Starting phenix.real_space_refine
on Sun Jul 27 22:03:46 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8d96_27256/07_2025/8d96_27256.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8d96_27256/07_2025/8d96_27256.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.35
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2025/8d96_27256.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2025/8d96_27256.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2025/8d96_27256.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8d96_27256/07_2025/8d96_27256.cif"
  }
  resolution = 3.35
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.020
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
     Fe      4      7.16       5
     P      35      5.49       5
     Mg      1      5.21       5
     S      55      5.16       5
     C    5782      2.51       5
     N    1567      2.21       5
     O    1759      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 19 residue(s): 0.02s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 9203
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "B"
      Number of atoms: 1525
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 187, 1525
          Classifications: {'peptide': 187}
          Link IDs: {'PTRANS': 10, 'TRANS': 176}
    Chain: "C"
      Number of atoms: 6988
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 869, 6988
          Classifications: {'peptide': 869}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 1, 'PTRANS': 42, 'TRANS': 825}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 3
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "E"
      Number of atoms: 264
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 12, 264
          Unusual residues: {'GTP': 1}
          Classifications: {'DNA': 3, 'RNA': 8, 'undetermined': 1}
          Modifications used: {'rna2p_pur': 1, 'rna3p_pur': 4, 'rna3p_pyr': 3}
          Link IDs: {'rna2p': 1, 'rna3p': 9, None: 1}
            Not linked:
              pdbres="GTP E   1 "
              pdbres="  G E   2 "
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 1
          Unresolved non-hydrogen chiralities: 1
    Chain: "F"
      Number of atoms: 387
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 19, 387
          Classifications: {'DNA': 19}
          Modifications used: {'5*END': 1}
          Link IDs: {'rna3p': 18}
    Chain: "B"
      Number of atoms: 9
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 9
          Unusual residues: {' MG': 1, 'SF4': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
    Chain: "C"
      Number of atoms: 30
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 30
          Unusual residues: {'DTP': 1}
          Classifications: {'undetermined': 1}

List of CYS excluded from plausible disulfide bonds:
  (reason: may participate in coordination)
  ATOM    810  SG  CYS B 367      70.443  91.366 103.166  1.00166.89           S
  ATOM    938  SG  CYS B 384      64.388  91.569 104.702  1.00238.63           S
  ATOM   1254  SG  CYS B 424      69.032  91.059 109.234  1.00264.10           S
  ATOM    139  SG  CYS B 287      67.225  85.996 105.788  1.00209.78           S

  Time building chain proxies: 6.33, per 1000 atoms: 0.69
  Number of scatterers: 9203
  At special positions: 0
  Unit cell: (95.2, 112, 132.16, 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)
     Fe      4     26.01
     S      55     16.00
     P      35     15.00
     Mg      1     11.99
     O    1759      8.00
     N    1567      7.00
     C    5782      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=2, symmetry=0
  Number of additional bonds: simple=2, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 2.32
  Conformation dependent library (CDL) restraints added in 1.1 seconds
  
  Dynamic metal coordination
    Iron sulfur cluster coordination
      pdb=" SF4 B 601 "
        pdb="FE3  SF4 B 601 " - pdb=" SG  CYS B 424 "
        pdb="FE1  SF4 B 601 " - pdb=" SG  CYS B 367 "
        pdb="FE2  SF4 B 601 " - pdb=" SG  CYS B 384 "
        pdb="FE4  SF4 B 601 " - pdb=" SG  CYS B 287 "
      Number of angles added : 12


