Starting phenix.real_space_refine
on Thu Aug  6 12:03:06 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9q14_72115/08_2026/9q14_72115.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9q14_72115/08_2026/9q14_72115.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9q14_72115/08_2026/9q14_72115.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9q14_72115/08_2026/9q14_72115.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9q14_72115/08_2026/9q14_72115.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9q14_72115/08_2026/9q14_72115.map"
  }
  resolution = 3.0
  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=   0.014
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     215      5.49       5
     S      43      5.16       5
     C    8529      2.51       5
     N    2694      2.21       5
     O    3260      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 14741
  Number of models: 1
  Model: ""
    Number of chains: 7
    Chain: "C"
      Number of atoms: 1171
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 152, 1171
          Classifications: {'peptide': 152}
          Link IDs: {'PTRANS': 9, 'TRANS': 142}
    Chain: "F"
      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: "G"
      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: "D"
      Number of atoms: 170
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 8, 170
          Classifications: {'DNA': 8}
          Link IDs: {'rna3p': 7}
    Chain: "B"
      Number of atoms: 4400
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 207, 4400
          Classifications: {'RNA': 207}
          Modifications used: {'rna2p_pur': 12, 'rna2p_pyr': 15, 'rna3p_pur': 86, 'rna3p_pyr': 94}
          Link IDs: {'rna2p': 27, 'rna3p': 179}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 7634
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 951, 7634
          Classifications: {'peptide': 951}
          Modifications used: {'COO': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 57, 'TRANS': 892}
          Chain breaks: 3
    Chain: "A"
      Number of atoms: 25
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 25
          Unusual residues: {'55C': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 2.12, per 1000 atoms: 0.14
  Number of scatterers: 14741
  At special positions: 0
  Unit cell: (151.8, 118.8, 124.3, 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      43     16.00
     P     215     15.00
     O    3260      8.00
     N    2694      7.00
     C    8529      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 463.1 milliseconds
  

