Starting phenix.real_space_refine
on Tue Mar  3 14:17:54 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7to1_26026/03_2026/7to1_26026.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7to1_26026/03_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7to1_26026/03_2026/7to1_26026.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7to1_26026/03_2026/7to1_26026.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7to1_26026/03_2026/7to1_26026.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7to1_26026/03_2026/7to1_26026.cif"
  }
  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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/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: {'RNA': 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: 1.19, per 1000 atoms: 0.21
  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: 0.45
  Conformation dependent library (CDL) restraints added in 156.9 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: 0.61
  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: 0.98

  Time building geometry restraints manager: 0.57 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: 6868
        1.63 -     3.27: 981
        3.27 -     4.90: 18
        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: 3236
       20.24 -    40.47: 228
       40.47 -    60.70: 43
       60.70 -    80.93: 26
       80.93 -   101.17: 2
  Dihedral angle restraints: 3535
    sinusoidal: 1663
      harmonic: 1872
  Sorted by residual:
  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
  dihedral pdb=" C4' GTP B   1 "
           pdb=" C5' GTP B   1 "
           pdb=" O5' GTP B   1 "
           pdb=" PA  GTP B   1 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -99.13 -165.63   66.50     1      2.00e+01 2.50e-03 1.44e+01
  dihedral pdb=" CA  LEU A 449 "
           pdb=" C   LEU A 449 "
           pdb=" N   GLU A 450 "
           pdb=" CA  GLU A 450 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.31  -18.69     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 3532 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.041: 411
       0.041 -    0.081: 265
       0.081 -    0.122: 188
       0.122 -    0.162: 27
       0.162 -    0.203: 2
  Chirality restraints: 893
  Sorted by residual:
  chirality pdb=" CA  ILE A 360 "
            pdb=" N   ILE A 360 "
            pdb=" C   ILE A 360 "
            pdb=" CB  ILE A 360 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.64   -0.20 2.00e-01 2.50e+01 1.03e+00
  chirality pdb=" CA  ILE A 261 "
            pdb=" N   ILE A 261 "
            pdb=" C   ILE A 261 "
            pdb=" CB  ILE A 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.62   -0.19 2.00e-01 2.50e+01 9.10e-01
  chirality pdb=" CA  ILE A 386 "
            pdb=" N   ILE A 386 "
            pdb=" C   ILE A 386 "
            pdb=" CB  ILE A 386 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.52e-01
  ... (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:             0.370
  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:          0.050
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.030
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:0.920
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.410
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7863
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     :  1.047   8.173   7872  Z= 0.756
  Chirality :  0.063   0.203    893
  Planarity :  0.004   0.019    924
  Dihedral  : 15.282 101.166   2315
  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
  covalent geometry    : bond        0.01213 ( 5758)
  covalent geometry    : angle       1.04703 ( 7872)
  hydrogen bonds       : bond        0.13076 (  260)
  hydrogen bonds       : angle       5.07344 (  737)
  metal coordination   : bond        0.40819 (    3)
  Misc. bond           : bond        0.00023 (    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  : 0.139 
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: 0.0915
  time to fit residues: 14.8614
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  : 0.146 
-------------------------------------------------------------------------------
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:    5.9990
   overall best weight:    0.6580

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3654 r_free = 0.3654 target = 0.139576 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.113621 restraints weight = 6908.751|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.117214 restraints weight = 4336.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3428 r_free = 0.3428 target = 0.119760 restraints weight = 3167.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.121424 restraints weight = 2530.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.122798 restraints weight = 2162.572|
|-----------------------------------------------------------------------------|
r_work (final): 0.3467
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7590
moved from start:          0.1569

