Starting phenix.real_space_refine
on Sun Apr 27 06:24:03 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vti_43523/04_2025/8vti_43523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vti_43523/04_2025/8vti_43523.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.9
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8vti_43523/04_2025/8vti_43523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vti_43523/04_2025/8vti_43523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vti_43523/04_2025/8vti_43523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vti_43523/04_2025/8vti_43523.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 66 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      23      5.16       5
     C    2917      2.51       5
     N     808      2.21       5
     O     919      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4667
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "A"
      Number of atoms: 2781
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 358, 2781
          Classifications: {'peptide': 358}
          Link IDs: {'PCIS': 1, 'PTRANS': 12, 'TRANS': 344}
    Chain: "B"
      Number of atoms: 85
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 11, 85
          Classifications: {'peptide': 11}
          Link IDs: {'TRANS': 10}
    Chain: "C"
      Number of atoms: 792
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 105, 792
          Classifications: {'peptide': 105}
          Link IDs: {'PCIS': 2, 'PTRANS': 4, 'TRANS': 98}
    Chain: "D"
      Number of atoms: 956
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 122, 956
          Classifications: {'peptide': 122}
          Link IDs: {'PTRANS': 3, 'TRANS': 118}
    Chain: "E"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 5.49, per 1000 atoms: 1.18
  Number of scatterers: 4667
  At special positions: 0
  Unit cell: (79.9085, 98.039, 106.769, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      23     16.00
     O     919      8.00
     N     808      7.00
     C    2917      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 498 " - pdb=" SG  CYS A 533 " distance=2.00
    Simple disulfide: pdb=" SG  CYS A 521 " - pdb=" SG  CYS A 550 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 818 " - pdb=" SG  CYS A 849 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 837 " - pdb=" SG  CYS A 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C  24 " - pdb=" SG  CYS C  89 " distance=2.01
    Simple disulfide: pdb=" SG  CYS D  25 " - pdb=" SG  CYS D  99 " distance=2.04

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    BETA1-4
      " NAG E   1 " - " NAG E   2 "
      " NAG E   2 " - " BMA E   3 "
    NAG-ASN
      " NAG A 901 " - " ASN A 843 "
      " NAG E   1 " - " ASN A 817 "
  Time building additional restraints: 1.17
  Conformation dependent library (CDL) restraints added in 531.1 milliseconds
  

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1114

  Finding SS restraints...
    Secondary structure from input PDB file:
      11 helices and 10 sheets defined
      23.3% alpha, 29.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.62
  Creating SS restraints...
    Processing helix  chain 'A' and resid 553 through 565
      removed outlier: 4.042A  pdb=" N   HIS A 557 " --> pdb=" O   PRO A 553 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 579
      removed outlier: 3.682A  pdb=" N   ILE A 571 " --> pdb=" O   THR A 567 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 584 through 609
      removed outlier: 3.813A  pdb=" N   VAL A 599 " --> pdb=" O   MET A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 618 through 646
      removed outlier: 3.522A  pdb=" N   GLU A 640 " --> pdb=" O   GLN A 636 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 647 through 649
      No H-bonds generated for 'chain 'A' and resid 647 through 649'
    Processing helix  chain 'A' and resid 650 through 657
      removed outlier: 3.871A  pdb=" N   TRP A 654 " --> pdb=" O   ALA A 650 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 683
      removed outlier: 3.509A  pdb=" N   ARG A 664 " --> pdb=" O   SER A 660 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 728 through 735
    Processing helix  chain 'A' and resid 751 through 755
    Processing helix  chain 'D' and resid 64 through 68
    Processing helix  chain 'D' and resid 77 through 79
      No H-bonds generated for 'chain 'D' and resid 77 through 79'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 501 through 502
      removed outlier: 3.903A  pdb=" N   ILE A 506 " --> pdb=" O   GLU A 502 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 518 through 520
    Processing sheet with id=AA3, first strand: chain 'A' and resid 689 through 690
    Processing sheet with id=AA4, first strand: chain 'A' and resid 689 through 690
      removed outlier: 4.360A  pdb=" N   ASN B 856 " --> pdb=" O   TRP A 821 " (cutoff:3.500A)
      removed outlier: 3.897A  pdb=" N   THR A 829 " --> pdb=" O   SER A 824 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'A' and resid 714 through 715
      removed outlier: 3.565A  pdb=" N   VAL A 801 " --> pdb=" O   GLN A 726 " (cutoff:3.500A)
      removed outlier: 4.438A  pdb=" N   VAL A 794 " --> pdb=" O   LEU A 854 " (cutoff:3.500A)
      removed outlier: 6.768A  pdb=" N   ASN A 852 " --> pdb=" O   LEU A 796 " (cutoff:3.500A)
      removed outlier: 11.251A  pdb=" N   ASP A 798 " --> pdb=" O   SER A 850 " (cutoff:3.500A)
      removed outlier: 10.035A  pdb=" N   SER A 850 " --> pdb=" O   ASP A 798 " (cutoff:3.500A)
      removed outlier: 10.510A  pdb=" N   VAL A 800 " --> pdb=" O   THR A 848 " (cutoff:3.500A)
      removed outlier: 9.446A  pdb=" N   THR A 848 " --> pdb=" O   VAL A 800 " (cutoff:3.500A)
      removed outlier: 10.817A  pdb=" N   PHE A 802 " --> pdb=" O   HIS A 846 " (cutoff:3.500A)
      removed outlier: 9.157A  pdb=" N   HIS A 846 " --> pdb=" O   PHE A 802 " (cutoff:3.500A)
      removed outlier: 7.259A  pdb=" N   HIS A 846 " --> pdb=" O   THR A 842 " (cutoff:3.500A)
      removed outlier: 5.406A  pdb=" N   THR A 842 " --> pdb=" O   HIS A 846 " (cutoff:3.500A)
      removed outlier: 6.963A  pdb=" N   THR A 848 " --> pdb=" O   LEU A 840 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.640A  pdb=" N   THR C  86 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
      removed outlier: 6.442A  pdb=" N   VAL C  34 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
      removed outlier: 5.271A  pdb=" N   TYR C  50 " --> pdb=" O   VAL C  34 " (cutoff:3.500A)
      removed outlier: 6.552A  pdb=" N   TRP C  36 " --> pdb=" O   LEU C  48 " (cutoff:3.500A)
      removed outlier: 3.933A  pdb=" N   SER C  54 " --> pdb=" O   TYR C  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'C' and resid 11 through 12
      removed outlier: 3.640A  pdb=" N   THR C  86 " --> pdb=" O   GLN C  39 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'C' and resid 20 through 22
      removed outlier: 3.764A  pdb=" N   VAL C  20 " --> pdb=" O   ILE C  76 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'D' and resid 6 through 10
    Processing sheet with id=AB1, first strand: chain 'D' and resid 13 through 14
      removed outlier: 6.100A  pdb=" N   GLY D  13 " --> pdb=" O   THR D 124 " (cutoff:3.500A)
      removed outlier: 3.570A  pdb=" N   ALA D  95 " --> pdb=" O   VAL D 123 " (cutoff:3.500A)
      removed outlier: 7.082A  pdb=" N   ILE D  37 " --> pdb=" O   SER D  53 " (cutoff:3.500A)
      removed outlier: 4.692A  pdb=" N   SER D  53 " --> pdb=" O   ILE D  37 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   TRP D  39 " --> pdb=" O   VAL D  51 " (cutoff:3.500A)

