Starting phenix.real_space_refine
on Wed Mar  4 12:51:19 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7trf_26088/03_2026/7trf_26088.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trf_26088/03_2026/7trf_26088.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7trf_26088/03_2026/7trf_26088.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trf_26088/03_2026/7trf_26088.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trf_26088/03_2026/7trf_26088.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trf_26088/03_2026/7trf_26088.cif"
  }
  resolution = 3.7
  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=   0.003
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      38      5.16       5
     C    7774      2.51       5
     N    2469      2.21       5
     O    3076      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 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: 13581
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "F"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "E"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 642
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
    Chain: "B"
      Number of atoms: 4605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 4605
          Classifications: {'RNA': 217}
          Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 21, 'rna3p_pur': 85, 'rna3p_pyr': 96}
          Link IDs: {'rna2p': 36, 'rna3p': 180}
          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}
  Time building chain proxies: 3.11, per 1000 atoms: 0.23
  Number of scatterers: 13581
  At special positions: 0
  Unit cell: (117.7, 122.1, 121, 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      38     16.00
     P     224     15.00
     O    3076      8.00
     N    2469      7.00
     C    7774      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: 1.25
  Conformation dependent library (CDL) restraints added in 297.4 milliseconds
  

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2086

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 9 sheets defined
      59.4% alpha, 13.0% beta
      64 base pairs and 97 stacking pairs defined.
    Time for finding SS restraints: 1.71
  Creating SS restraints...
    Processing helix  chain 'F' and resid 38 through 50
      removed outlier: 3.800A  pdb=" N   TYR F  43 " --> pdb=" O   SER F  39 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLN F  48 " --> pdb=" O   LYS F  44 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL F  49 " --> pdb=" O   VAL F  45 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 56 through 86
      removed outlier: 4.107A  pdb=" N   SER F  65 " --> pdb=" O   GLY F  61 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE F  66 " --> pdb=" O   ILE F  62 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL F  67 " --> pdb=" O   MET F  63 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ASN F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE F  70 " --> pdb=" O   PHE F  66 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE F  74 " --> pdb=" O   ILE F  70 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 103
      removed outlier: 4.193A  pdb=" N   ILE F  95 " --> pdb=" O   THR F  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN F  96 " --> pdb=" O   SER F  92 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR F  97 " --> pdb=" O   ARG F  93 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA F  98 " --> pdb=" O   GLU F  94 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL F  99 " --> pdb=" O   ILE F  95 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG F 100 " --> pdb=" O   GLN F  96 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU F 101 " --> pdb=" O   THR F  97 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU F 102 " --> pdb=" O   ALA F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 105 through 124
      removed outlier: 3.548A  pdb=" N   LYS F 109 " --> pdb=" O   GLY F 105 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS F 121 " --> pdb=" O   LYS F 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 19 through 23
    Processing helix  chain 'E' and resid 27 through 38
      removed outlier: 3.854A  pdb=" N   GLY E  38 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 74
      removed outlier: 4.561A  pdb=" N   VAL E  50 " --> pdb=" O   ALA E  46 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR E  51 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL E  55 " --> pdb=" O   TYR E  51 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU E  56 " --> pdb=" O   LEU E  52 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLU E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR E  58 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU E  64 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU E  66 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA E  67 " --> pdb=" O   ILE E  63 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASP E  73 " --> pdb=" O   ASN E  69 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ASN E  74 " --> pdb=" O   ALA E  70 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 81 through 91
      removed outlier: 3.810A  pdb=" N   ALA E  87 " --> pdb=" O   HIS E  83 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 98
      removed outlier: 3.596A  pdb=" N   LEU E  97 " --> pdb=" O   GLU E  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 8 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 125 through 134
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 146 through 156
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.839A  pdb=" N   LEU A 178 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
      removed outlier: 4.000A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 332'
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
      removed outlier: 3.574A  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 401
      removed outlier: 4.037A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.782A  pdb=" N   LEU A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 454
      removed outlier: 3.781A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 471
      removed outlier: 3.717A  pdb=" N   ARG A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.506A  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: 3.654A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 560
      removed outlier: 3.764A  pdb=" N   HIS A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   VAL A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 4.388A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
      removed outlier: 3.515A  pdb=" N   GLU A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 672
      removed outlier: 3.532A  pdb=" N   SER A 656 " --> pdb=" O   GLU A 652 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.652A  pdb=" N   LEU A 676 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.762A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 4.005A  pdb=" N   LEU A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 3.583A  pdb=" N   PHE A 776 " --> pdb=" O   TYR A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 815
    Processing helix  chain 'A' and resid 837 through 854
    Processing helix  chain 'A' and resid 876 through 890
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.788A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 958
      removed outlier: 4.052A  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: 4.120A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1082
      removed outlier: 4.323A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TRP A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.651A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.508A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1119
      removed outlier: 3.712A  pdb=" N   ALA A1119 " --> pdb=" O   LEU A1115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 89 through 90
      removed outlier: 3.756A  pdb=" N   ILE F  90 " --> pdb=" O   ARG E  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600
      removed outlier: 6.601A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 862 through 865
      removed outlier: 3.640A  pdb=" N   VAL A 904 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ASP A 712 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LYS A 902 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 927 through 930

