Starting phenix.real_space_refine
on Sat Sep 12 04:32:42 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7trf_26088/09_2026/7trf_26088.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trf_26088/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trf_26088/09_2026/7trf_26088.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trf_26088/09_2026/7trf_26088.cif"
    restraint_files = "/net/cci-nas-00/data/ceres_data/7trf_26088/09_2026/7trf_26088.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7trf_26088/09_2026/7trf_26088.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7trf_26088/09_2026/7trf_26088.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trf_26088/09_2026/7trf_26088.map"
  }
  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-2.2.1-6174/lib/python3.11/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: {'RNAv2': 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: 2.73, per 1000 atoms: 0.20
  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: 1.08
  Conformation dependent library (CDL) restraints added in 414.7 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: 1.59
  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: 2.40

  Time building geometry restraints manager: 1.44 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 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: 18713
        1.52 -     3.05: 1440
        3.05 -     4.57: 264
        4.57 -     6.09: 56
        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=" N3   DT D  13 "
        pdb=" C4   DT D  13 "
        pdb=" O4   DT D  13 "
      ideal   model   delta    sigma   weight residual
     119.90  122.38   -2.48 6.00e-01 2.78e+00 1.71e+01
  angle pdb=" N3   DT D  12 "
        pdb=" C4   DT D  12 "
        pdb=" O4   DT D  12 "
      ideal   model   delta    sigma   weight residual
     119.90  122.37   -2.47 6.00e-01 2.78e+00 1.70e+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
  ... (remaining 20471 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    22.35: 7094
       22.35 -    44.69: 685
       44.69 -    67.04: 305
       67.04 -    89.39: 53
       89.39 -   111.73: 1
  Dihedral angle restraints: 8138
    sinusoidal: 4917
      harmonic: 3221
  Sorted by residual:
  dihedral pdb=" C4'   A B 281 "
           pdb=" C3'   A B 281 "
           pdb=" C2'   A B 281 "
           pdb=" C1'   A B 281 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.97   75.32     1      3.10e+00 1.04e-01 7.46e+02
  dihedral pdb=" C4'   A B 301 "
           pdb=" C3'   A B 301 "
           pdb=" C2'   A B 301 "
           pdb=" C1'   A B 301 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -38.27   74.62     1      3.10e+00 1.04e-01 7.34e+02
  dihedral pdb=" C4'   C B 256 "
           pdb=" C3'   C B 256 "
           pdb=" C2'   C B 256 "
           pdb=" C1'   C B 256 "
      ideal   model   delta sinusoidal    sigma   weight residual
      36.34  -37.77   74.11     1      3.10e+00 1.04e-01 7.25e+02
  ... (remaining 8135 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.161: 2174
       0.161 -    0.322: 312
       0.322 -    0.483: 9
       0.483 -    0.644: 0
       0.644 -    0.804: 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       2.17    2.98   -0.80 2.00e-01 2.50e+01 1.62e+01
  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       2.17   -2.65   -0.47 2.00e-01 2.50e+01 5.58e+00
  chirality pdb=" P     G B 315 "
            pdb=" OP1   G B 315 "
            pdb=" OP2   G B 315 "
            pdb=" O5'   G B 315 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.64   -0.47 2.00e-01 2.50e+01 5.56e+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:             1.270
  Set stop_for_unknowns flag:              0.010
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.230
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.120
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.840
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
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= 0.328
  Angle     :  0.914   7.614  20476  Z= 0.490
  Chirality :  0.096   0.804   2496
  Planarity :  0.004   0.041   1776
  Dihedral  : 19.302 111.733   6052
  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/Z
  covalent geometry    : bond        0.00530 /  0.33 (14328)
  covalent geometry    : angle       0.91375 /  0.49 (20476)
  hydrogen bonds       : bond        0.15745 /  9.62 (  626)
  hydrogen bonds       : angle       6.10120 /  4.27 ( 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  : 0.379 
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: 0.1288
  time to fit residues: 25.5141
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  : 0.350 
-------------------------------------------------------------------------------
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:    0.9980
   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:    5.9990
   overall best weight:    1.7386

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 608 GLN
A 827 GLN
A1023 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3897 r_free = 0.3897 target = 0.101458 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.065523 restraints weight = 47777.284|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3201 r_free = 0.3201 target = 0.067370 restraints weight = 23399.437|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.068436 restraints weight = 16284.786|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3236 r_free = 0.3236 target = 0.069002 restraints weight = 13667.829|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 15)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.069140 restraints weight = 12585.882|
|-----------------------------------------------------------------------------|
r_work (final): 0.3178
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8166
moved from start:          0.1641

