Starting phenix.real_space_refine
on Fri Sep 11 00:17:06 2026 by dcliebschner
===============================================================================

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

  Found model, restraint, /net/cci-nas-00/data/ceres_data/7to1_26026/09_2026/7to1_26026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7to1_26026/09_2026/7to1_26026.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.66
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    restraint_files = "/net/cci-nas-00/data/ceres_data/7to1_26026/09_2026/7to1_26026.cif"
    default_restraint = "/net/cci-nas-00/data/ceres_data/7to1_26026/09_2026/7to1_26026.cif"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7to1_26026/09_2026/7to1_26026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7to1_26026/09_2026/7to1_26026.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/7to1_26026/09_2026/7to1_26026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7to1_26026/09_2026/7to1_26026.map"
  }
  resolution = 3.66
  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=   0.005
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: 6
    Type Number    sf(0)   Gaussians
     Zn      1      6.06       5
     P      24      5.49       5
     S      31      5.16       5
     C    3492      2.51       5
     N     947      2.21       5
     O    1106      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 5601
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5123
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 635, 5123
          Classifications: {'peptide': 635}
          Incomplete info: {'truncation_to_alanine': 3}
          Link IDs: {'PTRANS': 27, 'TRANS': 607}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 16
          Unresolved non-hydrogen angles: 18
          Unresolved non-hydrogen dihedrals: 14
          Planarities with less than four sites: {'ARG:plan': 2}
          Unresolved non-hydrogen planarities: 10
    Chain: "B"
      Number of atoms: 477
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 22, 477
          Unusual residues: {'GTP': 1}
          Classifications: {'RNAv2': 21, 'undetermined': 1}
          Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11}
          Link IDs: {'rna3p': 20, None: 1}
            Not linked:
              pdbres="GTP B   1 "
              pdbres="  G B   2 "
          Chain breaks: 1
    Chain: "A"
      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   4191  SG  CYS A 810      43.045  22.013  23.953  1.00 50.21           S
  ATOM   4630  SG  CYS A 864      42.729  20.263  20.098  1.00 64.66           S
  ATOM   4669  SG  CYS A 869      39.685  21.192  21.887  1.00 60.38           S

  Time building chain proxies: 1.43, per 1000 atoms: 0.26
  Number of scatterers: 5601
  At special positions: 0
  Unit cell: (89.25, 94.5, 66.15, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Zn      1     29.99
     S      31     16.00
     P      24     15.00
     O    1106      8.00
     N     947      7.00
     C    3492      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=1, symmetry=0
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.54
  Conformation dependent library (CDL) restraints added in 333.2 milliseconds
  
  Dynamic metal coordination
    Zn2+ tetrahedral coordination
      pdb="  ZN A1001 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 869 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 864 "
        pdb="ZN    ZN A1001 " - pdb=" SG  CYS A 810 "


  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1220

  Finding SS restraints...
    Secondary structure from input PDB file:
      22 helices and 5 sheets defined
      50.2% alpha, 8.7% beta
      10 base pairs and 15 stacking pairs defined.
    Time for finding SS restraints: 0.53
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 256
      removed outlier: 3.711A  pdb=" N   LEU A 250 " --> pdb=" O   TYR A 246 " (cutoff:3.500A)
      removed outlier: 3.651A  pdb=" N   ALA A 251 " --> pdb=" O   GLN A 247 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
      removed outlier: 3.725A  pdb=" N   LYS A 256 " --> pdb=" O   LEU A 252 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 284
    Processing helix  chain 'A' and resid 299 through 314
    Processing helix  chain 'A' and resid 333 through 340
    Processing helix  chain 'A' and resid 347 through 358
      removed outlier: 3.534A  pdb=" N   LEU A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 374 through 377
    Processing helix  chain 'A' and resid 381 through 396
    Processing helix  chain 'A' and resid 419 through 434
    Processing helix  chain 'A' and resid 448 through 452
      removed outlier: 4.068A  pdb=" N   GLN A 451 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
      removed outlier: 4.374A  pdb=" N   VAL A 452 " --> pdb=" O   LEU A 449 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 448 through 452'
    Processing helix  chain 'A' and resid 469 through 487
    Processing helix  chain 'A' and resid 492 through 497
      removed outlier: 4.366A  pdb=" N   SER A 497 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 521
    Processing helix  chain 'A' and resid 529 through 558
      removed outlier: 3.674A  pdb=" N   ARG A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 576
      removed outlier: 3.698A  pdb=" N   ALA A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   ALA A 576 " --> pdb=" O   SER A 572 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 602
      removed outlier: 3.598A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 4.663A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
      removed outlier: 4.277A  pdb=" N   SER A 599 " --> pdb=" O   GLN A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 607
      removed outlier: 3.960A  pdb=" N   GLU A 607 " --> pdb=" O   PRO A 604 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 608 through 625
    Processing helix  chain 'A' and resid 636 through 650
      removed outlier: 3.714A  pdb=" N   VAL A 640 " --> pdb=" O   THR A 636 " (cutoff:3.500A)
      removed outlier: 4.382A  pdb=" N   ASP A 641 " --> pdb=" O   ARG A 637 " (cutoff:3.500A)
      removed outlier: 4.117A  pdb=" N   ALA A 642 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   LYS A 644 " --> pdb=" O   VAL A 640 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 771
      removed outlier: 4.107A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 773 through 794
    Processing helix  chain 'A' and resid 835 through 840
      removed outlier: 3.561A  pdb=" N   LYS A 839 " --> pdb=" O   GLY A 835 " (cutoff:3.500A)
      removed outlier: 4.120A  pdb=" N   GLU A 840 " --> pdb=" O   ASP A 836 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 835 through 840'
    Processing helix  chain 'A' and resid 889 through 892
    Processing sheet with id=AA1, first strand: chain 'A' and resid 294 through 296
      removed outlier: 7.202A  pdb=" N   LEU A 408 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
      removed outlier: 6.199A  pdb=" N   PHE A 371 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 461 through 462
      removed outlier: 3.744A  pdb=" N   THR A 742 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
      removed outlier: 6.443A  pdb=" N   VAL A 712 " --> pdb=" O   PHE A 739 " (cutoff:3.500A)
      removed outlier: 7.580A  pdb=" N   LEU A 741 " --> pdb=" O   VAL A 712 " (cutoff:3.500A)
      removed outlier: 6.344A  pdb=" N   LEU A 714 " --> pdb=" O   LEU A 741 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   ILE A 631 " --> pdb=" O   ILE A 713 " (cutoff:3.500A)
      removed outlier: 6.907A  pdb=" N   TYR A 715 " --> pdb=" O   ILE A 631 " (cutoff:3.500A)
      removed outlier: 6.087A  pdb=" N   PHE A 633 " --> pdb=" O   TYR A 715 " (cutoff:3.500A)
      removed outlier: 7.068A  pdb=" N   THR A 630 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 7.240A  pdb=" N   ALA A 696 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
      removed outlier: 5.863A  pdb=" N   LEU A 632 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 816 through 819
      removed outlier: 3.857A  pdb=" N   CYS A 818 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 831 through 833
      removed outlier: 4.405A  pdb=" N   ILE A 916 " --> pdb=" O   VAL A 823 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 842 through 846
      removed outlier: 5.729A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
      removed outlier: 6.098A  pdb=" N   LYS A 878 " --> pdb=" O   LYS A 858 " (cutoff:3.500A)
      removed outlier: 3.772A  pdb=" N   ILE A 862 " --> pdb=" O   GLY A 874 " (cutoff:3.500A)
      removed outlier: 3.799A  pdb=" N   GLY A 874 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)
      removed outlier: 6.606A  pdb=" N   CYS A 864 " --> pdb=" O   ASP A 872 " (cutoff:3.500A)
      removed outlier: 7.351A  pdb=" N   ASP A 872 " --> pdb=" O   CYS A 864 " (cutoff:3.500A)