    467 hydrogen bonds defined for protein.
    1344 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      173 hydrogen bonds
      330 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      97 stacking parallelities
  Total time for adding SS restraints: 3.08

  Time building geometry restraints manager: 1.65 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 3548
        1.34 -     1.46: 4450
        1.46 -     1.58: 5835
        1.58 -     1.71: 444
        1.71 -     1.83: 51
  Bond restraints: 14328
  Sorted by residual:
  bond pdb=" C   LYS A 973 "
       pdb=" N   LEU A 974 "
    ideal  model  delta    sigma   weight residual
    1.334  1.384 -0.049 1.27e-02 6.20e+03 1.50e+01
  bond pdb=" CA  ILE E  79 "
       pdb=" CB  ILE E  79 "
    ideal  model  delta    sigma   weight residual
    1.540  1.575 -0.035 1.10e-02 8.26e+03 1.04e+01
  bond pdb=" N   VAL E  31 "
       pdb=" CA  VAL E  31 "
    ideal  model  delta    sigma   weight residual
    1.461  1.498 -0.037 1.19e-02 7.06e+03 9.83e+00
  bond pdb=" N   ILE E  79 "
       pdb=" CA  ILE E  79 "
    ideal  model  delta    sigma   weight residual
    1.457  1.498 -0.041 1.32e-02 5.74e+03 9.48e+00
  bond pdb=" N   VAL A 697 "
       pdb=" CA  VAL A 697 "
    ideal  model  delta    sigma   weight residual
    1.460  1.496 -0.036 1.21e-02 6.83e+03 8.98e+00
  ... (remaining 14323 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.52: 19326
        1.52 -     3.05: 987
        3.05 -     4.57: 141
        4.57 -     6.09: 19
        6.09 -     7.61: 3
  Bond angle restraints: 20476
  Sorted by residual:
  angle pdb=" O   LYS A 973 "
        pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
      ideal   model   delta    sigma   weight residual
     122.07  117.21    4.86 1.03e+00 9.43e-01 2.23e+01
  angle pdb=" N   VAL A 596 "
        pdb=" CA  VAL A 596 "
        pdb=" C   VAL A 596 "
      ideal   model   delta    sigma   weight residual
     112.43  108.64    3.79 9.20e-01 1.18e+00 1.70e+01
  angle pdb=" C   ILE E  80 "
        pdb=" N   PRO E  81 "
        pdb=" CA  PRO E  81 "
      ideal   model   delta    sigma   weight residual
     119.84  124.98   -5.14 1.25e+00 6.40e-01 1.69e+01
  angle pdb=" CA  LYS A 973 "
        pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
      ideal   model   delta    sigma   weight residual
     117.07  121.61   -4.54 1.14e+00 7.69e-01 1.59e+01
  angle pdb=" C   LYS A 973 "
        pdb=" N   LEU A 974 "
        pdb=" CA  LEU A 974 "
      ideal   model   delta    sigma   weight residual
     120.44  125.58   -5.14 1.30e+00 5.92e-01 1.56e+01
  ... (remaining 20471 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.84: 8266
       35.84 -    71.69: 627
       71.69 -   107.53: 95
      107.53 -   143.38: 5
      143.38 -   179.22: 3
  Dihedral angle restraints: 8996
    sinusoidal: 5775
      harmonic: 3221
  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   52.78  179.22     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
    -128.00   48.72 -176.72     1      1.70e+01 3.46e-03 6.64e+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   40.43 -168.43     1      1.70e+01 3.46e-03 6.58e+01
  ... (remaining 8993 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.113: 2401
       0.113 -    0.227: 86
       0.227 -    0.340: 8
       0.340 -    0.454: 0
       0.454 -    0.567: 1
  Chirality restraints: 2496
  Sorted by residual:
  chirality pdb=" P     G B 251 "
            pdb=" OP1   G B 251 "
            pdb=" OP2   G B 251 "
            pdb=" O5'   G B 251 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.98   -0.57 2.00e-01 2.50e+01 8.05e+00
  chirality pdb=" CA  MET F  63 "
            pdb=" N   MET F  63 "
            pdb=" C   MET F  63 "
            pdb=" CB  MET F  63 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.26    0.25 2.00e-01 2.50e+01 1.61e+00
  chirality pdb=" P     G B 319 "
            pdb=" OP1   G B 319 "
            pdb=" OP2   G B 319 "
            pdb=" O5'   G B 319 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.65   -0.24 2.00e-01 2.50e+01 1.39e+00
  ... (remaining 2493 not shown)