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= 0.224
  Angle     :  1.320  22.406  20476  Z= 0.531
  Chirality :  0.114   1.144   2496
  Planarity :  0.005   0.054   1776
  Dihedral  : 18.358 142.861   3911
  Min Nonbonded Distance : 2.155

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  1.26 %
    Allowed  :  7.66 %
    Favored  : 91.08 %
  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: -0.05 (0.26), residues: 1092
  helix:  0.90 (0.22), residues: 565
  sheet: -0.08 (0.51), residues: 93
  loop : -1.25 (0.30), residues: 434

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG A 901 
 TYR   0.015   0.001   TYR F  43 
 PHE   0.014   0.001   PHE F  66 
 TRP   0.010   0.001   TRP A 547 
 HIS   0.015   0.001   HIS E  32 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00449 /  0.22 (14328)
  covalent geometry    : angle       1.32008 /  0.53 (20476)
  hydrogen bonds       : bond        0.05641 /  3.87 (  626)
  hydrogen bonds       : angle       4.45380 /  3.14 ( 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
  106 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 94
  time to evaluate  : 0.378 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   18 ARG cc_start: 0.7501 (mtm110) cc_final: 0.7161 (ptt-90)
REVERT: E   62 GLU cc_start: 0.9050 (tp30) cc_final: 0.8767 (mm-30)
REVERT: E   69 ASN cc_start: 0.9104 (m110) cc_final: 0.8043 (m110)
REVERT: E   76 LYS cc_start: 0.8685 (mmtt) cc_final: 0.7993 (mmmt)
  outliers start: 12
  outliers final: 4
  residues processed: 99
  average time/residue: 0.1190
  time to fit residues: 16.8714
Evaluate side-chains
  89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain E residue   77 THR
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:    9.9990
   chunk 17 optimal weight:   20.0000
   chunk 19 optimal weight:    9.9990
   chunk 7 optimal weight:    7.9990
   chunk 112 optimal weight:    2.9990
   chunk 88 optimal weight:    5.9990
   chunk 30 optimal weight:    7.9990
   chunk 72 optimal weight:    1.9990
   chunk 29 optimal weight:    9.9990
   chunk 37 optimal weight:    4.9990
   chunk 48 optimal weight:    6.9990
   overall best weight:    4.5990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  50 HIS
A 400 HIS
** A 635 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 762 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.097656 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3074 r_free = 0.3074 target = 0.061636 restraints weight = 49037.895|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.063364 restraints weight = 24440.649|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 53)----------------|
| r_work = 0.3137 r_free = 0.3137 target = 0.064343 restraints weight = 17283.430|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 45)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.064860 restraints weight = 14668.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.065075 restraints weight = 13581.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3091
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8297
moved from start:          0.2685

