: 131
  loop : -1.25 (0.29), residues: 458

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 657 
 TYR   0.009   0.001   TYR A 168 
 PHE   0.024   0.002   PHE A  27 
 TRP   0.025   0.002   TRP A 137 
 HIS   0.006   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 (14161)
  covalent geometry    : angle       0.57889 (20266)
  hydrogen bonds       : bond        0.04638 (  576)
  hydrogen bonds       : angle       4.06293 ( 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
  89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 GLU cc_start: 0.8334 (tp30) cc_final: 0.8001 (mt-10)
REVERT: A  787 ARG cc_start: 0.5506 (ptt90) cc_final: 0.5286 (ptt90)
REVERT: A  794 GLN cc_start: 0.7878 (OUTLIER) cc_final: 0.7617 (mm110)
REVERT: A 1054 MET cc_start: 0.7706 (tpp) cc_final: 0.7294 (ttt)
REVERT: C   98 TRP cc_start: 0.8690 (p-90) cc_final: 0.8297 (p-90)
REVERT: C  101 GLU cc_start: 0.8710 (OUTLIER) cc_final: 0.8419 (tm-30)
REVERT: C  144 LEU cc_start: 0.8441 (mt) cc_final: 0.8198 (mp)
  outliers start: 19
  outliers final: 12
  residues processed: 83
  average time/residue: 0.1133
  time to fit residues: 14.0659
Evaluate side-chains
  81 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 67
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  791 VAL
Chi-restraints excluded: chain A residue  792 ILE
Chi-restraints excluded: chain A residue  794 GLN
Chi-restraints excluded: chain A residue 1016 VAL
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  189 VAL
Chi-restraints excluded: chain C residue  214 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 88 optimal weight:    3.9990
   chunk 20 optimal weight:    4.9990
   chunk 31 optimal weight:    0.9980
   chunk 18 optimal weight:   10.0000
   chunk 62 optimal weight:    0.8980
   chunk 41 optimal weight:    0.1980
   chunk 128 optimal weight:    5.9990
   chunk 36 optimal weight:    7.9990
   chunk 23 optimal weight:   10.0000
   chunk 103 optimal weight:    1.9990
   chunk 85 optimal weight:    1.9990
   overall best weight:    1.2184

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

Flipped N/Q/H residues before XYZ refinement:
A  73 GLN
A1051 ASN
C 151 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4036 r_free = 0.4036 target = 0.139202 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.089585 restraints weight = 27915.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3283 r_free = 0.3283 target = 0.089623 restraints weight = 15551.756|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.089752 restraints weight = 12453.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3288 r_free = 0.3288 target = 0.090116 restraints weight = 11638.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.090123 restraints weight = 11162.406|
|-----------------------------------------------------------------------------|
r_work (final): 0.3225
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8117
moved from start:          0.4405

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14161  Z= 0.127
  Angle     :  0.549  10.394  20266  Z= 0.272
  Chirality :  0.033   0.206   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 22.720 177.575   4740
  Min Nonbonded Distance : 2.476

Molprobity Statistics.
  All-atom Clashscore : 6.07
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.10 %
    Favored  : 95.90 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 16.91 %
    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:  0.28 (0.26), residues: 1074
  helix:  1.60 (0.25), residues: 486
  sheet: -0.43 (0.41), residues: 137
  loop : -1.21 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  19 
 TYR   0.007   0.001   TYR A 168 
 PHE   0.024   0.001   PHE A  47 
 TRP   0.028   0.002   TRP A  60 
 HIS   0.009   0.001   HIS C 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (14161)
  covalent geometry    : angle       0.54911 (20266)
  hydrogen bonds       : bond        0.04288 (  576)
  hydrogen bonds       : angle       3.90687 ( 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
  92 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 75
  time to evaluate  : 0.317 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 GLU cc_start: 0.8309 (tp30) cc_final: 0.8003 (mt-10)
REVERT: A  787 ARG cc_start: 0.5509 (ptt90) cc_final: 0.5113 (ptt90)
REVERT: A 1054 MET cc_start: 0.7650 (tpp) cc_final: 0.7400 (ttt)
REVERT: C   98 TRP cc_start: 0.8731 (p-90) cc_final: 0.8273 (p-90)
REVERT: C  101 GLU cc_start: 0.8775 (OUTLIER) cc_final: 0.8511 (tm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 87
  average time/residue: 0.1112
  time to fit residues: 14.3883
Evaluate side-chains
  80 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 67
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  791 VAL
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue 1016 VAL
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  120 VAL
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 74 optimal weight:    0.0270
   chunk 2 optimal weight:    9.9990
   chunk 83 optimal weight:    0.9990
   chunk 113 optimal weight:    0.9990
   chunk 121 optimal weight:    0.0270
   chunk 96 optimal weight:    4.9990
   chunk 17 optimal weight:   10.0000
   chunk 42 optimal weight:    4.9990
   chunk 80 optimal weight:    3.9990
   chunk 54 optimal weight:    3.9990
   overall best weight:    1.2102