  Planarity restraints: 1776
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE E  26 "    0.015 2.00e-02 2.50e+03   2.98e-02 8.89e+00
        pdb=" C   PHE E  26 "   -0.052 2.00e-02 2.50e+03
        pdb=" O   PHE E  26 "    0.019 2.00e-02 2.50e+03
        pdb=" N   PRO E  27 "    0.017 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B 312 "   -0.000 2.00e-02 2.50e+03   1.70e-02 6.49e+00
        pdb=" N1    U B 312 "    0.015 2.00e-02 2.50e+03
        pdb=" C2    U B 312 "    0.001 2.00e-02 2.50e+03
        pdb=" O2    U B 312 "   -0.000 2.00e-02 2.50e+03
        pdb=" N3    U B 312 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    U B 312 "   -0.016 2.00e-02 2.50e+03
        pdb=" O4    U B 312 "    0.000 2.00e-02 2.50e+03
        pdb=" C5    U B 312 "    0.032 2.00e-02 2.50e+03
        pdb=" C6    U B 312 "   -0.033 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F  43 "    0.023 2.00e-02 2.50e+03   1.70e-02 5.76e+00
        pdb=" CG  TYR F  43 "   -0.021 2.00e-02 2.50e+03
        pdb=" CD1 TYR F  43 "    0.003 2.00e-02 2.50e+03
        pdb=" CD2 TYR F  43 "   -0.022 2.00e-02 2.50e+03
        pdb=" CE1 TYR F  43 "   -0.015 2.00e-02 2.50e+03
        pdb=" CE2 TYR F  43 "    0.010 2.00e-02 2.50e+03
        pdb=" CZ  TYR F  43 "    0.024 2.00e-02 2.50e+03
        pdb=" OH  TYR F  43 "   -0.002 2.00e-02 2.50e+03
  ... (remaining 1773 not shown)

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1519
        2.75 -     3.28: 12437
        3.28 -     3.82: 23235
        3.82 -     4.36: 26628
        4.36 -     4.90: 41800
  Nonbonded interactions: 105619
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1079 "
            pdb=" OG1 THR A1083 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NE  ARG E  78 "
            pdb=" O6    G B 315 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O2'   G B  71 "
            pdb=" OP1   C B  72 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   TYR F  38 "
            pdb=" N   VAL F  40 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OG  SER A 619 "
            pdb=" O   ASN A 635 "
     model   vdw
     2.261 3.040
  ... (remaining 105614 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:             1.050
  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:          0.180
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     14.940
  Find NCS groups from input model:        0.050
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.410
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   17.750
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
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      :  0.005   0.049  14328  Z= 0.320
  Angle     :  0.743   7.614  20476  Z= 0.460
  Chirality :  0.049   0.567   2496
  Planarity :  0.004   0.041   1776
  Dihedral  : 21.473 179.219   6910
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.58 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.26 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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: -0.55 (0.26), residues: 1092
  helix:  0.47 (0.23), residues: 546
  sheet: -0.29 (0.51), residues: 93
  loop : -1.38 (0.29), residues: 453

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 470 
 TYR   0.024   0.002   TYR F  43 
 PHE   0.030   0.002   PHE F  66 
 TRP   0.015   0.001   TRP A 581 
 HIS   0.012   0.002   HIS F  50 

Details of bonding type rmsd
  covalent geometry    : bond        0.00509 (14328)
  covalent geometry    : angle       0.74349 (20476)
  hydrogen bonds       : bond        0.15745 (  626)
  hydrogen bonds       : angle       6.10120 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   63 MET cc_start: 0.9253 (ptt) cc_final: 0.9052 (mmt)
REVERT: E   37 LYS cc_start: 0.5136 (tptp) cc_final: 0.4891 (mptt)
REVERT: E   62 GLU cc_start: 0.9252 (tp30) cc_final: 0.8818 (mm-30)
REVERT: E   80 ILE cc_start: 0.6512 (tt) cc_final: 0.6153 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.1392
  time to fit residues: 27.2038
Evaluate side-chains
  85 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.392 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 98 optimal weight:    4.9990
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    7.9990
   chunk 103 optimal weight:   10.0000
   chunk 77 optimal weight:    4.9990
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    3.9990
   chunk 55 optimal weight:    6.9990
   overall best weight:    1.7186

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

Flipped N/Q/H residues before XYZ refinement:
A 384 GLN
A 608 GLN
A 827 GLN
A1023 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3902 r_free = 0.3902 target = 0.101332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.065409 restraints weight = 47583.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.067264 restraints weight = 23209.314|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3235 r_free = 0.3235 target = 0.068344 restraints weight = 16209.636|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3247 r_free = 0.3247 target = 0.068919 restraints weight = 13624.117|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3251 r_free = 0.3251 target = 0.069121 restraints weight = 12551.806|
|-----------------------------------------------------------------------------|
r_work (final): 0.3189
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8175
moved from start:          0.1529

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  14328  Z= 0.149
  Angle     :  0.595   8.898  20476  Z= 0.299
  Chirality :  0.034   0.171   2496
  Planarity :  0.004   0.040   1776
  Dihedral  : 23.044 177.444   4769
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 6.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.66 %
    Favored  : 96.34 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  7.76 %
    Favored  : 90.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.12 (0.26), residues: 1092
  helix:  1.05 (0.22), residues: 565
  sheet: -0.09 (0.51), residues: 93
  loop : -1.15 (0.31), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG E  33 
 TYR   0.019   0.002   TYR F  43 
 PHE   0.016   0.002   PHE F  66 
 TRP   0.010   0.001   TRP A 459 
 HIS   0.009   0.001   HIS E  32 