  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  2004

  Finding SS restraints...
    Secondary structure from input PDB file:
      43 helices and 7 sheets defined
      50.1% alpha, 16.2% beta
      2 base pairs and 21 stacking pairs defined.
    Time for finding SS restraints: 2.64
  Creating SS restraints...
    Processing helix  chain 'B' and resid 275 through 283
    Processing helix  chain 'B' and resid 285 through 299
    Processing helix  chain 'B' and resid 302 through 317
      removed outlier: 3.523A  pdb=" N   GLY B 317 " --> pdb=" O   LEU B 313 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 319 through 334
    Processing helix  chain 'B' and resid 337 through 345
    Processing helix  chain 'B' and resid 345 through 353
    Processing helix  chain 'B' and resid 366 through 373
    Processing helix  chain 'B' and resid 390 through 401
      removed outlier: 3.929A  pdb=" N   GLN B 396 " --> pdb=" O   GLU B 392 " (cutoff:3.500A)
    Processing helix  chain 'B' and resid 404 through 417
    Processing helix  chain 'B' and resid 420 through 432
    Processing helix  chain 'B' and resid 443 through 456
    Processing helix  chain 'C' and resid 409 through 420
    Processing helix  chain 'C' and resid 420 through 426
    Processing helix  chain 'C' and resid 482 through 492
    Processing helix  chain 'C' and resid 522 through 524
      No H-bonds generated for 'chain 'C' and resid 522 through 524'
    Processing helix  chain 'C' and resid 597 through 606
    Processing helix  chain 'C' and resid 614 through 630
    Processing helix  chain 'C' and resid 642 through 655
    Processing helix  chain 'C' and resid 658 through 663
      removed outlier: 3.512A  pdb=" N   ILE C 662 " --> pdb=" O   TRP C 659 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 679 through 685
    Processing helix  chain 'C' and resid 693 through 701
    Processing helix  chain 'C' and resid 707 through 716
    Processing helix  chain 'C' and resid 725 through 733
      removed outlier: 3.691A  pdb=" N   GLN C 729 " --> pdb=" O   GLU C 726 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER C 733 " --> pdb=" O   ASN C 730 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 734 through 760
    Processing helix  chain 'C' and resid 760 through 773
      removed outlier: 3.586A  pdb=" N   LEU C 764 " --> pdb=" O   ASN C 760 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 775 through 780
    Processing helix  chain 'C' and resid 784 through 799
    Processing helix  chain 'C' and resid 863 through 873
    Processing helix  chain 'C' and resid 909 through 931
      removed outlier: 4.006A  pdb=" N   LYS C 917 " --> pdb=" O   ARG C 913 " (cutoff:3.500A)
      removed outlier: 3.960A  pdb=" N   LEU C 918 " --> pdb=" O   GLU C 914 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   GLN C 931 " --> pdb=" O   GLN C 927 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 935 through 960
      removed outlier: 3.696A  pdb=" N   MET C 956 " --> pdb=" O   THR C 952 " (cutoff:3.500A)
      removed outlier: 4.410A  pdb=" N   TYR C 957 " --> pdb=" O   ALA C 953 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   GLY C 958 " --> pdb=" O   ASN C 954 " (cutoff:3.500A)
      removed outlier: 3.636A  pdb=" N   LEU C 960 " --> pdb=" O   MET C 956 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 969 through 993
      removed outlier: 3.857A  pdb=" N   ALA C 973 " --> pdb=" O   ALA C 969 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1014 through 1033
      removed outlier: 3.513A  pdb=" N   VAL C1018 " --> pdb=" O   ASN C1014 " (cutoff:3.500A)
      removed outlier: 4.188A  pdb=" N   LEU C1032 " --> pdb=" O   GLU C1028 " (cutoff:3.500A)
      removed outlier: 4.274A  pdb=" N   TYR C1033 " --> pdb=" O   VAL C1029 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1077 through 1081
    Processing helix  chain 'C' and resid 1085 through 1101
    Processing helix  chain 'C' and resid 1104 through 1126
      removed outlier: 3.537A  pdb=" N   ILE C1108 " --> pdb=" O   SER C1104 " (cutoff:3.500A)
      removed outlier: 3.876A  pdb=" N   VAL C1109 " --> pdb=" O   ARG C1105 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   GLU C1110 " --> pdb=" O   ASP C1106 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1129 through 1134
      removed outlier: 3.879A  pdb=" N   GLU C1134 " --> pdb=" O   SER C1131 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1142 through 1146
      removed outlier: 3.784A  pdb=" N   TYR C1146 " --> pdb=" O   PRO C1143 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1152 through 1165
    Processing helix  chain 'C' and resid 1187 through 1190
    Processing helix  chain 'C' and resid 1194 through 1201
      removed outlier: 3.556A  pdb=" N   LEU C1198 " --> pdb=" O   ALA C1194 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   GLN C1199 " --> pdb=" O   PRO C1195 " (cutoff:3.500A)
      removed outlier: 3.914A  pdb=" N   LYS C1200 " --> pdb=" O   GLU C1196 " (cutoff:3.500A)
      removed outlier: 3.737A  pdb=" N   GLN C1201 " --> pdb=" O   GLN C1197 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'C' and resid 1194 through 1201'
    Processing helix  chain 'C' and resid 1207 through 1215
      removed outlier: 3.535A  pdb=" N   TYR C1211 " --> pdb=" O   ASP C1207 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1215 through 1224
      removed outlier: 4.264A  pdb=" N   VAL C1219 " --> pdb=" O   GLN C1215 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 1231 through 1240
    Processing sheet with id=AA1, first strand: chain 'C' and resid 516 through 520
      removed outlier: 9.929A  pdb=" N   VAL C 516 " --> pdb=" O   HIS C 373 " (cutoff:3.500A)
      removed outlier: 7.152A  pdb=" N   SER C 375 " --> pdb=" O   VAL C 516 " (cutoff:3.500A)
      removed outlier: 8.937A  pdb=" N   ALA C 518 " --> pdb=" O   SER C 375 " (cutoff:3.500A)
      removed outlier: 6.715A  pdb=" N   CYS C 377 " --> pdb=" O   ALA C 518 " (cutoff:3.500A)
      removed outlier: 8.205A  pdb=" N   ALA C 520 " --> pdb=" O   CYS C 377 " (cutoff:3.500A)
      removed outlier: 6.274A  pdb=" N   MET C 379 " --> pdb=" O   ALA C 520 " (cutoff:3.500A)
      removed outlier: 3.567A  pdb=" N   THR C 372 " --> pdb=" O   ILE C 367 " (cutoff:3.500A)
      removed outlier: 3.543A  pdb=" N   ILE C 367 " --> pdb=" O   THR C 372 " (cutoff:3.500A)
      removed outlier: 8.484A  pdb=" N   VAL C 358 " --> pdb=" O   GLU C 350 " (cutoff:3.500A)
      removed outlier: 5.274A  pdb=" N   GLU C 350 " --> pdb=" O   VAL C 358 " (cutoff:3.500A)
      removed outlier: 6.646A  pdb=" N   PHE C 360 " --> pdb=" O   ALA C 348 " (cutoff:3.500A)
      removed outlier: 4.337A  pdb=" N   ALA C 348 " --> pdb=" O   PHE C 360 " (cutoff:3.500A)
      removed outlier: 6.955A  pdb=" N   PHE C 362 " --> pdb=" O   LEU C 346 " (cutoff:3.500A)
      removed outlier: 5.396A  pdb=" N   TRP C 366 " --> pdb=" O   HIS C 342 " (cutoff:3.500A)
      removed outlier: 7.054A  pdb=" N   HIS C 342 " --> pdb=" O   TRP C 366 " (cutoff:3.500A)
      removed outlier: 3.841A  pdb=" N   PHE C 341 " --> pdb=" O   VAL C 501 " (cutoff:3.500A)
      removed outlier: 4.177A  pdb=" N   TRP C 498 " --> pdb=" O   ILE C 529 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 431 through 438
      removed outlier: 3.508A  pdb=" N   SER C 450 " --> pdb=" O   LYS C 437 " (cutoff:3.500A)
      removed outlier: 7.570A  pdb=" N   GLU C 451 " --> pdb=" O   PRO C 391 " (cutoff:3.500A)
      removed outlier: 4.186A  pdb=" N   HIS C 475 " --> pdb=" O   LEU C 390 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 609 through 612
      removed outlier: 9.006A  pdb=" N   GLU C 610 " --> pdb=" O   HIS C 582 " (cutoff:3.500A)
      removed outlier: 6.788A  pdb=" N   CYS C 584 " --> pdb=" O   GLU C 610 " (cutoff:3.500A)
      removed outlier: 7.716A  pdb=" N   ALA C 612 " --> pdb=" O   CYS C 584 " (cutoff:3.500A)
      removed outlier: 6.437A  pdb=" N   VAL C 586 " --> pdb=" O   ALA C 612 " (cutoff:3.500A)
      removed outlier: 4.885A  pdb=" N   ILE C 558 " --> pdb=" O   SER C 587 " (cutoff:3.500A)
      removed outlier: 6.962A  pdb=" N   ILE C 558 " --> pdb=" O   MET C 547 " (cutoff:3.500A)
      removed outlier: 8.754A  pdb=" N   MET C 547 " --> pdb=" O   ILE C 558 " (cutoff:3.500A)
      removed outlier: 6.082A  pdb=" N   MET C 560 " --> pdb=" O   LYS C 545 " (cutoff:3.500A)
      removed outlier: 7.601A  pdb=" N   LYS C 545 " --> pdb=" O   MET C 560 " (cutoff:3.500A)
      removed outlier: 5.578A  pdb=" N   ALA C 562 " --> pdb=" O   SER C 543 " (cutoff:3.500A)
      removed outlier: 7.504A  pdb=" N   SER C 543 " --> pdb=" O   ALA C 562 " (cutoff:3.500A)
      removed outlier: 5.320A  pdb=" N   VAL C 564 " --> pdb=" O   ALA C 541 " (cutoff:3.500A)
      removed outlier: 7.304A  pdb=" N   ALA C 541 " --> pdb=" O   VAL C 564 " (cutoff:3.500A)
      removed outlier: 5.574A  pdb=" N   HIS C 566 " --> pdb=" O   VAL C 539 " (cutoff:3.500A)
      removed outlier: 6.456A  pdb=" N   VAL C 539 " --> pdb=" O   HIS C 566 " (cutoff:3.500A)
      removed outlier: 3.502A  pdb=" N   PHE C 542 " --> pdb=" O   VAL C 635 " (cutoff:3.500A)
      removed outlier: 6.169A  pdb=" N   ILE C 634 " --> pdb=" O   CYS C 691 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'C' and resid 850 through 852
      removed outlier: 3.558A  pdb=" N   GLY C 850 " --> pdb=" O   LEU C1049 " (cutoff:3.500A)
      removed outlier: 6.511A  pdb=" N   PHE C1044 " --> pdb=" O   VAL C1060 " (cutoff:3.500A)
      removed outlier: 6.212A  pdb=" N   VAL C1060 " --> pdb=" O   PHE C1044 " (cutoff:3.500A)
      removed outlier: 4.421A  pdb=" N   SER C1046 " --> pdb=" O   LEU C1058 " (cutoff:3.500A)
      removed outlier: 7.184A  pdb=" N   LYS C1054 " --> pdb=" O   LEU C1050 " (cutoff:3.500A)
      removed outlier: 6.725A  pdb=" N   ASN C1067 " --> pdb=" O   THR C1063 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'C' and resid 997 through 1000
      removed outlier: 4.488A  pdb=" N   GLU C 997 " --> pdb=" O   ASN C1009 " (cutoff:3.500A)
      removed outlier: 6.712A  pdb=" N   MET C1007 " --> pdb=" O   ILE C 999 " (cutoff:3.500A)
      removed outlier: 3.545A  pdb=" N   ILE C1008 " --> pdb=" O   LEU C 857 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 1135 through 1138
    Processing sheet with id=AA7, first strand: chain 'C' and resid 1135 through 1138
      removed outlier: 3.686A  pdb=" N   THR C1205 " --> pdb=" O   GLN C1181 " (cutoff:3.500A)

