Starting phenix.real_space_refine
on Thu Jun 12 08:47:40 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7trf_26088/06_2025/7trf_26088.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7trf_26088/06_2025/7trf_26088.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7trf_26088/06_2025/7trf_26088.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7trf_26088/06_2025/7trf_26088.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7trf_26088/06_2025/7trf_26088.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7trf_26088/06_2025/7trf_26088.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 5
    Type Number    sf(0)   Gaussians
     P     224      5.49       5
     S      38      5.16       5
     C    7774      2.51       5
     N    2469      2.21       5
     O    3076      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 66 residue(s): 0.03s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 13581
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "F"
      Number of atoms: 699
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 90, 699
          Classifications: {'peptide': 90}
          Link IDs: {'PTRANS': 2, 'TRANS': 87}
    Chain: "E"
      Number of atoms: 642
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 82, 642
          Classifications: {'peptide': 82}
          Link IDs: {'PTRANS': 3, 'TRANS': 78}
    Chain: "B"
      Number of atoms: 4605
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 217, 4605
          Classifications: {'RNA': 217}
          Modifications used: {'rna2p_pur': 15, 'rna2p_pyr': 21, 'rna3p_pur': 85, 'rna3p_pyr': 96}
          Link IDs: {'rna2p': 36, 'rna3p': 180}
          Chain breaks: 2
    Chain: "A"
      Number of atoms: 7488
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 934, 7488
          Classifications: {'peptide': 934}
          Link IDs: {'PCIS': 1, 'PTRANS': 55, 'TRANS': 877}
          Chain breaks: 4
    Chain: "D"
      Number of atoms: 147
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 7, 147
          Classifications: {'DNA': 7}
          Link IDs: {'rna3p': 6}
  Time building chain proxies: 7.75, per 1000 atoms: 0.57
  Number of scatterers: 13581
  At special positions: 0
  Unit cell: (117.7, 122.1, 121, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      38     16.00
     P     224     15.00
     O    3076      8.00
     N    2469      7.00
     C    7774      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 3.09
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      51 helices and 9 sheets defined
      59.4% alpha, 13.0% beta
      64 base pairs and 97 stacking pairs defined.
    Time for finding SS restraints: 5.73
  Creating SS restraints...
    Processing helix  chain 'F' and resid 38 through 50
      removed outlier: 3.800A  pdb=" N   TYR F  43 " --> pdb=" O   SER F  39 " (cutoff:3.500A)
      removed outlier: 3.597A  pdb=" N   GLN F  48 " --> pdb=" O   LYS F  44 " (cutoff:3.500A)
      removed outlier: 3.940A  pdb=" N   VAL F  49 " --> pdb=" O   VAL F  45 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 56 through 86
      removed outlier: 4.107A  pdb=" N   SER F  65 " --> pdb=" O   GLY F  61 " (cutoff:3.500A)
      removed outlier: 3.713A  pdb=" N   PHE F  66 " --> pdb=" O   ILE F  62 " (cutoff:3.500A)
      removed outlier: 3.878A  pdb=" N   VAL F  67 " --> pdb=" O   MET F  63 " (cutoff:3.500A)
      removed outlier: 3.978A  pdb=" N   ASN F  68 " --> pdb=" O   ASN F  64 " (cutoff:3.500A)
      removed outlier: 3.717A  pdb=" N   ILE F  70 " --> pdb=" O   PHE F  66 " (cutoff:3.500A)
      removed outlier: 3.512A  pdb=" N   ILE F  74 " --> pdb=" O   ILE F  70 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 91 through 103
      removed outlier: 4.193A  pdb=" N   ILE F  95 " --> pdb=" O   THR F  91 " (cutoff:3.500A)
      removed outlier: 3.716A  pdb=" N   GLN F  96 " --> pdb=" O   SER F  92 " (cutoff:3.500A)
      removed outlier: 4.227A  pdb=" N   THR F  97 " --> pdb=" O   ARG F  93 " (cutoff:3.500A)
      removed outlier: 3.829A  pdb=" N   ALA F  98 " --> pdb=" O   GLU F  94 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   VAL F  99 " --> pdb=" O   ILE F  95 " (cutoff:3.500A)
      removed outlier: 3.559A  pdb=" N   ARG F 100 " --> pdb=" O   GLN F  96 " (cutoff:3.500A)
      removed outlier: 3.870A  pdb=" N   LEU F 101 " --> pdb=" O   THR F  97 " (cutoff:3.500A)
      removed outlier: 3.500A  pdb=" N   LEU F 102 " --> pdb=" O   ALA F  98 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 105 through 124
      removed outlier: 3.548A  pdb=" N   LYS F 109 " --> pdb=" O   GLY F 105 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   LYS F 121 " --> pdb=" O   LYS F 117 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 19 through 23
    Processing helix  chain 'E' and resid 27 through 38
      removed outlier: 3.854A  pdb=" N   GLY E  38 " --> pdb=" O   LEU E  34 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 46 through 74
      removed outlier: 4.561A  pdb=" N   VAL E  50 " --> pdb=" O   ALA E  46 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   TYR E  51 " --> pdb=" O   GLY E  47 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   VAL E  55 " --> pdb=" O   TYR E  51 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU E  56 " --> pdb=" O   LEU E  52 " (cutoff:3.500A)
      removed outlier: 3.916A  pdb=" N   GLU E  57 " --> pdb=" O   ALA E  53 " (cutoff:3.500A)
      removed outlier: 3.598A  pdb=" N   TYR E  58 " --> pdb=" O   ALA E  54 " (cutoff:3.500A)
      removed outlier: 3.537A  pdb=" N   LEU E  64 " --> pdb=" O   THR E  60 " (cutoff:3.500A)
      removed outlier: 3.835A  pdb=" N   LEU E  66 " --> pdb=" O   GLU E  62 " (cutoff:3.500A)
      removed outlier: 3.660A  pdb=" N   ALA E  67 " --> pdb=" O   ILE E  63 " (cutoff:3.500A)
      removed outlier: 4.026A  pdb=" N   ASP E  73 " --> pdb=" O   ASN E  69 " (cutoff:3.500A)
      removed outlier: 4.154A  pdb=" N   ASN E  74 " --> pdb=" O   ALA E  70 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 81 through 91
      removed outlier: 3.810A  pdb=" N   ALA E  87 " --> pdb=" O   HIS E  83 " (cutoff:3.500A)
      removed outlier: 3.908A  pdb=" N   ARG E  89 " --> pdb=" O   GLN E  85 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 92 through 98
      removed outlier: 3.596A  pdb=" N   LEU E  97 " --> pdb=" O   GLU E  93 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 8 through 18
    Processing helix  chain 'A' and resid 24 through 32
    Processing helix  chain 'A' and resid 44 through 53
    Processing helix  chain 'A' and resid 76 through 92
    Processing helix  chain 'A' and resid 125 through 134
    Processing helix  chain 'A' and resid 134 through 145
    Processing helix  chain 'A' and resid 146 through 156
    Processing helix  chain 'A' and resid 174 through 178
      removed outlier: 3.839A  pdb=" N   LEU A 178 " --> pdb=" O   LEU A 175 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 329 through 332
      removed outlier: 4.000A  pdb=" N   LEU A 332 " --> pdb=" O   LYS A 329 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 329 through 332'
