Starting phenix.real_space_refine
on Fri Oct 23 17:12:02 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9nhc_49408/10_2026/9nhc_49408.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9nhc_49408/10_2026/9nhc_49408.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.6
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9nhc_49408/10_2026/9nhc_49408.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9nhc_49408/10_2026/9nhc_49408.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9nhc_49408/10_2026/9nhc_49408.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9nhc_49408/10_2026/9nhc_49408.cif"
  }
  resolution = 3.6
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.080
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: 7
    Type Number    sf(0)   Gaussians
     Zn      3      6.06       5
     P      52      5.49       5
     Mg      2      5.21       5
     S      49      5.16       5
     C    6442      2.51       5
     N    1796      2.21       5
     O    2087      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 67 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 10431
  Number of models: 1
  Model: ""
    Number of chains: 8
    Chain: "A"
      Number of atoms: 6075
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 753, 6075
          Classifications: {'peptide': 753}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 35, 'TRANS': 717}
          Chain breaks: 1
    Chain: "B"
      Number of atoms: 541
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 25, 541
          Classifications: {'RNA': 25}
          Modifications used: {'p5*END': 1, 'rna2p_pyr': 2, 'rna3p_pur': 14, 'rna3p_pyr': 8}
          Link IDs: {'rna2p': 2, 'rna3p': 22}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
    Chain: "C"
      Number of atoms: 565
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 27, 565
          Classifications: {'RNA': 27}
          Modifications used: {'rna2p_pur': 1, 'rna2p_pyr': 2, 'rna3p_pur': 11, 'rna3p_pyr': 13}
          Link IDs: {'rna2p': 2, 'rna3p': 24}
    Chain: "E"
      Number of atoms: 1215
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 149, 1215
          Classifications: {'peptide': 149}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 12, 'TRANS': 136}
    Chain: "F"
      Number of atoms: 2030
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 253, 2030
          Classifications: {'peptide': 253}
          Link IDs: {'PTRANS': 14, 'TRANS': 238}
          Chain breaks: 4
    Chain: "A"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' MG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "E"
      Number of atoms: 2
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 2
          Unusual residues: {' ZN': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "F"
      Number of atoms: 1
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 1
          Unusual residues: {' ZN': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM   7302  SG  CYS E  16      39.646  31.860  60.521  1.00 49.44           S
  ATOM   7479  SG  CYS E  36      41.411  28.862  61.747  1.00 47.76           S
  ATOM   7575  SG  CYS E  48      37.174  33.729  43.988  1.00 47.12           S
  ATOM   7733  SG  CYS E  68      35.944  37.046  43.967  1.00 51.50           S
  ATOM  10084  SG  CYS F 302      41.609  72.226  40.488  1.00 58.82           S

  Time building chain proxies: 2.52, per 1000 atoms: 0.24
  Number of scatterers: 10431
  At special positions: 0
  Unit cell: (108.29, 94.64, 107.38, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Zn      3     29.99
     S      49     16.00
     P      52     15.00
     Mg      2     11.99
     O    2087      8.00
     N    1796      7.00
     C    6442      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Time building additional restraints: 0.82
  Conformation dependent library (CDL) restraints added in 330.5 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN E 201 "
        pdb="ZN    ZN E 201 " - pdb=" NE2 HIS E  32 "
        pdb="ZN    ZN E 201 " - pdb=" SG  CYS E  16 "
        pdb="ZN    ZN E 201 " - pdb=" SG  CYS E  36 "
        pdb="ZN    ZN E 201 " - pdb=" ND1 HIS E  22 "
      pdb="  ZN E 202 "
        pdb="ZN    ZN E 202 " - pdb=" NE2 HIS E  64 "
        pdb="ZN    ZN E 202 " - pdb=" SG  CYS E  68 "
        pdb="ZN    ZN E 202 " - pdb=" ND1 HIS E  54 "
        pdb="ZN    ZN E 202 " - pdb=" SG  CYS E  48 "
      pdb="  ZN F 501 "
        pdb="ZN    ZN F 501 " - pdb=" SG  CYS F 302 "
        pdb="ZN    ZN F 501 " - pdb=" ND1 HIS F 293 "
      Number of angles added : 2