Details of bonding type rmsd
  covalent geometry    : bond        0.00312 (14328)
  covalent geometry    : angle       0.59539 (20476)
  hydrogen bonds       : bond        0.05037 (  626)
  hydrogen bonds       : angle       4.31700 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 93
  time to evaluate  : 0.419 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   18 ARG cc_start: 0.7660 (mtm110) cc_final: 0.7204 (ptt-90)
REVERT: E   62 GLU cc_start: 0.9050 (tp30) cc_final: 0.8807 (mm-30)
REVERT: E   76 LYS cc_start: 0.8605 (mmtt) cc_final: 0.7825 (mmmt)
REVERT: A  512 MET cc_start: 0.8995 (mtp) cc_final: 0.8784 (mtp)
REVERT: A  813 MET cc_start: 0.8538 (tmm) cc_final: 0.8149 (tmm)
  outliers start: 12
  outliers final: 3
  residues processed: 98
  average time/residue: 0.1295
  time to fit residues: 18.1691
Evaluate side-chains
  87 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 84
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue 1016 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 11 optimal weight:    7.9990
   chunk 17 optimal weight:   30.0000
   chunk 19 optimal weight:   10.0000
   chunk 7 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 88 optimal weight:    0.0060
   chunk 30 optimal weight:    8.9990
   chunk 72 optimal weight:    0.8980
   chunk 29 optimal weight:    9.9990
   chunk 37 optimal weight:    5.9990
   chunk 48 optimal weight:   10.0000
   overall best weight:    3.3802

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

Flipped N/Q/H residues before XYZ refinement:
A 400 HIS
A 762 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3837 r_free = 0.3837 target = 0.097605 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.061784 restraints weight = 49004.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.063556 restraints weight = 23957.252|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.064586 restraints weight = 16818.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 47)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.065125 restraints weight = 14170.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3160 r_free = 0.3160 target = 0.065371 restraints weight = 13066.808|
|-----------------------------------------------------------------------------|
r_work (final): 0.3096
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8265
moved from start:          0.2553

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  14328  Z= 0.228
  Angle     :  0.644   8.684  20476  Z= 0.324
  Chirality :  0.036   0.205   2496
  Planarity :  0.005   0.035   1776
  Dihedral  : 23.054 175.781   4769
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 10.70 %
    Favored  : 87.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.27 (0.26), residues: 1092
  helix:  1.18 (0.22), residues: 568
  sheet: -0.17 (0.50), residues: 94
  loop : -1.08 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 901 
 TYR   0.018   0.002   TYR A  18 
 PHE   0.018   0.002   PHE A1021 
 TRP   0.012   0.001   TRP A 581 
 HIS   0.006   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00490 (14328)
  covalent geometry    : angle       0.64433 (20476)
  hydrogen bonds       : bond        0.05206 (  626)
  hydrogen bonds       : angle       4.23020 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 80
  time to evaluate  : 0.380 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   38 TYR cc_start: 0.8456 (m-10) cc_final: 0.8220 (m-10)
REVERT: F   43 TYR cc_start: 0.7927 (t80) cc_final: 0.7647 (t80)
REVERT: E   62 GLU cc_start: 0.9183 (tp30) cc_final: 0.8864 (mm-30)
REVERT: E   76 LYS cc_start: 0.8609 (mmtt) cc_final: 0.7854 (mmmt)
REVERT: A  512 MET cc_start: 0.9098 (mtp) cc_final: 0.8883 (mtp)
REVERT: A  813 MET cc_start: 0.8754 (tmm) cc_final: 0.8225 (tmm)
  outliers start: 19
  outliers final: 13
  residues processed: 90
  average time/residue: 0.1111
  time to fit residues: 15.0957
Evaluate side-chains
  87 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 74
  time to evaluate  : 0.389 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain E residue   83 HIS
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1036 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 59 optimal weight:    3.9990
   chunk 17 optimal weight:   30.0000
   chunk 108 optimal weight:    2.9990
   chunk 99 optimal weight:    8.9990
   chunk 97 optimal weight:    9.9990
   chunk 87 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 5 optimal weight:    0.9990
   chunk 105 optimal weight:    0.5980
   chunk 83 optimal weight:   10.0000
   chunk 43 optimal weight:   20.0000
   overall best weight:    1.9186

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

Flipped N/Q/H residues before XYZ refinement:
F  96 GLN
A 687 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3858 r_free = 0.3858 target = 0.098814 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.063036 restraints weight = 49209.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3152 r_free = 0.3152 target = 0.064873 restraints weight = 24159.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.065940 restraints weight = 16962.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3187 r_free = 0.3187 target = 0.066486 restraints weight = 14305.532|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3193 r_free = 0.3193 target = 0.066734 restraints weight = 13225.491|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8228
moved from start:          0.2819

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  14328  Z= 0.143
  Angle     :  0.552  10.480  20476  Z= 0.277
  Chirality :  0.034   0.182   2496
  Planarity :  0.004   0.034   1776
  Dihedral  : 22.944 174.858   4769
  Min Nonbonded Distance : 2.396