    Processing helix  chain 'A' and resid 345 through 350
    Processing helix  chain 'A' and resid 353 through 366
      removed outlier: 3.574A  pdb=" N   ALA A 357 " --> pdb=" O   SER A 353 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 388
    Processing helix  chain 'A' and resid 389 through 401
      removed outlier: 4.037A  pdb=" N   PHE A 393 " --> pdb=" O   MET A 389 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 413
      removed outlier: 3.782A  pdb=" N   LEU A 408 " --> pdb=" O   PRO A 404 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 446 through 454
      removed outlier: 3.781A  pdb=" N   GLN A 454 " --> pdb=" O   GLN A 450 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 457 through 471
      removed outlier: 3.717A  pdb=" N   ARG A 471 " --> pdb=" O   ALA A 467 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 474 through 479
    Processing helix  chain 'A' and resid 480 through 496
      removed outlier: 3.506A  pdb=" N   GLU A 484 " --> pdb=" O   SER A 480 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 505 through 509
    Processing helix  chain 'A' and resid 517 through 521
      removed outlier: 3.654A  pdb=" N   LEU A 520 " --> pdb=" O   CYS A 517 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 530 through 560
      removed outlier: 3.764A  pdb=" N   HIS A 534 " --> pdb=" O   PRO A 530 " (cutoff:3.500A)
      removed outlier: 4.124A  pdb=" N   VAL A 553 " --> pdb=" O   MET A 549 " (cutoff:3.500A)
      removed outlier: 5.267A  pdb=" N   VAL A 554 " --> pdb=" O   SER A 550 " (cutoff:3.500A)
      removed outlier: 4.101A  pdb=" N   PHE A 560 " --> pdb=" O   LEU A 556 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 578 through 596
      removed outlier: 4.388A  pdb=" N   ILE A 587 " --> pdb=" O   LYS A 583 " (cutoff:3.500A)
      removed outlier: 3.813A  pdb=" N   GLY A 588 " --> pdb=" O   LEU A 584 " (cutoff:3.500A)
      removed outlier: 3.788A  pdb=" N   VAL A 596 " --> pdb=" O   HIS A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 602 through 612
      removed outlier: 3.515A  pdb=" N   GLU A 611 " --> pdb=" O   ARG A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 652 through 672
      removed outlier: 3.532A  pdb=" N   SER A 656 " --> pdb=" O   GLU A 652 " (cutoff:3.500A)
      removed outlier: 3.750A  pdb=" N   ARG A 672 " --> pdb=" O   GLU A 668 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 673 through 677
      removed outlier: 3.652A  pdb=" N   LEU A 676 " --> pdb=" O   PRO A 673 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 682 through 698
      removed outlier: 3.762A  pdb=" N   ILE A 686 " --> pdb=" O   GLY A 682 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 721 through 733
    Processing helix  chain 'A' and resid 765 through 769
      removed outlier: 4.005A  pdb=" N   LEU A 769 " --> pdb=" O   LEU A 766 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 784
      removed outlier: 3.583A  pdb=" N   PHE A 776 " --> pdb=" O   TYR A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 815
    Processing helix  chain 'A' and resid 837 through 854
    Processing helix  chain 'A' and resid 876 through 890
    Processing helix  chain 'A' and resid 946 through 950
      removed outlier: 3.788A  pdb=" N   ALA A 950 " --> pdb=" O   SER A 947 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 954 through 958
      removed outlier: 4.052A  pdb=" N   LEU A 958 " --> pdb=" O   ARG A 955 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 965 through 982
    Processing helix  chain 'A' and resid 983 through 988
    Processing helix  chain 'A' and resid 993 through 1017
    Processing helix  chain 'A' and resid 1024 through 1027
    Processing helix  chain 'A' and resid 1028 through 1051
      removed outlier: 4.120A  pdb=" N   PHE A1032 " --> pdb=" O   ASN A1028 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   TYR A1044 " --> pdb=" O   ALA A1040 " (cutoff:3.500A)
      removed outlier: 3.568A  pdb=" N   ASN A1051 " --> pdb=" O   LEU A1047 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1066 through 1082
      removed outlier: 4.323A  pdb=" N   VAL A1070 " --> pdb=" O   PRO A1066 " (cutoff:3.500A)
      removed outlier: 4.022A  pdb=" N   GLN A1071 " --> pdb=" O   SER A1067 " (cutoff:3.500A)
      removed outlier: 3.943A  pdb=" N   TRP A1072 " --> pdb=" O   GLU A1068 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1085 through 1107
      removed outlier: 3.651A  pdb=" N   TYR A1089 " --> pdb=" O   HIS A1085 " (cutoff:3.500A)
      Proline residue:  A1091  - end of helix
      removed outlier: 4.508A  pdb=" N   GLY A1094 " --> pdb=" O   VAL A1090 " (cutoff:3.500A)
      removed outlier: 5.654A  pdb=" N   SER A1095 " --> pdb=" O   PRO A1091 " (cutoff:3.500A)
      removed outlier: 3.658A  pdb=" N   ARG A1105 " --> pdb=" O   THR A1101 " (cutoff:3.500A)
      removed outlier: 3.755A  pdb=" N   LYS A1106 " --> pdb=" O   GLN A1102 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 1108 through 1119
      removed outlier: 3.712A  pdb=" N   ALA A1119 " --> pdb=" O   LEU A1115 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'F' and resid 89 through 90
      removed outlier: 3.756A  pdb=" N   ILE F  90 " --> pdb=" O   ARG E  43 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1
    Processing sheet with id=AA2, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
      removed outlier: 3.523A  pdb=" N   TYR A 744 " --> pdb=" O   LYS A 760 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 21 through 23
      removed outlier: 6.418A  pdb=" N   LEU A 158 " --> pdb=" O   VAL A 170 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   VAL A 160 " --> pdb=" O   TYR A 168 " (cutoff:3.500A)
      removed outlier: 3.540A  pdb=" N   TYR A 168 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 5.715A  pdb=" N   ALA A 167 " --> pdb=" O   VAL A 791 " (cutoff:3.500A)
      removed outlier: 7.471A  pdb=" N   GLU A 793 " --> pdb=" O   ALA A 167 " (cutoff:3.500A)
      removed outlier: 7.582A  pdb=" N   GLN A 169 " --> pdb=" O   GLU A 793 " (cutoff:3.500A)
      removed outlier: 10.472A  pdb=" N   SER A 795 " --> pdb=" O   GLN A 169 " (cutoff:3.500A)
      removed outlier: 14.579A  pdb=" N   CYS A 171 " --> pdb=" O   SER A 795 " (cutoff:3.500A)
      removed outlier: 6.926A  pdb=" N   ARG A 743 " --> pdb=" O   GLN A 794 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 101 through 103
    Processing sheet with id=AA5, first strand: chain 'A' and resid 325 through 327
    Processing sheet with id=AA6, first strand: chain 'A' and resid 561 through 564
    Processing sheet with id=AA7, first strand: chain 'A' and resid 598 through 600
      removed outlier: 6.601A  pdb=" N   SER A 619 " --> pdb=" O   ARG A 819 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 862 through 865
      removed outlier: 3.640A  pdb=" N   VAL A 904 " --> pdb=" O   LYS A 710 " (cutoff:3.500A)
      removed outlier: 4.203A  pdb=" N   ASP A 712 " --> pdb=" O   LYS A 902 " (cutoff:3.500A)
      removed outlier: 6.745A  pdb=" N   LYS A 902 " --> pdb=" O   ASP A 712 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 927 through 930