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.049  14328  Z= 0.321
  Angle     :  1.145  20.016  20476  Z= 0.472
  Chirality :  0.081   0.947   2496
  Planarity :  0.006   0.076   1776
  Dihedral  : 18.734 155.848   3911
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 9.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 11.96 %
    Favored  : 86.15 %
  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: -0.15 (0.25), residues: 1092
  helix:  0.89 (0.21), residues: 566
  sheet: -0.40 (0.50), residues: 93
  loop : -1.33 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG A 901 
 TYR   0.036   0.002   TYR A  18 
 PHE   0.027   0.002   PHE F  66 
 TRP   0.013   0.002   TRP A 581 
 HIS   0.008   0.002   HIS A 482 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00682 /  0.32 (14328)
  covalent geometry    : angle       1.14487 /  0.47 (20476)
  hydrogen bonds       : bond        0.06004 /  4.16 (  626)
  hydrogen bonds       : angle       4.52509 /  3.22 ( 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
  98 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 80
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9176 (tp30) cc_final: 0.8846 (mm-30)
REVERT: E   76 LYS cc_start: 0.8623 (mmtt) cc_final: 0.7874 (mmmt)
REVERT: E   78 ARG cc_start: 0.8475 (tpp80) cc_final: 0.8175 (tpp80)
REVERT: E   86 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8628 (tp)
REVERT: A  813 MET cc_start: 0.8969 (tmm) cc_final: 0.8385 (tmm)
  outliers start: 18
  outliers final: 12
  residues processed: 87
  average time/residue: 0.0963
  time to fit residues: 12.7122
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  : 0.240 
-------------------------------------------------------------------------------
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  114 GLU
Chi-restraints excluded: chain E residue   19 SER
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 E residue   97 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
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 59 optimal weight:    4.9990
   chunk 17 optimal weight:   20.0000
   chunk 108 optimal weight:    0.3980
   chunk 99 optimal weight:    7.9990
   chunk 97 optimal weight:    7.9990
   chunk 87 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9980
   chunk 5 optimal weight:    9.9990
   chunk 105 optimal weight:    0.6980
   chunk 83 optimal weight:   10.0000
   chunk 43 optimal weight:    8.9990
   overall best weight:    1.6184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 384 GLN
A 635 ASN
A 687 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3879 r_free = 0.3879 target = 0.099823 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.063881 restraints weight = 48131.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.065716 restraints weight = 23217.908|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 65)----------------|
| r_work = 0.3196 r_free = 0.3196 target = 0.066767 restraints weight = 16151.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3208 r_free = 0.3208 target = 0.067302 restraints weight = 13580.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 45)----------------|
| r_work = 0.3214 r_free = 0.3214 target = 0.067567 restraints weight = 12563.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8222
moved from start:          0.2834

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= 0.155
  Angle     :  0.943  13.420  20476  Z= 0.387
  Chirality :  0.070   0.606   2496
  Planarity :  0.004   0.033   1776
  Dihedral  : 18.312 156.015   3911
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 13.12 %
    Favored  : 85.10 %
  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:  0.33 (0.26), residues: 1092
  helix:  1.24 (0.22), residues: 569
  sheet:  0.05 (0.52), residues: 94
  loop : -1.12 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A  83 
 TYR   0.013   0.001   TYR F  38 
 PHE   0.014   0.002   PHE A1021 
 TRP   0.012   0.001   TRP A 547 
 HIS   0.004   0.001   HIS A 482 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00325 /  0.16 (14328)
  covalent geometry    : angle       0.94322 /  0.39 (20476)
  hydrogen bonds       : bond        0.04761 /  3.33 (  626)
  hydrogen bonds       : angle       4.08902 /  2.89 ( 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
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.402 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   38 TYR cc_start: 0.8434 (m-10) cc_final: 0.8158 (m-10)
REVERT: E   18 ARG cc_start: 0.7686 (mtm110) cc_final: 0.7374 (ptt-90)
REVERT: E   62 GLU cc_start: 0.9145 (tp30) cc_final: 0.8799 (mm-30)
REVERT: E   76 LYS cc_start: 0.8643 (mmtt) cc_final: 0.8011 (mmmt)
REVERT: E   78 ARG cc_start: 0.8454 (tpp80) cc_final: 0.8166 (tpp80)
REVERT: A  125 ASN cc_start: 0.7149 (t0) cc_final: 0.6878 (t0)
REVERT: A  512 MET cc_start: 0.9040 (mtp) cc_final: 0.8839 (mtp)
REVERT: A  813 MET cc_start: 0.8974 (tmm) cc_final: 0.8425 (tmm)
  outliers start: 17
  outliers final: 8
  residues processed: 90
  average time/residue: 0.1106
  time to fit residues: 14.9671
Evaluate side-chains
  89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 81
  time to evaluate  : 0.301 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   97 THR
Chi-restraints excluded: chain E residue   59 LEU
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 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 69 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 23 optimal weight:   10.0000
   chunk 123 optimal weight:    0.9980
   chunk 4 optimal weight:    5.9990
   chunk 42 optimal weight:    4.9990
   chunk 65 optimal weight:    4.9990
   chunk 17 optimal weight:   20.0000
   chunk 78 optimal weight:    5.9990
   chunk 22 optimal weight:   20.0000
   chunk 29 optimal weight:    9.9990
   overall best weight:    3.1988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** F  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  17 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3843 r_free = 0.3843 target = 0.098009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3078 r_free = 0.3078 target = 0.062094 restraints weight = 49698.422|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.063887 restraints weight = 24136.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 58)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.064907 restraints weight = 16869.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.065447 restraints weight = 14239.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.065714 restraints weight = 13179.212|
|-----------------------------------------------------------------------------|
r_work (final): 0.3103
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8255
moved from start:          0.3178

