Starting phenix.real_space_refine
on Fri Aug 22 16:18:02 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8sd0_40348/08_2025/8sd0_40348.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8sd0_40348/08_2025/8sd0_40348.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.8
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8sd0_40348/08_2025/8sd0_40348.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8sd0_40348/08_2025/8sd0_40348.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8sd0_40348/08_2025/8sd0_40348.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8sd0_40348/08_2025/8sd0_40348.map"
  }
  resolution = 3.8
  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      34      5.49       5
     S      31      5.16       5
     C    3598      2.51       5
     N     985      2.21       5
     O    1180      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 13 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5829
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 5140
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 636, 5140
          Classifications: {'peptide': 636}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PTRANS': 27, 'TRANS': 608}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 4
    Chain: "B"
      Number of atoms: 688
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 32, 688
          Unusual residues: {'GTP': 1}
          Classifications: {'RNA': 31, 'undetermined': 1}
          Modifications used: {'rna2p_pyr': 3, 'rna3p_pur': 14, 'rna3p_pyr': 14}
          Link IDs: {'rna2p': 3, 'rna3p': 27, None: 1}
            Not linked:
              pdbres="GTP B   1 "
              pdbres="  G B   2 "
    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   4208  SG  CYS A 810      27.805  58.529  40.084  1.00 67.93           S
  ATOM   4647  SG  CYS A 864      27.991  62.363  40.544  1.00 66.95           S
  ATOM   4686  SG  CYS A 869      27.689  60.503  42.864  1.00 72.48           S

  Time building chain proxies: 1.32, per 1000 atoms: 0.23
  Number of scatterers: 5829
  At special positions: 0
  Unit cell: (96.6, 81.9, 86.1, 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      34     15.00
     O    1180      8.00
     N     985      7.00
     C    3598      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: 0.48
  Conformation dependent library (CDL) restraints added in 382.3 milliseconds
  
  Enol-peptide restraints added in 1.2 microseconds
  
  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 "


  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1222

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 6 sheets defined
      51.4% alpha, 10.2% beta
      5 base pairs and 21 stacking pairs defined.
    Time for finding SS restraints: 0.69
  Creating SS restraints...
    Processing helix  chain 'A' and resid 244 through 256
      Proline residue:  A 253  - end of helix
      removed outlier: 3.741A  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: 3.690A  pdb=" N   LEU A 351 " --> pdb=" O   THR A 347 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 362 through 366
      removed outlier: 3.951A  pdb=" N   ILE A 365 " --> pdb=" O   SER A 362 " (cutoff:3.500A)
      removed outlier: 3.883A  pdb=" N   PHE A 366 " --> pdb=" O   LEU A 363 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 362 through 366'
    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 435
    Processing helix  chain 'A' and resid 445 through 452
      removed outlier: 3.803A  pdb=" N   LEU A 449 " --> pdb=" O   ASN A 445 " (cutoff:3.500A)
      removed outlier: 3.866A  pdb=" N   VAL A 452 " --> pdb=" O   GLU A 448 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 469 through 487
    Processing helix  chain 'A' and resid 492 through 496
      removed outlier: 3.856A  pdb=" N   LEU A 496 " --> pdb=" O   LEU A 493 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 506 through 520
    Processing helix  chain 'A' and resid 521 through 523
      No H-bonds generated for 'chain 'A' and resid 521 through 523'
    Processing helix  chain 'A' and resid 529 through 558
      removed outlier: 3.725A  pdb=" N   ARG A 533 " --> pdb=" O   ASP A 529 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 559 through 576
      removed outlier: 3.704A  pdb=" N   ALA A 563 " --> pdb=" O   ARG A 559 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 580 through 602
      removed outlier: 4.113A  pdb=" N   GLN A 595 " --> pdb=" O   GLU A 591 " (cutoff:3.500A)
      removed outlier: 5.048A  pdb=" N   GLU A 596 " --> pdb=" O   GLU A 592 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 603 through 607
      removed outlier: 3.555A  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 649
      removed outlier: 3.552A  pdb=" N   VAL A 640 " --> pdb=" O   THR A 636 " (cutoff:3.500A)
      removed outlier: 4.306A  pdb=" N   ASP A 641 " --> pdb=" O   ARG A 637 " (cutoff:3.500A)
      removed outlier: 4.064A  pdb=" N   ALA A 642 " --> pdb=" O   ALA A 638 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 744 through 771
      removed outlier: 4.087A  pdb=" N   ILE A 748 " --> pdb=" O   ASN A 744 " (cutoff:3.500A)
      removed outlier: 3.501A  pdb=" N   TRP A 771 " --> pdb=" O   ARG A 767 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 772 through 794
      removed outlier: 4.130A  pdb=" N   PHE A 776 " --> pdb=" O   ASP A 772 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 837 through 840
      removed outlier: 3.608A  pdb=" N   GLU A 840 " --> pdb=" O   ALA A 837 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 837 through 840'
    Processing helix  chain 'A' and resid 889 through 892
    Processing sheet with id=AA1, first strand: chain 'A' and resid 261 through 263
      removed outlier: 6.565A  pdb=" N   ILE A 262 " --> pdb=" O   THR A 409 " (cutoff:3.500A)
      removed outlier: 6.929A  pdb=" N   LEU A 408 " --> pdb=" O   MET A 369 " (cutoff:3.500A)
      removed outlier: 6.007A  pdb=" N   PHE A 371 " --> pdb=" O   LEU A 408 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 457 through 458
      removed outlier: 6.615A  pdb=" N   GLN A 457 " --> pdb=" O   CYS A 738 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   LEU A 740 " --> pdb=" O   GLN A 457 " (cutoff:3.500A)
      removed outlier: 3.855A  pdb=" N   THR A 742 " --> pdb=" O   ARG A 461 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 457 through 458
      removed outlier: 6.615A  pdb=" N   GLN A 457 " --> pdb=" O   CYS A 738 " (cutoff:3.500A)
      removed outlier: 7.495A  pdb=" N   LEU A 740 " --> pdb=" O   GLN A 457 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   THR A 630 " --> pdb=" O   LEU A 694 " (cutoff:3.500A)
      removed outlier: 7.509A  pdb=" N   ALA A 696 " --> pdb=" O   THR A 630 " (cutoff:3.500A)
      removed outlier: 5.837A  pdb=" N   LEU A 632 " --> pdb=" O   ALA A 696 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 816 through 819
      removed outlier: 3.754A  pdb=" N   CYS A 818 " --> pdb=" O   LEU A 808 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 823 through 825
    Processing sheet with id=AA6, first strand: chain 'A' and resid 842 through 846
      removed outlier: 5.865A  pdb=" N   LYS A 858 " --> pdb=" O   LYS A 878 " (cutoff:3.500A)
      removed outlier: 6.759A  pdb=" N   LYS A 878 " --> pdb=" O   LYS A 858 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   GLY A 874 " --> pdb=" O   ILE A 862 " (cutoff:3.500A)
      removed outlier: 6.847A  pdb=" N   CYS A 864 " --> pdb=" O   ASP A 872 " (cutoff:3.500A)
      removed outlier: 7.441A  pdb=" N   ASP A 872 " --> pdb=" O   CYS A 864 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    723 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      12 hydrogen bonds
      24 hydrogen bond angles
      0 basepair planarities
      5 basepair parallelities
      21 stacking parallelities
  Total time for adding SS restraints: 1.02