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2396

  Finding SS restraints...
    Secondary structure from input PDB file:
      66 helices and 11 sheets defined
      57.8% alpha, 13.8% beta
      70 base pairs and 116 stacking pairs defined.
    Time for finding SS restraints: 1.48
  Creating SS restraints...
    Processing helix  chain 'C' and resid 100 through 105
    Processing helix  chain 'C' and resid 134 through 138
    Processing helix  chain 'C' and resid 158 through 164
    Processing helix  chain 'C' and resid 167 through 173
    Processing helix  chain 'C' and resid 223 through 226
    Processing helix  chain 'C' and resid 227 through 240
      removed outlier: 4.008A  pdb=" N   GLU C 240 " --> pdb=" O   ASP C 236 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 18 through 22
    Processing helix  chain 'F' and resid 27 through 38
      removed outlier: 3.574A  pdb=" N   VAL F  31 " --> pdb=" O   PRO F  27 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 46 through 74
      removed outlier: 4.054A  pdb=" N   VAL F  50 " --> pdb=" O   ALA F  46 " (cutoff:3.500A)
      removed outlier: 3.672A  pdb=" N   LEU F  66 " --> pdb=" O   GLU F  62 " (cutoff:3.500A)
      removed outlier: 3.811A  pdb=" N   ASN F  74 " --> pdb=" O   ALA F  70 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 80 through 91
      removed outlier: 3.586A  pdb=" N   LEU F  84 " --> pdb=" O   ILE F  80 " (cutoff:3.500A)
      removed outlier: 4.045A  pdb=" N   ASP F  91 " --> pdb=" O   ALA F  87 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 98
    Processing helix  chain 'G' and resid 38 through 48
    Processing helix  chain 'G' and resid 56 through 85
      removed outlier: 3.861A  pdb=" N   ILE G  62 " --> pdb=" O   LYS G  58 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 91 through 103
      removed outlier: 3.639A  pdb=" N   ILE G  95 " --> pdb=" O   THR G  91 " (cutoff:3.500A)
      removed outlier: 3.637A  pdb=" N   VAL G  99 " --> pdb=" O   ILE G  95 " (cutoff:3.500A)
    Processing helix  chain 'G' and resid 106 through 125
    Processing helix  chain 'A' and resid 7 through 17
    Processing helix  chain 'A' and resid 24 through 32
      removed outlier: 3.641A  pdb=" N   ARG A  30 " --> pdb=" O   THR A  26 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 76 through 92
    Processing helix  chain 'A' and resid 95 through 99
    Processing helix  chain 'A' and resid 125 through 133
    Processing helix  chain 'A' and resid 135 through 145
    Processing helix  chain 'A' and resid 145 through 156
    Processing helix  chain 'A' and resid 174 through 178
    Processing helix  chain 'A' and resid 329 through 332
      removed outlier: 4.091A  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
    Processing helix  chain 'A' and resid 371 through 375
    Processing helix  chain 'A' and resid 383 through 388
      removed outlier: 3.805A  pdb=" N   GLN A 388 " --> pdb=" O   GLN A 384 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 3.581A  pdb=" N   GLU A 395 " --> pdb=" O   PRO A 391 " (cutoff:3.500A)
      removed outlier: 3.521A  pdb=" N   ALA A 401 " --> pdb=" O   LEU A 397 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
    Processing helix  chain 'A' and resid 444 through 452
      removed outlier: 3.975A  pdb=" N   VAL A 449 " --> pdb=" O   PRO A 445 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 473
      removed outlier: 3.848A  pdb=" N   VAL A 473 " --> pdb=" O   LEU A 469 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
      removed outlier: 3.884A  pdb=" N   TRP A 478 " --> pdb=" O   PRO A 474 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.542A  pdb=" N   SER A 496 " --> pdb=" O   LYS A 492 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 510
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.628A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 551
      removed outlier: 3.544A  pdb=" N   ILE A 540 " --> pdb=" O   LEU A 536 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 560
      removed outlier: 3.713A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 593
      removed outlier: 4.111A  pdb=" N   LYS A 583 " --> pdb=" O   SER A 579 " (cutoff:3.500A)
      removed outlier: 3.707A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 4.010A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   HIS A 592 " --> pdb=" O   GLY A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
    Processing helix  chain 'A' and resid 640 through 644
      removed outlier: 3.927A  pdb=" N   THR A 644 " --> pdb=" O   GLY A 641 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 645 through 646
      No H-bonds generated for 'chain 'A' and resid 645 through 646'
    Processing helix  chain 'A' and resid 647 through 672
      removed outlier: 3.817A  pdb=" N   GLU A 652 " --> pdb=" O   GLU A 648 " (cutoff:3.500A)
      removed outlier: 5.866A  pdb=" N   ARG A 653 " --> pdb=" O   LYS A 649 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   LEU A 654 " --> pdb=" O   ARG A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 676
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.870A  pdb=" N   THR A 692 " --> pdb=" O   ARG A 688 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 715 through 720
      removed outlier: 3.540A  pdb=" N   ILE A 720 " --> pdb=" O   ALA A 716 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 751 through 753
      No H-bonds generated for 'chain 'A' and resid 751 through 753'
    Processing helix  chain 'A' and resid 772 through 784
    Processing helix  chain 'A' and resid 802 through 815
      removed outlier: 3.774A  pdb=" N   ASP A 807 " --> pdb=" O   SER A 803 " (cutoff:3.500A)
      removed outlier: 3.723A  pdb=" N   VAL A 808 " --> pdb=" O   GLY A 804 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 853
      removed outlier: 3.927A  pdb=" N   ASP A 848 " --> pdb=" O   LEU A 844 " (cutoff:3.500A)
      removed outlier: 3.935A  pdb=" N   MET A 849 " --> pdb=" O   CYS A 845 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 856 through 860
      removed outlier: 4.459A  pdb=" N   ASP A 860 " --> pdb=" O   ILE A 857 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 876 through 888
      removed outlier: 3.766A  pdb=" N   ALA A 880 " --> pdb=" O   HIS A 876 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 891 through 895
    Processing helix  chain 'A' and resid 911 through 915
    Processing helix  chain 'A' and resid 965 through 982
      removed outlier: 3.636A  pdb=" N   MET A 970 " --> pdb=" O   ALA A 966 " (cutoff:3.500A)
      removed outlier: 3.625A  pdb=" N   ARG A 971 " --> pdb=" O   GLY A 967 " (cutoff:3.500A)
    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: 4.209A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
      removed outlier: 3.697A  pdb=" N   ILE A1036 " --> pdb=" O   PHE A1032 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   THR A1039 " --> pdb=" O   VAL A1035 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.569A  pdb=" N   ALA A1049 " --> pdb=" O   SER A1045 " (cutoff:3.500A)
      removed outlier: 3.527A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1058 through 1062
    Processing helix  chain 'A' and resid 1066 through 1083
      removed outlier: 4.001A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 3.632A  pdb=" N   LYS A1081 " --> pdb=" O   ALA A1077 " (cutoff:3.500A)
      removed outlier: 3.514A  pdb=" N   THR A1083 " --> pdb=" O   LEU A1079 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      Proline residue:  A1091  - end of helix
      removed outlier: 4.337A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 4.767A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.797A  pdb=" N   THR A1098 " --> pdb=" O   GLY A1094 " (cutoff:3.500A)
      removed outlier: 3.638A  pdb=" N   THR A1101 " --> pdb=" O   ARG A1097 " (cutoff:3.500A)
      removed outlier: 3.692A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1119
      removed outlier: 3.651A  pdb=" N   ALA A1114 " --> pdb=" O   THR A1110 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1126 through 1130
      removed outlier: 3.773A  pdb=" N   THR A1129 " --> pdb=" O   ASP A1126 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 113 through 122
      removed outlier: 7.233A  pdb=" N   LEU C 118 " --> pdb=" O   SER C 147 " (cutoff:3.500A)
      removed outlier: 8.838A  pdb=" N   SER C 147 " --> pdb=" O   LEU C 118 " (cutoff:3.500A)
      removed outlier: 5.825A  pdb=" N   VAL C 120 " --> pdb=" O   LEU C 145 " (cutoff:3.500A)
      removed outlier: 6.599A  pdb=" N   LEU C 145 " --> pdb=" O   VAL C 120 " (cutoff:3.500A)
      removed outlier: 11.039A  pdb=" N   SER C 152 " --> pdb=" O   PHE C 202 " (cutoff:3.500A)
      removed outlier: 9.400A  pdb=" N   LEU C 204 " --> pdb=" O   SER C 152 " (cutoff:3.500A)
      removed outlier: 7.097A  pdb=" N   ARG C 154 " --> pdb=" O   LEU C 204 " (cutoff:3.500A)
      removed outlier: 8.271A  pdb=" N   VAL C 206 " --> pdb=" O   ARG C 154 " (cutoff:3.500A)
      removed outlier: 7.084A  pdb=" N   LEU C 156 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 7.937A  pdb=" N   ARG C 208 " --> pdb=" O   LEU C 156 " (cutoff:3.500A)
      removed outlier: 6.841A  pdb=" N   PHE C 202 " --> pdb=" O   VAL C 191 " (cutoff:3.500A)
      removed outlier: 6.329A  pdb=" N   VAL C 191 " --> pdb=" O   PHE C 202 " (cutoff:3.500A)
      removed outlier: 6.903A  pdb=" N   LEU C 204 " --> pdb=" O   VAL C 189 " (cutoff:3.500A)
      removed outlier: 6.533A  pdb=" N   VAL C 189 " --> pdb=" O   LEU C 204 " (cutoff:3.500A)
      removed outlier: 6.480A  pdb=" N   VAL C 206 " --> pdb=" O   CYS C 187 " (cutoff:3.500A)
      removed outlier: 6.358A  pdb=" N   CYS C 187 " --> pdb=" O   VAL C 206 " (cutoff:3.500A)
      removed outlier: 6.211A  pdb=" N   ARG C 208 " --> pdb=" O   GLN C 185 " (cutoff:3.500A)
      removed outlier: 4.866A  pdb=" N   LEU C 181 " --> pdb=" O   LEU C 212 " (cutoff:3.500A)
      removed outlier: 4.400A  pdb=" N   ARG C 180 " --> pdb=" O   LEU C 117 " (cutoff:3.500A)
      removed outlier: 3.946A  pdb=" N   LEU C 117 " --> pdb=" O   ARG C 180 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'F' and resid 43 through 44
      removed outlier: 7.150A  pdb=" N   ARG F  43 " --> pdb=" O   ILE G  90 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA2
    Processing sheet with id=AA3, first strand: chain 'F' and resid 78 through 79
    Processing sheet with id=AA4, first strand: chain 'A' and resid 18 through 23
      removed outlier: 3.917A  pdb=" N   GLU A  20 " --> pdb=" O   VAL A  58 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   VAL A  58 " --> pdb=" O   GLU A  20 " (cutoff:3.500A)
      removed outlier: 6.391A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA7, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA8, first strand: chain 'A' and resid 598 through 600
      removed outlier: 3.638A  pdb=" N   LYS A 823 " --> pdb=" O   ILE A 820 " (cutoff:3.500A)
      removed outlier: 6.097A  pdb=" N   GLN A 827 " --> pdb=" O   HIS A 816 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   HIS A 816 " --> pdb=" O   GLN A 827 " (cutoff:3.500A)
      removed outlier: 6.298A  pdb=" N   LEU A 617 " --> pdb=" O   ALA A 817 " (cutoff:3.500A)
      removed outlier: 7.616A  pdb=" N   ARG A 819 " --> pdb=" O   LEU A 617 " (cutoff:3.500A)
      removed outlier: 6.718A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 862 through 865
      removed outlier: 3.766A  pdb=" N   VAL A 711 " --> pdb=" O   PHE A 870 " (cutoff:3.500A)
      removed outlier: 7.239A  pdb=" N   THR A 903 " --> pdb=" O   VAL A 920 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 754 through 764
      removed outlier: 5.836A  pdb=" N   TYR A 739 " --> pdb=" O   LEU A 798 " (cutoff:3.500A)
      removed outlier: 5.557A  pdb=" N   LEU A 798 " --> pdb=" O   TYR A 739 " (cutoff:3.500A)
      removed outlier: 6.861A  pdb=" N   VAL A 741 " --> pdb=" O   SER A 796 " (cutoff:3.500A)
      removed outlier: 4.869A  pdb=" N   SER A 796 " --> pdb=" O   VAL A 741 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 927 through 930