    415 hydrogen bonds defined for protein.
    1188 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      5 hydrogen bonds
      10 hydrogen bond angles
      0 basepair planarities
      2 basepair parallelities
      21 stacking parallelities
  Total time for adding SS restraints: 3.22

  Time building geometry restraints manager: 2.74 seconds

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

  Histogram of bond lengths:
        1.22 -     1.43: 3975
        1.43 -     1.64: 5404
        1.64 -     1.86: 80
        1.86 -     2.07: 0
        2.07 -     2.28: 12
  Bond restraints: 9471
  Sorted by residual:
  bond pdb=" C2  GTP E   1 "
       pdb=" N3  GTP E   1 "
    ideal  model  delta    sigma   weight residual
    1.380  1.329  0.051 2.00e-02 2.50e+03 6.43e+00
  bond pdb=" C8  GTP E   1 "
       pdb=" N7  GTP E   1 "
    ideal  model  delta    sigma   weight residual
    1.350  1.311  0.039 2.00e-02 2.50e+03 3.85e+00
  bond pdb=" C4' GTP E   1 "
       pdb=" O4' GTP E   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.448 -0.038 2.00e-02 2.50e+03 3.57e+00
  bond pdb=" C5  GTP E   1 "
       pdb=" N7  GTP E   1 "
    ideal  model  delta    sigma   weight residual
    1.350  1.387 -0.037 2.00e-02 2.50e+03 3.36e+00
  bond pdb=" O5'   G E   2 "
       pdb=" C5'   G E   2 "
    ideal  model  delta    sigma   weight residual
    1.420  1.447 -0.027 1.50e-02 4.44e+03 3.26e+00
  ... (remaining 9466 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.08: 12776
        2.08 -     4.15: 133
        4.15 -     6.23: 24
        6.23 -     8.31: 6
        8.31 -    10.39: 6
  Bond angle restraints: 12945
  Sorted by residual:
  angle pdb=" O1B GTP E   1 "
        pdb=" PB  GTP E   1 "
        pdb=" O2B GTP E   1 "
      ideal   model   delta    sigma   weight residual
     109.50  119.89  -10.39 3.00e+00 1.11e-01 1.20e+01
  angle pdb=" C2' GTP E   1 "
        pdb=" C3' GTP E   1 "
        pdb=" C4' GTP E   1 "
      ideal   model   delta    sigma   weight residual
     111.00  100.80   10.20 3.00e+00 1.11e-01 1.16e+01
  angle pdb=" C1' GTP E   1 "
        pdb=" C2' GTP E   1 "
        pdb=" C3' GTP E   1 "
      ideal   model   delta    sigma   weight residual
     111.00  100.92   10.08 3.00e+00 1.11e-01 1.13e+01
  angle pdb=" C3'   G E   2 "
        pdb=" O3'   G E   2 "
        pdb=" P     C E   3 "
      ideal   model   delta    sigma   weight residual
     120.20  115.47    4.73 1.50e+00 4.44e-01 9.95e+00
  angle pdb=" CA  MET B 430 "
        pdb=" CB  MET B 430 "
        pdb=" CG  MET B 430 "
      ideal   model   delta    sigma   weight residual
     114.10  120.30   -6.20 2.00e+00 2.50e-01 9.61e+00
  ... (remaining 12940 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    31.27: 5398
       31.27 -    62.53: 282
       62.53 -    93.80: 39
       93.80 -   125.06: 1
      125.06 -   156.33: 3
  Dihedral angle restraints: 5723
    sinusoidal: 2626
      harmonic: 3097
  Sorted by residual:
  dihedral pdb=" C5' GTP E   1 "
           pdb=" O5' GTP E   1 "
           pdb=" PA  GTP E   1 "
           pdb=" O3A GTP E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
      69.27  -87.06  156.33     1      2.00e+01 2.50e-03 4.60e+01
  dihedral pdb=" O3B GTP E   1 "
           pdb=" O3A GTP E   1 "
           pdb=" PB  GTP E   1 "
           pdb=" PA  GTP E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     291.08  154.30  136.78     1      2.00e+01 2.50e-03 4.15e+01
  dihedral pdb=" O5' GTP E   1 "
           pdb=" O3A GTP E   1 "
           pdb=" PA  GTP E   1 "
           pdb=" PB  GTP E   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -85.88   41.35 -127.22     1      2.00e+01 2.50e-03 3.85e+01
  ... (remaining 5720 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.072: 1318
       0.072 -    0.144: 113
       0.144 -    0.217: 4
       0.217 -    0.289: 0
       0.289 -    0.361: 1
  Chirality restraints: 1436
  Sorted by residual:
  chirality pdb=" P     G E   2 "
            pdb=" OP1   G E   2 "
            pdb=" OP2   G E   2 "
            pdb=" O5'   G E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.41   -2.77   -0.36 2.00e-01 2.50e+01 3.26e+00
  chirality pdb=" C3' GTP E   1 "
            pdb=" C2' GTP E   1 "
            pdb=" C4' GTP E   1 "
            pdb=" O3' GTP E   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.47   -2.64    0.17 2.00e-01 2.50e+01 7.47e-01
  chirality pdb=" C3'   G E   2 "
            pdb=" C4'   G E   2 "
            pdb=" O3'   G E   2 "
            pdb=" C2'   G E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.48   -2.65    0.17 2.00e-01 2.50e+01 7.47e-01
  ... (remaining 1433 not shown)