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.39 %
    Favored  : 96.61 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.80 %
    Favored  : 85.31 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.65 (0.26), residues: 1092
  helix:  1.49 (0.22), residues: 568
  sheet:  0.18 (0.54), residues: 87
  loop : -0.92 (0.31), residues: 437

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 901 
 TYR   0.013   0.001   TYR F  43 
 PHE   0.013   0.001   PHE A 776 
 TRP   0.016   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 (14328)
  covalent geometry    : angle       0.55183 (20476)
  hydrogen bonds       : bond        0.04225 (  626)
  hydrogen bonds       : angle       3.91445 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   38 TYR cc_start: 0.8529 (m-10) cc_final: 0.8236 (m-10)
REVERT: E   18 ARG cc_start: 0.7662 (mtm110) cc_final: 0.7350 (ptt-90)
REVERT: E   62 GLU cc_start: 0.9238 (tp30) cc_final: 0.8875 (mm-30)
REVERT: E   76 LYS cc_start: 0.8643 (mmtt) cc_final: 0.7915 (mmmt)
REVERT: E   78 ARG cc_start: 0.8395 (tpp80) cc_final: 0.7965 (tpp80)
REVERT: E   86 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8713 (tp)
REVERT: A  125 ASN cc_start: 0.7193 (t0) cc_final: 0.6938 (t0)
REVERT: A  512 MET cc_start: 0.9052 (mtp) cc_final: 0.8839 (mtp)
REVERT: A  813 MET cc_start: 0.8780 (tmm) cc_final: 0.8189 (tmm)
  outliers start: 18
  outliers final: 11
  residues processed: 92
  average time/residue: 0.1145
  time to fit residues: 15.7918
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 69 optimal weight:    0.3980
   chunk 16 optimal weight:    2.9990
   chunk 23 optimal weight:   10.0000
   chunk 123 optimal weight:    5.9990
   chunk 4 optimal weight:    8.9990
   chunk 42 optimal weight:    6.9990
   chunk 65 optimal weight:    5.9990
   chunk 17 optimal weight:   30.0000
   chunk 78 optimal weight:    7.9990
   chunk 22 optimal weight:   20.0000
   chunk 29 optimal weight:   10.0000
   overall best weight:    4.4788

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

Flipped N/Q/H residues before XYZ refinement:
A  17 HIS
A 340 GLN
A 779 HIS
A 827 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3810 r_free = 0.3810 target = 0.096240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 66)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.060396 restraints weight = 50034.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 60)----------------|
| r_work = 0.3083 r_free = 0.3083 target = 0.062108 restraints weight = 25397.092|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 64)----------------|
| r_work = 0.3106 r_free = 0.3106 target = 0.063069 restraints weight = 18156.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3117 r_free = 0.3117 target = 0.063558 restraints weight = 15490.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.063758 restraints weight = 14407.159|
|-----------------------------------------------------------------------------|
r_work (final): 0.3059
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8321
moved from start:          0.3288

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.050  14328  Z= 0.275
  Angle     :  0.649  10.095  20476  Z= 0.327
  Chirality :  0.037   0.181   2496
  Planarity :  0.005   0.034   1776
  Dihedral  : 23.042 174.327   4769
  Min Nonbonded Distance : 2.377

Molprobity Statistics.
  All-atom Clashscore : 9.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.95 %
    Favored  : 95.05 %
  Rotamer:
    Outliers :  3.04 %
    Allowed  : 13.96 %
    Favored  : 83.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.42 (0.26), residues: 1092
  helix:  1.31 (0.22), residues: 568
  sheet: -0.23 (0.51), residues: 94
  loop : -0.98 (0.31), residues: 430

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 901 
 TYR   0.018   0.002   TYR F  43 
 PHE   0.021   0.002   PHE A 331 
 TRP   0.018   0.002   TRP A 581 
 HIS   0.006   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00589 (14328)
  covalent geometry    : angle       0.64871 (20476)
  hydrogen bonds       : bond        0.05229 (  626)
  hydrogen bonds       : angle       4.16416 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 79
  time to evaluate  : 0.388 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   38 TYR cc_start: 0.8609 (m-10) cc_final: 0.8328 (m-10)
REVERT: E   62 GLU cc_start: 0.9259 (tp30) cc_final: 0.8920 (mm-30)
REVERT: E   76 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8081 (mmmt)
REVERT: E   78 ARG cc_start: 0.8410 (tpp80) cc_final: 0.8116 (tpp80)
REVERT: A  125 ASN cc_start: 0.7282 (t0) cc_final: 0.7007 (t0)
REVERT: A  512 MET cc_start: 0.9097 (mtp) cc_final: 0.8866 (mtp)
REVERT: A  813 MET cc_start: 0.8789 (tmm) cc_final: 0.8176 (tmm)
  outliers start: 29
  outliers final: 20
  residues processed: 98
  average time/residue: 0.1019
  time to fit residues: 15.3770
Evaluate side-chains
  97 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 77
  time to evaluate  : 0.395 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   69 ASN
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  827 GLN
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 30 optimal weight:    7.9990
   chunk 17 optimal weight:   30.0000
   chunk 32 optimal weight:   10.0000
   chunk 111 optimal weight:    0.9980
   chunk 59 optimal weight:    0.0010
   chunk 48 optimal weight:    7.9990
   chunk 19 optimal weight:   10.0000
   chunk 46 optimal weight:    0.9980
   chunk 26 optimal weight:   20.0000
   chunk 31 optimal weight:   10.0000
   chunk 93 optimal weight:    9.9990
   overall best weight:    3.5990