    515 hydrogen bonds defined for protein.
    1434 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      183 hydrogen bonds
      348 hydrogen bond angles
      0 basepair planarities
      70 basepair parallelities
      116 stacking parallelities
  Total time for adding SS restraints: 3.56

  Time building geometry restraints manager: 1.18 seconds

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

  Histogram of bond lengths:
        1.21 -     1.33: 3253
        1.33 -     1.45: 4310
        1.45 -     1.57: 7452
        1.57 -     1.69: 425
        1.69 -     1.81: 57
  Bond restraints: 15497
  Sorted by residual:
  bond pdb=" C1'  DT D  20 "
       pdb=" N1   DT D  20 "
    ideal  model  delta    sigma   weight residual
    1.468  1.509 -0.041 1.40e-02 5.10e+03 8.74e+00
  bond pdb=" C5'  DA D  21 "
       pdb=" C4'  DA D  21 "
    ideal  model  delta    sigma   weight residual
    1.512  1.529 -0.017 7.00e-03 2.04e+04 6.02e+00
  bond pdb=" N9    A B  59 "
       pdb=" C4    A B  59 "
    ideal  model  delta    sigma   weight residual
    1.374  1.388 -0.014 6.00e-03 2.78e+04 5.30e+00
  bond pdb=" P     U B  38 "
       pdb=" O5'   U B  38 "
    ideal  model  delta    sigma   weight residual
    1.593  1.616 -0.023 1.00e-02 1.00e+04 5.21e+00
  bond pdb=" C5'  DT D  20 "
       pdb=" C4'  DT D  20 "
    ideal  model  delta    sigma   weight residual
    1.512  1.526 -0.014 7.00e-03 2.04e+04 3.83e+00
  ... (remaining 15492 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.56: 21013
        1.56 -     3.12: 926
        3.12 -     4.67: 69
        4.67 -     6.23: 10
        6.23 -     7.79: 4
  Bond angle restraints: 22022
  Sorted by residual:
  angle pdb=" O4'  DA D  21 "
        pdb=" C4'  DA D  21 "
        pdb=" C3'  DA D  21 "
      ideal   model   delta    sigma   weight residual
     106.00  102.63    3.37 6.00e-01 2.78e+00 3.15e+01
  angle pdb=" C1'   G B  60 "
        pdb=" N9    G B  60 "
        pdb=" C8    G B  60 "
      ideal   model   delta    sigma   weight residual
     127.00  120.46    6.54 1.30e+00 5.92e-01 2.53e+01
  angle pdb=" C1'   G B  60 "
        pdb=" N9    G B  60 "
        pdb=" C4    G B  60 "
      ideal   model   delta    sigma   weight residual
     126.50  133.00   -6.50 1.30e+00 5.92e-01 2.50e+01
  angle pdb=" C1'   U B 133 "
        pdb=" N1    U B 133 "
        pdb=" C2    U B 133 "
      ideal   model   delta    sigma   weight residual
     117.70  123.43   -5.73 1.20e+00 6.94e-01 2.28e+01
  angle pdb=" O4'   A B  59 "
        pdb=" C1'   A B  59 "
        pdb=" N9    A B  59 "
      ideal   model   delta    sigma   weight residual
     108.50  111.70   -3.20 7.00e-01 2.04e+00 2.09e+01
  ... (remaining 22017 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    32.68: 9007
       32.68 -    65.36: 570
       65.36 -    98.04: 92
       98.04 -   130.71: 4
      130.71 -   163.39: 2
  Dihedral angle restraints: 9675
    sinusoidal: 5973
      harmonic: 3702
  Sorted by residual:
  dihedral pdb=" O4'   U B 291 "
           pdb=" C1'   U B 291 "
           pdb=" N1    U B 291 "
           pdb=" C2    U B 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   35.39 -163.39     1      1.70e+01 3.46e-03 6.51e+01
  dihedral pdb=" O4'   U B 133 "
           pdb=" C1'   U B 133 "
           pdb=" N1    U B 133 "
           pdb=" C2    U B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
     200.00   97.05  102.95     1      1.50e+01 4.44e-03 5.22e+01
  dihedral pdb=" CA  TRP C  98 "
           pdb=" C   TRP C  98 "
           pdb=" N   ILE C  99 "
           pdb=" CA  ILE C  99 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -153.46  -26.54     0      5.00e+00 4.00e-02 2.82e+01
  ... (remaining 9672 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.090: 2391
       0.090 -    0.180: 257
       0.180 -    0.270: 3
       0.270 -    0.360: 0
       0.360 -    0.450: 1
  Chirality restraints: 2652
  Sorted by residual:
  chirality pdb=" P     U B  38 "
            pdb=" OP1   U B  38 "
            pdb=" OP2   U B  38 "
            pdb=" O5'   U B  38 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.86   -0.45 2.00e-01 2.50e+01 5.06e+00
  chirality pdb=" C1'   A B  59 "
            pdb=" O4'   A B  59 "
            pdb=" C2'   A B  59 "
            pdb=" N9    A B  59 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.47    2.28    0.19 2.00e-01 2.50e+01 9.22e-01
  chirality pdb=" C3'  DA D  21 "
            pdb=" C4'  DA D  21 "
            pdb=" O3'  DA D  21 "
            pdb=" C2'  DA D  21 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.73   -2.55   -0.18 2.00e-01 2.50e+01 8.34e-01
  ... (remaining 2649 not shown)

  Planarity restraints: 2018
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C10 55C A1201 "    0.055 2.00e-02 2.50e+03   6.12e-02 4.67e+01
        pdb=" C11 55C A1201 "   -0.019 2.00e-02 2.50e+03
        pdb=" C12 55C A1201 "   -0.099 2.00e-02 2.50e+03
        pdb=" C13 55C A1201 "    0.073 2.00e-02 2.50e+03
        pdb=" C14 55C A1201 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C12 55C A1201 "    0.027 2.00e-02 2.50e+03   2.94e-02 1.08e+01
        pdb=" C13 55C A1201 "   -0.014 2.00e-02 2.50e+03
        pdb=" C15 55C A1201 "    0.035 2.00e-02 2.50e+03
        pdb=" N1  55C A1201 "   -0.047 2.00e-02 2.50e+03
        pdb=" O21 55C A1201 "   -0.002 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE F  80 "    0.024 5.00e-02 4.00e+02   3.59e-02 2.06e+00
        pdb=" N   PRO F  81 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO F  81 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO F  81 "    0.020 5.00e-02 4.00e+02
  ... (remaining 2015 not shown)