    203 hydrogen bonds defined for protein.
    561 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.38

  Time building geometry restraints manager: 1.40 seconds

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

  Histogram of bond lengths:
        1.20 -     1.33: 901
        1.33 -     1.45: 1195
        1.45 -     1.57: 2633
        1.57 -     1.69: 0
        1.69 -     1.81: 33
  Bond restraints: 4762
  Sorted by residual:
  bond pdb=" N   LYS A 518 "
       pdb=" CA  LYS A 518 "
    ideal  model  delta    sigma   weight residual
    1.454  1.503 -0.049 1.29e-02 6.01e+03 1.42e+01
  bond pdb=" N   ILE A 516 "
       pdb=" CA  ILE A 516 "
    ideal  model  delta    sigma   weight residual
    1.457  1.497 -0.040 1.19e-02 7.06e+03 1.13e+01
  bond pdb=" N   VAL A 775 "
       pdb=" CA  VAL A 775 "
    ideal  model  delta    sigma   weight residual
    1.457  1.495 -0.038 1.15e-02 7.56e+03 1.09e+01
  bond pdb=" N   ILE A 776 "
       pdb=" CA  ILE A 776 "
    ideal  model  delta    sigma   weight residual
    1.461  1.500 -0.039 1.22e-02 6.72e+03 1.02e+01
  bond pdb=" N   GLU A 499 "
       pdb=" CA  GLU A 499 "
    ideal  model  delta    sigma   weight residual
    1.454  1.494 -0.040 1.27e-02 6.20e+03 9.95e+00
  ... (remaining 4757 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.26: 5530
        2.26 -     4.53: 917
        4.53 -     6.79: 22
        6.79 -     9.06: 2
        9.06 -    11.32: 1
  Bond angle restraints: 6472
  Sorted by residual:
  angle pdb=" C   THR A 511 "
        pdb=" CA  THR A 511 "
        pdb=" CB  THR A 511 "
      ideal   model   delta    sigma   weight residual
     110.77  122.09  -11.32 1.67e+00 3.59e-01 4.60e+01
  angle pdb=" N   GLU A 812 "
        pdb=" CA  GLU A 812 "
        pdb=" C   GLU A 812 "
      ideal   model   delta    sigma   weight residual
     114.12  106.43    7.69 1.39e+00 5.18e-01 3.06e+01
  angle pdb=" C   LEU A 645 "
        pdb=" N   LEU A 646 "
        pdb=" CA  LEU A 646 "
      ideal   model   delta    sigma   weight residual
     122.73  115.00    7.73 1.61e+00 3.86e-01 2.31e+01
  angle pdb=" CA  GLN A 515 "
        pdb=" C   GLN A 515 "
        pdb=" O   GLN A 515 "
      ideal   model   delta    sigma   weight residual
     121.28  115.81    5.47 1.18e+00 7.18e-01 2.15e+01
  angle pdb=" N   LEU A 751 "
        pdb=" CA  LEU A 751 "
        pdb=" C   LEU A 751 "
      ideal   model   delta    sigma   weight residual
     113.18  107.60    5.58 1.33e+00 5.65e-01 1.76e+01
  ... (remaining 6467 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.25: 2709
       21.25 -    42.50: 153
       42.50 -    63.76: 33
       63.76 -    85.01: 7
       85.01 -   106.26: 5
  Dihedral angle restraints: 2907
    sinusoidal: 1176
      harmonic: 1731
  Sorted by residual:
  dihedral pdb=" CA  PHE A 715 "
           pdb=" C   PHE A 715 "
           pdb=" N   PRO A 716 "
           pdb=" CA  PRO A 716 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00  -38.08   38.08     0      5.00e+00 4.00e-02 5.80e+01
  dihedral pdb=" CA  TYR C  95 "
           pdb=" C   TYR C  95 "
           pdb=" N   PRO C  96 "
           pdb=" CA  PRO C  96 "
      ideal   model   delta  harmonic     sigma   weight residual
       0.00   31.99  -31.99     0      5.00e+00 4.00e-02 4.09e+01
  dihedral pdb=" C   THR A 511 "
           pdb=" N   THR A 511 "
           pdb=" CA  THR A 511 "
           pdb=" CB  THR A 511 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.00 -134.78   12.78     0      2.50e+00 1.60e-01 2.61e+01
  ... (remaining 2904 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.084: 435
       0.084 -    0.167: 261
       0.167 -    0.250: 44
       0.250 -    0.334: 2
       0.334 -    0.417: 1
  Chirality restraints: 743
  Sorted by residual:
  chirality pdb=" C1  BMA E   3 "
            pdb=" O4  NAG E   2 "
            pdb=" C2  BMA E   3 "
            pdb=" O5  BMA E   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-02 2.50e+03 8.11e+01
  chirality pdb=" C1  NAG E   2 "
            pdb=" O4  NAG E   1 "
            pdb=" C2  NAG E   2 "
            pdb=" O5  NAG E   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.33   -0.07 2.00e-02 2.50e+03 1.16e+01
  chirality pdb=" C1  NAG A 901 "
            pdb=" ND2 ASN A 843 "
            pdb=" C2  NAG A 901 "
            pdb=" O5  NAG A 901 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.98   -0.42 2.00e-01 2.50e+01 4.34e+00
  ... (remaining 740 not shown)

  Planarity restraints: 827
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 901 "    0.116 2.00e-02 2.50e+03   9.66e-02 1.17e+02
        pdb=" C7  NAG A 901 "   -0.033 2.00e-02 2.50e+03
        pdb=" C8  NAG A 901 "    0.087 2.00e-02 2.50e+03
        pdb=" N2  NAG A 901 "   -0.155 2.00e-02 2.50e+03
        pdb=" O7  NAG A 901 "   -0.016 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   2 "    0.044 2.00e-02 2.50e+03   3.61e-02 1.63e+01
        pdb=" C7  NAG E   2 "   -0.012 2.00e-02 2.50e+03
        pdb=" C8  NAG E   2 "    0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG E   2 "   -0.057 2.00e-02 2.50e+03
        pdb=" O7  NAG E   2 "   -0.007 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG E   1 "    0.042 2.00e-02 2.50e+03   3.47e-02 1.50e+01
        pdb=" C7  NAG E   1 "   -0.014 2.00e-02 2.50e+03
        pdb=" C8  NAG E   1 "    0.033 2.00e-02 2.50e+03
        pdb=" N2  NAG E   1 "   -0.055 2.00e-02 2.50e+03
        pdb=" O7  NAG E   1 "   -0.005 2.00e-02 2.50e+03
  ... (remaining 824 not shown)