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   5762  Z= 0.116
  Angle     :  0.535   8.036   7872  Z= 0.266
  Chirality :  0.039   0.234    893
  Planarity :  0.003   0.040    924
  Dihedral  : 13.633  88.612   1009
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  1.93 %
    Allowed  : 12.43 %
    Favored  : 85.64 %
  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:  1.30 (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
  covalent geometry    : bond        0.00264 ( 5758)
  covalent geometry    : angle       0.53479 ( 7872)
  hydrogen bonds       : bond        0.03778 (  260)
  hydrogen bonds       : angle       3.72749 (  737)
  metal coordination   : bond        0.00937 (    3)
  Misc. bond           : bond        0.00030 (    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  : 0.211 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.8240 (mtt) cc_final: 0.7984 (mtt)
REVERT: A  298 ASN cc_start: 0.8049 (t0) cc_final: 0.7819 (t0)
REVERT: A  511 GLN cc_start: 0.7903 (tm-30) cc_final: 0.7509 (tm-30)
REVERT: A  529 ASP cc_start: 0.8061 (t0) cc_final: 0.7840 (t0)
REVERT: A  541 TYR cc_start: 0.8147 (m-80) cc_final: 0.7891 (m-80)
REVERT: A  556 GLU cc_start: 0.7372 (tt0) cc_final: 0.7152 (mt-10)
REVERT: A  596 GLU cc_start: 0.8417 (tm-30) cc_final: 0.8160 (tm-30)
REVERT: A  598 GLU cc_start: 0.8059 (tp30) cc_final: 0.7761 (tp30)
REVERT: A  907 LYS cc_start: 0.8591 (mttt) cc_final: 0.8069 (mtmm)
  outliers start: 11
  outliers final: 6
  residues processed: 97
  average time/residue: 0.0852
  time to fit residues: 10.7296
Evaluate side-chains
  81 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 75
  time to evaluate  : 0.212 
-------------------------------------------------------------------------------
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  513 ILE
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:    2.9990
   chunk 15 optimal weight:    0.7980
   chunk 40 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 41 optimal weight:    1.9990
   chunk 9 optimal weight:    8.9990
   chunk 55 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.1184

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

Flipped N/Q/H residues before XYZ refinement:
A 384 ASN
A 608 ASN
A 619 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.144160 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3464 r_free = 0.3464 target = 0.121468 restraints weight = 6648.671|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.124020 restraints weight = 4757.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3504 r_free = 0.3504 target = 0.125573 restraints weight = 4252.822|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.125799 restraints weight = 3138.214|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3509 r_free = 0.3509 target = 0.126051 restraints weight = 2965.795|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7743
moved from start:          0.2004

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= 0.139
  Angle     :  0.545   7.713   7872  Z= 0.273
  Chirality :  0.039   0.174    893
  Planarity :  0.003   0.035    924
  Dihedral  : 13.467  89.452   1009
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 16.46 %
    Favored  : 80.91 %
  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: -0.89 (0.35), residues: 627
  helix:  1.60 (0.31), residues: 293
  sheet: -3.24 (0.58), residues: 68
  loop : -2.47 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 602 
 TYR   0.012   0.002   TYR A 622 
 PHE   0.011   0.001   PHE A 295 
 TRP   0.006   0.001   TRP A 512 
 HIS   0.004   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 5758)
  covalent geometry    : angle       0.54538 ( 7872)
  hydrogen bonds       : bond        0.03956 (  260)
  hydrogen bonds       : angle       3.73515 (  737)
  metal coordination   : bond        0.00309 (    3)
  Misc. bond           : bond        0.00024 (    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
  99 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 84
  time to evaluate  : 0.199 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8813 (tppt) cc_final: 0.8448 (mmtt)
REVERT: A  298 ASN cc_start: 0.8080 (t0) cc_final: 0.7820 (t0)
REVERT: A  511 GLN cc_start: 0.8061 (tm-30) cc_final: 0.7714 (tm-30)
REVERT: A  541 TYR cc_start: 0.8056 (m-80) cc_final: 0.7771 (m-80)
REVERT: A  907 LYS cc_start: 0.8575 (mttt) cc_final: 0.8262 (mtmm)
  outliers start: 15
  outliers final: 10
  residues processed: 95
  average time/residue: 0.0818
  time to fit residues: 10.0590
Evaluate side-chains
  82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 72
  time to evaluate  : 0.207 
-------------------------------------------------------------------------------
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  893 VAL
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:    0.8980
   chunk 51 optimal weight:    7.9990
   chunk 50 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 62 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 5 optimal weight:    1.9990
   chunk 53 optimal weight:    0.8980
   chunk 41 optimal weight:    5.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.148772 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.124810 restraints weight = 6521.941|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.127310 restraints weight = 4711.551|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.129002 restraints weight = 4285.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.129358 restraints weight = 3079.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3551 r_free = 0.3551 target = 0.129759 restraints weight = 2942.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3443
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7777
moved from start:          0.2300