  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:
        1.22 -     1.34: 1673
        1.34 -     1.46: 1226
        1.46 -     1.58: 3002
        1.58 -     1.70: 67
        1.70 -     1.82: 43
  Bond restraints: 6011
  Sorted by residual:
  bond pdb=" C   LEU A 252 "
       pdb=" N   PRO A 253 "
    ideal  model  delta    sigma   weight residual
    1.336  1.367 -0.031 1.20e-02 6.94e+03 6.61e+00
  bond pdb=" CA  PRO A 626 "
       pdb=" C   PRO A 626 "
    ideal  model  delta    sigma   weight residual
    1.522  1.545 -0.023 9.80e-03 1.04e+04 5.31e+00
  bond pdb=" CB  GLU A 751 "
       pdb=" CG  GLU A 751 "
    ideal  model  delta    sigma   weight residual
    1.520  1.587 -0.067 3.00e-02 1.11e+03 5.00e+00
  bond pdb=" CB  GLU A 620 "
       pdb=" CG  GLU A 620 "
    ideal  model  delta    sigma   weight residual
    1.520  1.474  0.046 3.00e-02 1.11e+03 2.35e+00
  bond pdb=" CB  GLU A 581 "
       pdb=" CG  GLU A 581 "
    ideal  model  delta    sigma   weight residual
    1.520  1.563 -0.043 3.00e-02 1.11e+03 2.04e+00
  ... (remaining 6006 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.32: 8054
        2.32 -     4.65: 162
        4.65 -     6.97: 34
        6.97 -     9.30: 11
        9.30 -    11.62: 3
  Bond angle restraints: 8264
  Sorted by residual:
  angle pdb=" CB  GLU A 751 "
        pdb=" CG  GLU A 751 "
        pdb=" CD  GLU A 751 "
      ideal   model   delta    sigma   weight residual
     112.60  120.19   -7.59 1.70e+00 3.46e-01 2.00e+01
  angle pdb=" N   ASP A 392 "
        pdb=" CA  ASP A 392 "
        pdb=" C   ASP A 392 "
      ideal   model   delta    sigma   weight residual
     111.36  106.58    4.78 1.09e+00 8.42e-01 1.93e+01
  angle pdb=" CB  ARG A 316 "
        pdb=" CG  ARG A 316 "
        pdb=" CD  ARG A 316 "
      ideal   model   delta    sigma   weight residual
     111.30  121.01   -9.71 2.30e+00 1.89e-01 1.78e+01
  angle pdb=" CA  GLU A 751 "
        pdb=" CB  GLU A 751 "
        pdb=" CG  GLU A 751 "
      ideal   model   delta    sigma   weight residual
     114.10  122.16   -8.06 2.00e+00 2.50e-01 1.62e+01
  angle pdb=" C   ARG A 559 "
        pdb=" N   MET A 560 "
        pdb=" CA  MET A 560 "
      ideal   model   delta    sigma   weight residual
     120.44  125.78   -5.34 1.36e+00 5.41e-01 1.54e+01
  ... (remaining 8259 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    18.47: 3164
       18.47 -    36.94: 390
       36.94 -    55.42: 96
       55.42 -    73.89: 52
       73.89 -    92.36: 10
  Dihedral angle restraints: 3712
    sinusoidal: 1837
      harmonic: 1875
  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   24.12   80.48     1      2.00e+01 2.50e-03 2.00e+01
  dihedral pdb=" CA  VAL A 877 "
           pdb=" C   VAL A 877 "
           pdb=" N   LYS A 878 "
           pdb=" CA  LYS A 878 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  159.55   20.45     0      5.00e+00 4.00e-02 1.67e+01
  dihedral pdb=" CA  PHE A 853 "
           pdb=" C   PHE A 853 "
           pdb=" N   SER A 854 "
           pdb=" CA  SER A 854 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.29   18.71     0      5.00e+00 4.00e-02 1.40e+01
  ... (remaining 3709 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 732
       0.050 -    0.100: 170
       0.100 -    0.150: 31
       0.150 -    0.200: 10
       0.200 -    0.250: 3
  Chirality restraints: 946
  Sorted by residual:
  chirality pdb=" CB  ILE A 261 "
            pdb=" CA  ILE A 261 "
            pdb=" CG1 ILE A 261 "
            pdb=" CG2 ILE A 261 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.89   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CB  ILE A 693 "
            pdb=" CA  ILE A 693 "
            pdb=" CG1 ILE A 693 "
            pdb=" CG2 ILE A 693 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.40    0.25 2.00e-01 2.50e+01 1.54e+00
  chirality pdb=" CB  ILE A 695 "
            pdb=" CA  ILE A 695 "
            pdb=" CG1 ILE A 695 "
            pdb=" CG2 ILE A 695 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.44    0.21 2.00e-01 2.50e+01 1.07e+00
  ... (remaining 943 not shown)