  Histogram of nonbonded interaction distances:
        2.50 -     2.98: 2411
        2.98 -     3.46: 4319
        3.46 -     3.94: 7753
        3.94 -     4.42: 8548
        4.42 -     4.90: 13639
  Nonbonded interactions: 36670
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 596 "
            pdb=" OD1 ASP A 596 "
     model   vdw
     2.503 3.040
  nonbonded pdb=" O   GLN C  80 "
            pdb=" N   GLU C  82 "
     model   vdw
     2.529 3.120
  nonbonded pdb=" OD1 ASP A 615 "
            pdb=" N   ARG A 619 "
     model   vdw
     2.547 3.120
  nonbonded pdb=" O   LEU A 601 "
            pdb=" OE1 GLN A 605 "
     model   vdw
     2.550 3.040
  nonbonded pdb=" N   PHE A 509 "
            pdb=" O   PHE A 509 "
     model   vdw
     2.571 2.496
  ... (remaining 36665 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:             13.780
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.030
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.260
  Check model and map are aligned:         0.040
  Set scattering table:                    0.050
  Process input model:                     18.020
  Find NCS groups from input model:        0.060
  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:2.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   35.050
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6751
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.012   0.049   4772  Z= 0.911
  Angle     :  1.495  11.324   6496  Z= 1.100
  Chirality :  0.094   0.417    743
  Planarity :  0.006   0.097    825
  Dihedral  : 14.581 106.262   1775
  Min Nonbonded Distance : 2.503

Molprobity Statistics.
  All-atom Clashscore : 5.97
  Ramachandran Plot:
    Outliers :  0.17 %
    Allowed  :  9.18 %
    Favored  : 90.65 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  :  7.87 %
    Favored  : 88.58 %
  Cbeta Deviations :  0.18 %
  Peptide Plane:
    Cis-proline     : 4.55 %
    Cis-general     : 0.00 %
    Twisted Proline : 9.09 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -3.01 (0.32), residues: 588
  helix:  0.12 (0.45), residues: 124
  sheet: -2.45 (0.34), residues: 195
  loop : -2.62 (0.33), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP A 554 
 HIS   0.004   0.001   HIS A 846 
 PHE   0.015   0.002   PHE A 745 
 TYR   0.017   0.002   TYR D  36 
 ARG   0.003   0.000   ARG C  62 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01067 (    2)
  link_NAG-ASN         : angle       4.44112 (    6)
  link_BETA1-4         : bond        0.00192 (    2)
  link_BETA1-4         : angle       1.05732 (    6)
  hydrogen bonds       : bond        0.21557 (  181)
  hydrogen bonds       : angle       8.78856 (  561)
  SS BOND              : bond        0.01937 (    6)
  SS BOND              : angle       2.66828 (   12)
  covalent geometry    : bond        0.01218 ( 4762)
  covalent geometry    : angle       1.48667 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  225 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 207
  time to evaluate  : 0.579 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 TYR cc_start: 0.4269 (t80) cc_final: 0.4017 (t80)
REVERT: A  554 TRP cc_start: 0.7629 (p90) cc_final: 0.7172 (p90)
REVERT: A  573 ARG cc_start: 0.7588 (mtm-85) cc_final: 0.7294 (mtm-85)
REVERT: A  634 TYR cc_start: 0.7787 (t80) cc_final: 0.7355 (t80)
REVERT: A  688 ASP cc_start: 0.8574 (t0) cc_final: 0.7996 (m-30)
REVERT: A  701 VAL cc_start: 0.9408 (t) cc_final: 0.8988 (p)
REVERT: A  763 LYS cc_start: 0.7409 (ttpt) cc_final: 0.7140 (ttmm)
REVERT: A  782 ILE cc_start: 0.8420 (tp) cc_final: 0.8198 (tt)
REVERT: A  790 PHE cc_start: 0.8482 (m-80) cc_final: 0.7743 (m-10)
REVERT: B  860 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8145 (mm)
REVERT: B  865 GLU cc_start: 0.7103 (mm-30) cc_final: 0.6758 (mm-30)
REVERT: C   24 CYS cc_start: 0.5699 (t) cc_final: 0.5046 (t)
REVERT: C   34 VAL cc_start: 0.7955 (OUTLIER) cc_final: 0.7680 (m)
REVERT: C   36 TRP cc_start: 0.8500 (m100) cc_final: 0.8203 (m100)
REVERT: C   48 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8368 (mm)
REVERT: C   83 ASP cc_start: 0.7748 (t70) cc_final: 0.7469 (t70)
REVERT: C   94 GLN cc_start: 0.7723 (pp30) cc_final: 0.6748 (pp30)
REVERT: C  104 LYS cc_start: 0.7498 (mtpt) cc_final: 0.6934 (mtpp)
REVERT: D   39 TRP cc_start: 0.7896 (m100) cc_final: 0.7251 (m100)
REVERT: D   40 VAL cc_start: 0.7922 (t) cc_final: 0.7679 (m)
REVERT: D   42 GLN cc_start: 0.7972 (tt0) cc_final: 0.7288 (tt0)
REVERT: D   48 LEU cc_start: 0.6942 (mt) cc_final: 0.5852 (mt)
REVERT: D   81 THR cc_start: 0.6707 (p) cc_final: 0.6246 (p)
REVERT: D   83 TYR cc_start: 0.7883 (m-80) cc_final: 0.7276 (m-80)
REVERT: D   87 ASN cc_start: 0.8501 (m-40) cc_final: 0.8171 (m110)
REVERT: D   96 VAL cc_start: 0.7433 (t) cc_final: 0.7205 (p)
REVERT: D   98 TYR cc_start: 0.6608 (m-80) cc_final: 0.6064 (m-80)
REVERT: D  101 ARG cc_start: 0.7492 (tmm160) cc_final: 0.5878 (tmm-80)
REVERT: D  107 TRP cc_start: 0.6382 (t60) cc_final: 0.6074 (t60)
  outliers start: 18
  outliers final: 4
  residues processed: 217
  average time/residue: 0.2060
  time to fit residues: 54.2196
Evaluate side-chains
  144 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 137
  time to evaluate  : 0.561 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  550 CYS
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain B residue  860 LEU
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   48 LEU
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 48 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 15 optimal weight:    0.1980
   chunk 29 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 45 optimal weight:    0.7980
   chunk 17 optimal weight:    0.5980
   chunk 27 optimal weight:    0.8980
   chunk 33 optimal weight:    1.9990
   chunk 52 optimal weight:    1.9990
   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 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 662 GLN
A 773 HIS
C  94 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.126184 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.112454 restraints weight = 12209.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.117018 restraints weight = 10651.680|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.119733 restraints weight = 4588.209|
|-----------------------------------------------------------------------------|
r_work (final): 0.3737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.3409