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5762  Z= 0.192
  Angle     :  0.592   8.077   7872  Z= 0.299
  Chirality :  0.040   0.175    893
  Planarity :  0.004   0.040    924
  Dihedral  : 13.408  89.578   1009
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.61 %
    Favored  : 91.39 %
  Rotamer:
    Outliers :  3.68 %
    Allowed  : 17.16 %
    Favored  : 79.16 %
  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: -0.80 (0.35), residues: 627
  helix:  1.64 (0.31), residues: 292
  sheet: -3.29 (0.59), residues: 69
  loop : -2.33 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A 811 
 TYR   0.015   0.002   TYR A 622 
 PHE   0.013   0.001   PHE A 295 
 TRP   0.006   0.001   TRP A 512 
 HIS   0.005   0.001   HIS A 871 

Details of bonding type rmsd
  covalent geometry    : bond        0.00451 ( 5758)
  covalent geometry    : angle       0.59246 ( 7872)
  hydrogen bonds       : bond        0.04310 (  260)
  hydrogen bonds       : angle       3.82343 (  737)
  metal coordination   : bond        0.00345 (    3)
  Misc. bond           : bond        0.00011 (    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
  96 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 75
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8927 (tppt) cc_final: 0.8535 (mmtt)
REVERT: A  298 ASN cc_start: 0.8137 (t0) cc_final: 0.7795 (t0)
REVERT: A  511 GLN cc_start: 0.8161 (tm-30) cc_final: 0.7728 (tm-30)
REVERT: A  879 TYR cc_start: 0.7880 (t80) cc_final: 0.7653 (t80)
REVERT: A  907 LYS cc_start: 0.8670 (mttt) cc_final: 0.8295 (mtmm)
  outliers start: 21
  outliers final: 13
  residues processed: 91
  average time/residue: 0.0759
  time to fit residues: 9.1894
Evaluate side-chains
  82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 69
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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  825 VAL
Chi-restraints excluded: chain A residue  882 PHE
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:    0.2980
   chunk 47 optimal weight:    0.6980
   chunk 0 optimal weight:    7.9990
   chunk 55 optimal weight:    0.7980
   chunk 58 optimal weight:    1.9990
   chunk 14 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0970
   chunk 5 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 64 optimal weight:    5.9990
   overall best weight:    0.5178

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.154837 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3577 r_free = 0.3577 target = 0.131128 restraints weight = 6491.662|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.134564 restraints weight = 4660.825|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.135739 restraints weight = 3935.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.136520 restraints weight = 2939.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.137531 restraints weight = 2662.669|
|-----------------------------------------------------------------------------|
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2400

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   5762  Z= 0.108
  Angle     :  0.534   7.109   7872  Z= 0.271
  Chirality :  0.038   0.148    893
  Planarity :  0.003   0.035    924
  Dihedral  : 13.451  88.897   1009
  Min Nonbonded Distance : 2.509