  Planarity restraints: 1533
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE C 642 "    0.007 2.00e-02 2.50e+03   7.37e-03 9.50e-01
        pdb=" CG  PHE C 642 "   -0.017 2.00e-02 2.50e+03
        pdb=" CD1 PHE C 642 "    0.002 2.00e-02 2.50e+03
        pdb=" CD2 PHE C 642 "    0.005 2.00e-02 2.50e+03
        pdb=" CE1 PHE C 642 "    0.003 2.00e-02 2.50e+03
        pdb=" CE2 PHE C 642 "   -0.000 2.00e-02 2.50e+03
        pdb=" CZ  PHE C 642 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   HIS B 443 "    0.016 5.00e-02 4.00e+02   2.41e-02 9.26e-01
        pdb=" N   PRO B 444 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO B 444 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO B 444 "    0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  HIS B 303 "    0.006 2.00e-02 2.50e+03   7.85e-03 9.24e-01
        pdb=" CG  HIS B 303 "   -0.017 2.00e-02 2.50e+03
        pdb=" ND1 HIS B 303 "    0.005 2.00e-02 2.50e+03
        pdb=" CD2 HIS B 303 "    0.006 2.00e-02 2.50e+03
        pdb=" CE1 HIS B 303 "    0.000 2.00e-02 2.50e+03
        pdb=" NE2 HIS B 303 "   -0.000 2.00e-02 2.50e+03
  ... (remaining 1530 not shown)

  Histogram of nonbonded interaction distances:
        1.84 -     2.45: 24
        2.45 -     3.06: 5654
        3.06 -     3.67: 13543
        3.67 -     4.29: 18869
        4.29 -     4.90: 31991
  Nonbonded interactions: 70081
  Sorted by model distance:
  nonbonded pdb=" O   ASP B 361 "
            pdb=" C2   DA F  19 "
     model   vdw
     1.836 3.340
  nonbonded pdb=" OH  TYR B 362 "
            pdb=" OP2  DA F  18 "
     model   vdw
     1.844 3.040
  nonbonded pdb=" OD1 ASN B 348 "
            pdb=" N4   DC F  17 "
     model   vdw
     1.845 3.120
  nonbonded pdb=" NE2 HIS B 300 "
            pdb=" O2G GTP E   1 "
     model   vdw
     2.005 3.120
  nonbonded pdb=" CE1 HIS B 300 "
            pdb=" O2G GTP E   1 "
     model   vdw
     2.009 2.608
  ... (remaining 70076 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.740
  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:          0.320
  Check model and map are aligned:         0.060
  Set scattering table:                    0.080
  Process input model:                     27.520
  Find NCS groups from input model:        0.090
  Set up NCS constraints:                  0.040
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   32.650
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8345
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      :  0.004   0.357   9477  Z= 0.390
  Angle     :  0.599  10.386  12957  Z= 0.303
  Chirality :  0.040   0.361   1436
  Planarity :  0.002   0.024   1533
  Dihedral  : 17.809 156.329   3719
  Min Nonbonded Distance : 1.836

Molprobity Statistics.
  All-atom Clashscore : 7.87
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.49 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  0.11 %
    Allowed  : 12.20 %
    Favored  : 87.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.00 (0.28), residues: 1046
  helix:  2.36 (0.25), residues: 476
  sheet:  0.67 (0.45), residues: 150
  loop :  0.47 (0.33), residues: 420

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP C1160 
 HIS   0.010   0.001   HIS B 303 
 PHE   0.017   0.001   PHE C 642 
 TYR   0.014   0.001   TYR C 596 
 ARG   0.001   0.000   ARG B 296 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.18749 (  416)
  hydrogen bonds       : angle       6.02799 ( 1198)
  metal coordination   : bond        0.00235 (    4)
  metal coordination   : angle       4.49527 (   12)
  covalent geometry    : bond        0.00236 ( 9471)
  covalent geometry    : angle       0.58313 (12945)
  Misc. bond           : bond        0.25439 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 49
  time to evaluate  : 0.956 
Fit side-chains
  outliers start: 1
  outliers final: 0
  residues processed: 49
  average time/residue: 0.2652
  time to fit residues: 17.9900
Evaluate side-chains
  39 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 39
  time to evaluate  : 0.941 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 89 optimal weight:    0.8980
   chunk 80 optimal weight:    0.9980
   chunk 44 optimal weight:    0.9990
   chunk 27 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9990
   chunk 83 optimal weight:    4.9990
   chunk 32 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 61 optimal weight:    4.9990
   chunk 96 optimal weight:    6.9990
   overall best weight:    0.9786

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 308 GLN
B 322 GLN
B 348 ASN
** B 351 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 433 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.061959 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 60)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.041740 restraints weight = 37653.402|
|-----------------------------------------------------------------------------|
r_work (start): 0.2838 rms_B_bonded: 3.97
r_work: 0.2681 rms_B_bonded: 4.57 restraints_weight: 0.5000
r_work (final): 0.2681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start:          0.1215