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.045   4772  Z= 0.158
  Angle     :  0.691   7.163   6496  Z= 0.356
  Chirality :  0.044   0.180    743
  Planarity :  0.005   0.046    825
  Dihedral  :  8.510  79.781    737
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.91 %
    Favored  : 96.09 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 15.55 %
    Favored  : 79.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.44 (0.34), residues: 588
  helix:  1.83 (0.43), residues: 129
  sheet: -2.10 (0.34), residues: 189
  loop : -1.40 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 554 
 HIS   0.003   0.001   HIS A 773 
 PHE   0.019   0.002   PHE A 745 
 TYR   0.029   0.002   TYR C  56 
 ARG   0.008   0.001   ARG A 593 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00163 (    2)
  link_NAG-ASN         : angle       3.29893 (    6)
  link_BETA1-4         : bond        0.00367 (    2)
  link_BETA1-4         : angle       2.04504 (    6)
  hydrogen bonds       : bond        0.04482 (  181)
  hydrogen bonds       : angle       5.76154 (  561)
  SS BOND              : bond        0.00461 (    6)
  SS BOND              : angle       0.93437 (   12)
  covalent geometry    : bond        0.00356 ( 4762)
  covalent geometry    : angle       0.68059 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  156 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 132
  time to evaluate  : 0.559 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  688 ASP cc_start: 0.8259 (t0) cc_final: 0.7926 (m-30)
REVERT: A  743 VAL cc_start: 0.9618 (t) cc_final: 0.9363 (m)
REVERT: A  790 PHE cc_start: 0.7667 (m-80) cc_final: 0.7410 (m-80)
REVERT: B  865 GLU cc_start: 0.7408 (mm-30) cc_final: 0.7172 (mm-30)
REVERT: C   36 TRP cc_start: 0.9295 (m100) cc_final: 0.8387 (m100)
REVERT: C   90 GLN cc_start: 0.9355 (tm-30) cc_final: 0.8605 (tm-30)
REVERT: C   94 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7598 (pp30)
REVERT: C  104 LYS cc_start: 0.7455 (mtpt) cc_final: 0.7224 (mtpp)
REVERT: D   39 TRP cc_start: 0.8141 (m100) cc_final: 0.7798 (m100)
REVERT: D   48 LEU cc_start: 0.8231 (mt) cc_final: 0.7837 (mt)
REVERT: D   87 ASN cc_start: 0.8083 (m-40) cc_final: 0.7583 (m-40)
REVERT: D   92 GLU cc_start: 0.8440 (mp0) cc_final: 0.8191 (mp0)
REVERT: D   93 ASP cc_start: 0.8042 (m-30) cc_final: 0.7795 (m-30)
REVERT: D  101 ARG cc_start: 0.7680 (tmm160) cc_final: 0.6850 (tmm-80)
  outliers start: 24
  outliers final: 16
  residues processed: 146
  average time/residue: 0.1877
  time to fit residues: 34.0372
Evaluate side-chains
  122 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 105
  time to evaluate  : 0.563 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  604 VAL
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   94 GLN
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 34 optimal weight:    4.9990
   chunk 56 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    0.9990
   chunk 7 optimal weight:    0.6980
   chunk 20 optimal weight:    4.9990
   chunk 45 optimal weight:    0.9980
   chunk 53 optimal weight:    0.6980
   chunk 3 optimal weight:    0.0980
   chunk 23 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN
A 671 HIS
C  94 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3779 r_free = 0.3779 target = 0.122373 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108116 restraints weight = 12172.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.112805 restraints weight = 10741.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3668 r_free = 0.3668 target = 0.115267 restraints weight = 4559.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3670
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.4183

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.063   4772  Z= 0.153
  Angle     :  0.650   7.990   6496  Z= 0.336
  Chirality :  0.042   0.149    743
  Planarity :  0.005   0.047    825
  Dihedral  :  6.370  77.344    728
  Min Nonbonded Distance : 2.456

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 18.11 %
    Favored  : 76.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.04 (0.35), residues: 588
  helix:  2.65 (0.46), residues: 123
  sheet: -1.91 (0.35), residues: 184
  loop : -1.31 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.032   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.016   0.001   PHE A 745 
 TYR   0.032   0.002   TYR A 634 
 ARG   0.012   0.001   ARG A 593 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00480 (    2)
  link_NAG-ASN         : angle       3.79691 (    6)
  link_BETA1-4         : bond        0.00362 (    2)
  link_BETA1-4         : angle       1.75435 (    6)
  hydrogen bonds       : bond        0.04281 (  181)
  hydrogen bonds       : angle       5.38061 (  561)
  SS BOND              : bond        0.00392 (    6)
  SS BOND              : angle       1.22064 (   12)
  covalent geometry    : bond        0.00348 ( 4762)
  covalent geometry    : angle       0.63682 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  134 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 109
  time to evaluate  : 0.576 
Fit side-chains
   revert: symmetry clash
REVERT: A  592 VAL cc_start: 0.9131 (OUTLIER) cc_final: 0.8846 (t)
REVERT: A  634 TYR cc_start: 0.8350 (t80) cc_final: 0.7744 (t80)
REVERT: A  638 MET cc_start: 0.8417 (OUTLIER) cc_final: 0.8121 (tpp)
REVERT: A  651 LEU cc_start: 0.8148 (pp) cc_final: 0.7881 (pp)
REVERT: A  688 ASP cc_start: 0.8237 (t0) cc_final: 0.7909 (m-30)
REVERT: A  715 PHE cc_start: 0.8819 (t80) cc_final: 0.8332 (t80)
REVERT: A  743 VAL cc_start: 0.9625 (t) cc_final: 0.9293 (m)
REVERT: A  790 PHE cc_start: 0.7780 (m-80) cc_final: 0.6946 (m-10)
REVERT: C   36 TRP cc_start: 0.9448 (m100) cc_final: 0.8529 (m100)
REVERT: C   90 GLN cc_start: 0.9396 (tm-30) cc_final: 0.8753 (tm-30)
REVERT: D   22 ARG cc_start: 0.7701 (ttt-90) cc_final: 0.7067 (mmm-85)
REVERT: D   39 TRP cc_start: 0.8619 (m100) cc_final: 0.8197 (m100)
REVERT: D   87 ASN cc_start: 0.8048 (m-40) cc_final: 0.7562 (m-40)
REVERT: D   92 GLU cc_start: 0.8398 (mp0) cc_final: 0.8108 (mp0)
REVERT: D   98 TYR cc_start: 0.8763 (m-80) cc_final: 0.8291 (m-80)
REVERT: D  101 ARG cc_start: 0.7904 (tmm160) cc_final: 0.7035 (tmm-80)
  outliers start: 25
  outliers final: 18
  residues processed: 124
  average time/residue: 0.1700
  time to fit residues: 27.1075
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 95
  time to evaluate  : 0.509 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  638 MET
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 56 optimal weight:    4.9990
   chunk 50 optimal weight:    2.9990
   chunk 46 optimal weight:    3.9990
   chunk 5 optimal weight:    0.7980
   chunk 24 optimal weight:    5.9990
   chunk 38 optimal weight:    4.9990
   chunk 47 optimal weight:    1.9990
   chunk 8 optimal weight:    0.8980
   chunk 45 optimal weight:    0.2980
   chunk 55 optimal weight:    0.7980
   chunk 36 optimal weight:    0.9980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3761 r_free = 0.3761 target = 0.121332 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3543 r_free = 0.3543 target = 0.106693 restraints weight = 12281.333|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3612 r_free = 0.3612 target = 0.111640 restraints weight = 11328.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.114100 restraints weight = 4661.140|
|-----------------------------------------------------------------------------|
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.4703