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 19.26 %
    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: -0.48 (0.35), residues: 627
  helix:  1.87 (0.31), residues: 293
  sheet: -2.94 (0.63), residues: 67
  loop : -2.21 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.013   0.001   TYR A 390 
 PHE   0.008   0.001   PHE A 460 
 TRP   0.009   0.001   TRP A 646 
 HIS   0.004   0.000   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5758)
  covalent geometry    : angle       0.53433 ( 7872)
  hydrogen bonds       : bond        0.03598 (  260)
  hydrogen bonds       : angle       3.61186 (  737)
  metal coordination   : bond        0.00149 (    3)
  Misc. bond           : bond        0.00009 (    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
  92 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8864 (tppt) cc_final: 0.8541 (mptt)
REVERT: A  298 ASN cc_start: 0.8082 (t0) cc_final: 0.7786 (t0)
REVERT: A  511 GLN cc_start: 0.8072 (tm-30) cc_final: 0.7649 (tm-30)
REVERT: A  541 TYR cc_start: 0.8065 (m-80) cc_final: 0.7792 (m-80)
REVERT: A  907 LYS cc_start: 0.8565 (mttt) cc_final: 0.8166 (mtmm)
  outliers start: 14
  outliers final: 11
  residues processed: 87
  average time/residue: 0.0703
  time to fit residues: 8.1325
Evaluate side-chains
  82 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 71
  time to evaluate  : 0.199 
-------------------------------------------------------------------------------
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  882 PHE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 37 optimal weight:    2.9990
   chunk 10 optimal weight:    0.5980
   chunk 24 optimal weight:    4.9990
   chunk 1 optimal weight:    0.7980
   chunk 28 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9990
   chunk 39 optimal weight:    0.0570
   chunk 52 optimal weight:    0.8980
   overall best weight:    0.6298

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

Flipped N/Q/H residues before XYZ refinement:
A 588 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3815 r_free = 0.3815 target = 0.153901 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.130431 restraints weight = 6414.939|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3603 r_free = 0.3603 target = 0.133800 restraints weight = 4302.567|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.135156 restraints weight = 3710.191|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.135473 restraints weight = 2724.001|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.135878 restraints weight = 2675.309|
|-----------------------------------------------------------------------------|
r_work (final): 0.3525
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   5762  Z= 0.109
  Angle     :  0.523   7.345   7872  Z= 0.264
  Chirality :  0.038   0.139    893
  Planarity :  0.003   0.035    924
  Dihedral  : 13.384  89.133   1009
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 8.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 18.21 %
    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: -0.27 (0.36), residues: 627
  helix:  2.05 (0.31), residues: 291
  sheet: -2.94 (0.64), residues: 67
  loop : -2.04 (0.38), residues: 269

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   0.009   0.001   TRP A 771 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 5758)
  covalent geometry    : angle       0.52324 ( 7872)
  hydrogen bonds       : bond        0.03535 (  260)
  hydrogen bonds       : angle       3.56362 (  737)
  metal coordination   : bond        0.00119 (    3)
  Misc. bond           : bond        0.00014 (    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
  98 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 78
  time to evaluate  : 0.185 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8937 (tppt) cc_final: 0.8631 (mmtt)
REVERT: A  298 ASN cc_start: 0.8062 (t0) cc_final: 0.7760 (t0)
REVERT: A  511 GLN cc_start: 0.8118 (tm-30) cc_final: 0.7680 (tm-30)
REVERT: A  907 LYS cc_start: 0.8550 (mttt) cc_final: 0.8159 (mtmm)
  outliers start: 20
  outliers final: 16
  residues processed: 92
  average time/residue: 0.0715
  time to fit residues: 8.8399
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  : 0.208 
-------------------------------------------------------------------------------
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  344 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  485 LEU
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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 47 optimal weight:    0.7980
   chunk 57 optimal weight:    2.9990
   chunk 19 optimal weight:    3.9990
   chunk 43 optimal weight:    0.8980
   chunk 48 optimal weight:    0.4980
   chunk 39 optimal weight:    0.8980
   chunk 64 optimal weight:    5.9990
   chunk 55 optimal weight:    0.9980
   chunk 34 optimal weight:    2.9990
   chunk 32 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0030
   overall best weight:    0.6190

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3830 r_free = 0.3830 target = 0.154999 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.131079 restraints weight = 6572.997|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.134884 restraints weight = 4453.399|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3632 r_free = 0.3632 target = 0.136214 restraints weight = 3627.558|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.136507 restraints weight = 2705.428|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.137561 restraints weight = 2691.563|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7672
moved from start:          0.2612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   5762  Z= 0.108
  Angle     :  0.530   7.363   7872  Z= 0.265
  Chirality :  0.038   0.133    893
  Planarity :  0.003   0.034    924
  Dihedral  : 13.359  88.499   1009
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 8.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.54 %
    Favored  : 93.46 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 19.96 %
    Favored  : 76.71 %
  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:  2.10 (0.31), residues: 291
  sheet: -2.85 (0.62), residues: 73
  loop : -1.91 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 811 
 TYR   0.016   0.001   TYR A 390 
 PHE   0.007   0.001   PHE A 460 
 TRP   0.008   0.001   TRP A 771 
 HIS   0.003   0.001   HIS A 281 