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= 0.235
  Angle     :  0.963  13.957  20476  Z= 0.397
  Chirality :  0.067   0.515   2496
  Planarity :  0.004   0.031   1776
  Dihedral  : 18.240 157.854   3911
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.40 %
    Favored  : 95.60 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 14.90 %
    Favored  : 83.21 %
  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:  0.26 (0.26), residues: 1092
  helix:  1.21 (0.22), residues: 569
  sheet: -0.22 (0.51), residues: 94
  loop : -1.12 (0.30), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  82 
 TYR   0.019   0.001   TYR F  43 
 PHE   0.014   0.002   PHE A 331 
 TRP   0.016   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A1075 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00503 /  0.24 (14328)
  covalent geometry    : angle       0.96300 /  0.40 (20476)
  hydrogen bonds       : bond        0.05010 /  3.49 (  626)
  hydrogen bonds       : angle       4.13838 /  2.95 ( 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
  97 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 79
  time to evaluate  : 0.375 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   18 ARG cc_start: 0.7672 (mtm110) cc_final: 0.7375 (ptt-90)
REVERT: E   62 GLU cc_start: 0.9210 (tp30) cc_final: 0.8870 (mm-30)
REVERT: E   74 ASN cc_start: 0.7626 (p0) cc_final: 0.7412 (p0)
REVERT: E   76 LYS cc_start: 0.8681 (mmtt) cc_final: 0.7971 (mmmt)
REVERT: A  125 ASN cc_start: 0.7378 (t0) cc_final: 0.7065 (t0)
REVERT: A  512 MET cc_start: 0.9113 (mtp) cc_final: 0.8905 (mtp)
REVERT: A  813 MET cc_start: 0.9060 (tmm) cc_final: 0.8471 (tmm)
  outliers start: 18
  outliers final: 15
  residues processed: 92
  average time/residue: 0.0980
  time to fit residues: 13.6724
Evaluate side-chains
  92 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
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   59 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain E residue   97 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  840 LEU
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
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:    6.9990
   chunk 17 optimal weight:   20.0000
   chunk 32 optimal weight:    7.9990
   chunk 111 optimal weight:    0.9990
   chunk 59 optimal weight:    0.3980
   chunk 48 optimal weight:    1.9990
   chunk 19 optimal weight:   10.0000
   chunk 46 optimal weight:    9.9990
   chunk 26 optimal weight:   20.0000
   chunk 31 optimal weight:    9.9990
   chunk 93 optimal weight:    4.9990
   overall best weight:    3.0788

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** 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 = 0.3850 r_free = 0.3850 target = 0.098019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.062734 restraints weight = 49148.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.064494 restraints weight = 23794.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.065510 restraints weight = 16591.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 59)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.066050 restraints weight = 13964.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.066260 restraints weight = 12869.786|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8271
moved from start:          0.3433

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= 0.214
  Angle     :  0.920  12.425  20476  Z= 0.384
  Chirality :  0.065   0.488   2496
  Planarity :  0.004   0.031   1776
  Dihedral  : 18.063 164.301   3911
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 8.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 15.63 %
    Favored  : 82.37 %
  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:  0.36 (0.26), residues: 1092
  helix:  1.32 (0.22), residues: 570
  sheet: -0.28 (0.50), residues: 94
  loop : -1.11 (0.30), residues: 428

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A  48 
 TYR   0.020   0.002   TYR A  18 
 PHE   0.015   0.002   PHE A 331 
 TRP   0.016   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A 482 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00458 /  0.21 (14328)
  covalent geometry    : angle       0.91962 /  0.38 (20476)
  hydrogen bonds       : bond        0.04813 /  3.36 (  626)
  hydrogen bonds       : angle       4.12637 /  2.93 ( 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
  98 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 79
  time to evaluate  : 0.311 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9184 (tp30) cc_final: 0.8798 (mm-30)
REVERT: E   72 ARG cc_start: 0.8441 (ppt170) cc_final: 0.7987 (ppt170)
REVERT: E   76 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8025 (mmmt)
REVERT: A  125 ASN cc_start: 0.7370 (t0) cc_final: 0.7051 (t0)
REVERT: A  813 MET cc_start: 0.8986 (tmm) cc_final: 0.8416 (tmm)
  outliers start: 19
  outliers final: 13
  residues processed: 93
  average time/residue: 0.0951
  time to fit residues: 13.5598
Evaluate side-chains
  89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 76
  time to evaluate  : 0.359 
-------------------------------------------------------------------------------
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   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   80 ILE
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  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 12 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 98 optimal weight:    0.9980
   chunk 1 optimal weight:    5.9990
   chunk 32 optimal weight:    7.9990
   chunk 101 optimal weight:    5.9990
   chunk 20 optimal weight:   20.0000
   chunk 125 optimal weight:    0.9980
   chunk 13 optimal weight:    5.9990
   chunk 63 optimal weight:    0.9990
   chunk 108 optimal weight:    0.0970
   overall best weight:    1.6182