    235 hydrogen bonds defined for protein.
    687 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      25 hydrogen bonds
      50 hydrogen bond angles
      0 basepair planarities
      10 basepair parallelities
      15 stacking parallelities
  Total time for adding SS restraints: 0.91

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 895
        1.32 -     1.44: 1579
        1.44 -     1.57: 3195
        1.57 -     1.69: 46
        1.69 -     1.82: 43
  Bond restraints: 5758
  Sorted by residual:
  bond pdb=" C1' GTP B   1 "
       pdb=" C2' GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.524  1.285  0.239 2.00e-02 2.50e+03 1.43e+02
  bond pdb=" C1' GTP B   1 "
       pdb=" O4' GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.410  1.613 -0.203 2.00e-02 2.50e+03 1.03e+02
  bond pdb=" C5  GTP B   1 "
       pdb=" C6  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.390  1.544 -0.154 2.00e-02 2.50e+03 5.91e+01
  bond pdb=" C4  GTP B   1 "
       pdb=" N3  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.355  1.490 -0.135 2.00e-02 2.50e+03 4.54e+01
  bond pdb=" C2  GTP B   1 "
       pdb=" N2  GTP B   1 "
    ideal  model  delta    sigma   weight residual
    1.330  1.452 -0.122 2.00e-02 2.50e+03 3.73e+01
  ... (remaining 5753 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 6831
        1.63 -     3.27: 1012
        3.27 -     4.90: 24
        4.90 -     6.54: 2
        6.54 -     8.17: 3
  Bond angle restraints: 7872
  Sorted by residual:
  angle pdb=" CA  GLY A 835 "
        pdb=" C   GLY A 835 "
        pdb=" O   GLY A 835 "
      ideal   model   delta    sigma   weight residual
     121.41  118.49    2.92 8.80e-01 1.29e+00 1.10e+01
  angle pdb=" C   VAL A 453 "
        pdb=" N   TYR A 454 "
        pdb=" CA  TYR A 454 "
      ideal   model   delta    sigma   weight residual
     121.54  127.68   -6.14 1.91e+00 2.74e-01 1.03e+01
  angle pdb=" CA  VAL A 414 "
        pdb=" C   VAL A 414 "
        pdb=" O   VAL A 414 "
      ideal   model   delta    sigma   weight residual
     120.34  117.52    2.82 9.10e-01 1.21e+00 9.62e+00
  angle pdb=" N   ILE A 489 "
        pdb=" CA  ILE A 489 "
        pdb=" C   ILE A 489 "
      ideal   model   delta    sigma   weight residual
     113.53  110.85    2.68 9.80e-01 1.04e+00 7.50e+00
  angle pdb=" C2' GTP B   1 "
        pdb=" C3' GTP B   1 "
        pdb=" C4' GTP B   1 "
      ideal   model   delta    sigma   weight residual
     111.00  102.83    8.17 3.00e+00 1.11e-01 7.42e+00
  ... (remaining 7867 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.24: 3191
       20.24 -    40.47: 227
       40.47 -    60.70: 31
       60.70 -    80.93: 10
       80.93 -   101.17: 2
  Dihedral angle restraints: 3461
    sinusoidal: 1589
      harmonic: 1872
  Sorted by residual:
  dihedral pdb=" O5'   A B  11 "
           pdb=" C5'   A B  11 "
           pdb=" C4'   A B  11 "
           pdb=" C3'   A B  11 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  134.73   45.27     3      6.40e+00 2.44e-02 4.47e+01
  dihedral pdb=" O5'   C B  55 "
           pdb=" C5'   C B  55 "
           pdb=" C4'   C B  55 "
           pdb=" C3'   C B  55 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  143.10   36.90     3      6.40e+00 2.44e-02 3.52e+01
  dihedral pdb=" C8  GTP B   1 "
           pdb=" C1' GTP B   1 "
           pdb=" N9  GTP B   1 "
           pdb=" O4' GTP B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     104.59    3.43  101.17     1      2.00e+01 2.50e-03 2.86e+01
  ... (remaining 3458 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.053: 470
       0.053 -    0.106: 318
       0.106 -    0.159: 81
       0.159 -    0.212: 7
       0.212 -    0.265: 17
  Chirality restraints: 893
  Sorted by residual:
  chirality pdb=" P     G B   2 "
            pdb=" OP1   G B   2 "
            pdb=" OP2   G B   2 "
            pdb=" O5'   G B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.44   -0.26 2.00e-01 2.50e+01 1.75e+00
  chirality pdb=" P     C B  64 "
            pdb=" OP1   C B  64 "
            pdb=" OP2   C B  64 "
            pdb=" O5'   C B  64 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.41   -0.24 2.00e-01 2.50e+01 1.45e+00
  chirality pdb=" P     C B   9 "
            pdb=" OP1   C B   9 "
            pdb=" OP2   C B   9 "
            pdb=" O5'   C B   9 "
    both_signs  ideal   model   delta    sigma   weight residual
      True       2.17   -2.41   -0.24 2.00e-01 2.50e+01 1.40e+00
  ... (remaining 890 not shown)