    467 hydrogen bonds defined for protein.
    1344 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      173 hydrogen bonds
      330 hydrogen bond angles
      0 basepair planarities
      64 basepair parallelities
      97 stacking parallelities
  Total time for adding SS restraints: 6.61

  Time building geometry restraints manager: 3.62 seconds

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

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

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

  Histogram of dihedral angle deviations from ideal:
        0.00 -    35.84: 8266
       35.84 -    71.69: 627
       71.69 -   107.53: 95
      107.53 -   143.38: 5
      143.38 -   179.22: 3
  Dihedral angle restraints: 8996
    sinusoidal: 5775
      harmonic: 3221
  Sorted by residual:
  dihedral pdb=" O4'   U B  43 "
           pdb=" C1'   U B  43 "
           pdb=" N1    U B  43 "
           pdb=" C2    U B  43 "
      ideal   model   delta sinusoidal    sigma   weight residual
     232.00   52.78  179.22     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B 133 "
           pdb=" C1'   U B 133 "
           pdb=" N1    U B 133 "
           pdb=" C2    U B 133 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   48.72 -176.72     1      1.70e+01 3.46e-03 6.64e+01
  dihedral pdb=" O4'   U B 291 "
           pdb=" C1'   U B 291 "
           pdb=" N1    U B 291 "
           pdb=" C2    U B 291 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00   40.43 -168.43     1      1.70e+01 3.46e-03 6.58e+01
  ... (remaining 8993 not shown)

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

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

  Histogram of nonbonded interaction distances:
        2.21 -     2.75: 1519
        2.75 -     3.28: 12437
        3.28 -     3.82: 23235
        3.82 -     4.36: 26628
        4.36 -     4.90: 41800
  Nonbonded interactions: 105619
  Sorted by model distance:
  nonbonded pdb=" O   LEU A1079 "
            pdb=" OG1 THR A1083 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" NE  ARG E  78 "
            pdb=" O6    G B 315 "
     model   vdw
     2.221 3.120
  nonbonded pdb=" O2'   G B  71 "
            pdb=" OP1   C B  72 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" O   TYR F  38 "
            pdb=" N   VAL F  40 "
     model   vdw
     2.245 3.120
  nonbonded pdb=" OG  SER A 619 "
            pdb=" O   ASN A 635 "
     model   vdw
     2.261 3.040
  ... (remaining 105614 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.250
  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:          0.450
  Check model and map are aligned:         0.080
  Set scattering table:                    0.110
  Process input model:                     36.840
  Find NCS groups from input model:        0.130
  Set up NCS constraints:                  0.050
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:3.010
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   41.940
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8122
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049  14328  Z= 0.320
  Angle     :  0.743   7.614  20476  Z= 0.460
  Chirality :  0.049   0.567   2496
  Planarity :  0.004   0.041   1776
  Dihedral  : 21.473 179.219   6910
  Min Nonbonded Distance : 2.206

