Starting phenix.real_space_refine
on Sat May 10 03:11:36 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vti_43523/05_2025/8vti_43523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vti_43523/05_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_43523/05_2025/8vti_43523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vti_43523/05_2025/8vti_43523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vti_43523/05_2025/8vti_43523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vti_43523/05_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-5687/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: 7.25, per 1000 atoms: 1.55
  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: 1.27
  Conformation dependent library (CDL) restraints added in 577.1 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: 0.57
  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: 1.28

  Time building geometry restraints manager: 1.47 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:             11.850
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.050
  Process input model:                     19.050
  Find NCS groups from input model:        0.050
  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:2.660
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   33.720
-------------------------------------------------------------------------------
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  : 0.592 
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: 0.1936
  time to fit residues: 51.0429
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  : 0.504 
-------------------------------------------------------------------------------
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:    0.8980
   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 = 12209.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3702 r_free = 0.3702 target = 0.117017 restraints weight = 10651.408|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3739 r_free = 0.3739 target = 0.119719 restraints weight = 4588.679|
|-----------------------------------------------------------------------------|
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  79.780    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       3.29892 (    6)
  link_BETA1-4         : bond        0.00366 (    2)
  link_BETA1-4         : angle       2.04510 (    6)
  hydrogen bonds       : bond        0.04482 (  181)
  hydrogen bonds       : angle       5.76152 (  561)
  SS BOND              : bond        0.00461 (    6)
  SS BOND              : angle       0.93439 (   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  : 0.508 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  688 ASP cc_start: 0.8260 (t0) cc_final: 0.7926 (m-30)
REVERT: A  743 VAL cc_start: 0.9618 (t) cc_final: 0.9362 (m)
REVERT: A  790 PHE cc_start: 0.7669 (m-80) cc_final: 0.7410 (m-80)
REVERT: B  865 GLU cc_start: 0.7409 (mm-30) cc_final: 0.7175 (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: 0.7223 (mtpp)
REVERT: D   39 TRP cc_start: 0.8141 (m100) cc_final: 0.7799 (m100)
REVERT: D   48 LEU cc_start: 0.8232 (mt) cc_final: 0.7837 (mt)
REVERT: D   87 ASN cc_start: 0.8084 (m-40) cc_final: 0.7584 (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: 0.7796 (m-30)
REVERT: D  101 ARG cc_start: 0.7679 (tmm160) cc_final: 0.6849 (tmm-80)
  outliers start: 24
  outliers final: 16
  residues processed: 146
  average time/residue: 0.1817
  time to fit residues: 32.9551
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  : 0.564 
-------------------------------------------------------------------------------
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:    3.9990
   chunk 56 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   chunk 6 optimal weight:    0.6980
   chunk 7 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 45 optimal weight:    0.5980
   chunk 53 optimal weight:    0.9990
   chunk 3 optimal weight:    0.6980
   chunk 23 optimal weight:    2.9990
   chunk 54 optimal weight:    0.9990
   overall best weight:    0.7982

-------------------------------------------------------------------------------
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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3767 r_free = 0.3767 target = 0.121595 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.107259 restraints weight = 12129.221|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.111975 restraints weight = 10848.131|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3655 r_free = 0.3655 target = 0.114470 restraints weight = 4574.642|
|-----------------------------------------------------------------------------|
r_work (final): 0.3659
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7614
moved from start:          0.4207