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.043   4772  Z= 0.155
  Angle     :  0.638   8.565   6496  Z= 0.329
  Chirality :  0.041   0.145    743
  Planarity :  0.005   0.049    825
  Dihedral  :  5.953  74.939    728
  Min Nonbonded Distance : 2.431

Molprobity Statistics.
  All-atom Clashscore : 9.34
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.76 %
    Favored  : 95.24 %
  Rotamer:
    Outliers :  5.71 %
    Allowed  : 18.31 %
    Favored  : 75.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.93 (0.35), residues: 588
  helix:  2.85 (0.47), residues: 123
  sheet: -1.63 (0.35), residues: 188
  loop : -1.47 (0.36), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.014   0.002   PHE A 745 
 TYR   0.033   0.002   TYR A 754 
 ARG   0.012   0.001   ARG A 593 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00105 (    2)
  link_NAG-ASN         : angle       3.95126 (    6)
  link_BETA1-4         : bond        0.00412 (    2)
  link_BETA1-4         : angle       1.51702 (    6)
  hydrogen bonds       : bond        0.04145 (  181)
  hydrogen bonds       : angle       5.13442 (  561)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       1.11292 (   12)
  covalent geometry    : bond        0.00351 ( 4762)
  covalent geometry    : angle       0.62407 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  138 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 109
  time to evaluate  : 0.574 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 TYR cc_start: 0.8345 (t80) cc_final: 0.7918 (t80)
REVERT: A  675 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7748 (mt-10)
REVERT: A  688 ASP cc_start: 0.8233 (t0) cc_final: 0.7912 (m-30)
REVERT: A  715 PHE cc_start: 0.8835 (t80) cc_final: 0.8369 (t80)
REVERT: A  743 VAL cc_start: 0.9620 (t) cc_final: 0.9314 (m)
REVERT: A  790 PHE cc_start: 0.7851 (m-80) cc_final: 0.7429 (m-10)
REVERT: C   36 TRP cc_start: 0.9497 (m100) cc_final: 0.8577 (m100)
REVERT: C   90 GLN cc_start: 0.9403 (tm-30) cc_final: 0.8754 (tm-30)
REVERT: D   22 ARG cc_start: 0.7727 (ttt-90) cc_final: 0.7463 (mtp85)
REVERT: D   39 TRP cc_start: 0.8830 (m100) cc_final: 0.8337 (m100)
REVERT: D   54 ILE cc_start: 0.9119 (mt) cc_final: 0.8356 (tp)
REVERT: D   83 TYR cc_start: 0.8599 (m-80) cc_final: 0.8328 (m-80)
REVERT: D   87 ASN cc_start: 0.8014 (m-40) cc_final: 0.7619 (m-40)
REVERT: D   92 GLU cc_start: 0.8238 (mp0) cc_final: 0.7961 (mp0)
REVERT: D  101 ARG cc_start: 0.8046 (tmm160) cc_final: 0.7182 (tmm-80)
  outliers start: 29
  outliers final: 21
  residues processed: 128
  average time/residue: 0.1565
  time to fit residues: 25.9340
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.550 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue  110 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    4.9990
   chunk 44 optimal weight:    0.6980
   chunk 57 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 23 optimal weight:    0.9980
   chunk 51 optimal weight:    0.8980
   chunk 16 optimal weight:    0.8980
   chunk 13 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9980
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0870
   overall best weight:    0.6958

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3744 r_free = 0.3744 target = 0.120308 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.105296 restraints weight = 12229.914|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.110407 restraints weight = 11264.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.112848 restraints weight = 4630.657|
|-----------------------------------------------------------------------------|
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7675
moved from start:          0.4991

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4772  Z= 0.150
  Angle     :  0.622   7.901   6496  Z= 0.321
  Chirality :  0.041   0.152    743
  Planarity :  0.004   0.050    825
  Dihedral  :  5.634  70.885    728
  Min Nonbonded Distance : 2.462

Molprobity Statistics.
  All-atom Clashscore : 9.12
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 20.08 %
    Favored  : 74.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.35), residues: 588
  helix:  2.98 (0.47), residues: 123
  sheet: -1.67 (0.36), residues: 181
  loop : -1.35 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 554 
 HIS   0.003   0.000   HIS D 102 
 PHE   0.015   0.002   PHE A 802 
 TYR   0.027   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00219 (    2)
  link_NAG-ASN         : angle       3.88434 (    6)
  link_BETA1-4         : bond        0.00383 (    2)
  link_BETA1-4         : angle       1.23759 (    6)
  hydrogen bonds       : bond        0.04082 (  181)
  hydrogen bonds       : angle       4.99967 (  561)
  SS BOND              : bond        0.00440 (    6)
  SS BOND              : angle       1.03022 (   12)
  covalent geometry    : bond        0.00340 ( 4762)
  covalent geometry    : angle       0.60915 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  127 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 100
  time to evaluate  : 0.660 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 TYR cc_start: 0.8513 (t80) cc_final: 0.7878 (t80)
REVERT: A  638 MET cc_start: 0.8396 (tpp) cc_final: 0.8051 (tpp)
REVERT: A  688 ASP cc_start: 0.8216 (t0) cc_final: 0.7929 (m-30)
REVERT: A  700 GLU cc_start: 0.8320 (tp30) cc_final: 0.7854 (tp30)
REVERT: A  715 PHE cc_start: 0.8818 (t80) cc_final: 0.8356 (t80)
REVERT: A  790 PHE cc_start: 0.7916 (m-80) cc_final: 0.7427 (m-10)
REVERT: A  846 HIS cc_start: 0.8206 (m-70) cc_final: 0.7976 (m-70)
REVERT: C   36 TRP cc_start: 0.9519 (m100) cc_final: 0.8554 (m100)
REVERT: C   90 GLN cc_start: 0.9385 (tm-30) cc_final: 0.8739 (tm-30)
REVERT: D   22 ARG cc_start: 0.7734 (ttt-90) cc_final: 0.7474 (mtp-110)
REVERT: D   41 ARG cc_start: 0.8661 (ptt180) cc_final: 0.8143 (ptm160)
REVERT: D   54 ILE cc_start: 0.9180 (mt) cc_final: 0.8443 (tp)
REVERT: D   87 ASN cc_start: 0.8048 (m-40) cc_final: 0.7678 (m-40)
REVERT: D   92 GLU cc_start: 0.8262 (mp0) cc_final: 0.7989 (mp0)
REVERT: D  101 ARG cc_start: 0.8179 (tmm160) cc_final: 0.7298 (tmm-80)
  outliers start: 27
  outliers final: 19
  residues processed: 116
  average time/residue: 0.1963
  time to fit residues: 30.5912
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 22 optimal weight:    0.7980
   chunk 50 optimal weight:    3.9990
   chunk 46 optimal weight:    0.0970
   chunk 43 optimal weight:    0.6980
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 31 optimal weight:    0.9980
   chunk 16 optimal weight:    0.7980
   chunk 10 optimal weight:    3.9990
   chunk 28 optimal weight:    0.6980
   chunk 45 optimal weight:    0.8980
   overall best weight:    0.6178