Molprobity Statistics.
  All-atom Clashscore : 7.56
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  4.58 %
    Favored  : 95.33 %
  Rotamer:
    Outliers :  0.10 %
    Allowed  :  1.26 %
    Favored  : 98.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.55 (0.26), residues: 1092
  helix:  0.47 (0.23), residues: 546
  sheet: -0.29 (0.51), residues: 93
  loop : -1.38 (0.29), residues: 453

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

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

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  140 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 139
  time to evaluate  : 1.038 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   63 MET cc_start: 0.9253 (ptt) cc_final: 0.9053 (mmt)
REVERT: E   37 LYS cc_start: 0.5136 (tptp) cc_final: 0.4891 (mptt)
REVERT: E   62 GLU cc_start: 0.9252 (tp30) cc_final: 0.8818 (mm-30)
REVERT: E   80 ILE cc_start: 0.6512 (tt) cc_final: 0.6149 (tp)
  outliers start: 1
  outliers final: 0
  residues processed: 140
  average time/residue: 0.3005
  time to fit residues: 58.6220
Evaluate side-chains
  86 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 86
  time to evaluate  : 1.179 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 110 optimal weight:    7.9990
   chunk 99 optimal weight:    6.9990
   chunk 55 optimal weight:    7.9990
   chunk 33 optimal weight:   10.0000
   chunk 66 optimal weight:    0.8980
   chunk 53 optimal weight:    0.8980
   chunk 102 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0370
   chunk 62 optimal weight:    0.9990
   chunk 76 optimal weight:    5.9990
   chunk 118 optimal weight:    0.8980
   overall best weight:    0.7458

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3926 r_free = 0.3926 target = 0.102794 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 64)----------------|
| r_work = 0.3209 r_free = 0.3209 target = 0.066926 restraints weight = 47452.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3249 r_free = 0.3249 target = 0.068818 restraints weight = 23177.519|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3272 r_free = 0.3272 target = 0.069896 restraints weight = 16123.715|
|-----------------------------------------------------------------------------|
r_work (final): 0.3204
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8130
moved from start:          0.1595

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.040  14328  Z= 0.120
  Angle     :  0.588   9.745  20476  Z= 0.293
  Chirality :  0.034   0.184   2496
  Planarity :  0.004   0.036   1776
  Dihedral  : 22.994 178.583   4769
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 5.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  :  7.45 %
    Favored  : 91.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.17 (0.26), residues: 1092
  helix:  1.06 (0.22), residues: 568
  sheet:  0.09 (0.52), residues: 86
  loop : -1.11 (0.31), residues: 438

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP A 547 
 HIS   0.008   0.001   HIS E  32 
 PHE   0.017   0.001   PHE A  27 
 TYR   0.017   0.001   TYR F  43 
 ARG   0.005   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04497 (  626)
  hydrogen bonds       : angle       4.23160 ( 1674)
  covalent geometry    : bond        0.00247 (14328)
  covalent geometry    : angle       0.58822 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 101
  time to evaluate  : 1.179 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   18 ARG cc_start: 0.7646 (mtm110) cc_final: 0.7119 (ptt-90)
REVERT: E   62 GLU cc_start: 0.9058 (tp30) cc_final: 0.8822 (mm-30)
REVERT: E   76 LYS cc_start: 0.8674 (mmtt) cc_final: 0.7778 (mmmt)
REVERT: A  512 MET cc_start: 0.8921 (mtp) cc_final: 0.8629 (mtp)
REVERT: A  813 MET cc_start: 0.8629 (tmm) cc_final: 0.8178 (tmm)
  outliers start: 10
  outliers final: 1
  residues processed: 107
  average time/residue: 0.2994
  time to fit residues: 45.6198
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 90
  time to evaluate  : 1.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue 1016 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 23 optimal weight:   10.0000
   chunk 71 optimal weight:    6.9990
   chunk 88 optimal weight:    4.9990
   chunk 40 optimal weight:    8.9990
   chunk 120 optimal weight:    0.7980
   chunk 102 optimal weight:    7.9990
   chunk 28 optimal weight:   30.0000
   chunk 57 optimal weight:    0.9990
   chunk 73 optimal weight:    2.9990
   chunk 3 optimal weight:    7.9990
   chunk 101 optimal weight:    1.9990
   overall best weight:    2.3588

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

Flipped N/Q/H residues before XYZ refinement:
A 400 HIS
A 608 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.099566 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 61)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.063161 restraints weight = 48165.445|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 53)----------------|
| r_work = 0.3155 r_free = 0.3155 target = 0.064978 restraints weight = 23700.073|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3179 r_free = 0.3179 target = 0.066052 restraints weight = 16620.055|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8253
moved from start:          0.2235

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.046  14328  Z= 0.169
  Angle     :  0.584   9.361  20476  Z= 0.291
  Chirality :  0.034   0.211   2496
  Planarity :  0.004   0.050   1776
  Dihedral  : 22.932 175.921   4769
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 6.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.12 %
    Favored  : 95.88 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  :  9.76 %
    Favored  : 88.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.52 (0.26), residues: 1092
  helix:  1.36 (0.22), residues: 569
  sheet:  0.12 (0.51), residues: 91
  loop : -0.98 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 581 
 HIS   0.005   0.001   HIS A 482 
 PHE   0.014   0.002   PHE A  47 
 TYR   0.020   0.002   TYR A  18 
 ARG   0.008   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04564 (  626)
  hydrogen bonds       : angle       4.03835 ( 1674)
  covalent geometry    : bond        0.00364 (14328)
  covalent geometry    : angle       0.58410 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 84
  time to evaluate  : 1.326 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   37 LYS cc_start: 0.4206 (tptp) cc_final: 0.3989 (mmtm)
REVERT: E   62 GLU cc_start: 0.9115 (tp30) cc_final: 0.8852 (mm-30)
REVERT: E   78 ARG cc_start: 0.8388 (tpp80) cc_final: 0.8111 (tpp80)
REVERT: E   86 LEU cc_start: 0.8908 (OUTLIER) cc_final: 0.8690 (tp)
REVERT: A  512 MET cc_start: 0.9097 (mtp) cc_final: 0.8870 (mtp)
REVERT: A  813 MET cc_start: 0.8740 (tmm) cc_final: 0.8214 (tmm)
  outliers start: 18
  outliers final: 10
  residues processed: 92
  average time/residue: 0.2444
  time to fit residues: 34.3684
Evaluate side-chains
  89 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 78
  time to evaluate  : 1.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   52 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain E residue   86 LEU
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 78 optimal weight:    5.9990
   chunk 60 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 76 optimal weight:    5.9990
   chunk 26 optimal weight:   20.0000
   chunk 24 optimal weight:    8.9990
   chunk 39 optimal weight:   10.0000
   chunk 96 optimal weight:    0.9990
   chunk 10 optimal weight:    4.9990
   chunk 5 optimal weight:    8.9990
   chunk 92 optimal weight:    2.9990
   overall best weight:    3.1788