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
F  64 ASN
A  53 GLN
A 754 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3867 r_free = 0.3867 target = 0.098936 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 63)----------------|
| r_work = 0.3138 r_free = 0.3138 target = 0.063719 restraints weight = 48739.257|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 59)----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.065484 restraints weight = 23912.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.066504 restraints weight = 16743.578|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3212 r_free = 0.3212 target = 0.067059 restraints weight = 14135.932|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3216 r_free = 0.3216 target = 0.067254 restraints weight = 13047.518|
|-----------------------------------------------------------------------------|
r_work (final): 0.3153
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8234
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14328  Z= 0.151
  Angle     :  0.881  11.715  20476  Z= 0.366
  Chirality :  0.062   0.437   2496
  Planarity :  0.004   0.030   1776
  Dihedral  : 17.977 164.447   3911
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.68
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.79 %
    Favored  : 81.22 %
  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:  0.57 (0.26), residues: 1092
  helix:  1.48 (0.22), residues: 570
  sheet: -0.00 (0.53), residues: 87
  loop : -1.02 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E  78 
 TYR   0.016   0.001   TYR F  43 
 PHE   0.023   0.002   PHE F  66 
 TRP   0.013   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A 482 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00319 /  0.15 (14328)
  covalent geometry    : angle       0.88073 /  0.37 (20476)
  hydrogen bonds       : bond        0.04448 /  3.09 (  626)
  hydrogen bonds       : angle       3.97463 /  2.81 ( 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
  101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 82
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9201 (tp30) cc_final: 0.8799 (mm-30)
REVERT: E   74 ASN cc_start: 0.7971 (p0) cc_final: 0.7711 (p0)
REVERT: E   76 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8076 (mmmt)
REVERT: A   38 LEU cc_start: 0.4243 (OUTLIER) cc_final: 0.4030 (pp)
REVERT: A  813 MET cc_start: 0.9005 (tmm) cc_final: 0.8455 (tmm)
  outliers start: 19
  outliers final: 14
  residues processed: 91
  average time/residue: 0.1003
  time to fit residues: 13.9625
Evaluate side-chains
  92 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
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   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue   38 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  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 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:    6.9990
   chunk 90 optimal weight:    0.6980
   chunk 26 optimal weight:   20.0000
   chunk 112 optimal weight:    3.9990
   chunk 2 optimal weight:    9.9990
   chunk 17 optimal weight:   30.0000
   chunk 47 optimal weight:   20.0000
   chunk 101 optimal weight:    0.9980
   chunk 125 optimal weight:    0.8980
   chunk 57 optimal weight:    5.9990
   chunk 44 optimal weight:    8.9990
   overall best weight:    2.5184

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 827 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.098332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.063134 restraints weight = 48865.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3161 r_free = 0.3161 target = 0.064866 restraints weight = 24368.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.065860 restraints weight = 17222.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.3195 r_free = 0.3195 target = 0.066373 restraints weight = 14580.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3200 r_free = 0.3200 target = 0.066618 restraints weight = 13511.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3135
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8264
moved from start:          0.3752