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= 0.163
  Angle     :  0.660   8.021   6496  Z= 0.342
  Chirality :  0.042   0.154    743
  Planarity :  0.005   0.047    825
  Dihedral  :  6.422  77.419    728
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 18.50 %
    Favored  : 76.57 %
  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:  2.60 (0.46), residues: 123
  sheet: -1.79 (0.35), residues: 191
  loop : -1.36 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.029   0.002   TRP A 554 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.015   0.001   PHE A 745 
 TYR   0.031   0.002   TYR A 634 
 ARG   0.013   0.001   ARG A 593 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00461 (    2)
  link_NAG-ASN         : angle       3.34156 (    6)
  link_BETA1-4         : bond        0.00332 (    2)
  link_BETA1-4         : angle       1.77634 (    6)
  hydrogen bonds       : bond        0.04339 (  181)
  hydrogen bonds       : angle       5.40503 (  561)
  SS BOND              : bond        0.00436 (    6)
  SS BOND              : angle       1.28689 (   12)
  covalent geometry    : bond        0.00366 ( 4762)
  covalent geometry    : angle       0.64841 ( 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
  132 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 107
  time to evaluate  : 0.563 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  593 ARG cc_start: 0.7631 (tpt90) cc_final: 0.7417 (tpt90)
REVERT: A  634 TYR cc_start: 0.8347 (t80) cc_final: 0.7771 (t80)
REVERT: A  638 MET cc_start: 0.8435 (OUTLIER) cc_final: 0.8115 (tpp)
REVERT: A  651 LEU cc_start: 0.8167 (pp) cc_final: 0.7898 (pp)
REVERT: A  688 ASP cc_start: 0.8257 (t0) cc_final: 0.7908 (m-30)
REVERT: A  715 PHE cc_start: 0.8827 (t80) cc_final: 0.8327 (t80)
REVERT: A  790 PHE cc_start: 0.7791 (m-80) cc_final: 0.6928 (m-10)
REVERT: C   13 SER cc_start: 0.4786 (OUTLIER) cc_final: 0.4431 (t)
REVERT: C   36 TRP cc_start: 0.9452 (m100) cc_final: 0.8533 (m100)
REVERT: C   90 GLN cc_start: 0.9397 (tm-30) cc_final: 0.8766 (tm-30)
REVERT: D   22 ARG cc_start: 0.7697 (ttt-90) cc_final: 0.7395 (mtp-110)
REVERT: D   39 TRP cc_start: 0.8665 (m100) cc_final: 0.8218 (m100)
REVERT: D   87 ASN cc_start: 0.8042 (m-40) cc_final: 0.7569 (m-40)
REVERT: D   92 GLU cc_start: 0.8388 (mp0) cc_final: 0.7964 (mp0)
REVERT: D   98 TYR cc_start: 0.8817 (m-80) cc_final: 0.8381 (m-80)
REVERT: D  101 ARG cc_start: 0.7951 (tmm160) cc_final: 0.7080 (tmm-80)
  outliers start: 25
  outliers final: 18
  residues processed: 122
  average time/residue: 0.1649
  time to fit residues: 25.7500
Evaluate side-chains
  119 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 99
  time to evaluate  : 0.525 
-------------------------------------------------------------------------------
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  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   13 SER
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:    3.9990
   chunk 50 optimal weight:    3.9990
   chunk 46 optimal weight:    3.9990
   chunk 5 optimal weight:    0.2980
   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:    3.9990
   chunk 55 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.6386

-------------------------------------------------------------------------------
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 = 0.3673 r_free = 0.3673 target = 0.115660 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 30)----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.100299 restraints weight = 12354.453|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.105566 restraints weight = 12096.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3534 r_free = 0.3534 target = 0.107032 restraints weight = 4889.277|
|-----------------------------------------------------------------------------|
r_work (final): 0.3534
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7828
moved from start:          0.5154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.006   0.069   4772  Z= 0.277
  Angle     :  0.765   8.249   6496  Z= 0.399
  Chirality :  0.044   0.172    743
  Planarity :  0.005   0.051    825
  Dihedral  :  6.434  75.947    728
  Min Nonbonded Distance : 2.405