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

Flipped N/Q/H residues before XYZ refinement:
A 687 HIS
A 779 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3841 r_free = 0.3841 target = 0.097965 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 65)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.061808 restraints weight = 49252.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3118 r_free = 0.3118 target = 0.063574 restraints weight = 24942.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 46)----------------|
| r_work = 0.3141 r_free = 0.3141 target = 0.064585 restraints weight = 17805.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3072
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8299
moved from start:          0.2810

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.046  14328  Z= 0.211
  Angle     :  0.603   9.920  20476  Z= 0.303
  Chirality :  0.036   0.185   2496
  Planarity :  0.004   0.036   1776
  Dihedral  : 22.950 175.191   4769
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.85 %
    Favored  : 96.15 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 12.17 %
    Favored  : 85.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.58 (0.26), residues: 1092
  helix:  1.42 (0.22), residues: 570
  sheet:  0.14 (0.54), residues: 87
  loop : -0.95 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  60 
 HIS   0.006   0.001   HIS A 482 
 PHE   0.019   0.002   PHE A1021 
 TYR   0.019   0.001   TYR F  43 
 ARG   0.006   0.001   ARG A  48 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04681 (  626)
  hydrogen bonds       : angle       4.08329 ( 1674)
  covalent geometry    : bond        0.00451 (14328)
  covalent geometry    : angle       0.60331 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 82
  time to evaluate  : 1.088 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   38 TYR cc_start: 0.8580 (m-10) cc_final: 0.8281 (m-10)
REVERT: E   62 GLU cc_start: 0.9306 (tp30) cc_final: 0.8983 (mm-30)
REVERT: E   76 LYS cc_start: 0.8740 (mmtt) cc_final: 0.7931 (mmmt)
REVERT: E   78 ARG cc_start: 0.8388 (tpp80) cc_final: 0.8124 (tpp80)
REVERT: A  125 ASN cc_start: 0.7637 (t0) cc_final: 0.7374 (t0)
REVERT: A  512 MET cc_start: 0.9108 (mtp) cc_final: 0.8876 (mtp)
REVERT: A  813 MET cc_start: 0.8789 (tmm) cc_final: 0.8160 (tmm)
REVERT: A 1129 THR cc_start: 0.9399 (OUTLIER) cc_final: 0.9194 (m)
  outliers start: 20
  outliers final: 11
  residues processed: 92
  average time/residue: 0.2352
  time to fit residues: 33.1888
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 79
  time to evaluate  : 1.094 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1129 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 122 optimal weight:    2.9990
   chunk 65 optimal weight:    1.9990
   chunk 123 optimal weight:    4.9990
   chunk 16 optimal weight:    2.9990
   chunk 39 optimal weight:    0.5980
   chunk 118 optimal weight:    0.6980
   chunk 77 optimal weight:    3.9990
   chunk 108 optimal weight:    0.8980
   chunk 125 optimal weight:    0.8980
   chunk 3 optimal weight:    5.9990
   chunk 40 optimal weight:   40.0000
   overall best weight:    1.0182

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3874 r_free = 0.3874 target = 0.099663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3143 r_free = 0.3143 target = 0.064285 restraints weight = 48394.277|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.3186 r_free = 0.3186 target = 0.066171 restraints weight = 23200.763|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3211 r_free = 0.3211 target = 0.067258 restraints weight = 15987.425|
|-----------------------------------------------------------------------------|
r_work (final): 0.3141
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8203
moved from start:          0.2979

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.046  14328  Z= 0.106
  Angle     :  0.525  11.081  20476  Z= 0.261
  Chirality :  0.032   0.183   2496
  Planarity :  0.004   0.036   1776
  Dihedral  : 22.868 174.554   4769
  Min Nonbonded Distance : 2.349

Molprobity Statistics.
  All-atom Clashscore : 5.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 13.22 %
    Favored  : 84.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.94 (0.26), residues: 1092
  helix:  1.73 (0.22), residues: 570
  sheet:  0.32 (0.54), residues: 87
  loop : -0.82 (0.31), residues: 435