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.120569 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.105690 restraints weight = 12257.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.110764 restraints weight = 11258.470|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.113220 restraints weight = 4652.443|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7677
moved from start:          0.5207

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.053   4772  Z= 0.146
  Angle     :  0.617   8.889   6496  Z= 0.318
  Chirality :  0.041   0.142    743
  Planarity :  0.004   0.051    825
  Dihedral  :  5.554  69.569    728
  Min Nonbonded Distance : 2.479

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.27 %
    Favored  : 94.73 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 20.28 %
    Favored  : 74.80 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.80 (0.35), residues: 588
  helix:  3.00 (0.47), residues: 123
  sheet: -1.60 (0.36), residues: 181
  loop : -1.38 (0.36), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.017   0.002   TRP A 554 
 HIS   0.003   0.001   HIS B 863 
 PHE   0.012   0.001   PHE A 745 
 TYR   0.027   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00366 (    2)
  link_NAG-ASN         : angle       4.38594 (    6)
  link_BETA1-4         : bond        0.00291 (    2)
  link_BETA1-4         : angle       1.18816 (    6)
  hydrogen bonds       : bond        0.03960 (  181)
  hydrogen bonds       : angle       4.89474 (  561)
  SS BOND              : bond        0.00398 (    6)
  SS BOND              : angle       1.00353 (   12)
  covalent geometry    : bond        0.00332 ( 4762)
  covalent geometry    : angle       0.60064 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 101
  time to evaluate  : 0.899 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8656 (OUTLIER) cc_final: 0.8337 (p90)
REVERT: A  634 TYR cc_start: 0.8550 (t80) cc_final: 0.7931 (t80)
REVERT: A  638 MET cc_start: 0.8422 (tpp) cc_final: 0.8061 (tpp)
REVERT: A  688 ASP cc_start: 0.8141 (t0) cc_final: 0.7873 (m-30)
REVERT: A  700 GLU cc_start: 0.8303 (tp30) cc_final: 0.7819 (tp30)
REVERT: A  715 PHE cc_start: 0.8835 (t80) cc_final: 0.8392 (t80)
REVERT: A  790 PHE cc_start: 0.7897 (m-80) cc_final: 0.7425 (m-10)
REVERT: A  846 HIS cc_start: 0.8174 (m-70) cc_final: 0.7957 (m-70)
REVERT: C   36 TRP cc_start: 0.9508 (m100) cc_final: 0.8569 (m100)
REVERT: C   90 GLN cc_start: 0.9363 (tm-30) cc_final: 0.8702 (tm-30)
REVERT: D   41 ARG cc_start: 0.8662 (ptt180) cc_final: 0.8224 (ptm160)
REVERT: D   54 ILE cc_start: 0.9211 (mt) cc_final: 0.8477 (tp)
REVERT: D   83 TYR cc_start: 0.8672 (m-80) cc_final: 0.8304 (m-80)
REVERT: D   87 ASN cc_start: 0.7982 (m-40) cc_final: 0.7604 (m-40)
REVERT: D   92 GLU cc_start: 0.8211 (mp0) cc_final: 0.7903 (mp0)
REVERT: D  101 ARG cc_start: 0.8226 (tmm160) cc_final: 0.7408 (tmm-80)
  outliers start: 25
  outliers final: 20
  residues processed: 115
  average time/residue: 0.2219
  time to fit residues: 33.0561
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 1.020 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   48 LEU
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    3.9990
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 29 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0970
   chunk 54 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 46 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9990
   overall best weight:    0.5758

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.120471 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3523 r_free = 0.3523 target = 0.105630 restraints weight = 12264.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.110600 restraints weight = 11388.757|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.113072 restraints weight = 4750.420|
|-----------------------------------------------------------------------------|
r_work (final): 0.3629
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7682
moved from start:          0.5384

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4772  Z= 0.136
  Angle     :  0.626   8.778   6496  Z= 0.315
  Chirality :  0.041   0.138    743
  Planarity :  0.004   0.050    825
  Dihedral  :  5.462  66.855    728
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 8.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  5.12 %
    Allowed  : 21.26 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.76 (0.36), residues: 588
  helix:  3.04 (0.47), residues: 123
  sheet: -1.50 (0.36), residues: 188
  loop : -1.41 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.027   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.012   0.001   PHE A 745 
 TYR   0.028   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D  22 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00113 (    2)
  link_NAG-ASN         : angle       4.65061 (    6)
  link_BETA1-4         : bond        0.00485 (    2)
  link_BETA1-4         : angle       1.17862 (    6)
  hydrogen bonds       : bond        0.03881 (  181)
  hydrogen bonds       : angle       4.78990 (  561)
  SS BOND              : bond        0.00383 (    6)
  SS BOND              : angle       0.98104 (   12)
  covalent geometry    : bond        0.00309 ( 4762)
  covalent geometry    : angle       0.60839 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  129 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 103
  time to evaluate  : 0.596 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8631 (OUTLIER) cc_final: 0.8306 (p90)
REVERT: A  634 TYR cc_start: 0.8556 (t80) cc_final: 0.7885 (t80)
REVERT: A  638 MET cc_start: 0.8400 (tpp) cc_final: 0.8037 (tpp)
REVERT: A  675 GLU cc_start: 0.8118 (mt-10) cc_final: 0.7696 (mt-10)
REVERT: A  688 ASP cc_start: 0.8124 (t0) cc_final: 0.7849 (m-30)
REVERT: A  700 GLU cc_start: 0.8269 (tp30) cc_final: 0.7799 (tp30)
REVERT: A  715 PHE cc_start: 0.8842 (t80) cc_final: 0.8407 (t80)
REVERT: A  790 PHE cc_start: 0.7905 (m-80) cc_final: 0.7474 (m-10)
REVERT: C   28 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8927 (tm-30)
REVERT: C   36 TRP cc_start: 0.9508 (m100) cc_final: 0.8597 (m100)
REVERT: C   90 GLN cc_start: 0.9340 (tm-30) cc_final: 0.8707 (tm-30)
REVERT: D   41 ARG cc_start: 0.8749 (ptt180) cc_final: 0.8357 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9244 (mt) cc_final: 0.8545 (tp)
REVERT: D   83 TYR cc_start: 0.8710 (m-80) cc_final: 0.8325 (m-80)
REVERT: D   87 ASN cc_start: 0.7908 (m-40) cc_final: 0.7529 (m-40)
REVERT: D   92 GLU cc_start: 0.8119 (mp0) cc_final: 0.7850 (mp0)
REVERT: D  101 ARG cc_start: 0.8285 (tmm160) cc_final: 0.7454 (tmm-80)
  outliers start: 26
  outliers final: 18
  residues processed: 118
  average time/residue: 0.1522
  time to fit residues: 23.3772
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 96
  time to evaluate  : 0.560 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 5 optimal weight:    0.9990
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 48 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0870
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.7560