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049  14328  Z= 0.188
  Angle     :  0.887  11.235  20476  Z= 0.369
  Chirality :  0.062   0.458   2496
  Planarity :  0.004   0.030   1776
  Dihedral  : 17.956 166.940   3911
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 8.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.68 %
    Allowed  : 17.73 %
    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:  1.44 (0.22), residues: 572
  sheet: -0.10 (0.53), residues: 87
  loop : -1.02 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E  89 
 TYR   0.019   0.001   TYR F  43 
 PHE   0.014   0.002   PHE F  71 
 TRP   0.023   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 482 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00405 /  0.19 (14328)
  covalent geometry    : angle       0.88696 /  0.37 (20476)
  hydrogen bonds       : bond        0.04577 /  3.20 (  626)
  hydrogen bonds       : angle       4.01095 /  2.84 ( 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
  95 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 79
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  114 GLU cc_start: 0.8111 (pt0) cc_final: 0.7748 (pp20)
REVERT: E   62 GLU cc_start: 0.9151 (tp30) cc_final: 0.8755 (mm-30)
REVERT: E   76 LYS cc_start: 0.8665 (mmtt) cc_final: 0.8158 (mmmt)
REVERT: A   38 LEU cc_start: 0.4217 (OUTLIER) cc_final: 0.3997 (pp)
REVERT: A  813 MET cc_start: 0.9002 (tmm) cc_final: 0.8447 (tmm)
  outliers start: 16
  outliers final: 14
  residues processed: 89
  average time/residue: 0.1012
  time to fit residues: 13.9801
Evaluate side-chains
  92 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.383 
-------------------------------------------------------------------------------
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   59 LEU
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue   38 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  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 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:    6.9990
   chunk 17 optimal weight:   30.0000
   chunk 20 optimal weight:   20.0000
   chunk 35 optimal weight:   10.0000
   chunk 41 optimal weight:   10.0000
   chunk 47 optimal weight:   20.0000
   chunk 97 optimal weight:    5.9990
   chunk 50 optimal weight:    2.9990
   chunk 51 optimal weight:    7.9990
   chunk 83 optimal weight:    9.9990
   chunk 129 optimal weight:    3.9990
   overall best weight:    5.5990

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3805 r_free = 0.3805 target = 0.095655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3054 r_free = 0.3054 target = 0.060493 restraints weight = 50393.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.062169 restraints weight = 25351.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3114 r_free = 0.3114 target = 0.063085 restraints weight = 18013.197|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 54)----------------|
| r_work = 0.3126 r_free = 0.3126 target = 0.063596 restraints weight = 15319.110|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3131 r_free = 0.3131 target = 0.063830 restraints weight = 14190.971|
|-----------------------------------------------------------------------------|
r_work (final): 0.3068
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8338
moved from start:          0.4027

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.008   0.054  14328  Z= 0.360
  Angle     :  1.038  15.624  20476  Z= 0.437
  Chirality :  0.067   0.556   2496
  Planarity :  0.005   0.064   1776
  Dihedral  : 18.107 170.887   3911
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 10.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.58 %
    Favored  : 95.42 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 17.73 %
    Favored  : 80.17 %
  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:  0.04 (0.25), residues: 1092
  helix:  1.03 (0.21), residues: 577
  sheet: -0.64 (0.51), residues: 94
  loop : -1.19 (0.30), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 672 
 TYR   0.025   0.002   TYR F  43 
 PHE   0.022   0.003   PHE A 331 
 TRP   0.024   0.002   TRP A  60 
 HIS   0.006   0.001   HIS A1075 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00776 /  0.36 (14328)
  covalent geometry    : angle       1.03790 /  0.44 (20476)
  hydrogen bonds       : bond        0.05686 /  3.98 (  626)
  hydrogen bonds       : angle       4.36782 /  3.14 ( 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
  95 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.415 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: F  117 LYS cc_start: 0.7872 (OUTLIER) cc_final: 0.7511 (pttm)
REVERT: E   62 GLU cc_start: 0.9240 (tp30) cc_final: 0.8849 (mm-30)
REVERT: E   76 LYS cc_start: 0.8699 (mmtt) cc_final: 0.8184 (mmmt)
REVERT: A  813 MET cc_start: 0.9029 (tmm) cc_final: 0.8438 (tmm)
  outliers start: 20
  outliers final: 16
  residues processed: 89
  average time/residue: 0.1080
  time to fit residues: 14.8960
Evaluate side-chains
  89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.407 
-------------------------------------------------------------------------------
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   67 VAL
Chi-restraints excluded: chain F residue  117 LYS
Chi-restraints excluded: chain E residue   59 LEU
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  999 THR
Chi-restraints excluded: chain A residue 1016 VAL
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 123 optimal weight:    0.8980
   chunk 62 optimal weight:    0.9980
   chunk 72 optimal weight:    2.9990
   chunk 114 optimal weight:    2.9990
   chunk 116 optimal weight:    2.9990
   chunk 124 optimal weight:    3.9990
   chunk 66 optimal weight:    0.7980
   chunk 117 optimal weight:    4.9990
   chunk 86 optimal weight:    3.9990
   chunk 35 optimal weight:   10.0000
   chunk 115 optimal weight:    0.9990
   overall best weight:    1.3384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3848 r_free = 0.3848 target = 0.098110 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.062732 restraints weight = 50327.595|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 65)----------------|
| r_work = 0.3147 r_free = 0.3147 target = 0.064509 restraints weight = 24933.485|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3170 r_free = 0.3170 target = 0.065529 restraints weight = 17602.390|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 48)----------------|
| r_work = 0.3181 r_free = 0.3181 target = 0.066060 restraints weight = 14947.734|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 23)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.066259 restraints weight = 13838.430|
|-----------------------------------------------------------------------------|
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8276
moved from start:          0.4023