  Planarity restraints: 924
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   U B  62 "    0.028 2.00e-02 2.50e+03   1.31e-02 3.86e+00
        pdb=" N1    U B  62 "   -0.011 2.00e-02 2.50e+03
        pdb=" C2    U B  62 "   -0.010 2.00e-02 2.50e+03
        pdb=" O2    U B  62 "   -0.008 2.00e-02 2.50e+03
        pdb=" N3    U B  62 "    0.003 2.00e-02 2.50e+03
        pdb=" C4    U B  62 "    0.004 2.00e-02 2.50e+03
        pdb=" O4    U B  62 "    0.014 2.00e-02 2.50e+03
        pdb=" C5    U B  62 "   -0.008 2.00e-02 2.50e+03
        pdb=" C6    U B  62 "   -0.013 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  THR A 697 "   -0.006 2.00e-02 2.50e+03   1.20e-02 1.43e+00
        pdb=" C   THR A 697 "    0.021 2.00e-02 2.50e+03
        pdb=" O   THR A 697 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   SER A 698 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C1'   G B  60 "    0.017 2.00e-02 2.50e+03   6.79e-03 1.38e+00
        pdb=" N9    G B  60 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8    G B  60 "   -0.006 2.00e-02 2.50e+03
        pdb=" N7    G B  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" C5    G B  60 "    0.001 2.00e-02 2.50e+03
        pdb=" C6    G B  60 "    0.001 2.00e-02 2.50e+03
        pdb=" O6    G B  60 "    0.006 2.00e-02 2.50e+03
        pdb=" N1    G B  60 "    0.003 2.00e-02 2.50e+03
        pdb=" C2    G B  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" N2    G B  60 "   -0.003 2.00e-02 2.50e+03
        pdb=" N3    G B  60 "   -0.001 2.00e-02 2.50e+03
        pdb=" C4    G B  60 "   -0.004 2.00e-02 2.50e+03
  ... (remaining 921 not shown)

  Histogram of nonbonded interaction distances:
        2.31 -     2.83: 1634
        2.83 -     3.35: 5465
        3.35 -     3.87: 9347
        3.87 -     4.38: 10237
        4.38 -     4.90: 17565
  Nonbonded interactions: 44248
  Sorted by model distance:
  nonbonded pdb=" O   HIS A 557 "
            pdb=" OH  TYR A 715 "
     model   vdw
     2.314 3.040
  nonbonded pdb=" OH  TYR A 622 "
            pdb=" OD1 ASN A 692 "
     model   vdw
     2.315 3.040
  nonbonded pdb=" NH1 ARG A 811 "
            pdb=" O   GLU A 890 "
     model   vdw
     2.336 3.120
  nonbonded pdb=" O   ILE A 337 "
            pdb=" ND2 ASN A 341 "
     model   vdw
     2.339 3.120
  nonbonded pdb=" OG  SER A 362 "
            pdb=" OG  SER A 364 "
     model   vdw
     2.364 3.040
  ... (remaining 44243 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:             0.490
  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:             0.000
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     7.750
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    9.600
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8099
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      :  0.015   0.676   5762  Z= 0.890
  Angle     :  1.066   8.173   7872  Z= 0.754
  Chirality :  0.072   0.265    893
  Planarity :  0.004   0.019    924
  Dihedral  : 13.794 101.166   2241
  Min Nonbonded Distance : 2.314

Molprobity Statistics.
  All-atom Clashscore : 6.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.29 %
    Favored  : 91.71 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  5.08 %
    Favored  : 94.92 %
  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: -2.28 (0.31), residues: 627
  helix:  0.24 (0.29), residues: 282
  sheet: -3.75 (0.50), residues: 67
  loop : -2.85 (0.32), residues: 278