  Histogram of nonbonded interaction distances:
        2.43 -     2.92: 5729
        2.92 -     3.42: 13991
        3.42 -     3.91: 24819
        3.91 -     4.41: 29412
        4.41 -     4.90: 43346
  Nonbonded interactions: 117297
  Sorted by model distance:
  nonbonded pdb=" O2'   G B 188 "
            pdb=" OP2   G B 189 "
     model   vdw
     2.430 3.040
  nonbonded pdb=" O2'   C B  74 "
            pdb=" OP1   C B  75 "
     model   vdw
     2.433 3.040
  nonbonded pdb=" O2'   G B  71 "
            pdb=" OP1   C B  72 "
     model   vdw
     2.433 3.040
  nonbonded pdb=" O   THR C 137 "
            pdb=" OG  SER C 138 "
     model   vdw
     2.444 3.040
  nonbonded pdb=" O2'   C B  75 "
            pdb=" O2    C B  75 "
     model   vdw
     2.451 3.040
  ... (remaining 117292 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             5.270
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.200
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     13.640
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  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:8.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   27.310
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7739
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042  15497  Z= 0.229
  Angle     :  0.651   7.788  22022  Z= 0.514
  Chirality :  0.045   0.450   2652
  Planarity :  0.004   0.061   2018
  Dihedral  : 19.145 163.393   7279
  Min Nonbonded Distance : 2.430

Molprobity Statistics.
  All-atom Clashscore : 1.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  0.09 %
    Allowed  :  3.93 %
    Favored  : 95.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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: -2.79 (0.21), residues: 1261
  helix: -2.00 (0.18), residues: 605
  sheet: -1.80 (0.40), residues: 132
  loop : -1.42 (0.26), residues: 524

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 962 
 TYR   0.008   0.001   TYR F  58 
 PHE   0.017   0.001   PHE A 331 
 TRP   0.005   0.001   TRP A 510 
 HIS   0.004   0.001   HIS A 816 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00328 /  0.23 (15497)
  covalent geometry    : angle       0.65108 /  0.51 (22022)
  hydrogen bonds       : bond        0.24815 / 17.03 (  698)
  hydrogen bonds       : angle       8.67699 /  5.94 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  147 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 146
  time to evaluate  : 0.270 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   99 ILE cc_start: 0.8544 (tt) cc_final: 0.8300 (tt)
REVERT: G   38 TYR cc_start: 0.8626 (m-80) cc_final: 0.8312 (m-80)
REVERT: G   41 TYR cc_start: 0.6194 (m-80) cc_final: 0.5900 (m-80)
REVERT: G   69 ASP cc_start: 0.7688 (t70) cc_final: 0.6840 (t70)
REVERT: G   73 ARG cc_start: 0.7053 (ttm170) cc_final: 0.6753 (ttm170)
REVERT: G  122 TYR cc_start: 0.8640 (t80) cc_final: 0.8335 (t80)
REVERT: A   99 PHE cc_start: 0.7833 (m-10) cc_final: 0.7452 (m-80)
REVERT: A  459 TRP cc_start: 0.8217 (t60) cc_final: 0.7933 (t-100)
REVERT: A  638 TYR cc_start: 0.7838 (m-80) cc_final: 0.7345 (m-80)
REVERT: A  772 TYR cc_start: 0.7833 (m-80) cc_final: 0.7374 (m-10)
REVERT: A  782 GLU cc_start: 0.8955 (pt0) cc_final: 0.8637 (pp20)
REVERT: A  823 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7581 (mmmm)
  outliers start: 1
  outliers final: 0
  residues processed: 147
  average time/residue: 0.5563
  time to fit residues: 89.1345
Evaluate side-chains
  94 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 94
  time to evaluate  : 0.342 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 98 optimal weight:   10.0000
   chunk 107 optimal weight:    0.9990
   chunk 10 optimal weight:    3.9990
   chunk 66 optimal weight:    4.9990
   chunk 130 optimal weight:    1.9990
   chunk 124 optimal weight:    2.9990
   chunk 103 optimal weight:    0.7980
   chunk 77 optimal weight:    0.2980
   chunk 122 optimal weight:    0.6980
   chunk 91 optimal weight:    1.9990
   chunk 55 optimal weight:    0.0980
   overall best weight:    0.5782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 190 HIS
C 205 GLN
C 216 GLN
C 225 ASN
A 534 HIS

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4288 r_free = 0.4288 target = 0.134277 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.081632 restraints weight = 33858.391|
|-----------------------------------------------------------------------------|
r_work (start): 0.3312 rms_B_bonded: 2.61
r_work: 0.3142 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3142
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1560

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.069  15497  Z= 0.152
  Angle     :  0.648  11.437  22022  Z= 0.354
  Chirality :  0.041   0.341   2652
  Planarity :  0.005   0.052   2018
  Dihedral  : 21.518 165.232   4814
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.19 %
    Allowed  : 10.32 %
    Favored  : 88.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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: -1.29 (0.23), residues: 1261
  helix: -0.35 (0.20), residues: 623
  sheet: -1.21 (0.41), residues: 133
  loop : -1.25 (0.27), residues: 505

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG C 100 
 TYR   0.024   0.001   TYR F  51 
 PHE   0.014   0.002   PHE A 331 
 TRP   0.018   0.001   TRP C 167 
 HIS   0.006   0.001   HIS A 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00298 /  0.15 (15497)
  covalent geometry    : angle       0.64776 /  0.35 (22022)
  hydrogen bonds       : bond        0.07608 /  5.11 (  698)
  hydrogen bonds       : angle       5.08731 /  3.50 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 100
  time to evaluate  : 0.422 
Fit side-chains
   revert: symmetry clash
REVERT: G   38 TYR cc_start: 0.8652 (m-80) cc_final: 0.8308 (m-80)
REVERT: G   41 TYR cc_start: 0.5980 (m-80) cc_final: 0.5738 (m-80)
REVERT: G   69 ASP cc_start: 0.7578 (t70) cc_final: 0.7337 (t70)
REVERT: G   73 ARG cc_start: 0.6950 (ttm170) cc_final: 0.6684 (ttm170)
REVERT: G  122 TYR cc_start: 0.8678 (t80) cc_final: 0.8352 (t80)
REVERT: A   99 PHE cc_start: 0.7788 (m-10) cc_final: 0.7508 (m-80)
REVERT: A  137 TRP cc_start: 0.9539 (m100) cc_final: 0.9285 (m-10)
REVERT: A  158 LEU cc_start: 0.8734 (mm) cc_final: 0.8516 (tm)
REVERT: A  459 TRP cc_start: 0.7829 (t60) cc_final: 0.7565 (t-100)
REVERT: A  638 TYR cc_start: 0.7925 (m-80) cc_final: 0.7368 (m-80)
REVERT: A  772 TYR cc_start: 0.7709 (m-80) cc_final: 0.7493 (m-10)
REVERT: A  782 GLU cc_start: 0.8855 (pt0) cc_final: 0.8608 (pp20)
  outliers start: 13
  outliers final: 2
  residues processed: 107
  average time/residue: 0.5337
  time to fit residues: 62.8142
Evaluate side-chains
  92 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 90
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 145 optimal weight:    0.6980
   chunk 128 optimal weight:    1.9990
   chunk 127 optimal weight:    1.9990
   chunk 28 optimal weight:   20.0000
   chunk 31 optimal weight:    2.9990
   chunk 100 optimal weight:    2.9990
   chunk 63 optimal weight:    3.9990
   chunk 79 optimal weight:    0.3980
   chunk 132 optimal weight:    0.0170
   chunk 47 optimal weight:    9.9990
   chunk 71 optimal weight:    0.9980
   overall best weight:    0.8220

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 190 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.134524 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 68)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.082239 restraints weight = 34309.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3313 rms_B_bonded: 2.59
r_work: 0.3141 rms_B_bonded: 3.75 restraints_weight: 0.5000
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.2009