Molprobity Statistics.
  All-atom Clashscore : 11.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.29 %
    Favored  : 93.71 %
  Rotamer:
    Outliers :  6.69 %
    Allowed  : 18.31 %
    Favored  : 75.00 %
  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: -1.24 (0.35), residues: 588
  helix:  1.99 (0.46), residues: 129
  sheet: -1.68 (0.35), residues: 187
  loop : -1.53 (0.37), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.023   0.002   TRP A 554 
 HIS   0.005   0.001   HIS A 773 
 PHE   0.024   0.002   PHE A 509 
 TYR   0.036   0.003   TYR A 754 
 ARG   0.003   0.001   ARG A 504 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00302 (    2)
  link_NAG-ASN         : angle       3.71974 (    6)
  link_BETA1-4         : bond        0.00420 (    2)
  link_BETA1-4         : angle       1.39906 (    6)
  hydrogen bonds       : bond        0.04788 (  181)
  hydrogen bonds       : angle       5.57761 (  561)
  SS BOND              : bond        0.00757 (    6)
  SS BOND              : angle       1.52253 (   12)
  covalent geometry    : bond        0.00629 ( 4762)
  covalent geometry    : angle       0.75371 ( 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
  134 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 34
    poor density    : 100
  time to evaluate  : 0.497 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 TYR cc_start: 0.8531 (t80) cc_final: 0.8095 (t80)
REVERT: A  654 TRP cc_start: 0.8331 (m100) cc_final: 0.7966 (m100)
REVERT: A  675 GLU cc_start: 0.8039 (mt-10) cc_final: 0.7684 (mt-10)
REVERT: A  688 ASP cc_start: 0.8297 (t0) cc_final: 0.7934 (m-30)
REVERT: A  715 PHE cc_start: 0.8993 (t80) cc_final: 0.8714 (t80)
REVERT: A  790 PHE cc_start: 0.7889 (m-80) cc_final: 0.7401 (m-10)
REVERT: C   13 SER cc_start: 0.5076 (OUTLIER) cc_final: 0.4687 (t)
REVERT: C   36 TRP cc_start: 0.9505 (m100) cc_final: 0.8557 (m100)
REVERT: C   90 GLN cc_start: 0.9367 (tm-30) cc_final: 0.8718 (tm-30)
REVERT: D   22 ARG cc_start: 0.7751 (ttt-90) cc_final: 0.7476 (mtp-110)
REVERT: D   54 ILE cc_start: 0.9358 (mt) cc_final: 0.8596 (tp)
REVERT: D   92 GLU cc_start: 0.8274 (mp0) cc_final: 0.8038 (mp0)
REVERT: D   93 ASP cc_start: 0.8109 (m-30) cc_final: 0.7792 (t0)
  outliers start: 34
  outliers final: 22
  residues processed: 121
  average time/residue: 0.1620
  time to fit residues: 25.0634
Evaluate side-chains
  117 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 94
  time to evaluate  : 0.499 
-------------------------------------------------------------------------------
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  635 VAL
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   13 SER
Chi-restraints excluded: chain C residue   47 LEU
Chi-restraints excluded: chain C residue   55 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 D residue   10 SER
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   81 THR
Chi-restraints excluded: chain D residue  102 HIS
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 19 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 57 optimal weight:    0.5980
   chunk 39 optimal weight:    0.7980
   chunk 23 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9990
   chunk 16 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 52 optimal weight:    0.8980
   chunk 21 optimal weight:    0.0870
   overall best weight:    0.5958

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.118734 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3493 r_free = 0.3493 target = 0.103591 restraints weight = 12305.149|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.108805 restraints weight = 11205.706|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3585 r_free = 0.3585 target = 0.110158 restraints weight = 4690.269|
|-----------------------------------------------------------------------------|
r_work (final): 0.3586
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.5345