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.071   9477  Z= 0.129
  Angle     :  0.527   8.879  12957  Z= 0.271
  Chirality :  0.041   0.123   1436
  Planarity :  0.003   0.025   1533
  Dihedral  : 15.762 175.467   1541
  Min Nonbonded Distance : 2.438

Molprobity Statistics.
  All-atom Clashscore : 4.62
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.39 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 11.57 %
    Favored  : 86.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.11 (0.28), residues: 1046
  helix:  2.46 (0.24), residues: 468
  sheet:  1.02 (0.48), residues: 137
  loop :  0.44 (0.33), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 366 
 HIS   0.003   0.001   HIS B 300 
 PHE   0.012   0.001   PHE C 341 
 TYR   0.013   0.001   TYR B 347 
 ARG   0.003   0.000   ARG B 296 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03671 (  416)
  hydrogen bonds       : angle       4.46759 ( 1198)
  metal coordination   : bond        0.00430 (    4)
  metal coordination   : angle       4.37161 (   12)
  covalent geometry    : bond        0.00281 ( 9471)
  covalent geometry    : angle       0.51051 (12945)
  Misc. bond           : bond        0.00374 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 42
  time to evaluate  : 0.986 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  553 HIS cc_start: 0.8561 (OUTLIER) cc_final: 0.7932 (t70)
  outliers start: 19
  outliers final: 8
  residues processed: 58
  average time/residue: 0.2172
  time to fit residues: 18.4758
Evaluate side-chains
  49 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 40
  time to evaluate  : 0.975 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  553 HIS
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1035 LEU
Chi-restraints excluded: chain C residue 1155 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 77 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 89 optimal weight:    0.5980
   chunk 64 optimal weight:    0.8980
   chunk 24 optimal weight:    7.9990
   chunk 72 optimal weight:    0.8980
   chunk 4 optimal weight:    0.8980
   chunk 11 optimal weight:    0.8980
   chunk 75 optimal weight:    5.9990
   chunk 85 optimal weight:    6.9990
   chunk 39 optimal weight:    2.9990
   overall best weight:    0.8380

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.061885 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2892 r_free = 0.2892 target = 0.041645 restraints weight = 37890.434|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 4.01
r_work: 0.2705 rms_B_bonded: 4.61 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.1350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9477  Z= 0.109
  Angle     :  0.496   8.808  12957  Z= 0.252
  Chirality :  0.039   0.122   1436
  Planarity :  0.003   0.028   1533
  Dihedral  : 15.075 142.393   1541
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 4.73
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.29 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 12.83 %
    Favored  : 85.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.28), residues: 1046
  helix:  2.45 (0.24), residues: 467
  sheet:  0.99 (0.47), residues: 138
  loop :  0.49 (0.33), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C1160 
 HIS   0.002   0.000   HIS B 388 
 PHE   0.017   0.001   PHE C 642 
 TYR   0.007   0.001   TYR C 732 
 ARG   0.002   0.000   ARG B 306 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03445 (  416)
  hydrogen bonds       : angle       4.28066 ( 1198)
  metal coordination   : bond        0.00333 (    4)
  metal coordination   : angle       4.48173 (   12)
  covalent geometry    : bond        0.00240 ( 9471)
  covalent geometry    : angle       0.47760 (12945)
  Misc. bond           : bond        0.00232 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.934 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  553 HIS cc_start: 0.8621 (OUTLIER) cc_final: 0.8010 (t70)
REVERT: C  990 MET cc_start: 0.8914 (tmm) cc_final: 0.8684 (tmm)
  outliers start: 14
  outliers final: 9
  residues processed: 51
  average time/residue: 0.2400
  time to fit residues: 17.8415
Evaluate side-chains
  50 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 40
  time to evaluate  : 1.099 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  433 ASN
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  553 HIS
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 66 optimal weight:    4.9990
   chunk 55 optimal weight:    0.3980
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    3.9990
   chunk 61 optimal weight:    5.9990
   chunk 81 optimal weight:    0.6980
   chunk 4 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 50 optimal weight:    0.1980
   chunk 68 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   overall best weight:    0.6180

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3448 r_free = 0.3448 target = 0.062126 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.042056 restraints weight = 37569.741|
|-----------------------------------------------------------------------------|
r_work (start): 0.2876 rms_B_bonded: 3.95
r_work: 0.2718 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2718
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8716
moved from start:          0.1527

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9477  Z= 0.097
  Angle     :  0.484   8.689  12957  Z= 0.244
  Chirality :  0.039   0.122   1436
  Planarity :  0.003   0.030   1533
  Dihedral  : 14.484 107.259   1541
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.01 %
    Favored  : 97.80 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 12.93 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.21 (0.28), residues: 1046
  helix:  2.52 (0.24), residues: 467
  sheet:  1.00 (0.46), residues: 138
  loop :  0.55 (0.33), residues: 441

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C1160 
 HIS   0.002   0.000   HIS B 388 
 PHE   0.018   0.001   PHE C 642 
 TYR   0.006   0.001   TYR C 732 
 ARG   0.003   0.000   ARG C 688 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02997 (  416)
  hydrogen bonds       : angle       4.12301 ( 1198)
  metal coordination   : bond        0.00293 (    4)
  metal coordination   : angle       4.71106 (   12)
  covalent geometry    : bond        0.00208 ( 9471)
  covalent geometry    : angle       0.46263 (12945)
  Misc. bond           : bond        0.00033 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 0.978 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  553 HIS cc_start: 0.8569 (OUTLIER) cc_final: 0.7960 (t70)
REVERT: C  686 CYS cc_start: 0.8863 (OUTLIER) cc_final: 0.8532 (p)
REVERT: C  990 MET cc_start: 0.8900 (tmm) cc_final: 0.8657 (tmm)
  outliers start: 18
  outliers final: 11
  residues processed: 54
  average time/residue: 0.2348
  time to fit residues: 18.2853
Evaluate side-chains
  54 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.969 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  553 HIS
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  686 CYS
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1035 LEU
Chi-restraints excluded: chain C residue 1155 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 54 optimal weight:    0.9990
   chunk 21 optimal weight:    7.9990
   chunk 44 optimal weight:    3.9990
   chunk 53 optimal weight:    0.6980
   chunk 72 optimal weight:    1.9990
   chunk 62 optimal weight:    4.9990
   chunk 30 optimal weight:    5.9990
   chunk 77 optimal weight:    2.9990
   chunk 73 optimal weight:    4.9990
   chunk 61 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   overall best weight:    1.5388