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14328  Z= 0.147
  Angle     :  0.883  11.939  20476  Z= 0.368
  Chirality :  0.062   0.460   2496
  Planarity :  0.004   0.030   1776
  Dihedral  : 17.963 171.544   3911
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 8.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  1.36 %
    Allowed  : 18.47 %
    Favored  : 80.17 %
  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:  0.41 (0.26), residues: 1092
  helix:  1.36 (0.22), residues: 572
  sheet: -0.18 (0.54), residues: 87
  loop : -1.09 (0.30), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG F  93 
 TYR   0.012   0.001   TYR F  43 
 PHE   0.015   0.002   PHE A  47 
 TRP   0.020   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A 482 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.15 (14328)
  covalent geometry    : angle       0.88333 /  0.37 (20476)
  hydrogen bonds       : bond        0.04643 /  3.25 (  626)
  hydrogen bonds       : angle       4.00894 /  2.86 ( 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: 13
    poor density    : 76
  time to evaluate  : 0.417 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9229 (tp30) cc_final: 0.8806 (mm-30)
REVERT: E   76 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8100 (mmmt)
REVERT: A  813 MET cc_start: 0.8989 (tmm) cc_final: 0.8443 (tmm)
  outliers start: 13
  outliers final: 13
  residues processed: 84
  average time/residue: 0.1089
  time to fit residues: 14.2541
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  : 0.415 
-------------------------------------------------------------------------------
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   67 VAL
Chi-restraints excluded: chain E residue   59 LEU
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  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
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:    5.9990
   chunk 100 optimal weight:    0.9980
   chunk 11 optimal weight:   10.0000
   chunk 29 optimal weight:    9.9990
   chunk 25 optimal weight:    7.9990
   chunk 63 optimal weight:    0.6980
   chunk 53 optimal weight:    1.9990
   chunk 76 optimal weight:    4.9990
   chunk 38 optimal weight:    8.9990
   chunk 49 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9980
   overall best weight:    1.9384

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3849 r_free = 0.3849 target = 0.098223 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 67)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.062898 restraints weight = 50666.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3151 r_free = 0.3151 target = 0.064683 restraints weight = 24990.915|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 60)----------------|
| r_work = 0.3174 r_free = 0.3174 target = 0.065707 restraints weight = 17622.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 57)----------------|
| r_work = 0.3185 r_free = 0.3185 target = 0.066236 restraints weight = 14897.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3189 r_free = 0.3189 target = 0.066418 restraints weight = 13798.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3126
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8273
moved from start:          0.4134

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050  14328  Z= 0.163
  Angle     :  0.862  10.862  20476  Z= 0.358
  Chirality :  0.060   0.442   2496
  Planarity :  0.004   0.031   1776
  Dihedral  : 17.893 171.910   3911
  Min Nonbonded Distance : 2.363

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 18.78 %
    Favored  : 79.75 %
  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:  1.49 (0.22), residues: 572
  sheet: -0.23 (0.54), residues: 87
  loop : -1.02 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A1011 
 TYR   0.017   0.001   TYR F  43 
 PHE   0.017   0.001   PHE E  26 
 TRP   0.014   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 687 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00349 /  0.16 (14328)
  covalent geometry    : angle       0.86177 /  0.36 (20476)
  hydrogen bonds       : bond        0.04421 /  3.08 (  626)
  hydrogen bonds       : angle       3.94327 /  2.81 ( 1674)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2426.53 seconds
wall clock time: 42 minutes 33.48 seconds (2553.48 seconds total)