  Planarity restraints: 936
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN A 625 "    0.053 5.00e-02 4.00e+02   8.09e-02 1.05e+01
        pdb=" N   PRO A 626 "   -0.140 5.00e-02 4.00e+02
        pdb=" CA  PRO A 626 "    0.044 5.00e-02 4.00e+02
        pdb=" CD  PRO A 626 "    0.043 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CG  GLU A 778 "   -0.015 2.00e-02 2.50e+03   3.04e-02 9.25e+00
        pdb=" CD  GLU A 778 "    0.053 2.00e-02 2.50e+03
        pdb=" OE1 GLU A 778 "   -0.019 2.00e-02 2.50e+03
        pdb=" OE2 GLU A 778 "   -0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 343 "    0.014 2.00e-02 2.50e+03   2.86e-02 8.17e+00
        pdb=" C   ILE A 343 "   -0.049 2.00e-02 2.50e+03
        pdb=" O   ILE A 343 "    0.019 2.00e-02 2.50e+03
        pdb=" N   ILE A 344 "    0.017 2.00e-02 2.50e+03
  ... (remaining 933 not shown)

  Histogram of nonbonded interaction distances:
        2.28 -     2.80: 1453
        2.80 -     3.33: 5383
        3.33 -     3.85: 9945
        3.85 -     4.38: 10803
        4.38 -     4.90: 18313
  Nonbonded interactions: 45897
  Sorted by model distance:
  nonbonded pdb=" C3' GTP B   1 "
            pdb=" OP2   G B   2 "
     model   vdw
     2.276 2.776
  nonbonded pdb=" O   GLU A 583 "
            pdb=" OG1 THR A 587 "
     model   vdw
     2.307 3.040
  nonbonded pdb=" O   SER A 891 "
            pdb=" OG  SER A 891 "
     model   vdw
     2.329 3.040
  nonbonded pdb=" CD1 LEU A 611 "
            pdb=" OH  TYR A 715 "
     model   vdw
     2.333 3.460
  nonbonded pdb=" O   HIS A 557 "
            pdb=" OH  TYR A 715 "
     model   vdw
     2.352 3.040
  ... (remaining 45892 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:             0.470
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     8.210
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.290
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.080
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7800
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.078   6015  Z= 0.215
  Angle     :  0.860  11.624   8264  Z= 0.451
  Chirality :  0.047   0.250    946
  Planarity :  0.007   0.094    936
  Dihedral  : 18.359  92.360   2490
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 9.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  0.52 %
    Allowed  : 24.70 %
    Favored  : 74.78 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.62 (0.31), residues: 628
  helix:  0.17 (0.29), residues: 283
  sheet: -2.01 (0.53), residues: 86
  loop : -2.12 (0.35), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.023   0.001   ARG A 316 
 TYR   0.036   0.002   TYR A 548 
 PHE   0.026   0.002   PHE A 776 
 TRP   0.045   0.003   TRP A 646 
 HIS   0.002   0.001   HIS A 782 

Details of bonding type rmsd
  covalent geometry    : bond        0.00402 ( 6011)
  covalent geometry    : angle       0.86020 ( 8264)
  hydrogen bonds       : bond        0.13540 (  260)
  hydrogen bonds       : angle       6.06561 (  747)
  metal coordination   : bond        0.00112 (    3)
  Misc. bond           : bond        0.07791 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  109 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 106
  time to evaluate  : 0.167 
Fit side-chains
REVERT: A  317 HIS cc_start: 0.6894 (m-70) cc_final: 0.5916 (m-70)
REVERT: A  503 GLU cc_start: 0.7620 (pm20) cc_final: 0.6557 (pm20)
REVERT: A  876 HIS cc_start: 0.7792 (OUTLIER) cc_final: 0.6992 (t70)
REVERT: A  895 GLU cc_start: 0.7731 (pt0) cc_final: 0.7286 (pt0)
  outliers start: 3
  outliers final: 1
  residues processed: 109
  average time/residue: 0.0781
  time to fit residues: 11.0637
Evaluate side-chains
  90 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 88
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  876 HIS
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 49 optimal weight:    0.9980
   chunk 53 optimal weight:    2.9990
   chunk 5 optimal weight:    3.9990
   chunk 33 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.5980
   chunk 51 optimal weight:    4.9990
   chunk 38 optimal weight:   10.0000
   chunk 61 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9990
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.8984