Details of bonding type rmsd
  covalent geometry    : bond        0.00244 ( 5758)
  covalent geometry    : angle       0.52973 ( 7872)
  hydrogen bonds       : bond        0.03510 (  260)
  hydrogen bonds       : angle       3.53363 (  737)
  metal coordination   : bond        0.00194 (    3)
  Misc. bond           : bond        0.00012 (    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
  102 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  298 ASN cc_start: 0.7868 (t0) cc_final: 0.7539 (t0)
REVERT: A  511 GLN cc_start: 0.8097 (tm-30) cc_final: 0.7684 (tm-30)
REVERT: A  907 LYS cc_start: 0.8590 (mttt) cc_final: 0.8185 (mtmm)
  outliers start: 19
  outliers final: 17
  residues processed: 97
  average time/residue: 0.0720
  time to fit residues: 9.4209
Evaluate side-chains
  91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 74
  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  344 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  527 ASP
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 31 optimal weight:    5.9990
   chunk 22 optimal weight:    6.9990
   chunk 44 optimal weight:    9.9990
   chunk 59 optimal weight:    0.0980
   chunk 43 optimal weight:    0.9990
   chunk 21 optimal weight:    0.2980
   chunk 49 optimal weight:    5.9990
   chunk 20 optimal weight:    0.1980
   chunk 57 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   overall best weight:    0.4980

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

Flipped N/Q/H residues before XYZ refinement:
A 588 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3859 r_free = 0.3859 target = 0.157500 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3608 r_free = 0.3608 target = 0.133341 restraints weight = 6482.564|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3638 r_free = 0.3638 target = 0.136334 restraints weight = 4409.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3653 r_free = 0.3653 target = 0.137825 restraints weight = 3826.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3658 r_free = 0.3658 target = 0.138313 restraints weight = 2825.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.138645 restraints weight = 2755.554|
|-----------------------------------------------------------------------------|
r_work (final): 0.3545
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7663
moved from start:          0.2718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   5762  Z= 0.106
  Angle     :  0.542   7.285   7872  Z= 0.273
  Chirality :  0.038   0.156    893
  Planarity :  0.003   0.034    924
  Dihedral  : 13.346  88.083   1009
  Min Nonbonded Distance : 2.496

Molprobity Statistics.
  All-atom Clashscore : 7.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.86 %
    Favored  : 93.14 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.14 %
    Favored  : 76.36 %
  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: -0.13 (0.36), residues: 627
  helix:  2.12 (0.31), residues: 291
  sheet: -2.81 (0.62), residues: 73
  loop : -1.89 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.013   0.001   TYR A 390 
 PHE   0.007   0.001   PHE A 460 
 TRP   0.009   0.001   TRP A 771 
 HIS   0.003   0.000   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 5758)
  covalent geometry    : angle       0.54166 ( 7872)
  hydrogen bonds       : bond        0.03435 (  260)
  hydrogen bonds       : angle       3.51051 (  737)
  metal coordination   : bond        0.00156 (    3)
  Misc. bond           : bond        0.00011 (    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
  100 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 80
  time to evaluate  : 0.211 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.8034 (tp30) cc_final: 0.7694 (tp30)
REVERT: A  283 LYS cc_start: 0.8835 (tppt) cc_final: 0.8549 (mmmt)
REVERT: A  298 ASN cc_start: 0.7861 (t0) cc_final: 0.7510 (t0)
REVERT: A  511 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7695 (tm-30)
REVERT: A  907 LYS cc_start: 0.8558 (mttt) cc_final: 0.8143 (mtmm)
  outliers start: 20
  outliers final: 17
  residues processed: 93
  average time/residue: 0.0690
  time to fit residues: 8.6405
Evaluate side-chains
  93 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 76
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
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  344 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  481 ASP
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  489 ILE
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  527 ASP
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 17 optimal weight:    0.8980
   chunk 58 optimal weight:    7.9990
   chunk 53 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 9 optimal weight:    7.9990
   chunk 2 optimal weight:    4.9990
   chunk 46 optimal weight:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   overall best weight:    1.3384