  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2198

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 12 sheets defined
      38.1% alpha, 19.4% beta
      21 base pairs and 32 stacking pairs defined.
    Time for finding SS restraints: 0.88
  Creating SS restraints...
    Processing helix  chain 'A' and resid 181 through 190
    Processing helix  chain 'A' and resid 191 through 193
      No H-bonds generated for 'chain 'A' and resid 191 through 193'
    Processing helix  chain 'A' and resid 246 through 261
    Processing helix  chain 'A' and resid 317 through 329
    Processing helix  chain 'A' and resid 333 through 342
      removed outlier: 3.689A  pdb=" N   VAL A 342 " --> pdb=" O   LEU A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 379 through 388
    Processing helix  chain 'A' and resid 404 through 409
      removed outlier: 3.975A  pdb=" N   ARG A 409 " --> pdb=" O   PRO A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 419 through 421
      No H-bonds generated for 'chain 'A' and resid 419 through 421'
    Processing helix  chain 'A' and resid 429 through 433
    Processing helix  chain 'A' and resid 435 through 445
    Processing helix  chain 'A' and resid 449 through 467
      removed outlier: 3.707A  pdb=" N   THR A 467 " --> pdb=" O   ARG A 463 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 467 through 477
      removed outlier: 3.627A  pdb=" N   TRP A 477 " --> pdb=" O   GLU A 473 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 515 through 520
      removed outlier: 4.015A  pdb=" N   ARG A 520 " --> pdb=" O   THR A 516 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 541 through 559
      removed outlier: 3.570A  pdb=" N   GLY A 558 " --> pdb=" O   LYS A 554 " (cutoff:3.500A)
      removed outlier: 4.055A  pdb=" N   VAL A 559 " --> pdb=" O   THR A 555 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 575 through 590
      removed outlier: 3.552A  pdb=" N   ALA A 580 " --> pdb=" O   PRO A 576 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 616
      removed outlier: 3.616A  pdb=" N   VAL A 616 " --> pdb=" O   LYS A 612 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 628 through 631
      removed outlier: 3.958A  pdb=" N   SER A 631 " --> pdb=" O   ARG A 628 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 628 through 631'
    Processing helix  chain 'A' and resid 634 through 650
      removed outlier: 3.647A  pdb=" N   ILE A 638 " --> pdb=" O   SER A 634 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 712 through 729
      removed outlier: 3.562A  pdb=" N   ILE A 717 " --> pdb=" O   MET A 713 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   ALA A 718 " --> pdb=" O   GLY A 714 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 746 through 754
    Processing helix  chain 'A' and resid 754 through 767
    Processing helix  chain 'A' and resid 842 through 853
    Processing helix  chain 'A' and resid 867 through 883
    Processing helix  chain 'A' and resid 889 through 893
      removed outlier: 3.829A  pdb=" N   ASN A 893 " --> pdb=" O   TYR A 890 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 26 through 37
      removed outlier: 4.530A  pdb=" N   HIS E  30 " --> pdb=" O   HIS E  26 " (cutoff:3.500A)
      removed outlier: 6.025A  pdb=" N   ILE E  31 " --> pdb=" O   TYR E  27 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 38 through 40
      No H-bonds generated for 'chain 'E' and resid 38 through 40'
    Processing helix  chain 'E' and resid 60 through 65
      removed outlier: 3.536A  pdb=" N   VAL E  65 " --> pdb=" O   LEU E  61 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 66 through 68
      No H-bonds generated for 'chain 'E' and resid 66 through 68'
    Processing helix  chain 'E' and resid 71 through 79
      removed outlier: 4.382A  pdb=" N   GLN E  77 " --> pdb=" O   MET E  73 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 130 through 135
    Processing helix  chain 'E' and resid 137 through 142
    Processing helix  chain 'F' and resid 78 through 110
      removed outlier: 3.906A  pdb=" N   LYS F  90 " --> pdb=" O   GLN F  86 " (cutoff:3.500A)
      removed outlier: 3.898A  pdb=" N   LYS F 107 " --> pdb=" O   ILE F 103 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   ASP F 110 " --> pdb=" O   LEU F 106 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 166 through 178
    Processing helix  chain 'F' and resid 190 through 199
    Processing helix  chain 'F' and resid 221 through 231
    Processing helix  chain 'F' and resid 248 through 260
    Processing helix  chain 'F' and resid 269 through 279
      removed outlier: 4.076A  pdb=" N   ALA F 273 " --> pdb=" O   LYS F 269 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   LEU F 274 " --> pdb=" O   GLU F 270 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 291 through 296
      removed outlier: 3.649A  pdb=" N   LEU F 296 " --> pdb=" O   ARG F 292 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 298 through 301
    Processing helix  chain 'F' and resid 302 through 323
      removed outlier: 4.064A  pdb=" N   ARG F 317 " --> pdb=" O   THR F 313 " (cutoff:3.500A)
      Proline residue:  F 320  - end of helix
    Processing helix  chain 'F' and resid 337 through 341
    Processing sheet with id=AA1, first strand: chain 'A' and resid 696 through 703
      removed outlier: 3.994A  pdb=" N   SER A 681 " --> pdb=" O   HIS A 703 " (cutoff:3.500A)
      removed outlier: 4.385A  pdb=" N   ASP A 674 " --> pdb=" O   SER A 677 " (cutoff:3.500A)
      removed outlier: 8.609A  pdb=" N   GLU A 679 " --> pdb=" O   CYS A 672 " (cutoff:3.500A)
      removed outlier: 10.841A  pdb=" N   CYS A 672 " --> pdb=" O   GLU A 679 " (cutoff:3.500A)
      removed outlier: 10.203A  pdb=" N   SER A 681 " --> pdb=" O   ASP A 670 " (cutoff:3.500A)
      removed outlier: 11.123A  pdb=" N   ASP A 670 " --> pdb=" O   SER A 681 " (cutoff:3.500A)
      removed outlier: 9.740A  pdb=" N   GLY A 683 " --> pdb=" O   GLY A 668 " (cutoff:3.500A)
      removed outlier: 10.832A  pdb=" N   GLY A 668 " --> pdb=" O   GLY A 683 " (cutoff:3.500A)
      removed outlier: 9.558A  pdb=" N   PHE A 685 " --> pdb=" O   VAL A 666 " (cutoff:3.500A)
      removed outlier: 10.582A  pdb=" N   VAL A 666 " --> pdb=" O   PHE A 685 " (cutoff:3.500A)
      removed outlier: 9.572A  pdb=" N   ALA A 687 " --> pdb=" O   LEU A 664 " (cutoff:3.500A)
      removed outlier: 10.757A  pdb=" N   LEU A 664 " --> pdb=" O   ALA A 687 " (cutoff:3.500A)
      removed outlier: 6.364A  pdb=" N   MET A 665 " --> pdb=" O   PHE A 736 " (cutoff:3.500A)
      removed outlier: 7.864A  pdb=" N   TYR A 738 " --> pdb=" O   MET A 665 " (cutoff:3.500A)
      removed outlier: 6.696A  pdb=" N   VAL A 667 " --> pdb=" O   TYR A 738 " (cutoff:3.500A)
      removed outlier: 6.765A  pdb=" N   ILE A 735 " --> pdb=" O   ALA A 774 " (cutoff:3.500A)
      removed outlier: 7.489A  pdb=" N   ILE A 776 " --> pdb=" O   ILE A 735 " (cutoff:3.500A)
      removed outlier: 5.907A  pdb=" N   ILE A 737 " --> pdb=" O   ILE A 776 " (cutoff:3.500A)
      removed outlier: 6.836A  pdb=" N   VAL A 778 " --> pdb=" O   ILE A 737 " (cutoff:3.500A)
      removed outlier: 6.675A  pdb=" N   ARG A 739 " --> pdb=" O   VAL A 778 " (cutoff:3.500A)
      removed outlier: 6.664A  pdb=" N   LEU A 773 " --> pdb=" O   ASP A 837 " (cutoff:3.500A)
      removed outlier: 4.441A  pdb=" N   ASP A 837 " --> pdb=" O   LEU A 773 " (cutoff:3.500A)
      removed outlier: 7.023A  pdb=" N   PHE A 775 " --> pdb=" O   ILE A 835 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   SER A 831 " --> pdb=" O   SER A 779 " (cutoff:3.500A)
      removed outlier: 6.455A  pdb=" N   ASP A 152 " --> pdb=" O   GLN A 789 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   SER A 793 " --> pdb=" O   ARG A 790 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 265 through 267
      removed outlier: 3.717A  pdb=" N   TYR A 271 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 265 through 267
      removed outlier: 3.717A  pdb=" N   TYR A 271 " --> pdb=" O   TYR A 291 " (cutoff:3.500A)
      removed outlier: 5.228A  pdb=" N   LEU A 302 " --> pdb=" O   VAL A 160 " (cutoff:3.500A)
      removed outlier: 6.467A  pdb=" N   LYS A 480 " --> pdb=" O   GLU A 161 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 205 through 208
      removed outlier: 6.186A  pdb=" N   LEU A 168 " --> pdb=" O   GLU A 239 " (cutoff:3.500A)
      removed outlier: 4.738A  pdb=" N   GLU A 239 " --> pdb=" O   LEU A 168 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   GLN A 170 " --> pdb=" O   THR A 237 " (cutoff:3.500A)
      removed outlier: 3.594A  pdb=" N   SER A 221 " --> pdb=" O   MET A 230 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 354 through 356
    Processing sheet with id=AA6, first strand: chain 'A' and resid 369 through 371
    Processing sheet with id=AA7, first strand: chain 'A' and resid 399 through 402
    Processing sheet with id=AA8, first strand: chain 'A' and resid 497 through 498
      removed outlier: 3.554A  pdb=" N   TYR A 506 " --> pdb=" O   ILE A 498 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 569 through 571
      removed outlier: 6.372A  pdb=" N   VAL A 534 " --> pdb=" O   LEU A 596 " (cutoff:3.500A)
      removed outlier: 7.903A  pdb=" N   VAL A 598 " --> pdb=" O   VAL A 534 " (cutoff:3.500A)
      removed outlier: 6.988A  pdb=" N   ILE A 536 " --> pdb=" O   VAL A 598 " (cutoff:3.500A)
      removed outlier: 6.339A  pdb=" N   ILE A 595 " --> pdb=" O   GLN A 623 " (cutoff:3.500A)
      removed outlier: 7.866A  pdb=" N   VAL A 625 " --> pdb=" O   ILE A 595 " (cutoff:3.500A)
      removed outlier: 6.174A  pdb=" N   CYS A 597 " --> pdb=" O   VAL A 625 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'E' and resid 13 through 15
    Processing sheet with id=AB2, first strand: chain 'E' and resid 45 through 47
    Processing sheet with id=AB3, first strand: chain 'F' and resid 148 through 156
      removed outlier: 4.825A  pdb=" N   VAL F 149 " --> pdb=" O   SER F 144 " (cutoff:3.500A)
      removed outlier: 6.609A  pdb=" N   SER F 144 " --> pdb=" O   VAL F 149 " (cutoff:3.500A)
      removed outlier: 6.417A  pdb=" N   ASP F 132 " --> pdb=" O   LYS F 128 " (cutoff:3.500A)
      removed outlier: 5.071A  pdb=" N   LYS F 128 " --> pdb=" O   ASP F 132 " (cutoff:3.500A)
      removed outlier: 6.750A  pdb=" N   LEU F 134 " --> pdb=" O   TYR F 126 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ASN F 124 " --> pdb=" O   GLY F 136 " (cutoff:3.500A)
      removed outlier: 4.657A  pdb=" N   PHE F 138 " --> pdb=" O   ASP F 122 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   ASP F 122 " --> pdb=" O   PHE F 138 " (cutoff:3.500A)
      removed outlier: 4.348A  pdb=" N   VAL F 140 " --> pdb=" O   VAL F 120 " (cutoff:3.500A)
      removed outlier: 6.384A  pdb=" N   VAL F 120 " --> pdb=" O   VAL F 140 " (cutoff:3.500A)
      removed outlier: 4.343A  pdb=" N   GLN F 142 " --> pdb=" O   PHE F 118 " (cutoff:3.500A)
      removed outlier: 6.407A  pdb=" N   PHE F 118 " --> pdb=" O   GLN F 142 " (cutoff:3.500A)
      removed outlier: 6.336A  pdb=" N   MET F 215 " --> pdb=" O   TYR F 246 " (cutoff:3.500A)