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 316 
 TYR   0.015   0.003   TYR A 390 
 PHE   0.016   0.003   PHE A 460 
 TRP   0.010   0.003   TRP A 873 
 HIS   0.005   0.002   HIS A 782 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.01214 /  0.83 ( 5758)
  covalent geometry    : angle       1.06644 /  0.75 ( 7872)
  hydrogen bonds       : bond        0.13076 /  8.55 (  260)
  hydrogen bonds       : angle       5.07344 /  3.51 (  737)
  metal coordination   : bond        0.40819 / 21.35 (    3)
  Misc. bond           : bond        0.00023 /  0.01 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  132 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 132
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  256 LYS cc_start: 0.9094 (mmtp) cc_final: 0.8601 (mptt)
REVERT: A  287 GLN cc_start: 0.8710 (tp40) cc_final: 0.8243 (pm20)
REVERT: A  298 ASN cc_start: 0.8022 (t0) cc_final: 0.7806 (t0)
REVERT: A  373 GLU cc_start: 0.7883 (mt-10) cc_final: 0.7668 (mt-10)
REVERT: A  388 PHE cc_start: 0.8300 (m-10) cc_final: 0.7722 (m-80)
REVERT: A  481 ASP cc_start: 0.7314 (m-30) cc_final: 0.7111 (m-30)
REVERT: A  525 MET cc_start: 0.7566 (mmt) cc_final: 0.7181 (mmp)
REVERT: A  531 GLU cc_start: 0.8973 (tm-30) cc_final: 0.8079 (tt0)
REVERT: A  556 GLU cc_start: 0.7822 (tt0) cc_final: 0.7565 (mt-10)
REVERT: A  598 GLU cc_start: 0.8597 (tp30) cc_final: 0.8378 (tp30)
REVERT: A  603 ASP cc_start: 0.8437 (t0) cc_final: 0.7931 (t70)
REVERT: A  773 GLU cc_start: 0.7947 (tt0) cc_final: 0.7544 (tm-30)
REVERT: A  803 LYS cc_start: 0.8942 (mmmt) cc_final: 0.8739 (mmmt)
REVERT: A  907 LYS cc_start: 0.8642 (mttt) cc_final: 0.8119 (mtmm)
  outliers start: 0
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0976
  time to fit residues: 16.0112
Evaluate side-chains
  87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 87
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 49 optimal weight:    0.9990
   chunk 53 optimal weight:    0.8980
   chunk 5 optimal weight:    0.9990
   chunk 33 optimal weight:    3.9990
   chunk 62 optimal weight:    0.7980
   chunk 51 optimal weight:    0.1980
   chunk 38 optimal weight:    2.9990
   chunk 61 optimal weight:    3.9990
   chunk 45 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.6580

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 380 GLN
A 495 ASN
A 517 GLN
A 557 HIS
A 595 GLN
A 769 GLN
A 784 GLN
A 876 HIS

Total number of N/Q/H flips: 8

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.139938 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.114344 restraints weight = 6892.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3405 r_free = 0.3405 target = 0.117813 restraints weight = 4315.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3438 r_free = 0.3438 target = 0.120400 restraints weight = 3154.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3458 r_free = 0.3458 target = 0.122134 restraints weight = 2513.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.3473 r_free = 0.3473 target = 0.123500 restraints weight = 2137.857|
|-----------------------------------------------------------------------------|
r_work (final): 0.3553
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.1587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5762  Z= 0.117
  Angle     :  0.577   8.018   7872  Z= 0.274
  Chirality :  0.042   0.230    893
  Planarity :  0.004   0.040    924
  Dihedral  :  8.895  88.692    935
  Min Nonbonded Distance : 2.494

Molprobity Statistics.
  All-atom Clashscore : 8.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.78 %
    Favored  : 85.29 %
  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: -1.23 (0.34), residues: 627
  helix:  1.29 (0.31), residues: 292
  sheet: -3.30 (0.54), residues: 74
  loop : -2.60 (0.35), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 602 
 TYR   0.013   0.001   TYR A 622 
 PHE   0.008   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 771 
 HIS   0.005   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00264 /  0.12 ( 5758)
  covalent geometry    : angle       0.57750 /  0.27 ( 7872)
  hydrogen bonds       : bond        0.03779 /  2.45 (  260)
  hydrogen bonds       : angle       3.73191 /  2.55 (  737)
  metal coordination   : bond        0.00568 /  0.27 (    3)
  Misc. bond           : bond        0.00013 /  0.01 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 90
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.8275 (mtt) cc_final: 0.8011 (mtt)
REVERT: A  298 ASN cc_start: 0.8063 (t0) cc_final: 0.7830 (t0)
REVERT: A  511 GLN cc_start: 0.7895 (tm-30) cc_final: 0.7495 (tm-30)
REVERT: A  529 ASP cc_start: 0.8088 (t0) cc_final: 0.7832 (t0)
REVERT: A  541 TYR cc_start: 0.8153 (m-80) cc_final: 0.7894 (m-80)
REVERT: A  556 GLU cc_start: 0.7397 (tt0) cc_final: 0.7165 (mt-10)
REVERT: A  596 GLU cc_start: 0.8457 (tm-30) cc_final: 0.8185 (tm-30)
REVERT: A  598 GLU cc_start: 0.8069 (tp30) cc_final: 0.7762 (tp30)
REVERT: A  907 LYS cc_start: 0.8584 (mttt) cc_final: 0.8032 (mtmm)
  outliers start: 11
  outliers final: 5
  residues processed: 97
  average time/residue: 0.0807
  time to fit residues: 10.2143
Evaluate side-chains
  81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 76
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  890 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 39 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 40 optimal weight:    0.9990
   chunk 32 optimal weight:    0.0870
   chunk 34 optimal weight:    0.6980
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.8980
   chunk 41 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 55 optimal weight:    1.9990
   chunk 43 optimal weight:    0.3980
   overall best weight:    0.6160