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

Flipped N/Q/H residues before XYZ refinement:
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 = 0.3623 r_free = 0.3623 target = 0.136514 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.110816 restraints weight = 7142.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.114309 restraints weight = 4470.647|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.116786 restraints weight = 3285.670|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3413 r_free = 0.3413 target = 0.118422 restraints weight = 2645.245|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.119694 restraints weight = 2272.380|
|-----------------------------------------------------------------------------|
r_work (final): 0.3435
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7664
moved from start:          0.2772

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   5762  Z= 0.162
  Angle     :  0.593   7.977   7872  Z= 0.299
  Chirality :  0.040   0.163    893
  Planarity :  0.004   0.036    924
  Dihedral  : 13.273  88.031   1009
  Min Nonbonded Distance : 2.380

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.13 %
    Favored  : 91.87 %
  Rotamer:
    Outliers :  3.50 %
    Allowed  : 20.49 %
    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: -0.20 (0.36), residues: 627
  helix:  2.05 (0.31), residues: 291
  sheet: -2.96 (0.64), residues: 67
  loop : -1.90 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 602 
 TYR   0.016   0.001   TYR A 390 
 PHE   0.011   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 512 
 HIS   0.004   0.001   HIS A 871 

Details of bonding type rmsd
  covalent geometry    : bond        0.00379 ( 5758)
  covalent geometry    : angle       0.59312 ( 7872)
  hydrogen bonds       : bond        0.03935 (  260)
  hydrogen bonds       : angle       3.68945 (  737)
  metal coordination   : bond        0.00247 (    3)
  Misc. bond           : bond        0.00010 (    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
  95 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 75
  time to evaluate  : 0.227 
Fit side-chains
   revert: symmetry clash
REVERT: A  279 GLU cc_start: 0.8154 (tp30) cc_final: 0.7878 (tp30)
REVERT: A  283 LYS cc_start: 0.8853 (tppt) cc_final: 0.8338 (mmtt)
REVERT: A  298 ASN cc_start: 0.7951 (t0) cc_final: 0.7560 (t0)
REVERT: A  511 GLN cc_start: 0.8141 (tm-30) cc_final: 0.7701 (tm-30)
REVERT: A  907 LYS cc_start: 0.8592 (mttt) cc_final: 0.8095 (mtmm)
  outliers start: 20
  outliers final: 18
  residues processed: 90
  average time/residue: 0.0632
  time to fit residues: 7.7600
Evaluate side-chains
  91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  259 ASN
Chi-restraints excluded: chain A residue  273 VAL
Chi-restraints excluded: chain A residue  293 VAL
Chi-restraints excluded: chain A residue  321 VAL
Chi-restraints excluded: chain A residue  343 ILE
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  406 ILE
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  485 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  527 ASP
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 8 optimal weight:    4.9990
   chunk 45 optimal weight:    1.9990
   chunk 13 optimal weight:    0.0870
   chunk 14 optimal weight:    0.7980
   chunk 64 optimal weight:    6.9990
   chunk 9 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9980
   chunk 43 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0980
   chunk 11 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0060
   overall best weight:    0.3174

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

Flipped N/Q/H residues before XYZ refinement:
A 588 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3688 r_free = 0.3688 target = 0.141889 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.118089 restraints weight = 7133.093|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.121134 restraints weight = 4360.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3468 r_free = 0.3468 target = 0.122226 restraints weight = 3525.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3478 r_free = 0.3478 target = 0.123149 restraints weight = 2774.548|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3482 r_free = 0.3482 target = 0.123464 restraints weight = 2561.897|
|-----------------------------------------------------------------------------|
r_work (final): 0.3484
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7598
moved from start:          0.2830