    361 hydrogen bonds defined for protein.
    1026 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      51 hydrogen bonds
      102 hydrogen bond angles
      0 basepair planarities
      21 basepair parallelities
      32 stacking parallelities
  Total time for adding SS restraints: 1.63

  Time building geometry restraints manager: 1.10 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 2969
        1.34 -     1.45: 2019
        1.45 -     1.57: 5589
        1.57 -     1.69: 103
        1.69 -     1.81: 75
  Bond restraints: 10755
  Sorted by residual:
  bond pdb=" P   A2M B  25 "
       pdb=" O5' A2M B  25 "
    ideal  model  delta    sigma   weight residual
    1.722  1.593  0.129 2.00e-02 2.50e+03 4.18e+01
  bond pdb=" C4    C C   8 "
       pdb=" N4    C C   8 "
    ideal  model  delta    sigma   weight residual
    1.335  1.301  0.034 9.00e-03 1.23e+04 1.45e+01
  bond pdb=" C   LEU A 412 "
       pdb=" N   PRO A 413 "
    ideal  model  delta    sigma   weight residual
    1.329  1.374 -0.045 1.25e-02 6.40e+03 1.30e+01
  bond pdb=" CB  PRO F 328 "
       pdb=" CG  PRO F 328 "
    ideal  model  delta    sigma   weight residual
    1.492  1.660 -0.168 5.00e-02 4.00e+02 1.13e+01
  bond pdb=" N3    C C   8 "
       pdb=" C4    C C   8 "
    ideal  model  delta    sigma   weight residual
    1.335  1.314  0.021 7.00e-03 2.04e+04 8.59e+00
  ... (remaining 10750 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.79: 14761
        4.79 -     9.57: 40
        9.57 -    14.36: 5
       14.36 -    19.14: 1
       19.14 -    23.93: 1
  Bond angle restraints: 14808
  Sorted by residual:
  angle pdb=" O   LEU A 412 "
        pdb=" C   LEU A 412 "
        pdb=" N   PRO A 413 "
      ideal   model   delta    sigma   weight residual
     120.56   96.63   23.93 1.79e+00 3.12e-01 1.79e+02
  angle pdb=" CA  PRO F 328 "
        pdb=" N   PRO F 328 "
        pdb=" CD  PRO F 328 "
      ideal   model   delta    sigma   weight residual
     112.00   96.22   15.78 1.40e+00 5.10e-01 1.27e+02
  angle pdb=" C3'   C C  24 "
        pdb=" O3'   C C  24 "
        pdb=" P     A C  25 "
      ideal   model   delta    sigma   weight residual
     119.70  107.01   12.69 1.20e+00 6.94e-01 1.12e+02
  angle pdb=" C5    A C   7 "
        pdb=" C6    A C   7 "
        pdb=" N1    A C   7 "
      ideal   model   delta    sigma   weight residual
     117.70  121.30   -3.60 5.00e-01 4.00e+00 5.19e+01
  angle pdb=" C   LEU A 412 "
        pdb=" N   PRO A 413 "
        pdb=" CA  PRO A 413 "
      ideal   model   delta    sigma   weight residual
     120.14  127.59   -7.45 1.06e+00 8.90e-01 4.94e+01
  ... (remaining 14803 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.56: 5709
       17.56 -    35.11: 618
       35.11 -    52.67: 182
       52.67 -    70.22: 78
       70.22 -    87.78: 17
  Dihedral angle restraints: 6604
    sinusoidal: 3203
      harmonic: 3401
  Sorted by residual:
  dihedral pdb=" CA  ILE F 341 "
           pdb=" C   ILE F 341 "
           pdb=" N   LEU F 342 "
           pdb=" CA  LEU F 342 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -154.42  -25.58     0      5.00e+00 4.00e-02 2.62e+01
  dihedral pdb=" CA  LEU A 412 "
           pdb=" C   LEU A 412 "
           pdb=" N   PRO A 413 "
           pdb=" CA  PRO A 413 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.04   22.96     0      5.00e+00 4.00e-02 2.11e+01
  dihedral pdb=" O4'   U B   1 "
           pdb=" C1'   U B   1 "
           pdb=" N1    U B   1 "
           pdb=" C2    U B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -128.00  -73.63  -54.37     1      1.70e+01 3.46e-03 1.39e+01
  ... (remaining 6601 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.131: 1636
       0.131 -    0.263: 65
       0.263 -    0.394: 4
       0.394 -    0.525: 2
       0.525 -    0.656: 1
  Chirality restraints: 1708
  Sorted by residual:
  chirality pdb=" C3' A2M B  25 "
            pdb=" C4' A2M B  25 "
            pdb=" O3' A2M B  25 "
            pdb=" C2' A2M B  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.74   -2.08   -0.66 2.00e-01 2.50e+01 1.08e+01
  chirality pdb=" P     A C  25 "
            pdb=" OP1   A C  25 "
            pdb=" OP2   A C  25 "
            pdb=" O5'   A C  25 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.92   -0.51 2.00e-01 2.50e+01 6.60e+00
  chirality pdb=" P     U B   1 "
            pdb=" OP1   U B   1 "
            pdb=" OP2   U B   1 "
            pdb=" O5'   U B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41    2.87   -0.46 2.00e-01 2.50e+01 5.38e+00
  ... (remaining 1705 not shown)

  Planarity restraints: 1698
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 412 "   -0.113 2.00e-02 2.50e+03   1.95e-01 3.81e+02
        pdb=" C   LEU A 412 "    0.338 2.00e-02 2.50e+03
        pdb=" O   LEU A 412 "   -0.118 2.00e-02 2.50e+03
        pdb=" N   PRO A 413 "   -0.107 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A 355 "    0.104 2.00e-02 2.50e+03   5.73e-02 6.56e+01
        pdb=" CG  TYR A 355 "   -0.031 2.00e-02 2.50e+03
        pdb=" CD1 TYR A 355 "   -0.045 2.00e-02 2.50e+03
        pdb=" CD2 TYR A 355 "   -0.047 2.00e-02 2.50e+03
        pdb=" CE1 TYR A 355 "   -0.036 2.00e-02 2.50e+03
        pdb=" CE2 TYR A 355 "   -0.035 2.00e-02 2.50e+03
        pdb=" CZ  TYR A 355 "    0.003 2.00e-02 2.50e+03
        pdb=" OH  TYR A 355 "    0.087 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR F 246 "   -0.082 2.00e-02 2.50e+03   4.31e-02 3.71e+01
        pdb=" CG  TYR F 246 "    0.036 2.00e-02 2.50e+03
        pdb=" CD1 TYR F 246 "    0.032 2.00e-02 2.50e+03
        pdb=" CD2 TYR F 246 "    0.034 2.00e-02 2.50e+03
        pdb=" CE1 TYR F 246 "    0.020 2.00e-02 2.50e+03
        pdb=" CE2 TYR F 246 "    0.021 2.00e-02 2.50e+03
        pdb=" CZ  TYR F 246 "    0.000 2.00e-02 2.50e+03
        pdb=" OH  TYR F 246 "   -0.062 2.00e-02 2.50e+03
  ... (remaining 1695 not shown)