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 547 
 HIS   0.003   0.001   HIS A 609 
 PHE   0.027   0.001   PHE A  47 
 TYR   0.013   0.001   TYR F  43 
 ARG   0.005   0.000   ARG A 132 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03833 (  626)
  hydrogen bonds       : angle       3.74796 ( 1674)
  covalent geometry    : bond        0.00221 (14328)
  covalent geometry    : angle       0.52539 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  108 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 88
  time to evaluate  : 1.187 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: F   38 TYR cc_start: 0.8475 (m-10) cc_final: 0.8225 (m-10)
REVERT: F   47 LYS cc_start: 0.8782 (tppt) cc_final: 0.8531 (mptt)
REVERT: E   18 ARG cc_start: 0.7596 (mtm110) cc_final: 0.7282 (ptt-90)
REVERT: E   62 GLU cc_start: 0.9307 (tp30) cc_final: 0.8947 (mm-30)
REVERT: E   76 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8094 (mmmt)
REVERT: E   78 ARG cc_start: 0.8387 (tpp80) cc_final: 0.8098 (tpp80)
REVERT: A  125 ASN cc_start: 0.7652 (t0) cc_final: 0.7379 (t0)
REVERT: A  512 MET cc_start: 0.8994 (mtp) cc_final: 0.8746 (mtp)
REVERT: A  813 MET cc_start: 0.8817 (tmm) cc_final: 0.8181 (tmm)
  outliers start: 20
  outliers final: 9
  residues processed: 102
  average time/residue: 0.2523
  time to fit residues: 39.6180
Evaluate side-chains
  93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 1.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 103 optimal weight:    7.9990
   chunk 121 optimal weight:    0.9990
   chunk 56 optimal weight:    0.9990
   chunk 89 optimal weight:   10.0000
   chunk 107 optimal weight:    5.9990
   chunk 71 optimal weight:    0.9980
   chunk 39 optimal weight:    0.0470
   chunk 50 optimal weight:    6.9990
   chunk 29 optimal weight:   10.0000
   chunk 101 optimal weight:    8.9990
   chunk 3 optimal weight:    8.9990
   overall best weight:    1.8084

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

Flipped N/Q/H residues before XYZ refinement:
F  64 ASN
A 340 GLN
A 827 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3862 r_free = 0.3862 target = 0.099008 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.3125 r_free = 0.3125 target = 0.063442 restraints weight = 48961.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3167 r_free = 0.3167 target = 0.065263 restraints weight = 24169.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 52)----------------|
| r_work = 0.3190 r_free = 0.3190 target = 0.066303 restraints weight = 16944.199|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8250
moved from start:          0.3176

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047  14328  Z= 0.137
  Angle     :  0.541  10.909  20476  Z= 0.269
  Chirality :  0.033   0.188   2496
  Planarity :  0.004   0.031   1776
  Dihedral  : 22.805 174.669   4769
  Min Nonbonded Distance : 2.341

Molprobity Statistics.
  All-atom Clashscore : 6.85
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  1.57 %
    Allowed  : 14.06 %
    Favored  : 84.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.26), residues: 1092
  helix:  1.75 (0.22), residues: 572
  sheet:  0.24 (0.53), residues: 87
  loop : -0.80 (0.31), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A 482 
 PHE   0.013   0.001   PHE A 331 
 TYR   0.013   0.001   TYR F  43 
 ARG   0.002   0.000   ARG A 613 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03987 (  626)
  hydrogen bonds       : angle       3.78150 ( 1674)
  covalent geometry    : bond        0.00292 (14328)
  covalent geometry    : angle       0.54091 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 88
  time to evaluate  : 1.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9273 (tp30) cc_final: 0.8911 (mm-30)
REVERT: E   76 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8028 (mmmt)
REVERT: A  125 ASN cc_start: 0.7636 (t0) cc_final: 0.7420 (t0)
REVERT: A  512 MET cc_start: 0.9032 (mtp) cc_final: 0.8804 (mtp)
REVERT: A  813 MET cc_start: 0.8833 (tmm) cc_final: 0.8177 (tmm)
  outliers start: 15
  outliers final: 13
  residues processed: 95
  average time/residue: 0.2580
  time to fit residues: 37.0984
Evaluate side-chains
  96 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 1.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   64 ASN
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  827 GLN
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 80 optimal weight:    6.9990
   chunk 73 optimal weight:    3.9990
   chunk 20 optimal weight:   30.0000
   chunk 110 optimal weight:    5.9990
   chunk 64 optimal weight:    5.9990
   chunk 94 optimal weight:    1.9990
   chunk 52 optimal weight:   10.0000
   chunk 84 optimal weight:    3.9990
   chunk 57 optimal weight:    2.9990
   chunk 30 optimal weight:    8.9990
   chunk 71 optimal weight:    0.8980
   overall best weight:    2.7788

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

Flipped N/Q/H residues before XYZ refinement:
F  64 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3844 r_free = 0.3844 target = 0.098045 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 72)----------------|
| r_work = 0.3098 r_free = 0.3098 target = 0.062425 restraints weight = 49429.468|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 68)----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.064210 restraints weight = 24694.159|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 62)----------------|
| r_work = 0.3162 r_free = 0.3162 target = 0.065230 restraints weight = 17449.163|
|-----------------------------------------------------------------------------|
r_work (final): 0.3092
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8284
moved from start:          0.3329

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056  14328  Z= 0.183
  Angle     :  0.569  10.285  20476  Z= 0.283
  Chirality :  0.034   0.191   2496
  Planarity :  0.004   0.030   1776
  Dihedral  : 22.810 174.725   4769
  Min Nonbonded Distance : 2.343

Molprobity Statistics.
  All-atom Clashscore : 7.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.94 %
    Favored  : 96.06 %
  Rotamer:
    Outliers :  2.10 %
    Allowed  : 15.01 %
    Favored  : 82.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1092
  helix:  1.68 (0.22), residues: 573
  sheet:  0.10 (0.53), residues: 87
  loop : -0.85 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP A  60 
 HIS   0.004   0.001   HIS A 482 
 PHE   0.020   0.002   PHE A1078 
 TYR   0.012   0.001   TYR F  43 
 ARG   0.002   0.000   ARG A 613 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04240 (  626)
  hydrogen bonds       : angle       3.86310 ( 1674)
  covalent geometry    : bond        0.00394 (14328)
  covalent geometry    : angle       0.56865 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 81
  time to evaluate  : 1.206 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9259 (tp30) cc_final: 0.8888 (mm-30)
REVERT: E   76 LYS cc_start: 0.8628 (mmtt) cc_final: 0.8065 (mmmt)
REVERT: A  125 ASN cc_start: 0.7570 (t0) cc_final: 0.7347 (t0)
REVERT: A  512 MET cc_start: 0.9064 (mtp) cc_final: 0.8836 (mtp)
REVERT: A  813 MET cc_start: 0.8821 (tmm) cc_final: 0.8160 (tmm)
  outliers start: 20
  outliers final: 15
  residues processed: 93
  average time/residue: 0.2572
  time to fit residues: 35.9520
Evaluate side-chains
  93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 78
  time to evaluate  : 1.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   64 ASN
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 97 optimal weight:    7.9990
   chunk 4 optimal weight:    7.9990
   chunk 52 optimal weight:   10.0000
   chunk 10 optimal weight:    9.9990
   chunk 119 optimal weight:    0.9990
   chunk 56 optimal weight:    5.9990
   chunk 79 optimal weight:    2.9990
   chunk 121 optimal weight:    0.6980
   chunk 78 optimal weight:   10.0000
   chunk 26 optimal weight:   20.0000
   chunk 28 optimal weight:   40.0000
   overall best weight:    3.7388