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.119563 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.104680 restraints weight = 12186.384|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.109656 restraints weight = 11364.005|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3602 r_free = 0.3602 target = 0.111108 restraints weight = 4707.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3604
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7733
moved from start:          0.5576

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   4772  Z= 0.156
  Angle     :  0.661   8.762   6496  Z= 0.332
  Chirality :  0.042   0.141    743
  Planarity :  0.004   0.051    825
  Dihedral  :  5.523  67.172    728
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 23.03 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.78 (0.36), residues: 588
  helix:  2.90 (0.47), residues: 123
  sheet: -1.47 (0.36), residues: 188
  loop : -1.39 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.021   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.012   0.001   PHE A 745 
 TYR   0.026   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D  41 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00077 (    2)
  link_NAG-ASN         : angle       4.93283 (    6)
  link_BETA1-4         : bond        0.00676 (    2)
  link_BETA1-4         : angle       1.19138 (    6)
  hydrogen bonds       : bond        0.03948 (  181)
  hydrogen bonds       : angle       4.82090 (  561)
  SS BOND              : bond        0.00421 (    6)
  SS BOND              : angle       1.02179 (   12)
  covalent geometry    : bond        0.00358 ( 4762)
  covalent geometry    : angle       0.64193 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 94
  time to evaluate  : 0.549 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8612 (OUTLIER) cc_final: 0.8295 (p90)
REVERT: A  596 ASP cc_start: 0.8436 (t0) cc_final: 0.8197 (t0)
REVERT: A  634 TYR cc_start: 0.8589 (t80) cc_final: 0.7889 (t80)
REVERT: A  638 MET cc_start: 0.8429 (tpp) cc_final: 0.8016 (tpp)
REVERT: A  675 GLU cc_start: 0.8123 (mt-10) cc_final: 0.7684 (mt-10)
REVERT: A  688 ASP cc_start: 0.8098 (t0) cc_final: 0.7843 (m-30)
REVERT: A  700 GLU cc_start: 0.8239 (tp30) cc_final: 0.7790 (tp30)
REVERT: A  715 PHE cc_start: 0.8892 (t80) cc_final: 0.8486 (t80)
REVERT: A  790 PHE cc_start: 0.7956 (m-80) cc_final: 0.7563 (m-80)
REVERT: B  861 MET cc_start: 0.6800 (tmm) cc_final: 0.6422 (tmm)
REVERT: C   36 TRP cc_start: 0.9508 (m100) cc_final: 0.8623 (m100)
REVERT: C   90 GLN cc_start: 0.9316 (tm-30) cc_final: 0.8688 (tm-30)
REVERT: D   41 ARG cc_start: 0.8815 (ptt180) cc_final: 0.8441 (ptm160)
REVERT: D   54 ILE cc_start: 0.9268 (mt) cc_final: 0.8569 (tp)
REVERT: D   83 TYR cc_start: 0.8755 (m-80) cc_final: 0.8357 (m-80)
REVERT: D   92 GLU cc_start: 0.8260 (mp0) cc_final: 0.7917 (mp0)
REVERT: D  101 ARG cc_start: 0.8353 (tmm160) cc_final: 0.7528 (tmm-80)
  outliers start: 21
  outliers final: 19
  residues processed: 108
  average time/residue: 0.1597
  time to fit residues: 22.3667
Evaluate side-chains
  113 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 93
  time to evaluate  : 0.576 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 53 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 25 optimal weight:    0.5980
   chunk 52 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 35 optimal weight:    3.9990
   chunk 11 optimal weight:    0.6980
   chunk 18 optimal weight:    0.7980
   chunk 12 optimal weight:    0.9990
   chunk 7 optimal weight:    2.9990
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.119507 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.106119 restraints weight = 12366.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3593 r_free = 0.3593 target = 0.110202 restraints weight = 11164.955|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3617 r_free = 0.3617 target = 0.111891 restraints weight = 4609.257|
|-----------------------------------------------------------------------------|
r_work (final): 0.3617
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7723
moved from start:          0.5718

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4772  Z= 0.153
  Angle     :  0.651   8.679   6496  Z= 0.327
  Chirality :  0.042   0.140    743
  Planarity :  0.004   0.051    825
  Dihedral  :  5.538  68.492    728
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 23.62 %
    Favored  : 72.05 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.36), residues: 588
  helix:  2.92 (0.47), residues: 123
  sheet: -1.53 (0.36), residues: 193
  loop : -1.40 (0.38), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 554 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.012   0.001   PHE A 745 
 TYR   0.027   0.002   TYR C  56 
 ARG   0.001   0.000   ARG A 504 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00131 (    2)
  link_NAG-ASN         : angle       4.81391 (    6)
  link_BETA1-4         : bond        0.00605 (    2)
  link_BETA1-4         : angle       1.15531 (    6)
  hydrogen bonds       : bond        0.03913 (  181)
  hydrogen bonds       : angle       4.80218 (  561)
  SS BOND              : bond        0.00430 (    6)
  SS BOND              : angle       1.05152 (   12)
  covalent geometry    : bond        0.00352 ( 4762)
  covalent geometry    : angle       0.63324 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.583 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8572 (OUTLIER) cc_final: 0.8265 (p90)
REVERT: A  634 TYR cc_start: 0.8619 (t80) cc_final: 0.8123 (t80)
REVERT: A  668 MET cc_start: 0.8658 (tpt) cc_final: 0.8282 (tpp)
REVERT: A  675 GLU cc_start: 0.8075 (mt-10) cc_final: 0.7635 (mt-10)
REVERT: A  700 GLU cc_start: 0.8209 (tp30) cc_final: 0.7806 (tp30)
REVERT: A  715 PHE cc_start: 0.8894 (t80) cc_final: 0.8477 (t80)
REVERT: A  790 PHE cc_start: 0.7839 (m-80) cc_final: 0.7522 (m-80)
REVERT: A  803 THR cc_start: 0.8430 (p) cc_final: 0.8190 (p)
REVERT: B  861 MET cc_start: 0.6916 (OUTLIER) cc_final: 0.6590 (tmm)
REVERT: C   28 GLN cc_start: 0.9140 (tm-30) cc_final: 0.8926 (tm-30)
REVERT: C   36 TRP cc_start: 0.9519 (m100) cc_final: 0.8616 (m100)
REVERT: C   90 GLN cc_start: 0.9351 (tm-30) cc_final: 0.9053 (tm-30)
REVERT: D   41 ARG cc_start: 0.8854 (ptt180) cc_final: 0.8533 (ptm160)
REVERT: D   54 ILE cc_start: 0.9294 (mt) cc_final: 0.8636 (tp)
REVERT: D   83 TYR cc_start: 0.8803 (m-80) cc_final: 0.8368 (m-80)
REVERT: D   92 GLU cc_start: 0.8193 (mp0) cc_final: 0.7871 (mp0)
REVERT: D  101 ARG cc_start: 0.8422 (tmm160) cc_final: 0.7619 (tmm-80)
  outliers start: 22
  outliers final: 18
  residues processed: 107
  average time/residue: 0.1510
  time to fit residues: 21.3613
Evaluate side-chains
  112 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 92
  time to evaluate  : 0.506 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain B residue  861 MET
Chi-restraints excluded: chain C residue   34 VAL
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   83 ASP
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 43 optimal weight:    1.9990
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    0.0470
   chunk 15 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 33 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 54 optimal weight:    1.9990
   chunk 23 optimal weight:    0.8980
   overall best weight:    0.5678