  Histogram of nonbonded interaction distances:
        1.22 -     1.96: 4
        1.96 -     2.69: 244
        2.69 -     3.43: 14078
        3.43 -     4.16: 24214
        4.16 -     4.90: 42832
  Nonbonded interactions: 81372
  Sorted by model distance:
  nonbonded pdb=" OXT LEU A 899 "
            pdb="MG    MG A 902 "
     model   vdw
     1.221 2.170
  nonbonded pdb=" NE2 GLN A 645 "
            pdb="MG    MG A 902 "
     model   vdw
     1.815 2.250
  nonbonded pdb=" C   LEU A 899 "
            pdb="MG    MG A 902 "
     model   vdw
     1.875 2.400
  nonbonded pdb=" OP1   U C  16 "
            pdb="MG    MG A 901 "
     model   vdw
     1.902 2.170
  nonbonded pdb=" OD2 ASP A 740 "
            pdb="MG    MG A 901 "
     model   vdw
     1.971 2.170
  ... (remaining 81367 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:             2.250
  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:          0.150
  Check model and map are aligned:         0.040
  Set scattering table:                    0.030
  Process input model:                     11.840
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.570
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8398
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      :  0.012   0.682  10765  Z= 0.446
  Angle     :  0.937  23.929  14810  Z= 0.603
  Chirality :  0.063   0.656   1708
  Planarity :  0.008   0.195   1698
  Dihedral  : 16.928  87.781   4406
  Min Nonbonded Distance : 1.221

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.65 %
    Favored  : 95.35 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  : 17.43 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.26), residues: 1139
  helix:  0.62 (0.27), residues: 387
  sheet:  0.77 (0.41), residues: 190
  loop : -0.48 (0.27), residues: 562

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 402 
 TYR   0.104   0.005   TYR A 355 
 PHE   0.051   0.002   PHE A 787 
 TRP   0.005   0.001   TRP A 288 
 HIS   0.004   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00544 /  0.31 (10755)
  covalent geometry    : angle       0.92479 /  0.60 (14808)
  hydrogen bonds       : bond        0.16170 / 10.06 (  407)
  hydrogen bonds       : angle       6.15317 /  4.08 ( 1128)
  metal coordination   : bond        0.34471 / 21.97 (   10)
  metal coordination   : angle      13.17465 /  7.16 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 127
  time to evaluate  : 0.291 
Fit side-chains
   revert: symmetry clash
REVERT: A  483 LYS cc_start: 0.8497 (mmtp) cc_final: 0.8045 (mmmt)
  outliers start: 0
  outliers final: 0
  residues processed: 127
  average time/residue: 0.1056
  time to fit residues: 18.9387
Evaluate side-chains
  111 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 111
  time to evaluate  : 0.381 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [108, 49, 97, 113, 53, 5, 33, 65, 62, 51, 117]
   chunk 108 optimal weight:    4.9990
   chunk 49 optimal weight:    3.9990
   chunk 97 optimal weight:    6.9990
   chunk 113 optimal weight:    4.9990
   chunk 53 optimal weight:    4.9990
   chunk 5 optimal weight:    4.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    0.4980
   chunk 62 optimal weight:    4.9990
   chunk 51 optimal weight:    2.9990
   chunk 117 optimal weight:    4.9990
   overall best weight:    2.6988

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 320 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.137180 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.117167 restraints weight = 13837.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 47)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.120768 restraints weight = 7538.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.123104 restraints weight = 5014.526|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.124551 restraints weight = 3776.089|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.125694 restraints weight = 3101.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8452
moved from start:          0.1022

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.052  10765  Z= 0.280
  Angle     :  0.654   8.188  14810  Z= 0.340
  Chirality :  0.048   0.167   1708
  Planarity :  0.005   0.054   1698
  Dihedral  : 13.614  73.861   2067
  Min Nonbonded Distance : 1.761

Molprobity Statistics.
  All-atom Clashscore : 4.81
  Ramachandran Plot:
    Outliers :  0.09 %
    Allowed  :  5.09 %
    Favored  : 94.82 %
  Rotamer:
    Outliers :  3.26 %
    Allowed  : 18.01 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.25), residues: 1139
  helix:  0.78 (0.27), residues: 392
  sheet:  0.38 (0.37), residues: 208
  loop : -0.57 (0.27), residues: 539

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 572 
 TYR   0.016   0.002   TYR A 245 
 PHE   0.013   0.002   PHE A 787 
 TRP   0.004   0.001   TRP A 533 
 HIS   0.007   0.002   HIS F 293 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00668 /  0.28 (10755)
  covalent geometry    : angle       0.64998 /  0.34 (14808)
  hydrogen bonds       : bond        0.06264 /  4.38 (  407)
  hydrogen bonds       : angle       4.87335 /  3.24 ( 1128)
  metal coordination   : bond        0.02081 /  1.48 (   10)
  metal coordination   : angle       5.95800 /  3.16 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  151 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 117
  time to evaluate  : 0.365 
Fit side-chains
REVERT: A  422 LEU cc_start: 0.8766 (OUTLIER) cc_final: 0.8244 (pp)
REVERT: A  483 LYS cc_start: 0.8519 (mmtp) cc_final: 0.8125 (mmmt)
REVERT: E   34 GLN cc_start: 0.8574 (mp10) cc_final: 0.8357 (mp10)
REVERT: E  145 TYR cc_start: 0.8268 (t80) cc_final: 0.7872 (t80)
REVERT: F  116 GLU cc_start: 0.7247 (mt-10) cc_final: 0.6990 (mt-10)
  outliers start: 34
  outliers final: 22
  residues processed: 141
  average time/residue: 0.0930
  time to fit residues: 19.1638
Evaluate side-chains
  129 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 106
  time to evaluate  : 0.305 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  247 TYR
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  550 ASP
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  215 MET
Chi-restraints excluded: chain F residue  223 ASP
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [28, 98, 104, 69, 9, 31, 112, 111, 11, 77, 22]
   chunk 28 optimal weight:    4.9990
   chunk 98 optimal weight:    2.9990
   chunk 104 optimal weight:    6.9990
   chunk 69 optimal weight:    4.9990
   chunk 9 optimal weight:    0.7980
   chunk 31 optimal weight:    0.8980
   chunk 112 optimal weight:    2.9990
   chunk 111 optimal weight:    0.6980
   chunk 11 optimal weight:    0.8980
   chunk 77 optimal weight:   10.0000
   chunk 22 optimal weight:    6.9990
   overall best weight:    1.2582

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3629 r_free = 0.3629 target = 0.139966 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3367 r_free = 0.3367 target = 0.119965 restraints weight = 13727.017|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3415 r_free = 0.3415 target = 0.123681 restraints weight = 7429.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 51)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.126094 restraints weight = 4891.416|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3466 r_free = 0.3466 target = 0.127673 restraints weight = 3654.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 63)----------------|
| r_work = 0.3481 r_free = 0.3481 target = 0.128786 restraints weight = 2962.298|
|-----------------------------------------------------------------------------|
r_work (final): 0.3492
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8415
moved from start:          0.1119