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

Flipped N/Q/H residues before XYZ refinement:
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.139546 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.089591 restraints weight = 27634.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.090139 restraints weight = 15723.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.090417 restraints weight = 12499.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.090603 restraints weight = 11181.668|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.090641 restraints weight = 10505.999|
|-----------------------------------------------------------------------------|
r_work (final): 0.3239
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8100
moved from start:          0.4563

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  14161  Z= 0.122
  Angle     :  0.544  11.267  20266  Z= 0.267
  Chirality :  0.033   0.207   2469
  Planarity :  0.004   0.042   1759
  Dihedral  : 22.630 177.366   4740
  Min Nonbonded Distance : 2.457

Molprobity Statistics.
  All-atom Clashscore : 5.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  2.23 %
    Allowed  : 16.70 %
    Favored  : 81.06 %
  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 (0.27), residues: 1074
  helix:  1.62 (0.25), residues: 488
  sheet: -0.29 (0.42), residues: 137
  loop : -1.14 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  15 
 TYR   0.007   0.001   TYR A 168 
 PHE   0.024   0.001   PHE A  47 
 TRP   0.022   0.001   TRP A 137 
 HIS   0.008   0.001   HIS C 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00268 (14161)
  covalent geometry    : angle       0.54423 (20266)
  hydrogen bonds       : bond        0.04188 (  576)
  hydrogen bonds       : angle       3.89665 ( 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
  96 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.356 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 GLU cc_start: 0.8323 (tp30) cc_final: 0.8039 (mt-10)
REVERT: A  787 ARG cc_start: 0.5672 (ptt90) cc_final: 0.5255 (ptt90)
REVERT: A 1054 MET cc_start: 0.7615 (tpp) cc_final: 0.7388 (ttt)
REVERT: C   98 TRP cc_start: 0.8719 (p-90) cc_final: 0.8250 (p-90)
REVERT: C  101 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8545 (tm-30)
  outliers start: 21
  outliers final: 12
  residues processed: 89
  average time/residue: 0.1066
  time to fit residues: 14.1642
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  : 0.382 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  780 LEU
Chi-restraints excluded: chain A residue  791 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1070 VAL
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  163 ASP
Chi-restraints excluded: chain C residue  189 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 129
   random chunks:
   chunk 41 optimal weight:    0.0670
   chunk 124 optimal weight:    2.9990
   chunk 100 optimal weight:    0.9980
   chunk 116 optimal weight:   10.0000
   chunk 51 optimal weight:    2.9990
   chunk 109 optimal weight:    1.9990
   chunk 66 optimal weight:    2.9990
   chunk 12 optimal weight:   10.0000
   chunk 20 optimal weight:    4.9990
   chunk 29 optimal weight:    0.8980
   chunk 25 optimal weight:    6.9990
   overall best weight:    1.3922

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

Flipped N/Q/H residues before XYZ refinement:
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.138860 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.088866 restraints weight = 27641.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.089954 restraints weight = 15074.506|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3282 r_free = 0.3282 target = 0.090072 restraints weight = 11781.711|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.090364 restraints weight = 10416.389|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.090348 restraints weight = 10134.433|
|-----------------------------------------------------------------------------|
r_work (final): 0.3232
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8120
moved from start:          0.4679

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045  14161  Z= 0.131
  Angle     :  0.551  11.547  20266  Z= 0.270
  Chirality :  0.033   0.208   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.594 177.071   4740
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 5.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  1.81 %
    Allowed  : 17.77 %
    Favored  : 80.43 %
  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:  0.34 (0.27), residues: 1074
  helix:  1.57 (0.25), residues: 488
  sheet: -0.25 (0.43), residues: 137
  loop : -1.13 (0.30), residues: 449