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 396 GLN
** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.060837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.040886 restraints weight = 37270.435|
|-----------------------------------------------------------------------------|
r_work (start): 0.2825 rms_B_bonded: 3.85
r_work: 0.2666 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8795
moved from start:          0.1765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   9477  Z= 0.148
  Angle     :  0.525   9.568  12957  Z= 0.262
  Chirality :  0.040   0.124   1436
  Planarity :  0.003   0.032   1533
  Dihedral  : 14.366 101.960   1541
  Min Nonbonded Distance : 2.195

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.49 %
    Favored  : 97.32 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.25 %
    Favored  : 84.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.12 (0.28), residues: 1046
  helix:  2.48 (0.25), residues: 473
  sheet:  0.92 (0.46), residues: 137
  loop :  0.46 (0.33), residues: 436

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C1160 
 HIS   0.004   0.001   HIS C1154 
 PHE   0.012   0.001   PHE B 447 
 TYR   0.007   0.001   TYR C 452 
 ARG   0.002   0.000   ARG C1167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03705 (  416)
  hydrogen bonds       : angle       4.13997 ( 1198)
  metal coordination   : bond        0.00475 (    4)
  metal coordination   : angle       5.15550 (   12)
  covalent geometry    : bond        0.00342 ( 9471)
  covalent geometry    : angle       0.50077 (12945)
  Misc. bond           : bond        0.00090 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 2.152 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  682 ARG cc_start: 0.8495 (tpt170) cc_final: 0.8122 (mmm-85)
REVERT: C  686 CYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8593 (p)
REVERT: C  990 MET cc_start: 0.8870 (tmm) cc_final: 0.8618 (tmm)
  outliers start: 18
  outliers final: 14
  residues processed: 54
  average time/residue: 0.2317
  time to fit residues: 19.2695
Evaluate side-chains
  56 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 41
  time to evaluate  : 1.050 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  432 HIS
Chi-restraints excluded: chain B residue  433 ASN
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  686 CYS
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1035 LEU
Chi-restraints excluded: chain C residue 1155 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 91 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 62 optimal weight:    1.9990
   chunk 71 optimal weight:    0.9990
   chunk 60 optimal weight:    0.2980
   chunk 105 optimal weight:    4.9990
   chunk 14 optimal weight:   20.0000
   chunk 23 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 67 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.2386

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** B 432 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.060826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2874 r_free = 0.2874 target = 0.040921 restraints weight = 37243.412|
|-----------------------------------------------------------------------------|
r_work (start): 0.2833 rms_B_bonded: 3.85
r_work: 0.2675 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8787
moved from start:          0.1857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   9477  Z= 0.125
  Angle     :  0.509  10.490  12957  Z= 0.253
  Chirality :  0.040   0.127   1436
  Planarity :  0.003   0.034   1533
  Dihedral  : 14.245 100.409   1541
  Min Nonbonded Distance : 2.017

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.29 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.79 %
    Allowed  : 13.56 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.22 (0.28), residues: 1046
  helix:  2.59 (0.24), residues: 467
  sheet:  0.96 (0.46), residues: 137
  loop :  0.49 (0.32), residues: 442

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP C 746 
 HIS   0.002   0.000   HIS C1154 
 PHE   0.012   0.001   PHE C 642 
 TYR   0.006   0.001   TYR C 732 
 ARG   0.002   0.000   ARG C 688 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03335 (  416)
  hydrogen bonds       : angle       4.07079 ( 1198)
  metal coordination   : bond        0.00408 (    4)
  metal coordination   : angle       5.47976 (   12)
  covalent geometry    : bond        0.00287 ( 9471)
  covalent geometry    : angle       0.48089 (12945)
  Misc. bond           : bond        0.00073 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 42
  time to evaluate  : 1.697 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  686 CYS cc_start: 0.8940 (OUTLIER) cc_final: 0.8638 (p)
REVERT: C  990 MET cc_start: 0.8829 (tmm) cc_final: 0.8592 (tmm)
  outliers start: 17
  outliers final: 12
  residues processed: 56
  average time/residue: 0.3397
  time to fit residues: 27.9303
Evaluate side-chains
  55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 1.819 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  686 CYS
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1035 LEU
Chi-restraints excluded: chain C residue 1155 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 51 optimal weight:    0.0050
   chunk 84 optimal weight:    0.7980
   chunk 72 optimal weight:    0.8980
   chunk 8 optimal weight:    7.9990
   chunk 36 optimal weight:    2.9990
   chunk 14 optimal weight:   20.0000
   chunk 20 optimal weight:    2.9990
   chunk 41 optimal weight:    4.9990
   chunk 64 optimal weight:    0.5980
   chunk 76 optimal weight:    0.0570
   chunk 19 optimal weight:    0.9980
   overall best weight:    0.4712

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
B 432 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.061773 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.041818 restraints weight = 38445.024|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 3.97
r_work: 0.2705 rms_B_bonded: 4.56 restraints_weight: 0.5000
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8750
moved from start:          0.1869

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   9477  Z= 0.093
  Angle     :  0.493  10.185  12957  Z= 0.246
  Chirality :  0.039   0.130   1436
  Planarity :  0.003   0.031   1533
  Dihedral  : 14.101  99.716   1541
  Min Nonbonded Distance : 2.021