-------------------------------------------------------------------------------
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 = 0.3753 r_free = 0.3753 target = 0.146941 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.123271 restraints weight = 6518.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3533 r_free = 0.3533 target = 0.126198 restraints weight = 4612.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3545 r_free = 0.3545 target = 0.127423 restraints weight = 3993.218|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.127808 restraints weight = 3076.304|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.128533 restraints weight = 2836.047|
|-----------------------------------------------------------------------------|
r_work (final): 0.3620
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
moved from start:          0.1956

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.029   5762  Z= 0.109
  Angle     :  0.559   7.112   7872  Z= 0.266
  Chirality :  0.042   0.181    893
  Planarity :  0.003   0.036    924
  Dihedral  :  8.702  89.975    935
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.28 %
    Allowed  : 15.41 %
    Favored  : 82.31 %
  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: -0.81 (0.34), residues: 627
  helix:  1.67 (0.31), residues: 293
  sheet: -3.09 (0.59), residues: 66
  loop : -2.49 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 602 
 TYR   0.012   0.001   TYR A 303 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 771 
 HIS   0.003   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00247 /  0.11 ( 5758)
  covalent geometry    : angle       0.55943 /  0.27 ( 7872)
  hydrogen bonds       : bond        0.03664 /  2.37 (  260)
  hydrogen bonds       : angle       3.64144 /  2.49 (  737)
  metal coordination   : bond        0.00221 /  0.11 (    3)
  Misc. bond           : bond        0.00012 /  0.01 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8822 (tppt) cc_final: 0.8427 (mmtt)
REVERT: A  298 ASN cc_start: 0.8057 (t0) cc_final: 0.7829 (t0)
REVERT: A  511 GLN cc_start: 0.8016 (tm-30) cc_final: 0.7662 (tm-30)
REVERT: A  529 ASP cc_start: 0.7981 (t0) cc_final: 0.7671 (t0)
REVERT: A  907 LYS cc_start: 0.8569 (mttt) cc_final: 0.8192 (mtmm)
  outliers start: 13
  outliers final: 9
  residues processed: 98
  average time/residue: 0.0814
  time to fit residues: 10.4009
Evaluate side-chains
  84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 75
  time to evaluate  : 0.203 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  890 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 0 optimal weight:    7.9990
   chunk 27 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 51 optimal weight:    8.9990
   chunk 50 optimal weight:    3.9990
   chunk 16 optimal weight:    0.7980
   chunk 62 optimal weight:    0.0570
   chunk 34 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.7700

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.155007 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3579 r_free = 0.3579 target = 0.131038 restraints weight = 6354.643|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3606 r_free = 0.3606 target = 0.133647 restraints weight = 4544.574|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.135241 restraints weight = 3999.019|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.135831 restraints weight = 2954.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.137006 restraints weight = 2798.444|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7857
moved from start:          0.2129

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   5762  Z= 0.118
  Angle     :  0.565   7.315   7872  Z= 0.271
  Chirality :  0.042   0.147    893
  Planarity :  0.003   0.036    924
  Dihedral  :  8.615  89.480    935
  Min Nonbonded Distance : 2.423

Molprobity Statistics.
  All-atom Clashscore : 6.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 16.46 %
    Favored  : 80.74 %
  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: -0.57 (0.35), residues: 627
  helix:  1.89 (0.31), residues: 293
  sheet: -3.16 (0.58), residues: 68
  loop : -2.31 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 602 
 TYR   0.012   0.001   TYR A 622 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.004   0.001   TRP A 512 
 HIS   0.002   0.000   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 ( 5758)
  covalent geometry    : angle       0.56531 /  0.27 ( 7872)
  hydrogen bonds       : bond        0.03612 /  2.34 (  260)
  hydrogen bonds       : angle       3.57261 /  2.46 (  737)
  metal coordination   : bond        0.00247 /  0.13 (    3)
  Misc. bond           : bond        0.00011 /  0.01 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 84
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.7938 (tp30) cc_final: 0.7633 (tp30)
REVERT: A  283 LYS cc_start: 0.8901 (tppt) cc_final: 0.8493 (mmtt)
REVERT: A  298 ASN cc_start: 0.8090 (t0) cc_final: 0.7851 (t0)
REVERT: A  511 GLN cc_start: 0.8041 (tm-30) cc_final: 0.7605 (tm-30)
REVERT: A  529 ASP cc_start: 0.8043 (t0) cc_final: 0.7785 (t0)
REVERT: A  907 LYS cc_start: 0.8582 (mttt) cc_final: 0.8191 (mtmm)
  outliers start: 16
  outliers final: 11
  residues processed: 94
  average time/residue: 0.0773
  time to fit residues: 9.6098
Evaluate side-chains
  84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 73
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 47 optimal weight:    0.8980
   chunk 0 optimal weight:    7.9990
   chunk 55 optimal weight:    0.5980
   chunk 58 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 5 optimal weight:    0.5980
   chunk 29 optimal weight:    2.9990
   chunk 30 optimal weight:    0.6980
   chunk 64 optimal weight:    4.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.3850 r_free = 0.3850 target = 0.157042 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.132141 restraints weight = 6427.343|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.135748 restraints weight = 4417.336|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.137039 restraints weight = 3662.434|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.137909 restraints weight = 2756.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.138790 restraints weight = 2500.920|
|-----------------------------------------------------------------------------|
r_work (final): 0.3549
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7823
moved from start:          0.2298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   5762  Z= 0.111
  Angle     :  0.572   7.237   7872  Z= 0.276
  Chirality :  0.041   0.157    893
  Planarity :  0.003   0.035    924
  Dihedral  :  8.529  89.146    935
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 7.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.18 %
    Favored  : 92.82 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 17.16 %
    Favored  : 80.04 %
  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: -0.31 (0.36), residues: 627
  helix:  2.09 (0.31), residues: 287
  sheet: -2.92 (0.59), residues: 74
  loop : -2.07 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.012   0.001   TYR A 622 
 PHE   0.008   0.001   PHE A 295 
 TRP   0.010   0.001   TRP A 646 
 HIS   0.002   0.000   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00254 /  0.11 ( 5758)
  covalent geometry    : angle       0.57231 /  0.28 ( 7872)
  hydrogen bonds       : bond        0.03509 /  2.27 (  260)
  hydrogen bonds       : angle       3.49686 /  2.42 (  737)
  metal coordination   : bond        0.00119 /  0.06 (    3)
  Misc. bond           : bond        0.00008 /  0.00 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 80
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.7982 (tp30) cc_final: 0.7705 (tp30)
REVERT: A  283 LYS cc_start: 0.8974 (tppt) cc_final: 0.8623 (mmtt)
REVERT: A  298 ASN cc_start: 0.8115 (t0) cc_final: 0.7863 (t0)
REVERT: A  511 GLN cc_start: 0.8096 (tm-30) cc_final: 0.7641 (tm-30)
REVERT: A  529 ASP cc_start: 0.8098 (t0) cc_final: 0.7684 (t0)
REVERT: A  907 LYS cc_start: 0.8559 (mttt) cc_final: 0.8195 (mtmm)
  outliers start: 16
  outliers final: 12
  residues processed: 90
  average time/residue: 0.0742
  time to fit residues: 8.9053
Evaluate side-chains
  87 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 75
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.9990
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    1.9990
   chunk 28 optimal weight:    0.0030
   chunk 29 optimal weight:    0.8980
   chunk 45 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.7794