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15497  Z= 0.152
  Angle     :  0.637  13.345  22022  Z= 0.338
  Chirality :  0.040   0.309   2652
  Planarity :  0.005   0.054   2018
  Dihedral  : 21.519 167.128   4814
  Min Nonbonded Distance : 2.458

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 10.96 %
    Favored  : 87.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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: -0.70 (0.23), residues: 1261
  helix:  0.21 (0.21), residues: 626
  sheet: -0.79 (0.43), residues: 133
  loop : -1.12 (0.27), residues: 502

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG A1105 
 TYR   0.019   0.001   TYR F  58 
 PHE   0.016   0.002   PHE C 202 
 TRP   0.012   0.001   TRP A1072 
 HIS   0.004   0.001   HIS A 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.15 (15497)
  covalent geometry    : angle       0.63674 /  0.34 (22022)
  hydrogen bonds       : bond        0.06256 /  4.19 (  698)
  hydrogen bonds       : angle       4.58188 /  3.16 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 95
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  167 TRP cc_start: 0.7813 (OUTLIER) cc_final: 0.7137 (p90)
REVERT: G   38 TYR cc_start: 0.8619 (m-80) cc_final: 0.8306 (m-80)
REVERT: G   41 TYR cc_start: 0.6396 (m-80) cc_final: 0.6137 (m-80)
REVERT: G   73 ARG cc_start: 0.7033 (ttm170) cc_final: 0.6760 (ttm170)
REVERT: G  122 TYR cc_start: 0.8690 (t80) cc_final: 0.8418 (t80)
REVERT: A   99 PHE cc_start: 0.7808 (m-10) cc_final: 0.7534 (m-80)
REVERT: A  638 TYR cc_start: 0.8002 (m-80) cc_final: 0.7437 (m-80)
REVERT: A  772 TYR cc_start: 0.7608 (m-80) cc_final: 0.7332 (m-10)
REVERT: A  782 GLU cc_start: 0.8811 (pt0) cc_final: 0.8589 (pp20)
  outliers start: 15
  outliers final: 4
  residues processed: 103
  average time/residue: 0.5336
  time to fit residues: 60.7577
Evaluate side-chains
  98 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 93
  time to evaluate  : 0.388 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  167 TRP
Chi-restraints excluded: chain F residue   63 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 63 optimal weight:    4.9990
   chunk 38 optimal weight:    7.9990
   chunk 128 optimal weight:    0.0870
   chunk 39 optimal weight:    6.9990
   chunk 20 optimal weight:    3.9990
   chunk 1 optimal weight:    0.0670
   chunk 144 optimal weight:    0.7980
   chunk 77 optimal weight:    1.9990
   chunk 48 optimal weight:   30.0000
   chunk 64 optimal weight:    1.9990
   chunk 66 optimal weight:   10.0000
   overall best weight:    0.9900

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS
C 190 HIS
** F  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 HIS
A1100 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4282 r_free = 0.4282 target = 0.134947 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 80)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.081857 restraints weight = 34927.461|
|-----------------------------------------------------------------------------|
r_work (start): 0.3300 rms_B_bonded: 2.69
r_work: 0.3127 rms_B_bonded: 3.83 restraints_weight: 0.5000
r_work (final): 0.3127
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8196
moved from start:          0.2333

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044  15497  Z= 0.158
  Angle     :  0.601   9.651  22022  Z= 0.320
  Chirality :  0.039   0.267   2652
  Planarity :  0.005   0.071   2018
  Dihedral  : 21.484 168.758   4814
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 5.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.09 %
    Favored  : 96.91 %
  Rotamer:
    Outliers :  1.64 %
    Allowed  : 11.96 %
    Favored  : 86.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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 (0.24), residues: 1261
  helix:  0.48 (0.21), residues: 630
  sheet: -0.68 (0.42), residues: 146
  loop : -1.04 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.016   0.000   ARG C 100 
 TYR   0.015   0.001   TYR F  58 
 PHE   0.014   0.002   PHE A 331 
 TRP   0.054   0.003   TRP C  98 
 HIS   0.009   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00343 /  0.16 (15497)
  covalent geometry    : angle       0.60118 /  0.32 (22022)
  hydrogen bonds       : bond        0.05791 /  3.86 (  698)
  hydrogen bonds       : angle       4.38457 /  3.02 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 94
  time to evaluate  : 0.330 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 ARG cc_start: 0.7629 (ptt-90) cc_final: 0.6505 (ptt90)
REVERT: C  159 ARG cc_start: 0.6016 (mmp80) cc_final: 0.5753 (mmm160)
REVERT: C  170 LYS cc_start: 0.8464 (ptpp) cc_final: 0.7995 (mttt)
REVERT: G   41 TYR cc_start: 0.6334 (m-80) cc_final: 0.6044 (m-80)
REVERT: G   60 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7660 (ttm)
REVERT: G  122 TYR cc_start: 0.8622 (t80) cc_final: 0.8408 (t80)
REVERT: A   99 PHE cc_start: 0.7763 (m-10) cc_final: 0.7467 (m-80)
REVERT: A  137 TRP cc_start: 0.9395 (m-10) cc_final: 0.8766 (m-10)
REVERT: A  638 TYR cc_start: 0.8064 (m-80) cc_final: 0.7591 (m-80)
REVERT: A  772 TYR cc_start: 0.7710 (m-80) cc_final: 0.7423 (m-10)
REVERT: A  782 GLU cc_start: 0.8880 (pt0) cc_final: 0.8610 (pp20)
REVERT: A  866 LEU cc_start: 0.7664 (OUTLIER) cc_final: 0.7461 (tt)
  outliers start: 18
  outliers final: 7
  residues processed: 103
  average time/residue: 0.4834
  time to fit residues: 55.1774
Evaluate side-chains
  99 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 90
  time to evaluate  : 0.296 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  158 THR
Chi-restraints excluded: chain F residue   63 ILE
Chi-restraints excluded: chain G residue   60 MET
Chi-restraints excluded: chain G residue   65 SER
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 41 optimal weight:   20.0000
   chunk 90 optimal weight:    0.7980
   chunk 83 optimal weight:    0.8980
   chunk 135 optimal weight:    0.6980
   chunk 86 optimal weight:    0.9980
   chunk 78 optimal weight:    0.6980
   chunk 119 optimal weight:    0.9990
   chunk 22 optimal weight:    3.9990
   chunk 82 optimal weight:    0.6980
   chunk 95 optimal weight:    5.9990
   chunk 2 optimal weight:   30.0000
   overall best weight:    0.7580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS
C 190 HIS
** F  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4295 r_free = 0.4295 target = 0.134529 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.082230 restraints weight = 34131.395|
|-----------------------------------------------------------------------------|
r_work (start): 0.3323 rms_B_bonded: 2.61
r_work: 0.3152 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3152
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8167
moved from start:          0.2617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039  15497  Z= 0.134
  Angle     :  0.569  10.556  22022  Z= 0.301
  Chirality :  0.037   0.262   2652
  Planarity :  0.005   0.055   2018
  Dihedral  : 21.416 168.776   4814
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 5.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 13.06 %
    Favored  : 85.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.12 (0.24), residues: 1261
  helix:  0.78 (0.21), residues: 630
  sheet: -0.62 (0.42), residues: 146
  loop : -0.97 (0.28), residues: 485