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

Flipped N/Q/H residues before XYZ refinement:
** F  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3813 r_free = 0.3813 target = 0.096429 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.060825 restraints weight = 49664.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.062566 restraints weight = 24647.936|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.063569 restraints weight = 17395.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.064069 restraints weight = 14747.320|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3136 r_free = 0.3136 target = 0.064274 restraints weight = 13667.153|
|-----------------------------------------------------------------------------|
r_work (final): 0.3071
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.3483

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14328  Z= 0.229
  Angle     :  0.620  10.595  20476  Z= 0.310
  Chirality :  0.036   0.183   2496
  Planarity :  0.004   0.035   1776
  Dihedral  : 23.039 173.663   4769
  Min Nonbonded Distance : 2.334

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.31 %
    Allowed  : 16.05 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.43 (0.26), residues: 1092
  helix:  1.35 (0.22), residues: 568
  sheet: -0.22 (0.49), residues: 99
  loop : -1.04 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 599 
 TYR   0.017   0.001   TYR F  43 
 PHE   0.015   0.002   PHE A 331 
 TRP   0.011   0.001   TRP A 581 
 HIS   0.006   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00491 (14328)
  covalent geometry    : angle       0.62009 (20476)
  hydrogen bonds       : bond        0.04865 (  626)
  hydrogen bonds       : angle       4.11307 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 72
  time to evaluate  : 0.305 
Fit side-chains
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9245 (tp30) cc_final: 0.8911 (mm-30)
REVERT: E   76 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8176 (mmmt)
REVERT: E   78 ARG cc_start: 0.8438 (tpp80) cc_final: 0.8068 (tpp80)
REVERT: A  512 MET cc_start: 0.9089 (mtp) cc_final: 0.8852 (mtp)
REVERT: A  813 MET cc_start: 0.8813 (tmm) cc_final: 0.8168 (tmm)
  outliers start: 22
  outliers final: 18
  residues processed: 87
  average time/residue: 0.0971
  time to fit residues: 13.0674
Evaluate side-chains
  90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   69 ASN
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1129 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 12 optimal weight:    5.9990
   chunk 46 optimal weight:    4.9990
   chunk 98 optimal weight:    7.9990
   chunk 1 optimal weight:    6.9990
   chunk 32 optimal weight:   10.0000
   chunk 101 optimal weight:    1.9990
   chunk 20 optimal weight:   30.0000
   chunk 125 optimal weight:    0.9990
   chunk 13 optimal weight:    1.9990
   chunk 63 optimal weight:    9.9990
   chunk 108 optimal weight:    3.9990
   overall best weight:    2.7990

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

Flipped N/Q/H residues before XYZ refinement:
** F  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.096760 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.061213 restraints weight = 49636.632|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 58)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.062958 restraints weight = 25098.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.063967 restraints weight = 17860.141|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3142 r_free = 0.3142 target = 0.064479 restraints weight = 15180.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3146 r_free = 0.3146 target = 0.064655 restraints weight = 14074.289|
|-----------------------------------------------------------------------------|
r_work (final): 0.3080
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8294
moved from start:          0.3685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14328  Z= 0.187
  Angle     :  0.585  10.484  20476  Z= 0.292
  Chirality :  0.035   0.184   2496
  Planarity :  0.004   0.034   1776
  Dihedral  : 22.974 173.006   4769
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 16.79 %
    Favored  : 81.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.56 (0.26), residues: 1092
  helix:  1.47 (0.22), residues: 570
  sheet: -0.13 (0.53), residues: 87
  loop : -0.98 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 811 
 TYR   0.017   0.001   TYR F  43 
 PHE   0.023   0.002   PHE A  47 
 TRP   0.012   0.001   TRP A 547 
 HIS   0.005   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00401 (14328)
  covalent geometry    : angle       0.58549 (20476)
  hydrogen bonds       : bond        0.04532 (  626)
  hydrogen bonds       : angle       3.99595 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.386 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9245 (tp30) cc_final: 0.8869 (mm-30)
REVERT: E   76 LYS cc_start: 0.8780 (mmtt) cc_final: 0.8223 (mmmt)
REVERT: A  813 MET cc_start: 0.8777 (tmm) cc_final: 0.8127 (tmm)
  outliers start: 20
  outliers final: 17
  residues processed: 86
  average time/residue: 0.0999
  time to fit residues: 13.0865
Evaluate side-chains
  90 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 73
  time to evaluate  : 0.240 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   69 ASN
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  827 GLN
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 103 optimal weight:    5.9990
   chunk 90 optimal weight:    4.9990
   chunk 26 optimal weight:   20.0000
   chunk 112 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9990
   chunk 17 optimal weight:   30.0000
   chunk 47 optimal weight:    7.9990
   chunk 101 optimal weight:    6.9990
   chunk 125 optimal weight:    3.9990
   chunk 57 optimal weight:    3.9990
   chunk 44 optimal weight:   50.0000
   overall best weight:    3.1990