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4772  Z= 0.142
  Angle     :  0.639   9.782   6496  Z= 0.325
  Chirality :  0.041   0.138    743
  Planarity :  0.005   0.056    825
  Dihedral  :  5.893  73.427    728
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.33 %
    Allowed  : 21.26 %
    Favored  : 74.41 %
  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: -0.98 (0.36), residues: 588
  helix:  2.84 (0.47), residues: 123
  sheet: -1.79 (0.34), residues: 198
  loop : -1.36 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 554 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.014   0.001   PHE A 745 
 TYR   0.027   0.002   TYR C  56 
 ARG   0.003   0.000   ARG A 580 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00411 (    2)
  link_NAG-ASN         : angle       4.53414 (    6)
  link_BETA1-4         : bond        0.00465 (    2)
  link_BETA1-4         : angle       1.18526 (    6)
  hydrogen bonds       : bond        0.04220 (  181)
  hydrogen bonds       : angle       5.10967 (  561)
  SS BOND              : bond        0.00336 (    6)
  SS BOND              : angle       1.00630 (   12)
  covalent geometry    : bond        0.00325 ( 4762)
  covalent geometry    : angle       0.62220 ( 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
  125 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 103
  time to evaluate  : 0.594 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.8332 (p90)
REVERT: A  634 TYR cc_start: 0.8585 (t80) cc_final: 0.7824 (t80)
REVERT: A  638 MET cc_start: 0.8421 (tpp) cc_final: 0.8051 (ttm)
REVERT: A  688 ASP cc_start: 0.8227 (t0) cc_final: 0.7913 (m-30)
REVERT: A  700 GLU cc_start: 0.8358 (tp30) cc_final: 0.7967 (tp30)
REVERT: A  715 PHE cc_start: 0.8913 (t80) cc_final: 0.8499 (t80)
REVERT: A  790 PHE cc_start: 0.7982 (m-80) cc_final: 0.7499 (m-10)
REVERT: C   36 TRP cc_start: 0.9499 (m100) cc_final: 0.8615 (m100)
REVERT: C   90 GLN cc_start: 0.9313 (tm-30) cc_final: 0.8661 (tm-30)
REVERT: D   22 ARG cc_start: 0.7694 (ttt-90) cc_final: 0.7472 (mtp-110)
REVERT: D   41 ARG cc_start: 0.8693 (ptt180) cc_final: 0.8217 (ptm160)
REVERT: D   54 ILE cc_start: 0.9323 (mt) cc_final: 0.8601 (tp)
REVERT: D   83 TYR cc_start: 0.8811 (m-80) cc_final: 0.8486 (m-80)
  outliers start: 22
  outliers final: 17
  residues processed: 117
  average time/residue: 0.1627
  time to fit residues: 24.7845
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  : 0.515 
-------------------------------------------------------------------------------
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  658 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 D residue   10 SER
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  102 HIS
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 22 optimal weight:    0.0670
   chunk 50 optimal weight:    1.9990
   chunk 46 optimal weight:    0.8980
   chunk 43 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 16 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 45 optimal weight:    3.9990
   overall best weight:    0.6518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3726 r_free = 0.3726 target = 0.118916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.103658 restraints weight = 12171.590|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3570 r_free = 0.3570 target = 0.108986 restraints weight = 11155.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3588 r_free = 0.3588 target = 0.110278 restraints weight = 4590.266|
|-----------------------------------------------------------------------------|
r_work (final): 0.3591
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7751
moved from start:          0.5559

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   4772  Z= 0.146
  Angle     :  0.647   9.300   6496  Z= 0.328
  Chirality :  0.041   0.150    743
  Planarity :  0.004   0.051    825
  Dihedral  :  5.662  68.816    728
  Min Nonbonded Distance : 2.467