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031  10765  Z= 0.149
  Angle     :  0.538   7.446  14810  Z= 0.281
  Chirality :  0.044   0.256   1708
  Planarity :  0.004   0.048   1698
  Dihedral  : 13.609  73.866   2067
  Min Nonbonded Distance : 1.861

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.78 %
    Allowed  : 19.44 %
    Favored  : 77.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.23 (0.25), residues: 1139
  helix:  1.02 (0.28), residues: 391
  sheet:  0.46 (0.38), residues: 202
  loop : -0.56 (0.27), residues: 546

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 572 
 TYR   0.012   0.001   TYR A 245 
 PHE   0.010   0.001   PHE A 685 
 TRP   0.003   0.001   TRP A 533 
 HIS   0.005   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00348 /  0.15 (10755)
  covalent geometry    : angle       0.53446 /  0.28 (14808)
  hydrogen bonds       : bond        0.04949 /  3.40 (  407)
  hydrogen bonds       : angle       4.53913 /  2.99 ( 1128)
  metal coordination   : bond        0.00835 /  0.46 (   10)
  metal coordination   : angle       5.47993 /  2.91 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 116
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  339 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7354 (mp0)
REVERT: A  422 LEU cc_start: 0.8731 (OUTLIER) cc_final: 0.8231 (pp)
REVERT: A  708 GLU cc_start: 0.7699 (tp30) cc_final: 0.7456 (tp30)
REVERT: E  145 TYR cc_start: 0.8311 (t80) cc_final: 0.7924 (t80)
REVERT: F  116 GLU cc_start: 0.7217 (mt-10) cc_final: 0.7016 (mt-10)
  outliers start: 29
  outliers final: 18
  residues processed: 134
  average time/residue: 0.0880
  time to fit residues: 17.4477
Evaluate side-chains
  124 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 104
  time to evaluate  : 0.330 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain F residue   77 ILE
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  223 ASP
Chi-restraints excluded: chain F residue  294 GLU
Chi-restraints excluded: chain F residue  336 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [11, 17, 77, 45, 13, 82, 89, 35, 117, 43, 109]
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 45 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 82 optimal weight:    1.9990
   chunk 89 optimal weight:    7.9990
   chunk 35 optimal weight:    3.9990
   chunk 117 optimal weight:    0.7980
   chunk 43 optimal weight:    0.9990
   chunk 109 optimal weight:    0.8980
   overall best weight:    1.3386

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.139521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3362 r_free = 0.3362 target = 0.119519 restraints weight = 13704.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.123232 restraints weight = 7388.053|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.125653 restraints weight = 4873.098|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.127286 restraints weight = 3620.380|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3476 r_free = 0.3476 target = 0.128398 restraints weight = 2915.080|
|-----------------------------------------------------------------------------|
r_work (final): 0.3486
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8418
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032  10765  Z= 0.154
  Angle     :  0.530   7.786  14810  Z= 0.276
  Chirality :  0.044   0.195   1708
  Planarity :  0.004   0.044   1698
  Dihedral  : 13.533  73.803   2067
  Min Nonbonded Distance : 1.841

Molprobity Statistics.
  All-atom Clashscore : 4.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.57 %
    Favored  : 95.43 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.35 %
    Favored  : 76.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.25), residues: 1139
  helix:  1.18 (0.28), residues: 386
  sheet:  0.44 (0.38), residues: 197
  loop : -0.61 (0.26), residues: 556

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 409 
 TYR   0.011   0.001   TYR A 245 
 PHE   0.009   0.001   PHE A 685 
 TRP   0.004   0.001   TRP A 533 
 HIS   0.004   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00364 /  0.15 (10755)
  covalent geometry    : angle       0.52797 /  0.28 (14808)
  hydrogen bonds       : bond        0.04692 /  3.26 (  407)
  hydrogen bonds       : angle       4.38193 /  2.89 ( 1128)
  metal coordination   : bond        0.00493 /  0.32 (   10)
  metal coordination   : angle       4.44696 /  2.35 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 41
    poor density    : 108
  time to evaluate  : 0.381 
Fit side-chains
REVERT: A  339 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7300 (mp0)
REVERT: A  422 LEU cc_start: 0.8783 (OUTLIER) cc_final: 0.8279 (pp)
REVERT: E  145 TYR cc_start: 0.8313 (t80) cc_final: 0.7909 (t80)
REVERT: F  154 HIS cc_start: 0.8242 (OUTLIER) cc_final: 0.7830 (t-90)
  outliers start: 41
  outliers final: 33
  residues processed: 136
  average time/residue: 0.0906
  time to fit residues: 18.3360
Evaluate side-chains
  137 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 36
    poor density    : 101
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  821 ASN
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue   24 VAL
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain F residue   77 ILE
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  154 HIS
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  195 LEU
Chi-restraints excluded: chain F residue  215 MET
Chi-restraints excluded: chain F residue  223 ASP
Chi-restraints excluded: chain F residue  294 GLU
Chi-restraints excluded: chain F residue  319 CYS
Chi-restraints excluded: chain F residue  324 ILE
Chi-restraints excluded: chain F residue  336 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [103, 16, 23, 4, 28, 6, 72, 91, 11, 54, 82]
   chunk 103 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 23 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 28 optimal weight:    0.8980
   chunk 6 optimal weight:    1.9990
   chunk 72 optimal weight:    0.9980
   chunk 91 optimal weight:    6.9990
   chunk 11 optimal weight:    0.7980
   chunk 54 optimal weight:    1.9990
   chunk 82 optimal weight:    5.9990
   overall best weight:    1.3384

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.139418 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.119640 restraints weight = 13674.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3412 r_free = 0.3412 target = 0.123278 restraints weight = 7349.254|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 47)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.125687 restraints weight = 4861.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3463 r_free = 0.3463 target = 0.127264 restraints weight = 3620.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.128372 restraints weight = 2930.371|
|-----------------------------------------------------------------------------|
r_work (final): 0.3487
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8422
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029  10765  Z= 0.150
  Angle     :  0.525   7.731  14810  Z= 0.273
  Chirality :  0.044   0.180   1708
  Planarity :  0.003   0.043   1698
  Dihedral  : 13.393  73.841   2067
  Min Nonbonded Distance : 1.848

Molprobity Statistics.
  All-atom Clashscore : 4.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.13 %
    Favored  : 95.87 %
  Rotamer:
    Outliers :  5.36 %
    Allowed  : 18.77 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.25), residues: 1139
  helix:  1.23 (0.28), residues: 384
  sheet:  0.39 (0.38), residues: 202
  loop : -0.63 (0.26), residues: 553