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= 0.106
  Angle     :  0.553   7.061   7872  Z= 0.279
  Chirality :  0.038   0.165    893
  Planarity :  0.004   0.035    924
  Dihedral  : 13.353  87.582   1009
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.74 %
    Favored  : 94.26 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 21.37 %
    Favored  : 76.18 %
  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: -0.13 (0.36), residues: 627
  helix:  2.19 (0.31), residues: 291
  sheet: -2.78 (0.58), residues: 84
  loop : -1.91 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 602 
 TYR   0.016   0.001   TYR A 541 
 PHE   0.008   0.001   PHE A 272 
 TRP   0.010   0.001   TRP A 771 
 HIS   0.003   0.000   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00239 ( 5758)
  covalent geometry    : angle       0.55267 ( 7872)
  hydrogen bonds       : bond        0.03404 (  260)
  hydrogen bonds       : angle       3.51034 (  737)
  metal coordination   : bond        0.00126 (    3)
  Misc. bond           : bond        0.00000 (    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
  97 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 83
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  283 LYS cc_start: 0.8860 (tppt) cc_final: 0.8449 (mmtt)
REVERT: A  298 ASN cc_start: 0.7880 (t0) cc_final: 0.7485 (t0)
REVERT: A  511 GLN cc_start: 0.8110 (tm-30) cc_final: 0.7664 (tm-30)
REVERT: A  556 GLU cc_start: 0.7350 (tt0) cc_final: 0.7110 (mt-10)
REVERT: A  588 GLN cc_start: 0.7470 (OUTLIER) cc_final: 0.7256 (pp30)
REVERT: A  759 LYS cc_start: 0.8480 (tppp) cc_final: 0.8079 (tppt)
REVERT: A  907 LYS cc_start: 0.8562 (mttt) cc_final: 0.8060 (mtmm)
  outliers start: 14
  outliers final: 12
  residues processed: 93
  average time/residue: 0.0765
  time to fit residues: 9.3438
Evaluate side-chains
  91 residues out of total 574 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 78
  time to evaluate  : 0.210 
-------------------------------------------------------------------------------
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  485 LEU
Chi-restraints excluded: chain A residue  513 ILE
Chi-restraints excluded: chain A residue  588 GLN
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 65
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 23 optimal weight:    0.9980
   chunk 54 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 14 optimal weight:    0.6980
   chunk 55 optimal weight:    2.9990
   chunk 24 optimal weight:    2.9990
   chunk 58 optimal weight:    5.9990
   chunk 12 optimal weight:    0.1980
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
A 306 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.138663 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.3376 r_free = 0.3376 target = 0.114673 restraints weight = 7146.844|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.117764 restraints weight = 4597.980|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3425 r_free = 0.3425 target = 0.119331 restraints weight = 3503.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3430 r_free = 0.3430 target = 0.119861 restraints weight = 2787.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3433 r_free = 0.3433 target = 0.120055 restraints weight = 2689.884|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7661
moved from start:          0.2841

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= 0.136
  Angle     :  0.575   7.616   7872  Z= 0.291
  Chirality :  0.039   0.184    893
  Planarity :  0.004   0.044    924
  Dihedral  : 13.257  88.158   1009
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 8.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.34 %
    Favored  : 92.66 %
  Rotamer:
    Outliers :  2.45 %
    Allowed  : 22.24 %
    Favored  : 75.31 %
  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: -0.16 (0.36), residues: 627
  helix:  2.13 (0.31), residues: 291
  sheet: -2.86 (0.61), residues: 78
  loop : -1.90 (0.38), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 589 
 TYR   0.015   0.001   TYR A 390 
 PHE   0.009   0.001   PHE A 295 
 TRP   0.007   0.001   TRP A 771 
 HIS   0.004   0.001   HIS A 871 

Details of bonding type rmsd
  covalent geometry    : bond        0.00317 ( 5758)
  covalent geometry    : angle       0.57521 ( 7872)
  hydrogen bonds       : bond        0.03669 (  260)
  hydrogen bonds       : angle       3.63516 (  737)
  metal coordination   : bond        0.00255 (    3)
  Misc. bond           : bond        0.00010 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 955.90 seconds
wall clock time: 17 minutes 16.23 seconds (1036.23 seconds total)