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 22.44 %
    Favored  : 72.24 %
  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: -0.87 (0.35), residues: 588
  helix:  2.84 (0.47), residues: 123
  sheet: -1.58 (0.36), residues: 188
  loop : -1.40 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.040   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.013   0.001   PHE A 745 
 TYR   0.027   0.002   TYR C  56 
 ARG   0.002   0.000   ARG A 504 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00141 (    2)
  link_NAG-ASN         : angle       4.25676 (    6)
  link_BETA1-4         : bond        0.00555 (    2)
  link_BETA1-4         : angle       1.16231 (    6)
  hydrogen bonds       : bond        0.04073 (  181)
  hydrogen bonds       : angle       5.00593 (  561)
  SS BOND              : bond        0.00389 (    6)
  SS BOND              : angle       0.97927 (   12)
  covalent geometry    : bond        0.00333 ( 4762)
  covalent geometry    : angle       0.63304 ( 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: 27
    poor density    : 99
  time to evaluate  : 0.577 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8632 (OUTLIER) cc_final: 0.8325 (p90)
REVERT: A  634 TYR cc_start: 0.8604 (t80) cc_final: 0.7828 (t80)
REVERT: A  638 MET cc_start: 0.8414 (tpp) cc_final: 0.8006 (ttm)
REVERT: A  688 ASP cc_start: 0.8156 (t0) cc_final: 0.7864 (m-30)
REVERT: A  700 GLU cc_start: 0.8296 (tp30) cc_final: 0.7859 (tp30)
REVERT: A  715 PHE cc_start: 0.8937 (t80) cc_final: 0.8508 (t80)
REVERT: A  790 PHE cc_start: 0.8018 (m-80) cc_final: 0.7594 (m-80)
REVERT: A  846 HIS cc_start: 0.8192 (m-70) cc_final: 0.7974 (m-70)
REVERT: B  861 MET cc_start: 0.6216 (OUTLIER) cc_final: 0.5876 (tpp)
REVERT: C   36 TRP cc_start: 0.9497 (m100) cc_final: 0.8616 (m100)
REVERT: C   90 GLN cc_start: 0.9302 (tm-30) cc_final: 0.8671 (tm-30)
REVERT: D   41 ARG cc_start: 0.8786 (ptt180) cc_final: 0.8361 (ptm160)
REVERT: D   54 ILE cc_start: 0.9339 (mt) cc_final: 0.8635 (tp)
  outliers start: 27
  outliers final: 20
  residues processed: 116
  average time/residue: 0.1774
  time to fit residues: 26.0203
Evaluate side-chains
  119 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 97
  time to evaluate  : 0.554 
-------------------------------------------------------------------------------
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  609 LEU
Chi-restraints excluded: chain A residue  627 ARG
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  847 THR
Chi-restraints excluded: chain B residue  861 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 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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 16 optimal weight:    0.5980
   chunk 34 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 29 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   chunk 11 optimal weight:    0.0040
   chunk 54 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    0.6980
   chunk 46 optimal weight:    3.9990
   chunk 10 optimal weight:    0.7980
   overall best weight:    0.6192

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

Flipped N/Q/H residues before XYZ refinement:
C   4 GLN
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3727 r_free = 0.3727 target = 0.119115 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.103453 restraints weight = 12339.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.108653 restraints weight = 11919.618|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3584 r_free = 0.3584 target = 0.110398 restraints weight = 5211.679|
|-----------------------------------------------------------------------------|
r_work (final): 0.3587
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.5724

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4772  Z= 0.140
  Angle     :  0.645   8.624   6496  Z= 0.324
  Chirality :  0.041   0.146    743
  Planarity :  0.004   0.053    825
  Dihedral  :  5.569  67.713    728
  Min Nonbonded Distance : 2.482