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 306 GLN
A 619 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3834 r_free = 0.3834 target = 0.155391 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.131084 restraints weight = 6420.037|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.134097 restraints weight = 4647.016|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.135681 restraints weight = 4139.713|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.136200 restraints weight = 2970.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.136519 restraints weight = 2811.695|
|-----------------------------------------------------------------------------|
r_work (final): 0.3530
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.2385

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5762  Z= 0.119
  Angle     :  0.577   8.221   7872  Z= 0.273
  Chirality :  0.042   0.150    893
  Planarity :  0.003   0.034    924
  Dihedral  :  8.479  89.007    935
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 7.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.66 %
    Favored  : 92.34 %
  Rotamer:
    Outliers :  2.98 %
    Allowed  : 18.04 %
    Favored  : 78.98 %
  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: -0.22 (0.36), residues: 627
  helix:  2.16 (0.31), residues: 288
  sheet: -2.94 (0.60), residues: 74
  loop : -2.00 (0.38), residues: 265

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.013   0.001   TYR A 622 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 646 
 HIS   0.003   0.000   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00270 /  0.12 ( 5758)
  covalent geometry    : angle       0.57692 /  0.27 ( 7872)
  hydrogen bonds       : bond        0.03605 /  2.34 (  260)
  hydrogen bonds       : angle       3.52234 /  2.45 (  737)
  metal coordination   : bond        0.00152 /  0.08 (    3)
  Misc. bond           : bond        0.00004 /  0.00 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 78
  time to evaluate  : 0.198 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.7978 (tp30) cc_final: 0.7678 (tp30)
REVERT: A  283 LYS cc_start: 0.8934 (tppt) cc_final: 0.8533 (mmtt)
REVERT: A  298 ASN cc_start: 0.8089 (t0) cc_final: 0.7797 (t0)
REVERT: A  388 PHE cc_start: 0.8066 (m-10) cc_final: 0.7631 (m-80)
REVERT: A  511 GLN cc_start: 0.8121 (tm-30) cc_final: 0.7672 (tm-30)
REVERT: A  907 LYS cc_start: 0.8557 (mttt) cc_final: 0.8216 (mtmm)
  outliers start: 17
  outliers final: 13
  residues processed: 87
  average time/residue: 0.0715
  time to fit residues: 8.3881
Evaluate side-chains
  84 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 71
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 57 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    0.7980
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    4.9990
   chunk 55 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9990
   chunk 32 optimal weight:    4.9990
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.7980

-------------------------------------------------------------------------------
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 = 0.3725 r_free = 0.3725 target = 0.145210 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.122722 restraints weight = 6788.286|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.125265 restraints weight = 4887.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.126562 restraints weight = 4185.904|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.127747 restraints weight = 3110.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3536 r_free = 0.3536 target = 0.128131 restraints weight = 2853.646|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7867
moved from start:          0.2482