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 962 
 TYR   0.014   0.001   TYR F  58 
 PHE   0.012   0.001   PHE A 331 
 TRP   0.032   0.002   TRP C  98 
 HIS   0.009   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00287 /  0.13 (15497)
  covalent geometry    : angle       0.56923 /  0.30 (22022)
  hydrogen bonds       : bond        0.05312 /  3.50 (  698)
  hydrogen bonds       : angle       4.17625 /  2.88 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 93
  time to evaluate  : 0.387 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 ARG cc_start: 0.7658 (ptt-90) cc_final: 0.6487 (ptt90)
REVERT: C  100 ARG cc_start: 0.8679 (ptm-80) cc_final: 0.8352 (ptm-80)
REVERT: G   41 TYR cc_start: 0.6260 (m-80) cc_final: 0.5957 (m-80)
REVERT: G   60 MET cc_start: 0.7938 (OUTLIER) cc_final: 0.7586 (ttm)
REVERT: G   69 ASP cc_start: 0.7846 (OUTLIER) cc_final: 0.7618 (t70)
REVERT: A   99 PHE cc_start: 0.7803 (m-10) cc_final: 0.7476 (m-80)
REVERT: A  638 TYR cc_start: 0.8040 (m-80) cc_final: 0.7572 (m-80)
REVERT: A  772 TYR cc_start: 0.7760 (m-80) cc_final: 0.7459 (m-10)
REVERT: A  782 GLU cc_start: 0.8870 (pt0) cc_final: 0.8636 (pp20)
  outliers start: 17
  outliers final: 10
  residues processed: 103
  average time/residue: 0.5069
  time to fit residues: 58.1829
Evaluate side-chains
  102 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.356 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain F residue   63 ILE
Chi-restraints excluded: chain G residue   60 MET
Chi-restraints excluded: chain G residue   69 ASP
Chi-restraints excluded: chain G residue   74 ILE
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  866 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 52 optimal weight:    0.8980
   chunk 122 optimal weight:    0.9980
   chunk 120 optimal weight:    1.9990
   chunk 76 optimal weight:    0.9980
   chunk 137 optimal weight:    0.9980
   chunk 82 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 38 optimal weight:    7.9990
   chunk 90 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   overall best weight:    0.9782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS
C 190 HIS
** F  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  86 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4290 r_free = 0.4290 target = 0.134218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.081680 restraints weight = 34066.718|
|-----------------------------------------------------------------------------|
r_work (start): 0.3310 rms_B_bonded: 2.61
r_work: 0.3140 rms_B_bonded: 3.74 restraints_weight: 0.5000
r_work (final): 0.3140
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8181
moved from start:          0.2737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041  15497  Z= 0.150
  Angle     :  0.581  15.453  22022  Z= 0.303
  Chirality :  0.038   0.295   2652
  Planarity :  0.005   0.056   2018
  Dihedral  : 21.395 168.911   4814
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 5.96
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.79 %
    Favored  : 84.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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 (0.24), residues: 1261
  helix:  0.86 (0.21), residues: 631
  sheet: -0.60 (0.42), residues: 146
  loop : -0.94 (0.28), residues: 484

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG C 100 
 TYR   0.012   0.001   TYR F  58 
 PHE   0.016   0.002   PHE C 174 
 TRP   0.021   0.002   TRP C  98 
 HIS   0.008   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00331 /  0.15 (15497)
  covalent geometry    : angle       0.58142 /  0.30 (22022)
  hydrogen bonds       : bond        0.05375 /  3.56 (  698)
  hydrogen bonds       : angle       4.17429 /  2.89 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.362 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 ARG cc_start: 0.7681 (ptt-90) cc_final: 0.6593 (ptt90)
REVERT: C  159 ARG cc_start: 0.5936 (mmp80) cc_final: 0.5718 (mmm160)
REVERT: C  177 THR cc_start: 0.8909 (p) cc_final: 0.8662 (p)
REVERT: G   41 TYR cc_start: 0.6256 (m-80) cc_final: 0.5945 (m-80)
REVERT: G   60 MET cc_start: 0.8018 (OUTLIER) cc_final: 0.7680 (ttm)
REVERT: A   86 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8437 (mm-40)
REVERT: A   99 PHE cc_start: 0.7827 (m-10) cc_final: 0.7529 (m-80)
REVERT: A  638 TYR cc_start: 0.8094 (m-80) cc_final: 0.7621 (m-80)
REVERT: A  772 TYR cc_start: 0.7740 (m-80) cc_final: 0.7511 (m-10)
  outliers start: 22
  outliers final: 9
  residues processed: 105
  average time/residue: 0.5402
  time to fit residues: 62.4336
Evaluate side-chains
  99 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.314 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain G residue   60 MET
Chi-restraints excluded: chain G residue   65 SER
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   86 GLN
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 49 optimal weight:    8.9990
   chunk 106 optimal weight:    1.9990
   chunk 59 optimal weight:    4.9990
   chunk 27 optimal weight:    7.9990
   chunk 2 optimal weight:    0.0010
   chunk 50 optimal weight:    9.9990
   chunk 1 optimal weight:    0.0970
   chunk 73 optimal weight:    0.8980
   chunk 131 optimal weight:    0.9980
   chunk 67 optimal weight:    3.9990
   chunk 92 optimal weight:    0.7980
   overall best weight:    0.5584

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS
C 190 HIS
** F  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A  86 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4298 r_free = 0.4298 target = 0.134831 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.082598 restraints weight = 33844.706|
|-----------------------------------------------------------------------------|
r_work (start): 0.3330 rms_B_bonded: 2.57
r_work: 0.3161 rms_B_bonded: 3.71 restraints_weight: 0.5000
r_work (final): 0.3161
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8163
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043  15497  Z= 0.120
  Angle     :  0.569  12.617  22022  Z= 0.297
  Chirality :  0.036   0.259   2652
  Planarity :  0.005   0.075   2018
  Dihedral  : 21.377 169.118   4814
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.85 %
    Favored  : 97.15 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 13.88 %
    Favored  : 84.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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:  0.06 (0.24), residues: 1261
  helix:  0.97 (0.21), residues: 636
  sheet: -0.56 (0.42), residues: 146
  loop : -0.96 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 962 
 TYR   0.012   0.001   TYR F  51 
 PHE   0.013   0.001   PHE A 159 
 TRP   0.026   0.001   TRP C  98 
 HIS   0.006   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00253 /  0.12 (15497)
  covalent geometry    : angle       0.56864 /  0.30 (22022)
  hydrogen bonds       : bond        0.05105 /  3.36 (  698)
  hydrogen bonds       : angle       4.08400 /  2.84 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.352 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 ARG cc_start: 0.7668 (ptt-90) cc_final: 0.6601 (ptt90)
REVERT: C  159 ARG cc_start: 0.6008 (mmp80) cc_final: 0.5720 (mmm160)
REVERT: C  177 THR cc_start: 0.8975 (p) cc_final: 0.8747 (p)
REVERT: C  219 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8222 (tm)
REVERT: G   41 TYR cc_start: 0.6266 (m-80) cc_final: 0.5954 (m-80)
REVERT: G   60 MET cc_start: 0.7984 (OUTLIER) cc_final: 0.7603 (ttm)
REVERT: A   99 PHE cc_start: 0.7824 (m-10) cc_final: 0.7502 (m-80)
REVERT: A  175 LEU cc_start: 0.9041 (tt) cc_final: 0.8411 (mt)
REVERT: A  638 TYR cc_start: 0.8106 (m-80) cc_final: 0.7617 (m-80)
REVERT: A  772 TYR cc_start: 0.7851 (m-80) cc_final: 0.7519 (m-80)
REVERT: A  773 MET cc_start: 0.8299 (tpt) cc_final: 0.8028 (tpt)
  outliers start: 22
  outliers final: 9
  residues processed: 107
  average time/residue: 0.4732
  time to fit residues: 56.3668
Evaluate side-chains
  99 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.294 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain G residue   60 MET
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  676 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  887 LEU
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 27 optimal weight:    8.9990
   chunk 135 optimal weight:    0.6980
   chunk 65 optimal weight:   20.0000
   chunk 62 optimal weight:    6.9990
   chunk 66 optimal weight:    6.9990
   chunk 37 optimal weight:    9.9990
   chunk 137 optimal weight:    0.6980
   chunk 54 optimal weight:    3.9990
   chunk 83 optimal weight:    0.5980
   chunk 74 optimal weight:    0.8980
   chunk 41 optimal weight:   20.0000
   overall best weight:    1.3782