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.10 %
    Favored  : 94.90 %
  Rotamer:
    Outliers :  5.51 %
    Allowed  : 22.83 %
    Favored  : 71.65 %
  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: -0.79 (0.36), residues: 588
  helix:  2.89 (0.47), residues: 123
  sheet: -1.55 (0.36), residues: 188
  loop : -1.33 (0.37), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.061   0.002   TRP A 654 
 HIS   0.004   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 A 655 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00127 (    2)
  link_NAG-ASN         : angle       4.70553 (    6)
  link_BETA1-4         : bond        0.00515 (    2)
  link_BETA1-4         : angle       1.09515 (    6)
  hydrogen bonds       : bond        0.04010 (  181)
  hydrogen bonds       : angle       4.94798 (  561)
  SS BOND              : bond        0.00402 (    6)
  SS BOND              : angle       1.00680 (   12)
  covalent geometry    : bond        0.00322 ( 4762)
  covalent geometry    : angle       0.62735 ( 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
  122 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 94
  time to evaluate  : 0.515 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  540 TRP cc_start: 0.4346 (OUTLIER) cc_final: 0.4136 (m100)
REVERT: A  554 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.8325 (p90)
REVERT: A  634 TYR cc_start: 0.8605 (t80) cc_final: 0.7952 (t80)
REVERT: A  668 MET cc_start: 0.8715 (tpt) cc_final: 0.8176 (tpp)
REVERT: A  688 ASP cc_start: 0.8135 (t0) cc_final: 0.7831 (m-30)
REVERT: A  700 GLU cc_start: 0.8303 (tp30) cc_final: 0.7842 (tp30)
REVERT: A  715 PHE cc_start: 0.8950 (t80) cc_final: 0.8504 (t80)
REVERT: A  790 PHE cc_start: 0.8053 (m-80) cc_final: 0.7563 (m-80)
REVERT: B  861 MET cc_start: 0.6052 (OUTLIER) cc_final: 0.5677 (tpp)
REVERT: C   28 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8932 (tm-30)
REVERT: C   90 GLN cc_start: 0.9284 (tm-30) cc_final: 0.9065 (tm-30)
REVERT: D   41 ARG cc_start: 0.8748 (ptt180) cc_final: 0.8519 (ptm160)
REVERT: D   54 ILE cc_start: 0.9354 (mt) cc_final: 0.8671 (tp)
  outliers start: 28
  outliers final: 20
  residues processed: 114
  average time/residue: 0.1540
  time to fit residues: 22.7186
Evaluate side-chains
  114 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 91
  time to evaluate  : 0.513 
-------------------------------------------------------------------------------
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  609 LEU
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  658 THR
Chi-restraints excluded: chain A residue  697 ILE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain B residue  861 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   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  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:    3.9990
   chunk 45 optimal weight:    0.9980
   chunk 42 optimal weight:    5.9990
   chunk 48 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 40 optimal weight:    0.4980
   chunk 9 optimal weight:    2.9990
   chunk 47 optimal weight:    1.9990
   chunk 34 optimal weight:    4.9990
   chunk 33 optimal weight:    2.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    1.0984

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

Flipped N/Q/H residues before XYZ refinement:
** A 671 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
C   4 GLN
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3690 r_free = 0.3690 target = 0.116651 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3452 r_free = 0.3452 target = 0.101302 restraints weight = 12233.013|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3529 r_free = 0.3529 target = 0.106569 restraints weight = 11700.224|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.107690 restraints weight = 4779.464|
|-----------------------------------------------------------------------------|
r_work (final): 0.3543
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7805
moved from start:          0.5940

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.064   4772  Z= 0.197
  Angle     :  0.693   9.281   6496  Z= 0.355
  Chirality :  0.043   0.150    743
  Planarity :  0.005   0.051    825
  Dihedral  :  5.794  69.166    728
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.80 %
    Favored  : 93.20 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 23.43 %
    Favored  : 71.65 %
  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: -0.92 (0.36), residues: 588
  helix:  2.82 (0.47), residues: 122
  sheet: -1.71 (0.35), residues: 199
  loop : -1.31 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.066   0.003   TRP A 654 
 HIS   0.005   0.001   HIS A 671 
 PHE   0.015   0.001   PHE A 509 
 TYR   0.029   0.002   TYR C  56 
 ARG   0.004   0.001   ARG A 826 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00355 (    2)
  link_NAG-ASN         : angle       4.98325 (    6)
  link_BETA1-4         : bond        0.00494 (    2)
  link_BETA1-4         : angle       1.19084 (    6)
  hydrogen bonds       : bond        0.04195 (  181)
  hydrogen bonds       : angle       5.09904 (  561)
  SS BOND              : bond        0.00568 (    6)
  SS BOND              : angle       1.19541 (   12)
  covalent geometry    : bond        0.00453 ( 4762)
  covalent geometry    : angle       0.67505 ( 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
  117 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.556 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 TYR cc_start: 0.8614 (t80) cc_final: 0.8183 (t80)
REVERT: A  675 GLU cc_start: 0.8086 (mt-10) cc_final: 0.7707 (mt-10)
REVERT: A  688 ASP cc_start: 0.8121 (t0) cc_final: 0.7830 (m-30)
REVERT: A  700 GLU cc_start: 0.8258 (tp30) cc_final: 0.7847 (tp30)
REVERT: A  715 PHE cc_start: 0.9023 (t80) cc_final: 0.8595 (t80)
REVERT: A  790 PHE cc_start: 0.8039 (m-80) cc_final: 0.7475 (m-10)
REVERT: B  861 MET cc_start: 0.6252 (OUTLIER) cc_final: 0.5874 (tpp)
REVERT: C   90 GLN cc_start: 0.9304 (tm-30) cc_final: 0.9086 (tm-30)
REVERT: D   41 ARG cc_start: 0.8960 (ptt180) cc_final: 0.8471 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9398 (mt) cc_final: 0.8697 (tp)
  outliers start: 25
  outliers final: 23
  residues processed: 108
  average time/residue: 0.1670
  time to fit residues: 23.0761
Evaluate side-chains
  109 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 85
  time to evaluate  : 0.555 
-------------------------------------------------------------------------------
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  609 LEU
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  697 ILE
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain A residue  810 SER
Chi-restraints excluded: chain A residue  817 ASN
Chi-restraints excluded: chain B residue  861 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   83 ASP
Chi-restraints excluded: chain D residue   10 SER
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:    3.9990
   chunk 33 optimal weight:    4.9990
   chunk 25 optimal weight:    0.4980
   chunk 52 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 35 optimal weight:    0.9980
   chunk 11 optimal weight:    0.4980
   chunk 18 optimal weight:    0.2980
   chunk 12 optimal weight:    0.5980
   chunk 7 optimal weight:    0.4980
   overall best weight:    0.4780