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

Flipped N/Q/H residues before XYZ refinement:
F  64 ASN
A  17 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.096692 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3067 r_free = 0.3067 target = 0.061339 restraints weight = 49957.281|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 49)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.063122 restraints weight = 24312.765|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 57)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.064138 restraints weight = 16969.042|
|-----------------------------------------------------------------------------|
r_work (final): 0.3063
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8310
moved from start:          0.3544

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.060  14328  Z= 0.239
  Angle     :  0.615   9.983  20476  Z= 0.306
  Chirality :  0.036   0.192   2496
  Planarity :  0.004   0.032   1776
  Dihedral  : 22.868 174.428   4769
  Min Nonbonded Distance : 2.353

Molprobity Statistics.
  All-atom Clashscore : 8.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.49 %
    Favored  : 95.51 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 15.84 %
    Favored  : 82.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.66 (0.26), residues: 1092
  helix:  1.52 (0.22), residues: 573
  sheet: -0.12 (0.53), residues: 87
  loop : -0.91 (0.31), residues: 432

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A 482 
 PHE   0.018   0.002   PHE A1078 
 TYR   0.016   0.001   TYR F  43 
 ARG   0.003   0.000   ARG A 672 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04696 (  626)
  hydrogen bonds       : angle       4.02694 ( 1674)
  covalent geometry    : bond        0.00512 (14328)
  covalent geometry    : angle       0.61474 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 76
  time to evaluate  : 1.087 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9272 (tp30) cc_final: 0.8895 (mm-30)
REVERT: E   76 LYS cc_start: 0.8653 (mmtt) cc_final: 0.8177 (mmmt)
REVERT: E   78 ARG cc_start: 0.8518 (tpp-160) cc_final: 0.8255 (tpp-160)
REVERT: A  125 ASN cc_start: 0.7563 (t0) cc_final: 0.7334 (t0)
REVERT: A  813 MET cc_start: 0.8852 (tmm) cc_final: 0.8199 (tmm)
  outliers start: 18
  outliers final: 16
  residues processed: 87
  average time/residue: 0.2719
  time to fit residues: 35.4842
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 1.113 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   64 ASN
Chi-restraints excluded: chain E residue   19 SER
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  788 ASP
Chi-restraints excluded: chain A residue  827 GLN
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue  900 LEU
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Chi-restraints excluded: chain A residue 1107 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 74 optimal weight:    0.1980
   chunk 33 optimal weight:   10.0000
   chunk 45 optimal weight:    9.9990
   chunk 130 optimal weight:    0.4980
   chunk 94 optimal weight:    9.9990
   chunk 90 optimal weight:    3.9990
   chunk 106 optimal weight:    0.8980
   chunk 122 optimal weight:    2.9990
   chunk 107 optimal weight:    3.9990
   chunk 124 optimal weight:    0.0000
   chunk 76 optimal weight:    2.9990
   overall best weight:    0.9186

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

Flipped N/Q/H residues before XYZ refinement:
F  64 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3861 r_free = 0.3861 target = 0.099073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 59)----------------|
| r_work = 0.3127 r_free = 0.3127 target = 0.063549 restraints weight = 48759.688|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 50)----------------|
| r_work = 0.3168 r_free = 0.3168 target = 0.065388 restraints weight = 24150.992|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 48)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.066410 restraints weight = 17004.419|
|-----------------------------------------------------------------------------|
r_work (final): 0.3123
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8249
moved from start:          0.3613

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  14328  Z= 0.105
  Angle     :  0.546  11.037  20476  Z= 0.267
  Chirality :  0.032   0.192   2496
  Planarity :  0.004   0.031   1776
  Dihedral  : 22.789 173.772   4769
  Min Nonbonded Distance : 2.329

Molprobity Statistics.
  All-atom Clashscore : 6.17
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.30 %
    Favored  : 96.70 %
  Rotamer:
    Outliers :  1.99 %
    Allowed  : 16.16 %
    Favored  : 81.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.86 (0.26), residues: 1092
  helix:  1.67 (0.22), residues: 574
  sheet:  0.16 (0.52), residues: 92
  loop : -0.86 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.001   TRP A  60 
 HIS   0.003   0.000   HIS A 609 
 PHE   0.019   0.001   PHE F  66 
 TYR   0.011   0.001   TYR F  43 
 ARG   0.003   0.000   ARG E  18 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03901 (  626)
  hydrogen bonds       : angle       3.79238 ( 1674)
  covalent geometry    : bond        0.00217 (14328)
  covalent geometry    : angle       0.54628 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 81
  time to evaluate  : 1.103 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   62 GLU cc_start: 0.9252 (tp30) cc_final: 0.8976 (mm-30)
REVERT: E   76 LYS cc_start: 0.8662 (mmtt) cc_final: 0.8161 (mmmt)
REVERT: A  125 ASN cc_start: 0.7509 (t0) cc_final: 0.7295 (t0)
REVERT: A  813 MET cc_start: 0.8772 (tmm) cc_final: 0.8102 (tmm)
  outliers start: 19
  outliers final: 13
  residues processed: 91
  average time/residue: 0.2557
  time to fit residues: 34.6837
Evaluate side-chains
  93 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 80
  time to evaluate  : 1.057 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   64 ASN
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  840 LEU
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 24 optimal weight:   10.0000
   chunk 20 optimal weight:   30.0000
   chunk 28 optimal weight:   30.0000
   chunk 95 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 12 optimal weight:    4.9990
   chunk 14 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 118 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 120 optimal weight:    6.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
** F  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  53 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.097119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 62)----------------|
| r_work = 0.3080 r_free = 0.3080 target = 0.061818 restraints weight = 49541.545|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3121 r_free = 0.3121 target = 0.063617 restraints weight = 23949.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 56)----------------|
| r_work = 0.3145 r_free = 0.3145 target = 0.064656 restraints weight = 16703.976|
|-----------------------------------------------------------------------------|
r_work (final): 0.3079
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8292
moved from start:          0.3748