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS
C 190 HIS
** F  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4280 r_free = 0.4280 target = 0.133506 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 75)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.080740 restraints weight = 34130.297|
|-----------------------------------------------------------------------------|
r_work (start): 0.3294 rms_B_bonded: 2.59
r_work: 0.3124 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3124
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8195
moved from start:          0.2934

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047  15497  Z= 0.190
  Angle     :  0.617  12.164  22022  Z= 0.319
  Chirality :  0.039   0.259   2652
  Planarity :  0.005   0.068   2018
  Dihedral  : 21.417 169.034   4814
  Min Nonbonded Distance : 2.352

Molprobity Statistics.
  All-atom Clashscore : 6.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  2.01 %
    Allowed  : 14.61 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.08 (0.24), residues: 1261
  helix:  0.88 (0.21), residues: 637
  sheet: -0.62 (0.42), residues: 146
  loop : -1.08 (0.28), residues: 478

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG C 175 
 TYR   0.011   0.001   TYR F  51 
 PHE   0.024   0.002   PHE A 159 
 TRP   0.023   0.002   TRP A 137 
 HIS   0.007   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00429 /  0.19 (15497)
  covalent geometry    : angle       0.61708 /  0.32 (22022)
  hydrogen bonds       : bond        0.05585 /  3.72 (  698)
  hydrogen bonds       : angle       4.20069 /  2.92 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  110 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 88
  time to evaluate  : 0.434 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 ARG cc_start: 0.7685 (ptt-90) cc_final: 0.6641 (ptt90)
REVERT: C  159 ARG cc_start: 0.6001 (mmp80) cc_final: 0.5732 (mmm160)
REVERT: C  177 THR cc_start: 0.8972 (p) cc_final: 0.8742 (p)
REVERT: C  219 LEU cc_start: 0.8352 (OUTLIER) cc_final: 0.8104 (tm)
REVERT: G   41 TYR cc_start: 0.6258 (m-80) cc_final: 0.5981 (m-80)
REVERT: G   60 MET cc_start: 0.8016 (OUTLIER) cc_final: 0.7653 (ttm)
REVERT: A   99 PHE cc_start: 0.7974 (m-10) cc_final: 0.7570 (m-80)
REVERT: A  175 LEU cc_start: 0.9032 (tt) cc_final: 0.8418 (mt)
REVERT: A  638 TYR cc_start: 0.8156 (m-80) cc_final: 0.7706 (m-80)
REVERT: A  772 TYR cc_start: 0.7832 (m-80) cc_final: 0.7518 (m-10)
REVERT: A 1105 ARG cc_start: 0.8601 (ttp-110) cc_final: 0.8134 (ttp-170)
  outliers start: 22
  outliers final: 10
  residues processed: 102
  average time/residue: 0.4895
  time to fit residues: 55.6494
Evaluate side-chains
  99 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.321 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain G residue   60 MET
Chi-restraints excluded: chain G residue   72 GLU
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  903 THR
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 137 optimal weight:    0.6980
   chunk 15 optimal weight:    5.9990
   chunk 10 optimal weight:   20.0000
   chunk 126 optimal weight:    0.0010
   chunk 141 optimal weight:    0.3980
   chunk 85 optimal weight:    0.6980
   chunk 146 optimal weight:    2.9990
   chunk 120 optimal weight:    0.9990
   chunk 86 optimal weight:    0.7980
   chunk 110 optimal weight:    3.9990
   overall best weight:    0.5186

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS
C 190 HIS
** F  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4302 r_free = 0.4302 target = 0.135068 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 69)----------------|
| r_work = 0.3492 r_free = 0.3492 target = 0.082838 restraints weight = 34169.536|
|-----------------------------------------------------------------------------|
r_work (start): 0.3335 rms_B_bonded: 2.56
r_work: 0.3165 rms_B_bonded: 3.72 restraints_weight: 0.5000
r_work (final): 0.3165
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8159
moved from start:          0.3095

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.059  15497  Z= 0.120
  Angle     :  0.594  14.509  22022  Z= 0.306
  Chirality :  0.036   0.255   2652
  Planarity :  0.005   0.056   2018
  Dihedral  : 21.378 169.140   4814
  Min Nonbonded Distance : 2.370