-------------------------------------------------------------------------------
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 = 0.3811 r_free = 0.3811 target = 0.096332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3059 r_free = 0.3059 target = 0.060802 restraints weight = 49182.278|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 61)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.062553 restraints weight = 24584.738|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.063549 restraints weight = 17399.381|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 44)----------------|
| r_work = 0.3134 r_free = 0.3134 target = 0.064054 restraints weight = 14757.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 41)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.064303 restraints weight = 13676.637|
|-----------------------------------------------------------------------------|
r_work (final): 0.3074
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8289
moved from start:          0.3883

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14328  Z= 0.210
  Angle     :  0.599  10.101  20476  Z= 0.301
  Chirality :  0.035   0.185   2496
  Planarity :  0.004   0.034   1776
  Dihedral  : 22.977 172.643   4769
  Min Nonbonded Distance : 2.294

Molprobity Statistics.
  All-atom Clashscore : 8.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.20 %
    Allowed  : 17.21 %
    Favored  : 80.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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 (0.26), residues: 1092
  helix:  1.38 (0.22), residues: 576
  sheet: -0.13 (0.52), residues: 92
  loop : -0.95 (0.31), residues: 424

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A  30 
 TYR   0.018   0.001   TYR F  43 
 PHE   0.016   0.002   PHE A  27 
 TRP   0.011   0.001   TRP A 547 
 HIS   0.004   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 (14328)
  covalent geometry    : angle       0.59945 (20476)
  hydrogen bonds       : bond        0.04747 (  626)
  hydrogen bonds       : angle       4.08392 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.389 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9252 (tp30) cc_final: 0.8879 (mm-30)
REVERT: E   76 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8210 (mmmt)
REVERT: A  773 MET cc_start: 0.7695 (mpp) cc_final: 0.7469 (mmm)
REVERT: A  813 MET cc_start: 0.8841 (tmm) cc_final: 0.8182 (tmm)
  outliers start: 21
  outliers final: 17
  residues processed: 89
  average time/residue: 0.1092
  time to fit residues: 14.6871
Evaluate side-chains
  88 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 71
  time to evaluate  : 0.292 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   69 ASN
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  827 GLN
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 39 optimal weight:    5.9990
   chunk 17 optimal weight:   30.0000
   chunk 20 optimal weight:   30.0000
   chunk 35 optimal weight:   10.0000
   chunk 41 optimal weight:    0.9980
   chunk 47 optimal weight:    9.9990
   chunk 97 optimal weight:    9.9990
   chunk 50 optimal weight:    4.9990
   chunk 51 optimal weight:    8.9990
   chunk 83 optimal weight:    0.9990
   chunk 129 optimal weight:    2.9990
   overall best weight:    3.1988

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

Flipped N/Q/H residues before XYZ refinement:
A  53 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3807 r_free = 0.3807 target = 0.096174 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3055 r_free = 0.3055 target = 0.060759 restraints weight = 50032.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 56)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.062472 restraints weight = 25219.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.063475 restraints weight = 17962.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.063984 restraints weight = 15259.231|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3135 r_free = 0.3135 target = 0.064173 restraints weight = 14128.507|
|-----------------------------------------------------------------------------|
r_work (final): 0.3070
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.4159

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14328  Z= 0.206
  Angle     :  0.606  10.288  20476  Z= 0.302
  Chirality :  0.035   0.184   2496
  Planarity :  0.004   0.033   1776
  Dihedral  : 22.975 171.947   4769
  Min Nonbonded Distance : 2.301

Molprobity Statistics.
  All-atom Clashscore : 8.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 17.31 %
    Favored  : 80.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.49 (0.26), residues: 1092
  helix:  1.40 (0.22), residues: 571
  sheet: -0.20 (0.53), residues: 92
  loop : -1.02 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 613 
 TYR   0.018   0.001   TYR F  43 
 PHE   0.018   0.002   PHE E  26 
 TRP   0.011   0.001   TRP A 547 
 HIS   0.005   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00441 (14328)
  covalent geometry    : angle       0.60642 (20476)
  hydrogen bonds       : bond        0.04706 (  626)
  hydrogen bonds       : angle       4.05973 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 75
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9306 (tp30) cc_final: 0.8941 (mm-30)
REVERT: E   76 LYS cc_start: 0.8746 (mmtt) cc_final: 0.8244 (mmmt)
REVERT: A  773 MET cc_start: 0.7703 (mpp) cc_final: 0.7490 (mpp)
REVERT: A  813 MET cc_start: 0.8823 (tmm) cc_final: 0.8178 (tmm)
  outliers start: 19
  outliers final: 18
  residues processed: 88
  average time/residue: 0.1056
  time to fit residues: 14.5584
Evaluate side-chains
  87 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 69
  time to evaluate  : 0.479 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   69 ASN
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  594 LYS
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Chi-restraints excluded: chain A residue 1129 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 123 optimal weight:    3.9990
   chunk 62 optimal weight:    2.9990
   chunk 72 optimal weight:    1.9990
   chunk 114 optimal weight:    2.9990
   chunk 116 optimal weight:    3.9990
   chunk 124 optimal weight:    0.5980
   chunk 66 optimal weight:    0.9980
   chunk 117 optimal weight:    5.9990
   chunk 86 optimal weight:    2.9990
   chunk 35 optimal weight:   10.0000
   chunk 115 optimal weight:    0.9990
   overall best weight:    1.5186