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

Flipped N/Q/H residues before XYZ refinement:
C   4 GLN
** C  94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.119482 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.104016 restraints weight = 12300.620|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.109187 restraints weight = 11834.327|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.111267 restraints weight = 5133.964|
|-----------------------------------------------------------------------------|
r_work (final): 0.3599
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.6055

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.045   4772  Z= 0.138
  Angle     :  0.654   8.657   6496  Z= 0.332
  Chirality :  0.041   0.143    743
  Planarity :  0.004   0.055    825
  Dihedral  :  5.602  70.488    728
  Min Nonbonded Distance : 2.490

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.93 %
    Favored  : 95.07 %
  Rotamer:
    Outliers :  4.13 %
    Allowed  : 23.82 %
    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: -0.80 (0.36), residues: 588
  helix:  2.86 (0.47), residues: 122
  sheet: -1.46 (0.36), residues: 186
  loop : -1.39 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.039   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.011   0.001   PHE A 745 
 TYR   0.052   0.002   TYR A 754 
 ARG   0.003   0.000   ARG A 655 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00109 (    2)
  link_NAG-ASN         : angle       4.93592 (    6)
  link_BETA1-4         : bond        0.00605 (    2)
  link_BETA1-4         : angle       1.19963 (    6)
  hydrogen bonds       : bond        0.04004 (  181)
  hydrogen bonds       : angle       4.91363 (  561)
  SS BOND              : bond        0.00339 (    6)
  SS BOND              : angle       1.03070 (   12)
  covalent geometry    : bond        0.00315 ( 4762)
  covalent geometry    : angle       0.63525 ( 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
  113 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 92
  time to evaluate  : 0.546 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8647 (OUTLIER) cc_final: 0.8328 (p90)
REVERT: A  634 TYR cc_start: 0.8502 (t80) cc_final: 0.8166 (t80)
REVERT: A  675 GLU cc_start: 0.8046 (mt-10) cc_final: 0.7623 (mt-10)
REVERT: A  688 ASP cc_start: 0.8124 (t0) cc_final: 0.7826 (m-30)
REVERT: A  700 GLU cc_start: 0.8263 (tp30) cc_final: 0.7843 (tp30)
REVERT: A  715 PHE cc_start: 0.8938 (t80) cc_final: 0.8539 (t80)
REVERT: A  790 PHE cc_start: 0.8048 (m-80) cc_final: 0.7429 (m-10)
REVERT: B  861 MET cc_start: 0.6031 (OUTLIER) cc_final: 0.5648 (tpp)
REVERT: C   28 GLN cc_start: 0.9163 (tm-30) cc_final: 0.8921 (tm-30)
REVERT: C   90 GLN cc_start: 0.9274 (tm-30) cc_final: 0.9029 (tm-30)
REVERT: D   41 ARG cc_start: 0.8917 (ptt180) cc_final: 0.8529 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9349 (mt) cc_final: 0.8685 (tp)
REVERT: D  119 GLN cc_start: 0.7907 (mm-40) cc_final: 0.7614 (mm-40)
  outliers start: 21
  outliers final: 18
  residues processed: 105
  average time/residue: 0.1704
  time to fit residues: 22.7124
Evaluate side-chains
  106 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 86
  time to evaluate  : 0.524 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  609 LEU
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  697 ILE
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   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   83 ASP
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 43 optimal weight:    0.7980
   chunk 18 optimal weight:    0.7980
   chunk 22 optimal weight:    1.9990
   chunk 0 optimal weight:    6.9990
   chunk 40 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 14 optimal weight:    0.5980
   chunk 33 optimal weight:    0.0470
   chunk 42 optimal weight:    1.9990
   chunk 54 optimal weight:    0.4980
   chunk 23 optimal weight:    1.9990
   overall best weight:    0.5078