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.022   5762  Z= 0.121
  Angle     :  0.588   7.427   7872  Z= 0.279
  Chirality :  0.042   0.160    893
  Planarity :  0.003   0.034    924
  Dihedral  :  8.449  88.781    935
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 7.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 18.91 %
    Favored  : 78.28 %
  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: -0.14 (0.36), residues: 627
  helix:  2.21 (0.31), residues: 291
  sheet: -2.99 (0.60), residues: 75
  loop : -1.95 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.013   0.001   TYR A 622 
 PHE   0.008   0.001   PHE A 295 
 TRP   0.006   0.001   TRP A 646 
 HIS   0.003   0.000   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.12 ( 5758)
  covalent geometry    : angle       0.58787 /  0.28 ( 7872)
  hydrogen bonds       : bond        0.03647 /  2.36 (  260)
  hydrogen bonds       : angle       3.54891 /  2.49 (  737)
  metal coordination   : bond        0.00074 /  0.04 (    3)
  Misc. bond           : bond        0.00007 /  0.00 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.203 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8905 (tppt) cc_final: 0.8624 (mptt)
REVERT: A  298 ASN cc_start: 0.8023 (t0) cc_final: 0.7722 (t0)
REVERT: A  388 PHE cc_start: 0.8080 (m-10) cc_final: 0.7606 (m-80)
REVERT: A  511 GLN cc_start: 0.8098 (tm-30) cc_final: 0.7687 (tm-30)
REVERT: A  907 LYS cc_start: 0.8533 (mttt) cc_final: 0.8225 (mtmm)
  outliers start: 16
  outliers final: 14
  residues processed: 84
  average time/residue: 0.0694
  time to fit residues: 8.0044
Evaluate side-chains
  83 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.204 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  890 GLU
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    6.9990
   chunk 59 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9980
   chunk 49 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 57 optimal weight:    3.9990
   chunk 10 optimal weight:    0.9990
   chunk 5 optimal weight:    0.4980
   overall best weight:    0.8382

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 306 GLN
A 588 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3831 r_free = 0.3831 target = 0.155177 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3589 r_free = 0.3589 target = 0.131801 restraints weight = 6420.728|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.134791 restraints weight = 4727.103|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.136002 restraints weight = 3942.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.136960 restraints weight = 2952.819|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3645 r_free = 0.3645 target = 0.137203 restraints weight = 2752.223|
|-----------------------------------------------------------------------------|
r_work (final): 0.3538
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7862
moved from start:          0.2588

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   5762  Z= 0.123
  Angle     :  0.589   7.472   7872  Z= 0.281
  Chirality :  0.042   0.154    893
  Planarity :  0.003   0.034    924
  Dihedral  :  8.436  88.673    935
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 7.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 19.26 %
    Favored  : 77.58 %
  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: -0.09 (0.36), residues: 627
  helix:  2.24 (0.31), residues: 291
  sheet: -3.08 (0.63), residues: 69
  loop : -1.91 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.033   0.002   TYR A 541 
 PHE   0.008   0.001   PHE A 295 
 TRP   0.006   0.001   TRP A 512 
 HIS   0.003   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.12 ( 5758)
  covalent geometry    : angle       0.58866 /  0.28 ( 7872)
  hydrogen bonds       : bond        0.03677 /  2.38 (  260)
  hydrogen bonds       : angle       3.55310 /  2.50 (  737)
  metal coordination   : bond        0.00117 /  0.06 (    3)
  Misc. bond           : bond        0.00008 /  0.00 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 71
  time to evaluate  : 0.190 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8957 (tppt) cc_final: 0.8646 (mptt)
REVERT: A  298 ASN cc_start: 0.7896 (t0) cc_final: 0.7534 (t0)
REVERT: A  388 PHE cc_start: 0.8093 (m-10) cc_final: 0.7650 (m-80)
REVERT: A  511 GLN cc_start: 0.8128 (tm-30) cc_final: 0.7704 (tm-30)
REVERT: A  907 LYS cc_start: 0.8565 (mttt) cc_final: 0.8183 (mtmm)
  outliers start: 18
  outliers final: 15
  residues processed: 83
  average time/residue: 0.0652
  time to fit residues: 7.4940
Evaluate side-chains
  79 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 64
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  890 GLU
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    5.9990
   chunk 17 optimal weight:    4.9990
   chunk 58 optimal weight:    0.9980
   chunk 53 optimal weight:    0.0980
   chunk 20 optimal weight:    0.3980
   chunk 9 optimal weight:    0.0050
   chunk 2 optimal weight:    2.9990
   chunk 46 optimal weight:    0.8980
   chunk 11 optimal weight:    0.5980
   chunk 21 optimal weight:    4.9990
   chunk 14 optimal weight:    0.5980
   overall best weight:    0.3394

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 384 ASN
A 588 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3876 r_free = 0.3876 target = 0.159082 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.137531 restraints weight = 6418.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3674 r_free = 0.3674 target = 0.139450 restraints weight = 5104.945|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3678 r_free = 0.3678 target = 0.140009 restraints weight = 5324.669|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.140853 restraints weight = 3773.458|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.142226 restraints weight = 3516.741|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.2729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   5762  Z= 0.106
  Angle     :  0.602   8.974   7872  Z= 0.289
  Chirality :  0.041   0.150    893
  Planarity :  0.003   0.034    924
  Dihedral  :  8.419  88.240    935
  Min Nonbonded Distance : 2.468