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 607 
 TYR   0.008   0.001   TYR A 744 
 PHE   0.025   0.001   PHE A  47 
 TRP   0.031   0.001   TRP A 137 
 HIS   0.008   0.001   HIS C 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00293 (14161)
  covalent geometry    : angle       0.55084 (20266)
  hydrogen bonds       : bond        0.04300 (  576)
  hydrogen bonds       : angle       3.92472 ( 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
  89 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 GLU cc_start: 0.8284 (tp30) cc_final: 0.7973 (mt-10)
REVERT: A  787 ARG cc_start: 0.5690 (ptt90) cc_final: 0.5272 (ptt90)
REVERT: A 1054 MET cc_start: 0.7606 (tpp) cc_final: 0.7383 (ttt)
REVERT: C   98 TRP cc_start: 0.8742 (p-90) cc_final: 0.8129 (p-90)
REVERT: C  101 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8311 (tm-30)
  outliers start: 17
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1109
  time to fit residues: 13.9596
Evaluate side-chains
  81 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  791 VAL
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1070 VAL
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  163 ASP
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:    9.9990
   chunk 106 optimal weight:    0.9990
   chunk 61 optimal weight:    1.9990
   chunk 98 optimal weight:    1.9990
   chunk 2 optimal weight:   10.0000
   chunk 12 optimal weight:   10.0000
   chunk 59 optimal weight:    0.7980
   chunk 8 optimal weight:    7.9990
   chunk 73 optimal weight:    4.9990
   chunk 67 optimal weight:    0.7980
   chunk 50 optimal weight:    2.9990
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 794 GLN
C 151 HIS
C 190 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.139424 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3243 r_free = 0.3243 target = 0.086773 restraints weight = 27874.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.089394 restraints weight = 14661.524|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.090909 restraints weight = 10685.383|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.091739 restraints weight = 9229.152|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3329 r_free = 0.3329 target = 0.092009 restraints weight = 8581.039|
|-----------------------------------------------------------------------------|
r_work (final): 0.3270
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.4840

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= 0.126
  Angle     :  0.541  11.555  20266  Z= 0.265
  Chirality :  0.033   0.213   2469
  Planarity :  0.004   0.043   1759
  Dihedral  : 22.551 177.024   4740
  Min Nonbonded Distance : 2.475