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

Flipped N/Q/H residues before XYZ refinement:
A 317 HIS
A 500 GLN
A 623 HIS
A 710 ASN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.142463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.116186 restraints weight = 9042.730|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.119739 restraints weight = 5236.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3527 r_free = 0.3527 target = 0.122151 restraints weight = 3670.222|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 46)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.123762 restraints weight = 2903.345|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.124698 restraints weight = 2468.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.3565
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7841
moved from start:          0.1290

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   6015  Z= 0.121
  Angle     :  0.550   7.702   8264  Z= 0.279
  Chirality :  0.038   0.154    946
  Planarity :  0.004   0.051    936
  Dihedral  : 15.506  93.942   1178
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.30 %
    Allowed  : 24.87 %
    Favored  : 71.83 %
  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 aren not related in a simple way.
  whole: -0.83 (0.33), residues: 628
  helix:  1.10 (0.31), residues: 291
  sheet: -1.92 (0.53), residues: 85
  loop : -2.05 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG A 316 
 TYR   0.027   0.001   TYR A 548 
 PHE   0.021   0.001   PHE A 616 
 TRP   0.017   0.001   TRP A 646 
 HIS   0.009   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00263 ( 6011)
  covalent geometry    : angle       0.55013 ( 8264)
  hydrogen bonds       : bond        0.04144 (  260)
  hydrogen bonds       : angle       4.24138 (  747)
  metal coordination   : bond        0.00178 (    3)
  Misc. bond           : bond        0.00050 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  114 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 95
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
REVERT: A  777 ARG cc_start: 0.8478 (tpp80) cc_final: 0.7997 (tpp-160)
  outliers start: 19
  outliers final: 11
  residues processed: 108
  average time/residue: 0.0657
  time to fit residues: 9.7460
Evaluate side-chains
  99 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 88
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  294 VAL
Chi-restraints excluded: chain A residue  344 ILE
Chi-restraints excluded: chain A residue  434 LEU
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 21 optimal weight:    6.9990
   chunk 2 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 20 optimal weight:    3.9990
   chunk 19 optimal weight:    0.8980
   chunk 10 optimal weight:    0.5980
   chunk 17 optimal weight:    8.9990
   chunk 23 optimal weight:    0.6980
   chunk 52 optimal weight:    2.9990
   chunk 49 optimal weight:    5.9990
   chunk 47 optimal weight:    5.9990
   overall best weight:    1.2384

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

Flipped N/Q/H residues before XYZ refinement:
A 280 HIS
A 500 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3764 r_free = 0.3764 target = 0.139910 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3409 r_free = 0.3409 target = 0.113538 restraints weight = 8941.008|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.117022 restraints weight = 5191.302|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3485 r_free = 0.3485 target = 0.119138 restraints weight = 3669.785|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.120841 restraints weight = 2956.622|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.121768 restraints weight = 2523.478|
|-----------------------------------------------------------------------------|
r_work (final): 0.3531
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7879
moved from start:          0.1533

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   6015  Z= 0.138
  Angle     :  0.556   8.230   8264  Z= 0.281
  Chirality :  0.038   0.150    946
  Planarity :  0.004   0.049    936
  Dihedral  : 15.446  92.368   1176
  Min Nonbonded Distance : 2.385

Molprobity Statistics.
  All-atom Clashscore : 8.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.52 %
    Allowed  : 23.65 %
    Favored  : 71.83 %
  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 aren not related in a simple way.
  whole: -0.50 (0.34), residues: 628
  helix:  1.32 (0.31), residues: 297
  sheet: -1.62 (0.60), residues: 70
  loop : -1.96 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 316 
 TYR   0.025   0.001   TYR A 548 
 PHE   0.028   0.001   PHE A 616 
 TRP   0.019   0.001   TRP A 646 
 HIS   0.003   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00306 ( 6011)
  covalent geometry    : angle       0.55609 ( 8264)
  hydrogen bonds       : bond        0.03961 (  260)
  hydrogen bonds       : angle       4.08352 (  747)
  metal coordination   : bond        0.00229 (    3)
  Misc. bond           : bond        0.00061 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  120 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 94
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
REVERT: A  777 ARG cc_start: 0.8526 (tpp80) cc_final: 0.8086 (tpp-160)
  outliers start: 26
  outliers final: 18
  residues processed: 115
  average time/residue: 0.0631
  time to fit residues: 9.8934
Evaluate side-chains
  106 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 88
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  282 LEU
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  434 LEU
Chi-restraints excluded: chain A residue  442 VAL
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  770 THR
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 25 optimal weight:    0.0020
   chunk 9 optimal weight:    4.9990
   chunk 10 optimal weight:    1.9990
   chunk 2 optimal weight:    6.9990
   chunk 38 optimal weight:   10.0000
   chunk 27 optimal weight:    0.9980
   chunk 41 optimal weight:    0.0970
   chunk 8 optimal weight:    6.9990
   chunk 29 optimal weight:    1.9990
   chunk 57 optimal weight:    6.9990
   chunk 61 optimal weight:    2.9990
   overall best weight:    1.0190