Molprobity Statistics.
  All-atom Clashscore : 3.80
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.39 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  2.21 %
    Allowed  : 13.25 %
    Favored  : 84.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.34 (0.28), residues: 1046
  helix:  2.62 (0.24), residues: 468
  sheet:  1.05 (0.46), residues: 138
  loop :  0.63 (0.33), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP C1160 
 HIS   0.001   0.000   HIS B 292 
 PHE   0.011   0.001   PHE B 447 
 TYR   0.006   0.001   TYR B 427 
 ARG   0.001   0.000   ARG C 688 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.02848 (  416)
  hydrogen bonds       : angle       3.99162 ( 1198)
  metal coordination   : bond        0.00299 (    4)
  metal coordination   : angle       5.26196 (   12)
  covalent geometry    : bond        0.00200 ( 9471)
  covalent geometry    : angle       0.46646 (12945)
  Misc. bond           : bond        0.00059 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 44
  time to evaluate  : 0.984 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  318 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9143 (tt)
REVERT: B  387 ARG cc_start: 0.9580 (tpt90) cc_final: 0.9312 (tpt90)
REVERT: C  553 HIS cc_start: 0.8519 (OUTLIER) cc_final: 0.7868 (t70)
REVERT: C  686 CYS cc_start: 0.8889 (OUTLIER) cc_final: 0.8600 (p)
REVERT: C  985 MET cc_start: 0.9063 (mmm) cc_final: 0.8837 (tpp)
REVERT: C  990 MET cc_start: 0.8836 (tmm) cc_final: 0.8593 (tmm)
  outliers start: 21
  outliers final: 13
  residues processed: 61
  average time/residue: 0.2641
  time to fit residues: 22.6895
Evaluate side-chains
  57 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 41
  time to evaluate  : 1.044 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  318 LEU
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  402 LYS
Chi-restraints excluded: chain C residue  553 HIS
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  686 CYS
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1035 LEU
Chi-restraints excluded: chain C residue 1155 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 92 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9990
   chunk 16 optimal weight:   20.0000
   chunk 65 optimal weight:    1.9990
   chunk 51 optimal weight:    0.3980
   chunk 98 optimal weight:    4.9990
   chunk 52 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 85 optimal weight:    5.9990
   chunk 42 optimal weight:    1.9990
   chunk 64 optimal weight:    0.6980
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.061355 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2888 r_free = 0.2888 target = 0.041400 restraints weight = 38089.599|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 3.91
r_work: 0.2693 rms_B_bonded: 4.50 restraints_weight: 0.5000
r_work (final): 0.2693
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8769
moved from start:          0.2007

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9477  Z= 0.114
  Angle     :  0.522  10.344  12957  Z= 0.260
  Chirality :  0.040   0.137   1436
  Planarity :  0.003   0.031   1533
  Dihedral  : 14.123  98.985   1541
  Min Nonbonded Distance : 1.951

Molprobity Statistics.
  All-atom Clashscore : 4.40
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.29 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.37 %
    Allowed  : 13.99 %
    Favored  : 84.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.36 (0.28), residues: 1046
  helix:  2.68 (0.24), residues: 468
  sheet:  0.96 (0.46), residues: 138
  loop :  0.63 (0.33), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.001   TRP C1160 
 HIS   0.004   0.000   HIS B 432 
 PHE   0.010   0.001   PHE C 642 
 TYR   0.007   0.001   TYR B 427 
 ARG   0.001   0.000   ARG C1167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03144 (  416)
  hydrogen bonds       : angle       3.94768 ( 1198)
  metal coordination   : bond        0.00353 (    4)
  metal coordination   : angle       5.40885 (   12)
  covalent geometry    : bond        0.00258 ( 9471)
  covalent geometry    : angle       0.49564 (12945)
  Misc. bond           : bond        0.00065 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 42
  time to evaluate  : 1.025 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  307 MET cc_start: 0.9306 (mtp) cc_final: 0.8980 (mtp)
REVERT: B  387 ARG cc_start: 0.9583 (tpt90) cc_final: 0.9275 (tpt90)
REVERT: C  686 CYS cc_start: 0.8904 (OUTLIER) cc_final: 0.8567 (p)
REVERT: C  990 MET cc_start: 0.8816 (tmm) cc_final: 0.8574 (tmm)
  outliers start: 13
  outliers final: 12
  residues processed: 53
  average time/residue: 0.2418
  time to fit residues: 18.1989
Evaluate side-chains
  54 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 41
  time to evaluate  : 0.958 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  402 LYS
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  686 CYS
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1035 LEU
Chi-restraints excluded: chain C residue 1155 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 96 optimal weight:    0.9990
   chunk 79 optimal weight:    0.0970
   chunk 11 optimal weight:   10.0000
   chunk 87 optimal weight:    0.4980
   chunk 99 optimal weight:    1.9990
   chunk 105 optimal weight:    4.9990
   chunk 35 optimal weight:    4.9990
   chunk 69 optimal weight:    2.9990
   chunk 88 optimal weight:    0.8980
   chunk 24 optimal weight:    8.9990
   chunk 14 optimal weight:   20.0000
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.061262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 57)----------------|
| r_work = 0.2876 r_free = 0.2876 target = 0.041158 restraints weight = 37330.757|
|-----------------------------------------------------------------------------|
r_work (start): 0.2849 rms_B_bonded: 3.88
r_work: 0.2692 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2692
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8778
moved from start:          0.2057

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   9477  Z= 0.110
  Angle     :  0.526  10.518  12957  Z= 0.261
  Chirality :  0.040   0.150   1436
  Planarity :  0.003   0.030   1533
  Dihedral  : 14.113  97.701   1541
  Min Nonbonded Distance : 1.954

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.39 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  1.89 %
    Allowed  : 13.04 %
    Favored  : 85.07 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.33 (0.28), residues: 1046
  helix:  2.66 (0.24), residues: 468
  sheet:  0.92 (0.46), residues: 138
  loop :  0.62 (0.33), residues: 440

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP C1160 
 HIS   0.002   0.000   HIS B 432 
 PHE   0.010   0.001   PHE C 642 
 TYR   0.008   0.001   TYR B 427 
 ARG   0.004   0.000   ARG C1167 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03093 (  416)
  hydrogen bonds       : angle       3.96276 ( 1198)
  metal coordination   : bond        0.00424 (    4)
  metal coordination   : angle       5.52302 (   12)
  covalent geometry    : bond        0.00248 ( 9471)
  covalent geometry    : angle       0.49815 (12945)
  Misc. bond           : bond        0.00070 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 41
  time to evaluate  : 1.036 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  307 MET cc_start: 0.9328 (mtp) cc_final: 0.8927 (mtp)
REVERT: B  321 GLU cc_start: 0.9419 (pm20) cc_final: 0.9217 (pm20)
REVERT: B  387 ARG cc_start: 0.9590 (tpt90) cc_final: 0.9335 (tpt90)
REVERT: C  686 CYS cc_start: 0.8882 (OUTLIER) cc_final: 0.8588 (p)
REVERT: C  725 MET cc_start: 0.8923 (ttp) cc_final: 0.8662 (ttt)
REVERT: C  990 MET cc_start: 0.8799 (tmm) cc_final: 0.8562 (tmm)
  outliers start: 18
  outliers final: 13
  residues processed: 56
  average time/residue: 0.2447
  time to fit residues: 19.5758
Evaluate side-chains
  55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 1.025 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain B residue  453 ARG
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  402 LYS
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  686 CYS
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1035 LEU
Chi-restraints excluded: chain C residue 1155 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 72 optimal weight:    1.9990
   chunk 81 optimal weight:    0.8980
   chunk 62 optimal weight:    5.9990
   chunk 90 optimal weight:    3.9990
   chunk 51 optimal weight:    4.9990
   chunk 15 optimal weight:    9.9990
   chunk 35 optimal weight:    3.9990
   chunk 56 optimal weight:    0.0170
   chunk 52 optimal weight:    2.9990
   chunk 86 optimal weight:    5.9990
   chunk 42 optimal weight:    0.8980
   overall best weight:    1.3622