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.06 %
    Favored  : 93.94 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 19.96 %
    Favored  : 77.23 %
  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: -0.06 (0.36), residues: 627
  helix:  2.22 (0.31), residues: 291
  sheet: -2.92 (0.62), residues: 75
  loop : -1.85 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.030   0.001   TYR A 541 
 PHE   0.006   0.001   PHE A 460 
 TRP   0.007   0.001   TRP A 771 
 HIS   0.003   0.000   HIS A 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00240 /  0.11 ( 5758)
  covalent geometry    : angle       0.60227 /  0.29 ( 7872)
  hydrogen bonds       : bond        0.03495 /  2.26 (  260)
  hydrogen bonds       : angle       3.52686 /  2.48 (  737)
  metal coordination   : bond        0.00053 /  0.03 (    3)
  Misc. bond           : bond        0.00007 /  0.00 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 76
  time to evaluate  : 0.210 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8807 (tppt) cc_final: 0.8556 (mptt)
REVERT: A  298 ASN cc_start: 0.7804 (t0) cc_final: 0.7415 (t0)
REVERT: A  388 PHE cc_start: 0.7997 (m-10) cc_final: 0.7546 (m-80)
REVERT: A  511 GLN cc_start: 0.8068 (tm-30) cc_final: 0.7655 (tm-30)
REVERT: A  907 LYS cc_start: 0.8589 (mttt) cc_final: 0.8250 (mtmm)
  outliers start: 16
  outliers final: 13
  residues processed: 85
  average time/residue: 0.0644
  time to fit residues: 7.5711
Evaluate side-chains
  81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  890 GLU
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 45 optimal weight:    0.0870
   chunk 13 optimal weight:    0.9990
   chunk 14 optimal weight:    0.7980
   chunk 64 optimal weight:    4.9990
   chunk 9 optimal weight:    0.0670
   chunk 41 optimal weight:    2.9990
   chunk 43 optimal weight:    0.9980
   chunk 28 optimal weight:    0.1980
   chunk 11 optimal weight:    0.7980
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.3896

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 588 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.142864 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.118492 restraints weight = 7194.010|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.121652 restraints weight = 4489.020|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.123075 restraints weight = 3473.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.124109 restraints weight = 2763.745|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.124528 restraints weight = 2564.116|
|-----------------------------------------------------------------------------|
r_work (final): 0.3494
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7775
moved from start:          0.2817

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   5762  Z= 0.110
  Angle     :  0.622  17.594   7872  Z= 0.293
  Chirality :  0.042   0.194    893
  Planarity :  0.003   0.035    924
  Dihedral  :  8.355  87.991    935
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.70 %
    Favored  : 93.30 %
  Rotamer:
    Outliers :  2.80 %
    Allowed  : 21.19 %
    Favored  : 76.01 %
  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: -0.17 (0.36), residues: 627
  helix:  2.13 (0.31), residues: 292
  sheet: -2.90 (0.58), residues: 86
  loop : -1.86 (0.39), residues: 249

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 589 
 TYR   0.029   0.001   TYR A 541 
 PHE   0.007   0.001   PHE A 523 
 TRP   0.008   0.001   TRP A 771 
 HIS   0.004   0.001   HIS A 281 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00248 /  0.11 ( 5758)
  covalent geometry    : angle       0.62199 /  0.29 ( 7872)
  hydrogen bonds       : bond        0.03456 /  2.23 (  260)
  hydrogen bonds       : angle       3.57196 /  2.51 (  737)
  metal coordination   : bond        0.00058 /  0.03 (    3)
  Misc. bond           : bond        0.00011 /  0.01 (    1)

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

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

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1254 Ramachandran restraints generated.
    627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.9063 (tppt) cc_final: 0.8689 (mmtt)
REVERT: A  298 ASN cc_start: 0.7807 (t0) cc_final: 0.7411 (t0)
REVERT: A  388 PHE cc_start: 0.7956 (m-10) cc_final: 0.7422 (m-80)
REVERT: A  511 GLN cc_start: 0.8143 (tm-30) cc_final: 0.7676 (tm-30)
REVERT: A  907 LYS cc_start: 0.8592 (mttt) cc_final: 0.8100 (mtmm)
  outliers start: 16
  outliers final: 13
  residues processed: 85
  average time/residue: 0.0763
  time to fit residues: 8.7695
Evaluate side-chains
  86 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 73
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  615 CYS
Chi-restraints excluded: chain A residue  760 MET
Chi-restraints excluded: chain A residue  771 TRP
Chi-restraints excluded: chain A residue  823 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  890 GLU
Chi-restraints excluded: chain A residue  893 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 17 optimal weight:    3.9990
   chunk 7 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 54 optimal weight:    3.9990
   chunk 33 optimal weight:    5.9990
   chunk 14 optimal weight:    0.6980
   chunk 55 optimal weight:    5.9990
   chunk 24 optimal weight:    3.9990
   chunk 58 optimal weight:    4.9990
   chunk 12 optimal weight:    0.9980
   chunk 10 optimal weight:    0.6980
   overall best weight:    1.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 588 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.138658 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114546 restraints weight = 7159.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3404 r_free = 0.3404 target = 0.117264 restraints weight = 4567.127|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.118235 restraints weight = 3648.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3426 r_free = 0.3426 target = 0.119243 restraints weight = 3116.090|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.119519 restraints weight = 2820.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7860
moved from start:          0.2831

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   5762  Z= 0.145
  Angle     :  0.660  16.563   7872  Z= 0.310
  Chirality :  0.044   0.186    893
  Planarity :  0.003   0.033    924
  Dihedral  :  8.369  87.685    935
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.81 %
    Favored  : 92.19 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.54 %
    Favored  : 76.01 %
  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: -0.16 (0.36), residues: 627
  helix:  2.10 (0.31), residues: 292
  sheet: -2.96 (0.64), residues: 74
  loop : -1.87 (0.38), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 589 
 TYR   0.022   0.001   TYR A 541 
 PHE   0.010   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 512 
 HIS   0.003   0.001   HIS A 280 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00341 /  0.15 ( 5758)
  covalent geometry    : angle       0.65953 /  0.31 ( 7872)
  hydrogen bonds       : bond        0.03839 /  2.52 (  260)
  hydrogen bonds       : angle       3.66641 /  2.57 (  737)
  metal coordination   : bond        0.00170 /  0.09 (    3)
  Misc. bond           : bond        0.00015 /  0.01 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 979.39 seconds
wall clock time: 17 minutes 42.48 seconds (1062.48 seconds total)