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 HIS
A 500 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3766 r_free = 0.3766 target = 0.140128 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3414 r_free = 0.3414 target = 0.113745 restraints weight = 9050.942|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3461 r_free = 0.3461 target = 0.117223 restraints weight = 5261.964|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3494 r_free = 0.3494 target = 0.119593 restraints weight = 3733.203|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3511 r_free = 0.3511 target = 0.120993 restraints weight = 2966.210|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3530 r_free = 0.3530 target = 0.122240 restraints weight = 2554.394|
|-----------------------------------------------------------------------------|
r_work (final): 0.3540
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7870
moved from start:          0.1695

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6015  Z= 0.124
  Angle     :  0.565   9.634   8264  Z= 0.281
  Chirality :  0.039   0.166    946
  Planarity :  0.004   0.048    936
  Dihedral  : 15.459  92.202   1176
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  4.35 %
    Allowed  : 24.70 %
    Favored  : 70.96 %
  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 aren not related in a simple way.
  whole: -0.38 (0.34), residues: 628
  helix:  1.45 (0.30), residues: 297
  sheet: -1.61 (0.60), residues: 70
  loop : -1.92 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 316 
 TYR   0.025   0.001   TYR A 548 
 PHE   0.033   0.001   PHE A 616 
 TRP   0.014   0.001   TRP A 646 
 HIS   0.005   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00276 ( 6011)
  covalent geometry    : angle       0.56486 ( 8264)
  hydrogen bonds       : bond        0.03843 (  260)
  hydrogen bonds       : angle       4.03454 (  747)
  metal coordination   : bond        0.00177 (    3)
  Misc. bond           : bond        0.00053 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  121 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 96
  time to evaluate  : 0.204 
Fit side-chains
   revert: symmetry clash
REVERT: A  493 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8437 (tt)
REVERT: A  623 HIS cc_start: 0.8329 (t-90) cc_final: 0.8110 (t-170)
REVERT: A  777 ARG cc_start: 0.8560 (tpp80) cc_final: 0.8091 (tpp-160)
  outliers start: 25
  outliers final: 17
  residues processed: 116
  average time/residue: 0.0681
  time to fit residues: 10.8031
Evaluate side-chains
  108 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  282 LEU
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  493 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  506 THR
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 13 optimal weight:    2.9990
   chunk 28 optimal weight:    0.7980
   chunk 6 optimal weight:    0.8980
   chunk 2 optimal weight:    5.9990
   chunk 46 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 60 optimal weight:    0.7980
   chunk 31 optimal weight:    0.7980
   chunk 32 optimal weight:    3.9990
   chunk 17 optimal weight:    0.0670
   chunk 42 optimal weight:   10.0000
   overall best weight:    0.6718

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.141750 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3436 r_free = 0.3436 target = 0.115449 restraints weight = 9079.229|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3486 r_free = 0.3486 target = 0.119022 restraints weight = 5200.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.121453 restraints weight = 3654.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.123047 restraints weight = 2886.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3555 r_free = 0.3555 target = 0.124099 restraints weight = 2457.724|
|-----------------------------------------------------------------------------|
r_work (final): 0.3561
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7840
moved from start:          0.1769

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6015  Z= 0.109
  Angle     :  0.575  10.213   8264  Z= 0.284
  Chirality :  0.039   0.184    946
  Planarity :  0.004   0.047    936
  Dihedral  : 15.487  91.810   1176
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 10.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 24.52 %
    Favored  : 70.61 %
  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 aren not related in a simple way.
  whole: -0.34 (0.34), residues: 628
  helix:  1.45 (0.31), residues: 297
  sheet: -1.50 (0.61), residues: 70
  loop : -1.89 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 466 
 TYR   0.026   0.001   TYR A 548 
 PHE   0.030   0.001   PHE A 616 
 TRP   0.011   0.001   TRP A 646 
 HIS   0.003   0.000   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00240 ( 6011)
  covalent geometry    : angle       0.57533 ( 8264)
  hydrogen bonds       : bond        0.03737 (  260)
  hydrogen bonds       : angle       3.96697 (  747)
  metal coordination   : bond        0.00116 (    3)
  Misc. bond           : bond        0.00051 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.247 
Fit side-chains
   revert: symmetry clash
REVERT: A  493 LEU cc_start: 0.9022 (OUTLIER) cc_final: 0.8415 (tt)
REVERT: A  777 ARG cc_start: 0.8565 (tpp80) cc_final: 0.8157 (tpp-160)
  outliers start: 28
  outliers final: 18
  residues processed: 121
  average time/residue: 0.0684
  time to fit residues: 11.1902
Evaluate side-chains
  108 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.206 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  282 LEU
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  493 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 11 optimal weight:    0.9980
   chunk 40 optimal weight:    6.9990
   chunk 7 optimal weight:    0.7980
   chunk 56 optimal weight:    0.0170
   chunk 39 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 28 optimal weight:    0.9990
   chunk 64 optimal weight:    8.9990
   chunk 45 optimal weight:    8.9990
   overall best weight:    0.9622