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN
C   4 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3746 r_free = 0.3746 target = 0.119991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3516 r_free = 0.3516 target = 0.105093 restraints weight = 12256.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.110106 restraints weight = 11119.782|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.112560 restraints weight = 4617.832|
|-----------------------------------------------------------------------------|
r_work (final): 0.3626
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7705
moved from start:          0.5846

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4772  Z= 0.136
  Angle     :  0.640   8.712   6496  Z= 0.320
  Chirality :  0.042   0.143    743
  Planarity :  0.004   0.051    825
  Dihedral  :  5.527  70.557    728
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  3.54 %
    Allowed  : 23.62 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.36), residues: 588
  helix:  2.98 (0.47), residues: 123
  sheet: -1.48 (0.36), residues: 188
  loop : -1.35 (0.38), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.011   0.001   PHE A 745 
 TYR   0.028   0.002   TYR C  56 
 ARG   0.002   0.000   ARG A 580 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00071 (    2)
  link_NAG-ASN         : angle       4.70213 (    6)
  link_BETA1-4         : bond        0.00590 (    2)
  link_BETA1-4         : angle       1.18059 (    6)
  hydrogen bonds       : bond        0.03814 (  181)
  hydrogen bonds       : angle       4.72738 (  561)
  SS BOND              : bond        0.00378 (    6)
  SS BOND              : angle       1.00566 (   12)
  covalent geometry    : bond        0.00311 ( 4762)
  covalent geometry    : angle       0.62267 ( 6472)

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

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

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1176 Ramachandran restraints generated.
    588 Oldfield, 0 Emsley, 588 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  113 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 95
  time to evaluate  : 0.522 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8603 (OUTLIER) cc_final: 0.8293 (p90)
REVERT: A  634 TYR cc_start: 0.8487 (t80) cc_final: 0.8242 (t80)
REVERT: A  675 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7648 (mt-10)
REVERT: A  700 GLU cc_start: 0.8314 (tp30) cc_final: 0.7862 (tp30)
REVERT: A  715 PHE cc_start: 0.8887 (t80) cc_final: 0.8446 (t80)
REVERT: A  790 PHE cc_start: 0.7905 (m-80) cc_final: 0.7531 (m-80)
REVERT: A  803 THR cc_start: 0.8424 (p) cc_final: 0.8182 (p)
REVERT: B  861 MET cc_start: 0.7000 (OUTLIER) cc_final: 0.6625 (tmm)
REVERT: C   28 GLN cc_start: 0.9150 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: C   36 TRP cc_start: 0.9491 (m100) cc_final: 0.8668 (m100)
REVERT: C   90 GLN cc_start: 0.9308 (tm-30) cc_final: 0.8985 (tm-30)
REVERT: D   41 ARG cc_start: 0.8888 (ptt180) cc_final: 0.8538 (ptm160)
REVERT: D   54 ILE cc_start: 0.9308 (mt) cc_final: 0.8642 (tp)
REVERT: D   83 TYR cc_start: 0.8791 (m-80) cc_final: 0.8356 (m-80)
REVERT: D   92 GLU cc_start: 0.8127 (mp0) cc_final: 0.7774 (mp0)
REVERT: D  101 ARG cc_start: 0.8427 (tmm160) cc_final: 0.7633 (tmm-80)
  outliers start: 18
  outliers final: 16
  residues processed: 107
  average time/residue: 0.1549
  time to fit residues: 21.6628
Evaluate side-chains
  109 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 91
  time to evaluate  : 0.594 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain B residue  861 MET
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 34 optimal weight:    3.9990
   chunk 41 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 6 optimal weight:    0.3980
   chunk 3 optimal weight:    0.7980
   chunk 0 optimal weight:    1.9990
   chunk 10 optimal weight:    0.7980
   chunk 28 optimal weight:    0.8980
   chunk 21 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN
C   4 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3730 r_free = 0.3730 target = 0.119029 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.103855 restraints weight = 12283.128|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3569 r_free = 0.3569 target = 0.109017 restraints weight = 11355.329|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.110344 restraints weight = 4679.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.3589
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.5975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4772  Z= 0.153
  Angle     :  0.648   8.422   6496  Z= 0.327
  Chirality :  0.042   0.141    743
  Planarity :  0.004   0.050    825
  Dihedral  :  5.451  65.202    728
  Min Nonbonded Distance : 2.471

Molprobity Statistics.
  All-atom Clashscore : 9.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 23.03 %
    Favored  : 72.83 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.77 (0.36), residues: 588
  helix:  2.90 (0.47), residues: 123
  sheet: -1.45 (0.35), residues: 191
  loop : -1.38 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.012   0.001   PHE A 745 
 TYR   0.027   0.002   TYR C  56 
 ARG   0.003   0.000   ARG A 655 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00134 (    2)
  link_NAG-ASN         : angle       4.60731 (    6)
  link_BETA1-4         : bond        0.00559 (    2)
  link_BETA1-4         : angle       1.18965 (    6)
  hydrogen bonds       : bond        0.03810 (  181)
  hydrogen bonds       : angle       4.76429 (  561)
  SS BOND              : bond        0.00416 (    6)
  SS BOND              : angle       1.05253 (   12)
  covalent geometry    : bond        0.00350 ( 4762)
  covalent geometry    : angle       0.63103 ( 6472)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2826.16 seconds
wall clock time: 51 minutes 25.79 seconds (3085.79 seconds total)