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.060691 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.040709 restraints weight = 37951.515|
|-----------------------------------------------------------------------------|
r_work (start): 0.2799 rms_B_bonded: 3.89
r_work: 0.2637 rms_B_bonded: 4.49 restraints_weight: 0.5000
r_work (final): 0.2637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8752
moved from start:          0.2152

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   9477  Z= 0.137
  Angle     :  0.544  11.032  12957  Z= 0.269
  Chirality :  0.040   0.166   1436
  Planarity :  0.003   0.031   1533
  Dihedral  : 14.169  96.063   1541
  Min Nonbonded Distance : 1.917

Molprobity Statistics.
  All-atom Clashscore : 4.24
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.29 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.47 %
    Allowed  : 13.35 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.19 (0.28), residues: 1046
  helix:  2.59 (0.24), residues: 474
  sheet:  0.61 (0.43), residues: 154
  loop :  0.55 (0.34), residues: 418

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C1160 
 HIS   0.003   0.000   HIS C1154 
 PHE   0.010   0.001   PHE B 447 
 TYR   0.007   0.001   TYR C 457 
 ARG   0.001   0.000   ARG C 650 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03457 (  416)
  hydrogen bonds       : angle       4.00805 ( 1198)
  metal coordination   : bond        0.00531 (    4)
  metal coordination   : angle       5.69880 (   12)
  covalent geometry    : bond        0.00317 ( 9471)
  covalent geometry    : angle       0.51605 (12945)
  Misc. bond           : bond        0.00088 (    2)

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

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

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  2092 Ramachandran restraints generated.
    1046 Oldfield, 0 Emsley, 1046 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 1.037 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: B  307 MET cc_start: 0.9366 (mtp) cc_final: 0.8910 (mtp)
REVERT: B  321 GLU cc_start: 0.9446 (pm20) cc_final: 0.9218 (pm20)
REVERT: B  387 ARG cc_start: 0.9577 (tpt90) cc_final: 0.9293 (tpt90)
REVERT: C  384 GLU cc_start: 0.8820 (OUTLIER) cc_final: 0.8550 (mt-10)
REVERT: C  686 CYS cc_start: 0.8931 (OUTLIER) cc_final: 0.8530 (p)
REVERT: C  725 MET cc_start: 0.8827 (ttp) cc_final: 0.8613 (ttt)
REVERT: C  990 MET cc_start: 0.8863 (tmm) cc_final: 0.8586 (tmm)
  outliers start: 14
  outliers final: 12
  residues processed: 53
  average time/residue: 0.2558
  time to fit residues: 19.2823
Evaluate side-chains
  55 residues out of total 952 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 41
  time to evaluate  : 1.075 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain B residue  374 ASN
Chi-restraints excluded: chain C residue  340 VAL
Chi-restraints excluded: chain C residue  384 GLU
Chi-restraints excluded: chain C residue  394 MET
Chi-restraints excluded: chain C residue  396 ILE
Chi-restraints excluded: chain C residue  402 LYS
Chi-restraints excluded: chain C residue  609 VAL
Chi-restraints excluded: chain C residue  611 VAL
Chi-restraints excluded: chain C residue  635 VAL
Chi-restraints excluded: chain C residue  686 CYS
Chi-restraints excluded: chain C residue  844 VAL
Chi-restraints excluded: chain C residue 1035 LEU
Chi-restraints excluded: chain C residue 1155 VAL
Chi-restraints excluded: chain C residue 1248 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 106
   random chunks:
   chunk 12 optimal weight:    6.9990
   chunk 42 optimal weight:    0.8980
   chunk 30 optimal weight:    4.9990
   chunk 15 optimal weight:    5.9990
   chunk 60 optimal weight:    0.9980
   chunk 11 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 41 optimal weight:    0.6980
   chunk 90 optimal weight:    1.9990
   chunk 78 optimal weight:    1.9990
   chunk 82 optimal weight:    0.9990
   overall best weight:    0.9184

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

Flipped N/Q/H residues before XYZ refinement:
** B 300 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.061029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2871 r_free = 0.2871 target = 0.041051 restraints weight = 37321.946|
|-----------------------------------------------------------------------------|
r_work (start): 0.2818 rms_B_bonded: 3.86
r_work: 0.2656 rms_B_bonded: 4.47 restraints_weight: 0.5000
r_work (final): 0.2656
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.2167

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   9477  Z= 0.110
  Angle     :  0.526  10.915  12957  Z= 0.260
  Chirality :  0.040   0.154   1436
  Planarity :  0.003   0.031   1533
  Dihedral  : 14.114  95.109   1541
  Min Nonbonded Distance : 1.968

Molprobity Statistics.
  All-atom Clashscore : 4.51
  Ramachandran Plot:
    Outliers :  0.19 %
    Allowed  :  2.29 %
    Favored  : 97.51 %
  Rotamer:
    Outliers :  1.58 %
    Allowed  : 13.25 %
    Favored  : 85.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 1.89 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.37 (0.28), residues: 1046
  helix:  2.73 (0.24), residues: 463
  sheet:  0.98 (0.45), residues: 138
  loop :  0.61 (0.33), residues: 445

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.001   TRP C1160 
 HIS   0.002   0.000   HIS B 419 
 PHE   0.010   0.001   PHE B 447 
 TYR   0.007   0.001   TYR B 427 
 ARG   0.001   0.000   ARG B 359 

Details of bonding type rmsd
  hydrogen bonds       : bond        0.03128 (  416)
  hydrogen bonds       : angle       3.95055 ( 1198)
  metal coordination   : bond        0.00381 (    4)
  metal coordination   : angle       5.66266 (   12)
  covalent geometry    : bond        0.00249 ( 9471)
  covalent geometry    : angle       0.49758 (12945)
  Misc. bond           : bond        0.00076 (    2)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 4541.11 seconds
wall clock time: 79 minutes 49.17 seconds (4789.17 seconds total)