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 GLN
A 623 HIS
A 784 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3781 r_free = 0.3781 target = 0.141197 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.114683 restraints weight = 9008.685|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.118162 restraints weight = 5257.529|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.120574 restraints weight = 3716.550|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.122017 restraints weight = 2951.841|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.123142 restraints weight = 2537.851|
|-----------------------------------------------------------------------------|
r_work (final): 0.3539
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7856
moved from start:          0.1879

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6015  Z= 0.125
  Angle     :  0.602  10.650   8264  Z= 0.298
  Chirality :  0.040   0.186    946
  Planarity :  0.004   0.047    936
  Dihedral  : 15.478  90.930   1176
  Min Nonbonded Distance : 2.425

Molprobity Statistics.
  All-atom Clashscore : 10.92
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.01 %
    Favored  : 92.99 %
  Rotamer:
    Outliers :  5.39 %
    Allowed  : 24.70 %
    Favored  : 69.91 %
  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 aren not related in a simple way.
  whole: -0.27 (0.35), residues: 628
  helix:  1.53 (0.31), residues: 297
  sheet: -1.67 (0.60), residues: 72
  loop : -1.80 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG A 466 
 TYR   0.028   0.001   TYR A 548 
 PHE   0.037   0.001   PHE A 616 
 TRP   0.009   0.001   TRP A 646 
 HIS   0.005   0.001   HIS A 623 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 6011)
  covalent geometry    : angle       0.60217 ( 8264)
  hydrogen bonds       : bond        0.03790 (  260)
  hydrogen bonds       : angle       3.95863 (  747)
  metal coordination   : bond        0.00164 (    3)
  Misc. bond           : bond        0.00051 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 31
    poor density    : 95
  time to evaluate  : 0.215 
Fit side-chains
   revert: symmetry clash
REVERT: A  493 LEU cc_start: 0.9020 (OUTLIER) cc_final: 0.8424 (tt)
REVERT: A  777 ARG cc_start: 0.8595 (tpp80) cc_final: 0.8193 (tpp-160)
  outliers start: 31
  outliers final: 19
  residues processed: 121
  average time/residue: 0.0705
  time to fit residues: 11.6247
Evaluate side-chains
  109 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 89
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  282 LEU
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  493 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 25 optimal weight:    2.9990
   chunk 24 optimal weight:    3.9990
   chunk 36 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   chunk 51 optimal weight:    0.1980
   chunk 30 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 22 optimal weight:    4.9990
   chunk 12 optimal weight:    0.3980
   chunk 64 optimal weight:    7.9990
   chunk 17 optimal weight:    3.9990
   overall best weight:    0.5980

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 876 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3798 r_free = 0.3798 target = 0.142413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.115823 restraints weight = 9037.142|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.119365 restraints weight = 5230.064|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3528 r_free = 0.3528 target = 0.121795 restraints weight = 3683.075|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 42)----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.123370 restraints weight = 2916.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.124219 restraints weight = 2496.845|
|-----------------------------------------------------------------------------|
r_work (final): 0.3554
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7833
moved from start:          0.1927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.031   6015  Z= 0.112
  Angle     :  0.610  11.140   8264  Z= 0.301
  Chirality :  0.039   0.182    946
  Planarity :  0.003   0.046    936
  Dihedral  : 15.506  90.441   1176
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.17 %
    Favored  : 92.83 %
  Rotamer:
    Outliers :  4.87 %
    Allowed  : 24.87 %
    Favored  : 70.26 %
  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 aren not related in a simple way.
  whole: -0.23 (0.35), residues: 628
  helix:  1.54 (0.31), residues: 297
  sheet: -1.64 (0.61), residues: 72
  loop : -1.78 (0.38), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.000   ARG A 466 
 TYR   0.029   0.001   TYR A 548 
 PHE   0.034   0.002   PHE A 616 
 TRP   0.013   0.001   TRP A 646 
 HIS   0.001   0.000   HIS A 847 

Details of bonding type rmsd
  covalent geometry    : bond        0.00247 ( 6011)
  covalent geometry    : angle       0.61011 ( 8264)
  hydrogen bonds       : bond        0.03738 (  260)
  hydrogen bonds       : angle       3.93221 (  747)
  metal coordination   : bond        0.00101 (    3)
  Misc. bond           : bond        0.00049 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 98
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
REVERT: A  479 MET cc_start: 0.8126 (mmt) cc_final: 0.7853 (mmt)
REVERT: A  493 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8428 (tt)
REVERT: A  777 ARG cc_start: 0.8588 (tpp80) cc_final: 0.8186 (tpp-160)
  outliers start: 28
  outliers final: 18
  residues processed: 122
  average time/residue: 0.0741
  time to fit residues: 12.1887
Evaluate side-chains
  111 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.214 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  285 PHE
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  493 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  546 ARG
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  694 LEU
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 11 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 10 optimal weight:    0.5980
   chunk 3 optimal weight:    0.7980
   chunk 55 optimal weight:    2.9990
   chunk 40 optimal weight:    8.9990
   chunk 1 optimal weight:    0.6980
   chunk 27 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 280 HIS
A 500 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3801 r_free = 0.3801 target = 0.142615 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3447 r_free = 0.3447 target = 0.116152 restraints weight = 8976.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.119635 restraints weight = 5239.497|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.122058 restraints weight = 3703.912|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 27)----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.123518 restraints weight = 2933.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 21)----------------|
| r_work = 0.3560 r_free = 0.3560 target = 0.124446 restraints weight = 2518.762|
|-----------------------------------------------------------------------------|
r_work (final): 0.3557
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2048