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 572 
 TYR   0.011   0.001   TYR A 298 
 PHE   0.010   0.001   PHE A 685 
 TRP   0.004   0.001   TRP A 533 
 HIS   0.004   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00356 /  0.15 (10755)
  covalent geometry    : angle       0.52280 /  0.27 (14808)
  hydrogen bonds       : bond        0.04512 /  3.13 (  407)
  hydrogen bonds       : angle       4.29911 /  2.84 ( 1128)
  metal coordination   : bond        0.00468 /  0.29 (   10)
  metal coordination   : angle       4.14589 /  2.19 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  165 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 56
    poor density    : 109
  time to evaluate  : 0.380 
Fit side-chains
REVERT: A  332 ASN cc_start: 0.8275 (m-40) cc_final: 0.7813 (p0)
REVERT: A  339 GLU cc_start: 0.7492 (OUTLIER) cc_final: 0.7260 (mp0)
REVERT: A  422 LEU cc_start: 0.8815 (OUTLIER) cc_final: 0.8323 (pp)
REVERT: A  582 MET cc_start: 0.8700 (tpp) cc_final: 0.8338 (tpt)
REVERT: E  145 TYR cc_start: 0.8300 (t80) cc_final: 0.7915 (t80)
REVERT: F  154 HIS cc_start: 0.8238 (OUTLIER) cc_final: 0.7800 (t-90)
  outliers start: 56
  outliers final: 41
  residues processed: 151
  average time/residue: 0.0868
  time to fit residues: 19.4267
Evaluate side-chains
  147 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 103
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  421 GLU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  673 HIS
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue   24 VAL
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  149 GLU
Chi-restraints excluded: chain F residue   77 ILE
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  154 HIS
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  195 LEU
Chi-restraints excluded: chain F residue  215 MET
Chi-restraints excluded: chain F residue  223 ASP
Chi-restraints excluded: chain F residue  294 GLU
Chi-restraints excluded: chain F residue  324 ILE
Chi-restraints excluded: chain F residue  336 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [111, 19, 46, 42, 4, 64, 90, 12, 35, 15, 78]
   chunk 111 optimal weight:    5.9990
   chunk 19 optimal weight:    1.9990
   chunk 46 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 64 optimal weight:    0.9990
   chunk 90 optimal weight:    8.9990
   chunk 12 optimal weight:    1.9990
   chunk 35 optimal weight:    3.9990
   chunk 15 optimal weight:    2.9990
   chunk 78 optimal weight:   10.0000
   overall best weight:    2.1990

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.140087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.118698 restraints weight = 14116.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.122506 restraints weight = 7567.543|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 45)----------------|
| r_work = 0.3406 r_free = 0.3406 target = 0.125036 restraints weight = 4997.355|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.126748 restraints weight = 3732.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3441 r_free = 0.3441 target = 0.127836 restraints weight = 3008.838|
|-----------------------------------------------------------------------------|
r_work (final): 0.3438
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8491
moved from start:          0.1617

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039  10765  Z= 0.229
  Angle     :  0.592   6.539  14810  Z= 0.305
  Chirality :  0.047   0.435   1708
  Planarity :  0.004   0.044   1698
  Dihedral  : 13.347  73.925   2067
  Min Nonbonded Distance : 1.791

Molprobity Statistics.
  All-atom Clashscore : 5.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.36 %
    Favored  : 94.64 %
  Rotamer:
    Outliers :  5.17 %
    Allowed  : 18.97 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.07 (0.25), residues: 1139
  helix:  1.10 (0.28), residues: 386
  sheet:  0.06 (0.37), residues: 206
  loop : -0.67 (0.26), residues: 547

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.013   0.002   TYR A 872 
 PHE   0.012   0.001   PHE A 787 
 TRP   0.004   0.001   TRP A 533 
 HIS   0.006   0.001   HIS A 855 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00546 /  0.23 (10755)
  covalent geometry    : angle       0.58983 /  0.30 (14808)
  hydrogen bonds       : bond        0.05276 /  3.68 (  407)
  hydrogen bonds       : angle       4.45843 /  2.96 ( 1128)
  metal coordination   : bond        0.00869 /  0.53 (   10)
  metal coordination   : angle       4.07323 /  2.15 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 54
    poor density    : 102
  time to evaluate  : 0.402 
Fit side-chains
REVERT: A  332 ASN cc_start: 0.8254 (m-40) cc_final: 0.7891 (p0)
REVERT: A  339 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7247 (mp0)
REVERT: A  340 ASP cc_start: 0.7884 (OUTLIER) cc_final: 0.7436 (t0)
REVERT: A  422 LEU cc_start: 0.8933 (OUTLIER) cc_final: 0.8459 (pp)
REVERT: E  145 TYR cc_start: 0.8267 (t80) cc_final: 0.7868 (t80)
REVERT: F  154 HIS cc_start: 0.8215 (OUTLIER) cc_final: 0.7718 (t-90)
  outliers start: 54
  outliers final: 42
  residues processed: 142
  average time/residue: 0.0848
  time to fit residues: 17.9983
Evaluate side-chains
  142 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 46
    poor density    : 96
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  317 THR
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  336 ILE
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  421 GLU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  512 THR
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  750 VAL
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  821 ASN
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue   24 VAL
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  149 GLU
Chi-restraints excluded: chain F residue   77 ILE
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  141 THR
Chi-restraints excluded: chain F residue  154 HIS
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  195 LEU
Chi-restraints excluded: chain F residue  215 MET
Chi-restraints excluded: chain F residue  319 CYS
Chi-restraints excluded: chain F residue  324 ILE
Chi-restraints excluded: chain F residue  336 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [42, 1, 86, 5, 77, 64, 73, 62, 67, 45, 31]
   chunk 42 optimal weight:    0.9990
   chunk 1 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   chunk 5 optimal weight:    2.9990
   chunk 77 optimal weight:    9.9990
   chunk 64 optimal weight:    0.7980
   chunk 73 optimal weight:    0.6980
   chunk 62 optimal weight:    1.9990
   chunk 67 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 31 optimal weight:    0.9990
   overall best weight:    0.8986

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 320 GLN
E 135 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3641 r_free = 0.3641 target = 0.143339 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.122396 restraints weight = 13909.861|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.126296 restraints weight = 7263.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3451 r_free = 0.3451 target = 0.128949 restraints weight = 4725.319|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3472 r_free = 0.3472 target = 0.130628 restraints weight = 3465.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.131811 restraints weight = 2783.761|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8435
moved from start:          0.1596

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030  10765  Z= 0.122
  Angle     :  0.522   7.243  14810  Z= 0.271
  Chirality :  0.043   0.290   1708
  Planarity :  0.003   0.049   1698
  Dihedral  : 13.313  73.895   2067
  Min Nonbonded Distance : 1.860

Molprobity Statistics.
  All-atom Clashscore : 5.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  4.89 %
    Allowed  : 19.35 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.26 (0.25), residues: 1139
  helix:  1.23 (0.28), residues: 386
  sheet:  0.23 (0.38), residues: 209
  loop : -0.58 (0.27), residues: 544

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 739 
 TYR   0.011   0.001   TYR E  27 
 PHE   0.009   0.001   PHE A 685 
 TRP   0.004   0.001   TRP A 533 
 HIS   0.003   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 (10755)
  covalent geometry    : angle       0.52007 /  0.27 (14808)
  hydrogen bonds       : bond        0.04300 /  2.96 (  407)
  hydrogen bonds       : angle       4.25767 /  2.80 ( 1128)
  metal coordination   : bond        0.00472 /  0.28 (   10)
  metal coordination   : angle       4.12638 /  2.18 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  154 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 51
    poor density    : 103
  time to evaluate  : 0.331 
Fit side-chains
REVERT: A  230 MET cc_start: 0.8387 (ptp) cc_final: 0.8186 (ptp)
REVERT: A  332 ASN cc_start: 0.8184 (m-40) cc_final: 0.7862 (p0)
REVERT: A  339 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.7268 (mp0)
REVERT: A  340 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7353 (t0)
REVERT: A  422 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8430 (pp)
REVERT: E  145 TYR cc_start: 0.8306 (t80) cc_final: 0.7902 (t80)
REVERT: F  154 HIS cc_start: 0.8280 (OUTLIER) cc_final: 0.7722 (t-90)
REVERT: F  167 MET cc_start: 0.8848 (tpt) cc_final: 0.8647 (tpp)
  outliers start: 51
  outliers final: 36
  residues processed: 140
  average time/residue: 0.0885
  time to fit residues: 18.5440
Evaluate side-chains
  137 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 40
    poor density    : 97
  time to evaluate  : 0.318 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  300 ASP
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  340 ASP
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  464 PHE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  673 HIS
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  821 ASN
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  141 THR
Chi-restraints excluded: chain F residue  154 HIS
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  195 LEU
Chi-restraints excluded: chain F residue  319 CYS
Chi-restraints excluded: chain F residue  324 ILE
Chi-restraints excluded: chain F residue  336 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [69, 1, 79, 19, 46, 56, 0, 3, 97, 32, 89]
   chunk 69 optimal weight:    0.9990
   chunk 1 optimal weight:    2.9990
   chunk 79 optimal weight:    5.9990
   chunk 19 optimal weight:    2.9990
   chunk 46 optimal weight:    4.9990
   chunk 56 optimal weight:    0.0010
   chunk 0 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 97 optimal weight:    7.9990
   chunk 32 optimal weight:    1.9990
   chunk 89 optimal weight:    1.9990
   overall best weight:    1.1392