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.62 %
    Favored  : 97.38 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 15.25 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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 (0.24), residues: 1261
  helix:  1.09 (0.21), residues: 636
  sheet: -0.50 (0.42), residues: 146
  loop : -0.99 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.000   ARG A 962 
 TYR   0.013   0.001   TYR F  51 
 PHE   0.013   0.001   PHE A 159 
 TRP   0.053   0.002   TRP A 137 
 HIS   0.007   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00261 /  0.12 (15497)
  covalent geometry    : angle       0.59380 /  0.31 (22022)
  hydrogen bonds       : bond        0.05006 /  3.29 (  698)
  hydrogen bonds       : angle       4.06731 /  2.84 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 90
  time to evaluate  : 0.300 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 ARG cc_start: 0.7772 (ptt-90) cc_final: 0.6728 (ptt90)
REVERT: C  159 ARG cc_start: 0.5941 (mmp80) cc_final: 0.5734 (mmm160)
REVERT: C  177 THR cc_start: 0.9015 (p) cc_final: 0.8790 (p)
REVERT: C  219 LEU cc_start: 0.8348 (OUTLIER) cc_final: 0.8101 (tm)
REVERT: G   41 TYR cc_start: 0.6256 (m-80) cc_final: 0.5977 (m-80)
REVERT: G   60 MET cc_start: 0.7968 (OUTLIER) cc_final: 0.7599 (ttm)
REVERT: A   99 PHE cc_start: 0.8016 (m-10) cc_final: 0.7597 (m-80)
REVERT: A  175 LEU cc_start: 0.9035 (tt) cc_final: 0.8456 (mt)
REVERT: A  638 TYR cc_start: 0.8159 (m-80) cc_final: 0.7703 (m-80)
REVERT: A  772 TYR cc_start: 0.7812 (m-80) cc_final: 0.7479 (m-10)
REVERT: A  773 MET cc_start: 0.8240 (tpt) cc_final: 0.7993 (tpt)
REVERT: A 1105 ARG cc_start: 0.8674 (ttp-110) cc_final: 0.8300 (ttp-170)
  outliers start: 15
  outliers final: 10
  residues processed: 97
  average time/residue: 0.4872
  time to fit residues: 52.6064
Evaluate side-chains
  99 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  167 TRP
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain C residue  219 LEU
Chi-restraints excluded: chain G residue   60 MET
Chi-restraints excluded: chain G residue   72 GLU
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  158 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 102 optimal weight:    2.9990
   chunk 139 optimal weight:    2.9990
   chunk 58 optimal weight:    7.9990
   chunk 79 optimal weight:    0.9990
   chunk 48 optimal weight:   20.0000
   chunk 109 optimal weight:   20.0000
   chunk 144 optimal weight:    1.9990
   chunk 47 optimal weight:    9.9990
   chunk 133 optimal weight:    0.6980
   chunk 2 optimal weight:    0.0470
   chunk 44 optimal weight:    7.9990
   overall best weight:    1.3484

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS
C 190 HIS
** F  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4278 r_free = 0.4278 target = 0.134559 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.081258 restraints weight = 34704.437|
|-----------------------------------------------------------------------------|
r_work (start): 0.3289 rms_B_bonded: 2.71
r_work: 0.3117 rms_B_bonded: 3.82 restraints_weight: 0.5000
r_work (final): 0.3117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8197
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.087  15497  Z= 0.191
  Angle     :  0.629  12.793  22022  Z= 0.322
  Chirality :  0.039   0.255   2652
  Planarity :  0.005   0.060   2018
  Dihedral  : 21.370 168.959   4814
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 7.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.65 %
    Favored  : 96.35 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.34 %
    Favored  : 83.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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:  0.01 (0.24), residues: 1261
  helix:  0.92 (0.21), residues: 637
  sheet: -0.48 (0.43), residues: 145
  loop : -1.00 (0.28), residues: 479

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG C 154 
 TYR   0.014   0.001   TYR F  51 
 PHE   0.025   0.002   PHE C 202 
 TRP   0.065   0.002   TRP A 137 
 HIS   0.007   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00439 /  0.19 (15497)
  covalent geometry    : angle       0.62923 /  0.32 (22022)
  hydrogen bonds       : bond        0.05540 /  3.68 (  698)
  hydrogen bonds       : angle       4.20714 /  2.92 ( 1782)

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

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

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2522 Ramachandran restraints generated.
    1261 Oldfield, 0 Emsley, 1261 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  107 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 90
  time to evaluate  : 0.331 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C   96 ARG cc_start: 0.7848 (ptt-90) cc_final: 0.6809 (ptt90)
REVERT: C  154 ARG cc_start: 0.8747 (pmt170) cc_final: 0.8323 (pmt170)
REVERT: C  177 THR cc_start: 0.9049 (p) cc_final: 0.8837 (p)
REVERT: C  220 ARG cc_start: 0.9090 (tmm160) cc_final: 0.8830 (mmp-170)
REVERT: G   41 TYR cc_start: 0.6235 (m-80) cc_final: 0.5965 (m-80)
REVERT: G   60 MET cc_start: 0.7995 (OUTLIER) cc_final: 0.7622 (ttm)
REVERT: A   99 PHE cc_start: 0.8066 (m-10) cc_final: 0.7687 (m-80)
REVERT: A  137 TRP cc_start: 0.9515 (m-10) cc_final: 0.9096 (m-10)
REVERT: A  175 LEU cc_start: 0.9026 (tt) cc_final: 0.8451 (mt)
REVERT: A  536 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8782 (tt)
REVERT: A  638 TYR cc_start: 0.8144 (m-80) cc_final: 0.7671 (m-80)
REVERT: A  773 MET cc_start: 0.8241 (tpt) cc_final: 0.7937 (tpt)
  outliers start: 17
  outliers final: 9
  residues processed: 99
  average time/residue: 0.4818
  time to fit residues: 53.1414
Evaluate side-chains
  98 residues out of total 1095 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 87
  time to evaluate  : 0.306 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  120 VAL
Chi-restraints excluded: chain C residue  184 LEU
Chi-restraints excluded: chain G residue   60 MET
Chi-restraints excluded: chain G residue   72 GLU
Chi-restraints excluded: chain A residue   27 PHE
Chi-restraints excluded: chain A residue   56 VAL
Chi-restraints excluded: chain A residue   88 LEU
Chi-restraints excluded: chain A residue  536 LEU
Chi-restraints excluded: chain A residue  841 LEU
Chi-restraints excluded: chain A residue  874 THR
Chi-restraints excluded: chain A residue  970 MET
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 147
   random chunks:
   chunk 38 optimal weight:    7.9990
   chunk 40 optimal weight:   20.0000
   chunk 81 optimal weight:    0.0370
   chunk 60 optimal weight:    7.9990
   chunk 36 optimal weight:   20.0000
   chunk 3 optimal weight:   10.0000
   chunk 55 optimal weight:   20.0000
   chunk 88 optimal weight:    0.7980
   chunk 107 optimal weight:    2.9990
   chunk 71 optimal weight:    3.9990
   chunk 14 optimal weight:    0.9990
   overall best weight:    1.7664

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
C 151 HIS
** F  83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 906 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4269 r_free = 0.4269 target = 0.133873 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.080301 restraints weight = 34532.108|
|-----------------------------------------------------------------------------|
r_work (start): 0.3271 rms_B_bonded: 2.72
r_work: 0.3098 rms_B_bonded: 3.81 restraints_weight: 0.5000
r_work (final): 0.3098
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8225
moved from start:          0.3177

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.075  15497  Z= 0.234
  Angle     :  0.678  13.349  22022  Z= 0.346
  Chirality :  0.042   0.257   2652
  Planarity :  0.006   0.068   2018
  Dihedral  : 21.421 168.561   4814
  Min Nonbonded Distance : 2.238

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 15.53 %
    Favored  : 83.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.41 %
    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 (0.24), residues: 1261
  helix:  0.80 (0.21), residues: 630
  sheet: -0.51 (0.43), residues: 143
  loop : -1.09 (0.28), residues: 488

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG C 100 
 TYR   0.014   0.001   TYR F  51 
 PHE   0.017   0.002   PHE A 331 
 TRP   0.054   0.002   TRP A 137 
 HIS   0.006   0.001   HIS C 151 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00536 /  0.23 (15497)
  covalent geometry    : angle       0.67832 /  0.35 (22022)
  hydrogen bonds       : bond        0.05952 /  3.98 (  698)
  hydrogen bonds       : angle       4.35527 /  3.03 ( 1782)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4133.23 seconds
wall clock time: 71 minutes 9.95 seconds (4269.95 seconds total)