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   6015  Z= 0.117
  Angle     :  0.621  11.236   8264  Z= 0.306
  Chirality :  0.040   0.177    946
  Planarity :  0.003   0.046    936
  Dihedral  : 15.491  89.711   1176
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.69 %
    Favored  : 93.31 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 26.61 %
    Favored  : 69.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.28 (0.35), residues: 628
  helix:  1.52 (0.31), residues: 297
  sheet: -1.71 (0.60), residues: 74
  loop : -1.79 (0.38), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.000   ARG A 466 
 TYR   0.032   0.001   TYR A 548 
 PHE   0.041   0.001   PHE A 616 
 TRP   0.012   0.001   TRP A 646 
 HIS   0.007   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00260 ( 6011)
  covalent geometry    : angle       0.62063 ( 8264)
  hydrogen bonds       : bond        0.03768 (  260)
  hydrogen bonds       : angle       3.94742 (  747)
  metal coordination   : bond        0.00116 (    3)
  Misc. bond           : bond        0.00050 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 96
  time to evaluate  : 0.226 
Fit side-chains
   revert: symmetry clash
REVERT: A  493 LEU cc_start: 0.9042 (OUTLIER) cc_final: 0.8444 (tt)
REVERT: A  777 ARG cc_start: 0.8568 (tpp80) cc_final: 0.8190 (tpp-160)
  outliers start: 22
  outliers final: 18
  residues processed: 114
  average time/residue: 0.0723
  time to fit residues: 11.1691
Evaluate side-chains
  111 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
Chi-restraints excluded: chain A residue  285 PHE
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  493 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  775 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 62 optimal weight:    6.9990
   chunk 61 optimal weight:    3.9990
   chunk 50 optimal weight:    7.9990
   chunk 25 optimal weight:    0.3980
   chunk 63 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 54 optimal weight:    6.9990
   chunk 45 optimal weight:    6.9990
   chunk 1 optimal weight:    0.1980
   chunk 42 optimal weight:    0.1980
   overall best weight:    1.1584

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3771 r_free = 0.3771 target = 0.140203 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.114151 restraints weight = 9062.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3470 r_free = 0.3470 target = 0.117617 restraints weight = 5167.773|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.119979 restraints weight = 3621.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3522 r_free = 0.3522 target = 0.121483 restraints weight = 2860.501|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3538 r_free = 0.3538 target = 0.122579 restraints weight = 2445.742|
|-----------------------------------------------------------------------------|
r_work (final): 0.3550
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7853
moved from start:          0.2111

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6015  Z= 0.140
  Angle     :  0.648  11.339   8264  Z= 0.320
  Chirality :  0.040   0.178    946
  Planarity :  0.004   0.046    936
  Dihedral  : 15.464  88.784   1176
  Min Nonbonded Distance : 2.419

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.32 %
    Favored  : 92.68 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 26.26 %
    Favored  : 69.91 %
  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 aren not related in a simple way.
  whole: -0.34 (0.35), residues: 628
  helix:  1.48 (0.31), residues: 297
  sheet: -1.83 (0.58), residues: 78
  loop : -1.80 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 466 
 TYR   0.035   0.001   TYR A 548 
 PHE   0.038   0.002   PHE A 616 
 TRP   0.014   0.001   TRP A 646 
 HIS   0.004   0.001   HIS A 280 

Details of bonding type rmsd
  covalent geometry    : bond        0.00314 ( 6011)
  covalent geometry    : angle       0.64767 ( 8264)
  hydrogen bonds       : bond        0.03850 (  260)
  hydrogen bonds       : angle       4.01388 (  747)
  metal coordination   : bond        0.00198 (    3)
  Misc. bond           : bond        0.00052 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  116 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 94
  time to evaluate  : 0.212 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  363 LEU cc_start: 0.8725 (tp) cc_final: 0.8506 (tp)
REVERT: A  493 LEU cc_start: 0.9015 (OUTLIER) cc_final: 0.8417 (tt)
REVERT: A  546 ARG cc_start: 0.8569 (OUTLIER) cc_final: 0.8276 (ttt-90)
REVERT: A  573 ASN cc_start: 0.8386 (m110) cc_final: 0.8170 (m110)
REVERT: A  777 ARG cc_start: 0.8559 (tpp80) cc_final: 0.8166 (tpp-160)
  outliers start: 22
  outliers final: 16
  residues processed: 113
  average time/residue: 0.0729
  time to fit residues: 11.1499
Evaluate side-chains
  108 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 90
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
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  493 LEU
Chi-restraints excluded: chain A residue  546 ARG
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 7 optimal weight:    2.9990
   chunk 16 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 58 optimal weight:    3.9990
   chunk 63 optimal weight:    4.9990
   chunk 2 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 19 optimal weight:    0.9990
   chunk 65 optimal weight:    5.9990
   chunk 5 optimal weight:    0.7980
   chunk 64 optimal weight:    7.9990
   overall best weight:    0.8584

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.141478 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.115632 restraints weight = 9086.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.119129 restraints weight = 5142.852|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3520 r_free = 0.3520 target = 0.121472 restraints weight = 3584.731|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3541 r_free = 0.3541 target = 0.123041 restraints weight = 2832.112|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.123961 restraints weight = 2403.613|
|-----------------------------------------------------------------------------|
r_work (final): 0.3555
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7830
moved from start:          0.2161