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3177 r_free = 0.3177 target = 0.110879 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2911 r_free = 0.2911 target = 0.090574 restraints weight = 14045.107|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.093606 restraints weight = 8120.729|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.2983 r_free = 0.2983 target = 0.095707 restraints weight = 5613.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 43)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.097154 restraints weight = 4314.166|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3017 r_free = 0.3017 target = 0.098168 restraints weight = 3574.101|
|-----------------------------------------------------------------------------|
r_work (final): 0.2996
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8369
moved from start:          0.1641

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10765  Z= 0.138
  Angle     :  0.526   7.228  14810  Z= 0.271
  Chirality :  0.044   0.284   1708
  Planarity :  0.003   0.047   1698
  Dihedral  : 13.166  73.817   2067
  Min Nonbonded Distance : 1.850

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.83 %
    Favored  : 95.17 %
  Rotamer:
    Outliers :  4.50 %
    Allowed  : 19.73 %
    Favored  : 75.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.25 (0.26), residues: 1139
  helix:  1.20 (0.28), residues: 388
  sheet:  0.23 (0.38), residues: 209
  loop : -0.57 (0.27), residues: 542

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 589 
 TYR   0.011   0.001   TYR A 872 
 PHE   0.009   0.001   PHE A 685 
 TRP   0.004   0.001   TRP A 533 
 HIS   0.003   0.001   HIS E  30 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00324 /  0.14 (10755)
  covalent geometry    : angle       0.52391 /  0.27 (14808)
  hydrogen bonds       : bond        0.04366 /  3.02 (  407)
  hydrogen bonds       : angle       4.21886 /  2.77 ( 1128)
  metal coordination   : bond        0.00472 /  0.28 (   10)
  metal coordination   : angle       3.82921 /  2.03 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  149 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 47
    poor density    : 102
  time to evaluate  : 0.316 
Fit side-chains
REVERT: A  332 ASN cc_start: 0.8356 (m-40) cc_final: 0.7969 (p0)
REVERT: A  339 GLU cc_start: 0.7694 (OUTLIER) cc_final: 0.7413 (mp0)
REVERT: A  422 LEU cc_start: 0.8837 (OUTLIER) cc_final: 0.8383 (pp)
REVERT: E  145 TYR cc_start: 0.8334 (t80) cc_final: 0.7945 (t80)
REVERT: F  154 HIS cc_start: 0.8231 (OUTLIER) cc_final: 0.7617 (t-90)
  outliers start: 47
  outliers final: 41
  residues processed: 138
  average time/residue: 0.0819
  time to fit residues: 16.9394
Evaluate side-chains
  142 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 44
    poor density    : 98
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  316 ASP
Chi-restraints excluded: chain A residue  321 MET
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  421 GLU
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  476 THR
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  570 VAL
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  673 HIS
Chi-restraints excluded: chain A residue  698 SER
Chi-restraints excluded: chain A residue  751 HIS
Chi-restraints excluded: chain A residue  821 ASN
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue    4 THR
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  149 GLU
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  141 THR
Chi-restraints excluded: chain F residue  154 HIS
Chi-restraints excluded: chain F residue  156 THR
Chi-restraints excluded: chain F residue  164 VAL
Chi-restraints excluded: chain F residue  195 LEU
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  319 CYS
Chi-restraints excluded: chain F residue  324 ILE
Chi-restraints excluded: chain F residue  336 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [18, 3, 94, 79, 112, 83, 2, 47, 40, 31, 86]
   chunk 18 optimal weight:    6.9990
   chunk 3 optimal weight:    0.7980
   chunk 94 optimal weight:    0.8980
   chunk 79 optimal weight:    0.0670
   chunk 112 optimal weight:    3.9990
   chunk 83 optimal weight:    5.9990
   chunk 2 optimal weight:    0.6980
   chunk 47 optimal weight:    1.9990
   chunk 40 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 86 optimal weight:    3.9990
   overall best weight:    0.6718

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3222 r_free = 0.3222 target = 0.114073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2954 r_free = 0.2954 target = 0.093188 restraints weight = 13941.473|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3000 r_free = 0.3000 target = 0.096502 restraints weight = 7732.588|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3030 r_free = 0.3030 target = 0.098760 restraints weight = 5210.817|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3050 r_free = 0.3050 target = 0.100269 restraints weight = 3949.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3066 r_free = 0.3066 target = 0.101451 restraints weight = 3244.730|
|-----------------------------------------------------------------------------|
r_work (final): 0.3029
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8331
moved from start:          0.1670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.027  10765  Z= 0.102
  Angle     :  0.499   7.573  14810  Z= 0.257
  Chirality :  0.042   0.260   1708
  Planarity :  0.003   0.043   1698
  Dihedral  : 13.161  73.778   2067
  Min Nonbonded Distance : 1.883

Molprobity Statistics.
  All-atom Clashscore : 5.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.78 %
    Favored  : 96.22 %
  Rotamer:
    Outliers :  4.02 %
    Allowed  : 20.40 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.37 (0.26), residues: 1139
  helix:  1.27 (0.28), residues: 392
  sheet:  0.41 (0.38), residues: 207
  loop : -0.53 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 589 
 TYR   0.011   0.001   TYR E  27 
 PHE   0.009   0.001   PHE A 685 
 TRP   0.004   0.001   TRP A 533 
 HIS   0.003   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00234 /  0.10 (10755)
  covalent geometry    : angle       0.49734 /  0.26 (14808)
  hydrogen bonds       : bond        0.03819 /  2.63 (  407)
  hydrogen bonds       : angle       4.08088 /  2.66 ( 1128)
  metal coordination   : bond        0.00629 /  0.33 (   10)
  metal coordination   : angle       3.61046 /  1.92 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 42
    poor density    : 103
  time to evaluate  : 0.305 
Fit side-chains
REVERT: A  332 ASN cc_start: 0.8334 (m-40) cc_final: 0.8008 (p0)
REVERT: A  339 GLU cc_start: 0.7556 (OUTLIER) cc_final: 0.7262 (mp0)
REVERT: A  391 ILE cc_start: 0.7798 (mm) cc_final: 0.7516 (mm)
REVERT: A  422 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.8283 (pp)
REVERT: A  708 GLU cc_start: 0.7680 (tp30) cc_final: 0.7388 (tp30)
REVERT: E   34 GLN cc_start: 0.8464 (mp10) cc_final: 0.8089 (mp10)
REVERT: F  154 HIS cc_start: 0.8218 (OUTLIER) cc_final: 0.7558 (t-90)
  outliers start: 42
  outliers final: 28
  residues processed: 136
  average time/residue: 0.0871
  time to fit residues: 17.7925
Evaluate side-chains
  130 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 99
  time to evaluate  : 0.358 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  673 HIS
Chi-restraints excluded: chain A residue  821 ASN
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  149 GLU
Chi-restraints excluded: chain F residue  141 THR
Chi-restraints excluded: chain F residue  154 HIS
Chi-restraints excluded: chain F residue  195 LEU
Chi-restraints excluded: chain F residue  215 MET
Chi-restraints excluded: chain F residue  281 LEU
Chi-restraints excluded: chain F residue  319 CYS
Chi-restraints excluded: chain F residue  336 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [114, 84, 45, 96, 85, 80, 48, 59, 94, 4, 61]
   chunk 114 optimal weight:    0.5980
   chunk 84 optimal weight:    5.9990
   chunk 45 optimal weight:    0.0870
   chunk 96 optimal weight:    7.9990
   chunk 85 optimal weight:    8.9990
   chunk 80 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9980
   chunk 59 optimal weight:    3.9990
   chunk 94 optimal weight:    3.9990
   chunk 4 optimal weight:    2.9990
   chunk 61 optimal weight:    0.8980
   overall best weight:    0.9160