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051  14328  Z= 0.197
  Angle     :  0.587  10.245  20476  Z= 0.290
  Chirality :  0.035   0.191   2496
  Planarity :  0.004   0.030   1776
  Dihedral  : 22.785 174.241   4769
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.30 %
    Favored  : 95.70 %
  Rotamer:
    Outliers :  1.78 %
    Allowed  : 16.68 %
    Favored  : 81.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.75 (0.26), residues: 1092
  helix:  1.60 (0.22), residues: 574
  sheet: -0.09 (0.52), residues: 92
  loop : -0.88 (0.31), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A  60 
 HIS   0.005   0.001   HIS A 482 
 PHE   0.016   0.002   PHE A 331 
 TYR   0.016   0.001   TYR F  43 
 ARG   0.003   0.000   ARG A1011 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.04372 (  626)
  hydrogen bonds       : angle       3.91650 ( 1674)
  covalent geometry    : bond        0.00422 (14328)
  covalent geometry    : angle       0.58736 (20476)

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

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

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

  2184 Ramachandran restraints generated.
    1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 77
  time to evaluate  : 1.226 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   18 ARG cc_start: 0.6887 (mtm-85) cc_final: 0.5810 (ptp-110)
REVERT: E   62 GLU cc_start: 0.9295 (tp30) cc_final: 0.8891 (mm-30)
REVERT: E   76 LYS cc_start: 0.8659 (mmtt) cc_final: 0.8174 (mmmt)
REVERT: A  125 ASN cc_start: 0.7669 (t0) cc_final: 0.7436 (t0)
REVERT: A  813 MET cc_start: 0.8846 (tmm) cc_final: 0.8184 (tmm)
  outliers start: 17
  outliers final: 14
  residues processed: 86
  average time/residue: 0.2681
  time to fit residues: 34.4997
Evaluate side-chains
  91 residues out of total 953 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 77
  time to evaluate  : 1.190 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain F residue   41 TYR
Chi-restraints excluded: chain F residue   49 VAL
Chi-restraints excluded: chain F residue   64 ASN
Chi-restraints excluded: chain E residue   56 LEU
Chi-restraints excluded: chain E residue   59 LEU
Chi-restraints excluded: chain E residue   72 ARG
Chi-restraints excluded: chain E residue   77 THR
Chi-restraints excluded: chain E residue   80 ILE
Chi-restraints excluded: chain A residue  127 VAL
Chi-restraints excluded: chain A residue  709 VAL
Chi-restraints excluded: chain A residue  729 ILE
Chi-restraints excluded: chain A residue  898 VAL
Chi-restraints excluded: chain A residue 1016 VAL
Chi-restraints excluded: chain A residue 1090 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 131
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 127 optimal weight:    1.9990
   chunk 96 optimal weight:    0.0060
   chunk 12 optimal weight:    0.0050
   chunk 117 optimal weight:    0.8980
   chunk 53 optimal weight:    0.0470
   chunk 98 optimal weight:    0.2980
   chunk 77 optimal weight:    4.9990
   chunk 23 optimal weight:   10.0000
   chunk 78 optimal weight:    3.9990
   chunk 25 optimal weight:    8.9990
   overall best weight:    0.2508

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

Flipped N/Q/H residues before XYZ refinement:
** F  64 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 666 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3886 r_free = 0.3886 target = 0.100346 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 55)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.065627 restraints weight = 48265.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 55)----------------|
| r_work = 0.3224 r_free = 0.3224 target = 0.067492 restraints weight = 23131.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3248 r_free = 0.3248 target = 0.068585 restraints weight = 15906.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.3179
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8182
moved from start:          0.3873

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.048  14328  Z= 0.097
  Angle     :  0.533  11.555  20476  Z= 0.259
  Chirality :  0.032   0.192   2496
  Planarity :  0.004   0.032   1776
  Dihedral  : 22.641 174.164   4769
  Min Nonbonded Distance : 2.345

Molprobity Statistics.
  All-atom Clashscore : 5.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.56 %
    Favored  : 97.44 %
  Rotamer:
    Outliers :  0.84 %
    Allowed  : 17.52 %
    Favored  : 81.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.67 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.01 (0.26), residues: 1092
  helix:  1.86 (0.22), residues: 571
  sheet:  0.12 (0.52), residues: 92
  loop : -0.84 (0.31), residues: 429

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  60 
 HIS   0.003   0.001   HIS A 534 
 PHE   0.018   0.001   PHE A 776 
 TYR   0.012   0.001   TYR F  43 
 ARG   0.003   0.000   ARG E  78 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03637 (  626)
  hydrogen bonds       : angle       3.67072 ( 1674)
  covalent geometry    : bond        0.00199 (14328)
  covalent geometry    : angle       0.53349 (20476)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4559.85 seconds
wall clock time: 79 minutes 30.52 seconds (4770.52 seconds total)