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6015  Z= 0.126
  Angle     :  0.655  11.269   8264  Z= 0.321
  Chirality :  0.040   0.189    946
  Planarity :  0.004   0.046    936
  Dihedral  : 15.489  87.987   1176
  Min Nonbonded Distance : 2.463

Molprobity Statistics.
  All-atom Clashscore : 11.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.85 %
    Favored  : 93.15 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 26.43 %
    Favored  : 69.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.29 (0.35), residues: 628
  helix:  1.50 (0.31), residues: 297
  sheet: -1.77 (0.57), residues: 78
  loop : -1.76 (0.39), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 466 
 TYR   0.037   0.001   TYR A 548 
 PHE   0.040   0.001   PHE A 616 
 TRP   0.016   0.001   TRP A 646 
 HIS   0.002   0.000   HIS A 871 

Details of bonding type rmsd
  covalent geometry    : bond        0.00284 ( 6011)
  covalent geometry    : angle       0.65459 ( 8264)
  hydrogen bonds       : bond        0.03833 (  260)
  hydrogen bonds       : angle       4.03044 (  747)
  metal coordination   : bond        0.00152 (    3)
  Misc. bond           : bond        0.00051 (    1)

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

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

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1256 Ramachandran restraints generated.
    628 Oldfield, 0 Emsley, 628 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.259 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  363 LEU cc_start: 0.8739 (tp) cc_final: 0.8512 (tp)
REVERT: A  470 LYS cc_start: 0.8135 (tppt) cc_final: 0.7817 (tppt)
REVERT: A  479 MET cc_start: 0.7637 (mmt) cc_final: 0.7060 (mmp)
REVERT: A  493 LEU cc_start: 0.9046 (OUTLIER) cc_final: 0.8448 (tt)
REVERT: A  573 ASN cc_start: 0.8382 (m110) cc_final: 0.8153 (m110)
REVERT: A  777 ARG cc_start: 0.8562 (tpp80) cc_final: 0.8187 (tpp-160)
  outliers start: 22
  outliers final: 18
  residues processed: 110
  average time/residue: 0.0738
  time to fit residues: 10.9017
Evaluate side-chains
  111 residues out of total 576 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  270 LYS
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  449 LEU
Chi-restraints excluded: chain A residue  493 LEU
Chi-restraints excluded: chain A residue  500 GLN
Chi-restraints excluded: chain A residue  567 LEU
Chi-restraints excluded: chain A residue  630 THR
Chi-restraints excluded: chain A residue  640 VAL
Chi-restraints excluded: chain A residue  660 ILE
Chi-restraints excluded: chain A residue  695 ILE
Chi-restraints excluded: chain A residue  718 VAL
Chi-restraints excluded: chain A residue  825 VAL
Chi-restraints excluded: chain A residue  834 LEU
Chi-restraints excluded: chain A residue  855 SER
Chi-restraints excluded: chain A residue  882 PHE
Chi-restraints excluded: chain A residue  894 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 66
   random chunks:
   chunk 65 optimal weight:    5.9990
   chunk 35 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 45 optimal weight:    7.9990
   chunk 61 optimal weight:    5.9990
   chunk 22 optimal weight:   10.0000
   chunk 23 optimal weight:    1.9990
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 14 optimal weight:    2.9990
   chunk 47 optimal weight:    6.9990
   overall best weight:    2.3988

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

Flipped N/Q/H residues before XYZ refinement:
** A 247 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 500 GLN
** A 868 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.134868 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.108702 restraints weight = 9002.391|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.111984 restraints weight = 5325.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3427 r_free = 0.3427 target = 0.114195 restraints weight = 3800.907|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.115582 restraints weight = 3043.032|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 42)----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.116626 restraints weight = 2622.162|
|-----------------------------------------------------------------------------|
r_work (final): 0.3472
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7950
moved from start:          0.2350

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6015  Z= 0.235
  Angle     :  0.745  10.979   8264  Z= 0.366
  Chirality :  0.044   0.207    946
  Planarity :  0.004   0.046    936
  Dihedral  : 15.461  87.965   1176
  Min Nonbonded Distance : 2.324

Molprobity Statistics.
  All-atom Clashscore : 11.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.60 %
    Favored  : 91.40 %
  Rotamer:
    Outliers :  3.83 %
    Allowed  : 26.09 %
    Favored  : 70.09 %
  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 aren not related in a simple way.
  whole: -0.52 (0.35), residues: 628
  helix:  1.48 (0.31), residues: 291
  sheet: -2.23 (0.55), residues: 77
  loop : -1.90 (0.39), residues: 260

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.001   ARG A 466 
 TYR   0.042   0.002   TYR A 548 
 PHE   0.042   0.002   PHE A 616 
 TRP   0.014   0.001   TRP A 646 
 HIS   0.005   0.001   HIS A 871 

Details of bonding type rmsd
  covalent geometry    : bond        0.00529 ( 6011)
  covalent geometry    : angle       0.74509 ( 8264)
  hydrogen bonds       : bond        0.04356 (  260)
  hydrogen bonds       : angle       4.26565 (  747)
  metal coordination   : bond        0.00424 (    3)
  Misc. bond           : bond        0.00072 (    1)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1026.41 seconds
wall clock time: 18 minutes 26.41 seconds (1106.41 seconds total)