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.00 %
    Favored  : 96.00 %
  Rotamer:
    Outliers :  1.60 %
    Allowed  : 18.30 %
    Favored  : 80.11 %
  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:  0.38 (0.27), residues: 1074
  helix:  1.60 (0.25), residues: 488
  sheet: -0.19 (0.44), residues: 135
  loop : -1.11 (0.30), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 657 
 TYR   0.007   0.001   TYR A 168 
 PHE   0.024   0.001   PHE A  47 
 TRP   0.027   0.001   TRP A 137 
 HIS   0.009   0.001   HIS C 151 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 (14161)
  covalent geometry    : angle       0.54073 (20266)
  hydrogen bonds       : bond        0.04244 (  576)
  hydrogen bonds       : angle       3.89707 ( 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
  92 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.408 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 GLU cc_start: 0.8332 (tp30) cc_final: 0.8014 (mt-10)
REVERT: A  787 ARG cc_start: 0.5791 (ptt90) cc_final: 0.5409 (ptt90)
REVERT: C   98 TRP cc_start: 0.8774 (p-90) cc_final: 0.8259 (p-90)
REVERT: C  101 GLU cc_start: 0.8909 (OUTLIER) cc_final: 0.8387 (tm-30)
  outliers start: 15
  outliers final: 12
  residues processed: 88
  average time/residue: 0.1153
  time to fit residues: 14.8186
Evaluate side-chains
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.285 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
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  791 VAL
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1070 VAL
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  163 ASP
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:    0.0000
   chunk 117 optimal weight:    7.9990
   chunk 112 optimal weight:    0.9990
   chunk 13 optimal weight:    6.9990
   chunk 113 optimal weight:    0.9980
   chunk 124 optimal weight:   20.0000
   chunk 77 optimal weight:    0.0980
   chunk 69 optimal weight:    0.9980
   chunk 78 optimal weight:    1.9990
   chunk 18 optimal weight:   10.0000
   overall best weight:    0.6186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.141144 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.091567 restraints weight = 27855.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.092279 restraints weight = 16098.202|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.092623 restraints weight = 11960.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.092837 restraints weight = 10993.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3340 r_free = 0.3340 target = 0.092933 restraints weight = 10351.540|
|-----------------------------------------------------------------------------|
r_work (final): 0.3280
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8061
moved from start:          0.4975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.047  14161  Z= 0.097
  Angle     :  0.524  11.372  20266  Z= 0.255
  Chirality :  0.032   0.212   2469
  Planarity :  0.004   0.044   1759
  Dihedral  : 22.500 177.372   4740
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.58
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  1.49 %
    Allowed  : 18.30 %
    Favored  : 80.21 %
  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:  0.53 (0.27), residues: 1074
  helix:  1.81 (0.25), residues: 484
  sheet: -0.13 (0.43), residues: 135
  loop : -1.12 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 132 
 TYR   0.008   0.001   TYR A 168 
 PHE   0.026   0.001   PHE A  47 
 TRP   0.026   0.001   TRP A 137 
 HIS   0.008   0.001   HIS C 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00211 (14161)
  covalent geometry    : angle       0.52409 (20266)
  hydrogen bonds       : bond        0.03806 (  576)
  hydrogen bonds       : angle       3.79452 ( 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
  88 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 74
  time to evaluate  : 0.449 
Fit side-chains
   revert: symmetry clash
REVERT: A  362 GLU cc_start: 0.8181 (tp30) cc_final: 0.7914 (mt-10)
REVERT: A  539 GLU cc_start: 0.8145 (tt0) cc_final: 0.7900 (tt0)
REVERT: C   98 TRP cc_start: 0.8650 (p-90) cc_final: 0.8319 (p-90)
REVERT: C  101 GLU cc_start: 0.8809 (OUTLIER) cc_final: 0.8606 (tm-30)
REVERT: C  122 GLN cc_start: 0.7634 (mm-40) cc_final: 0.7290 (tt0)
  outliers start: 14
  outliers final: 12
  residues processed: 84
  average time/residue: 0.1088
  time to fit residues: 13.6645
Evaluate side-chains
  83 residues out of total 940 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 70
  time to evaluate  : 0.337 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   31 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  791 VAL
Chi-restraints excluded: chain A residue  962 ARG
Chi-restraints excluded: chain A residue 1070 VAL
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  163 ASP
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:    0.3980
   chunk 60 optimal weight:    0.8980
   chunk 17 optimal weight:   20.0000
   chunk 59 optimal weight:    0.9990
   chunk 31 optimal weight:    0.4980
   chunk 25 optimal weight:    5.9990
   chunk 79 optimal weight:    6.9990
   chunk 116 optimal weight:    6.9990
   chunk 48 optimal weight:    0.8980
   chunk 66 optimal weight:    0.9980
   chunk 65 optimal weight:    2.9990
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
C 151 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.141099 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3281 r_free = 0.3281 target = 0.088809 restraints weight = 27782.207|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.091444 restraints weight = 14496.151|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.093010 restraints weight = 10533.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.093872 restraints weight = 9030.385|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 18)----------------|
| r_work = 0.3368 r_free = 0.3368 target = 0.094175 restraints weight = 8394.625|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8029
moved from start:          0.5055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.043  14161  Z= 0.100
  Angle     :  0.524  11.873  20266  Z= 0.254
  Chirality :  0.032   0.214   2469
  Planarity :  0.004   0.044   1759
  Dihedral  : 22.448 177.104   4740
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 5.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.63 %
    Favored  : 96.37 %
  Rotamer:
    Outliers :  1.28 %
    Allowed  : 18.40 %
    Favored  : 80.32 %
  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:  0.58 (0.27), residues: 1074
  helix:  1.87 (0.25), residues: 484
  sheet: -0.13 (0.44), residues: 135
  loop : -1.12 (0.30), residues: 455

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 132 
 TYR   0.007   0.001   TYR A 168 
 PHE   0.026   0.001   PHE A  47 
 TRP   0.049   0.002   TRP A 137 
 HIS   0.008   0.001   HIS C 241 

Details of bonding type rmsd
  covalent geometry    : bond        0.00218 (14161)
  covalent geometry    : angle       0.52371 (20266)
  hydrogen bonds       : bond        0.03877 (  576)
  hydrogen bonds       : angle       3.81006 ( 1489)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2026.44 seconds
wall clock time: 35 minutes 40.63 seconds (2140.63 seconds total)