-------------------------------------------------------------------------------
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 = 0.3833 r_free = 0.3833 target = 0.097572 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.062704 restraints weight = 48832.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.064518 restraints weight = 23914.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3172 r_free = 0.3172 target = 0.065550 restraints weight = 16687.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.066090 restraints weight = 14023.353|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3188 r_free = 0.3188 target = 0.066289 restraints weight = 12942.617|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8243
moved from start:          0.4196

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048  14328  Z= 0.127
  Angle     :  0.553  10.740  20476  Z= 0.273
  Chirality :  0.033   0.184   2496
  Planarity :  0.004   0.034   1776
  Dihedral  : 22.869 171.995   4769
  Min Nonbonded Distance : 2.308

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 17.63 %
    Favored  : 80.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.71 (0.26), residues: 1092
  helix:  1.63 (0.22), residues: 569
  sheet: -0.10 (0.52), residues: 92
  loop : -0.98 (0.31), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A  30 
 TYR   0.012   0.001   TYR F  43 
 PHE   0.010   0.001   PHE A 331 
 TRP   0.016   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00271 (14328)
  covalent geometry    : angle       0.55304 (20476)
  hydrogen bonds       : bond        0.04162 (  626)
  hydrogen bonds       : angle       3.88578 ( 1674)

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 75
  time to evaluate  : 0.369 
Fit side-chains
   revert: symmetry clash
REVERT: F   36 GLU cc_start: 0.8049 (pp20) cc_final: 0.7768 (pp20)
REVERT: E   62 GLU cc_start: 0.9275 (tp30) cc_final: 0.8792 (mm-30)
REVERT: E   76 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8235 (mmmt)
REVERT: A  773 MET cc_start: 0.7825 (mpp) cc_final: 0.7614 (mmm)
REVERT: A  813 MET cc_start: 0.8825 (tmm) cc_final: 0.8175 (tmm)
  outliers start: 14
  outliers final: 14
  residues processed: 84
  average time/residue: 0.1093
  time to fit residues: 13.8812
Evaluate side-chains
  85 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 71
  time to evaluate  : 0.373 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  594 LYS
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  827 GLN
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1036 ILE
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 67 optimal weight:    0.8980
   chunk 100 optimal weight:    8.9990
   chunk 11 optimal weight:    7.9990
   chunk 29 optimal weight:   10.0000
   chunk 25 optimal weight:   10.0000
   chunk 63 optimal weight:    1.9990
   chunk 53 optimal weight:    2.9990
   chunk 76 optimal weight:    4.9990
   chunk 38 optimal weight:    6.9990
   chunk 49 optimal weight:    5.9990
   chunk 61 optimal weight:    0.9990
   overall best weight:    2.3788

-------------------------------------------------------------------------------
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 = 0.3819 r_free = 0.3819 target = 0.096849 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.061600 restraints weight = 49354.258|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.063362 restraints weight = 24677.091|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.064355 restraints weight = 17472.569|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 22)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.064775 restraints weight = 14796.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 44)----------------|
| r_work = 0.3158 r_free = 0.3158 target = 0.065087 restraints weight = 13812.291|
|-----------------------------------------------------------------------------|
r_work (final): 0.3094
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8281
moved from start:          0.4302

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.050  14328  Z= 0.165
  Angle     :  0.579  10.315  20476  Z= 0.286
  Chirality :  0.034   0.185   2496
  Planarity :  0.004   0.032   1776
  Dihedral  : 22.842 172.632   4769
  Min Nonbonded Distance : 2.346

Molprobity Statistics.
  All-atom Clashscore : 8.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 17.94 %
    Favored  : 80.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    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:  0.69 (0.26), residues: 1092
  helix:  1.63 (0.22), residues: 568
  sheet: -0.18 (0.52), residues: 92
  loop : -0.98 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  72 
 TYR   0.014   0.001   TYR F  43 
 PHE   0.015   0.002   PHE A 331 
 TRP   0.011   0.001   TRP A 547 
 HIS   0.005   0.001   HIS A 482 

Details of bonding type rmsd
  covalent geometry    : bond        0.00354 (14328)
  covalent geometry    : angle       0.57900 (20476)
  hydrogen bonds       : bond        0.04383 (  626)
  hydrogen bonds       : angle       3.94897 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2510.64 seconds
wall clock time: 44 minutes 0.95 seconds (2640.95 seconds total)