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3217 r_free = 0.3217 target = 0.113667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2946 r_free = 0.2946 target = 0.092772 restraints weight = 13912.179|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.096009 restraints weight = 7767.443|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3022 r_free = 0.3022 target = 0.098340 restraints weight = 5259.171|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3041 r_free = 0.3041 target = 0.099764 restraints weight = 3977.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 48)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.100936 restraints weight = 3275.739|
|-----------------------------------------------------------------------------|
r_work (final): 0.3020
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.1692

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027  10765  Z= 0.119
  Angle     :  0.519   9.701  14810  Z= 0.264
  Chirality :  0.043   0.266   1708
  Planarity :  0.003   0.043   1698
  Dihedral  : 13.114  73.778   2067
  Min Nonbonded Distance : 1.862

Molprobity Statistics.
  All-atom Clashscore : 5.25
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 20.88 %
    Favored  : 75.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.36 (0.26), residues: 1139
  helix:  1.27 (0.28), residues: 392
  sheet:  0.40 (0.39), residues: 207
  loop : -0.54 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.010   0.001   TYR A 298 
 PHE   0.008   0.001   PHE A 685 
 TRP   0.005   0.001   TRP A 533 
 HIS   0.004   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00281 /  0.12 (10755)
  covalent geometry    : angle       0.51773 /  0.26 (14808)
  hydrogen bonds       : bond        0.03963 /  2.74 (  407)
  hydrogen bonds       : angle       4.08659 /  2.67 ( 1128)
  metal coordination   : bond        0.00527 /  0.29 (   10)
  metal coordination   : angle       3.47046 /  1.84 (    2)

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

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

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2278 Ramachandran restraints generated.
    1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 37
    poor density    : 101
  time to evaluate  : 0.362 
Fit side-chains
REVERT: A  332 ASN cc_start: 0.8324 (m-40) cc_final: 0.8006 (p0)
REVERT: A  339 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7238 (mp0)
REVERT: A  391 ILE cc_start: 0.7804 (mm) cc_final: 0.7519 (mm)
REVERT: A  422 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8283 (pp)
REVERT: F  154 HIS cc_start: 0.8219 (OUTLIER) cc_final: 0.7578 (t-90)
  outliers start: 37
  outliers final: 31
  residues processed: 128
  average time/residue: 0.0921
  time to fit residues: 17.5572
Evaluate side-chains
  131 residues out of total 1044 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 97
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  146 THR
Chi-restraints excluded: chain A residue  149 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  225 THR
Chi-restraints excluded: chain A residue  266 LEU
Chi-restraints excluded: chain A residue  282 GLU
Chi-restraints excluded: chain A residue  293 THR
Chi-restraints excluded: chain A residue  294 THR
Chi-restraints excluded: chain A residue  306 THR
Chi-restraints excluded: chain A residue  315 MET
Chi-restraints excluded: chain A residue  339 GLU
Chi-restraints excluded: chain A residue  341 VAL
Chi-restraints excluded: chain A residue  348 THR
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  422 LEU
Chi-restraints excluded: chain A residue  454 ILE
Chi-restraints excluded: chain A residue  470 VAL
Chi-restraints excluded: chain A residue  527 ILE
Chi-restraints excluded: chain A residue  664 LEU
Chi-restraints excluded: chain A residue  665 MET
Chi-restraints excluded: chain A residue  821 ASN
Chi-restraints excluded: chain A residue  827 ILE
Chi-restraints excluded: chain A residue  838 THR
Chi-restraints excluded: chain E residue    3 VAL
Chi-restraints excluded: chain E residue   73 MET
Chi-restraints excluded: chain E residue   97 LEU
Chi-restraints excluded: chain E residue  149 GLU
Chi-restraints excluded: chain F residue  108 VAL
Chi-restraints excluded: chain F residue  141 THR
Chi-restraints excluded: chain F residue  154 HIS
Chi-restraints excluded: chain F residue  164 VAL
Chi-restraints excluded: chain F residue  215 MET
Chi-restraints excluded: chain F residue  319 CYS
Chi-restraints excluded: chain F residue  336 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 118
   random chunks: [29, 69, 45, 53, 58, 67, 35, 19, 63, 10, 4]
   chunk 29 optimal weight:    5.9990
   chunk 69 optimal weight:    1.9990
   chunk 45 optimal weight:    0.7980
   chunk 53 optimal weight:    4.9990
   chunk 58 optimal weight:    1.9990
   chunk 67 optimal weight:    2.9990
   chunk 35 optimal weight:    3.9990
   chunk 19 optimal weight:    3.9990
   chunk 63 optimal weight:    0.0170
   chunk 10 optimal weight:    0.9980
   chunk 4 optimal weight:    2.9990
   overall best weight:    1.1622

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
E 135 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3173 r_free = 0.3173 target = 0.110492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2919 r_free = 0.2919 target = 0.091211 restraints weight = 13924.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.2960 r_free = 0.2960 target = 0.094170 restraints weight = 7864.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.096222 restraints weight = 5304.818|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3007 r_free = 0.3007 target = 0.097580 restraints weight = 4018.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.098550 restraints weight = 3289.205|
|-----------------------------------------------------------------------------|
r_work (final): 0.3018
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8356
moved from start:          0.1722

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028  10765  Z= 0.135
  Angle     :  0.528   8.973  14810  Z= 0.269
  Chirality :  0.043   0.269   1708
  Planarity :  0.003   0.042   1698
  Dihedral  : 13.116  73.805   2067
  Min Nonbonded Distance : 1.842

Molprobity Statistics.
  All-atom Clashscore : 5.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.48 %
    Favored  : 95.52 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 20.79 %
    Favored  : 75.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.33 (0.26), residues: 1139
  helix:  1.26 (0.27), residues: 392
  sheet:  0.34 (0.38), residues: 207
  loop : -0.56 (0.27), residues: 540

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 739 
 TYR   0.010   0.001   TYR A 298 
 PHE   0.008   0.001   PHE A 685 
 TRP   0.005   0.001   TRP A 533 
 HIS   0.004   0.001   HIS A 673 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00321 /  0.14 (10755)
  covalent geometry    : angle       0.52637 /  0.27 (14808)
  hydrogen bonds       : bond        0.04128 /  2.87 (  407)
  hydrogen bonds       : angle       4.10827 /  2.69 ( 1128)
  metal coordination   : bond        0.00432 /  0.26 (   10)
  metal coordination   : angle       3.56360 /  1.88 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1549.75 seconds
wall clock time: 27 minutes 37.33 seconds (1657.33 seconds total)