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

Flipped N/Q/H residues before XYZ refinement:
C  94 GLN

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 = 0.120047 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3506 r_free = 0.3506 target = 0.104738 restraints weight = 12103.723|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.110104 restraints weight = 11196.587|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3600 r_free = 0.3600 target = 0.111332 restraints weight = 4597.067|
|-----------------------------------------------------------------------------|
r_work (final): 0.3602
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
moved from start:          0.6197

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   4772  Z= 0.138
  Angle     :  0.655   8.424   6496  Z= 0.333
  Chirality :  0.041   0.138    743
  Planarity :  0.004   0.052    825
  Dihedral  :  5.401  62.436    728
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  3.74 %
    Allowed  : 24.41 %
    Favored  : 71.85 %
  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:  2.84 (0.47), residues: 122
  sheet: -1.41 (0.36), residues: 186
  loop : -1.31 (0.38), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.047   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 
 PHE   0.011   0.001   PHE A 745 
 TYR   0.030   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D 101 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00136 (    2)
  link_NAG-ASN         : angle       4.66103 (    6)
  link_BETA1-4         : bond        0.00556 (    2)
  link_BETA1-4         : angle       1.21990 (    6)
  hydrogen bonds       : bond        0.03933 (  181)
  hydrogen bonds       : angle       4.89907 (  561)
  SS BOND              : bond        0.00368 (    6)
  SS BOND              : angle       1.02347 (   12)
  covalent geometry    : bond        0.00314 ( 4762)
  covalent geometry    : angle       0.63820 ( 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
  108 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 89
  time to evaluate  : 0.510 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8623 (OUTLIER) cc_final: 0.8301 (p90)
REVERT: A  634 TYR cc_start: 0.8454 (t80) cc_final: 0.8087 (t80)
REVERT: A  675 GLU cc_start: 0.8048 (mt-10) cc_final: 0.7507 (mt-10)
REVERT: A  688 ASP cc_start: 0.8045 (t0) cc_final: 0.7824 (m-30)
REVERT: A  700 GLU cc_start: 0.8185 (tp30) cc_final: 0.7767 (tp30)
REVERT: A  715 PHE cc_start: 0.8935 (t80) cc_final: 0.8528 (t80)
REVERT: A  790 PHE cc_start: 0.8041 (m-80) cc_final: 0.7425 (m-10)
REVERT: B  861 MET cc_start: 0.6100 (OUTLIER) cc_final: 0.5707 (tpp)
REVERT: C   28 GLN cc_start: 0.9135 (tm-30) cc_final: 0.8849 (tm-30)
REVERT: C   90 GLN cc_start: 0.9236 (tm-30) cc_final: 0.9033 (tm-30)
REVERT: D   41 ARG cc_start: 0.8916 (ptt180) cc_final: 0.8567 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9337 (mt) cc_final: 0.8703 (tp)
REVERT: D   60 TYR cc_start: 0.8630 (t80) cc_final: 0.8402 (t80)
REVERT: D  119 GLN cc_start: 0.7881 (mm-40) cc_final: 0.7536 (mm-40)
  outliers start: 19
  outliers final: 15
  residues processed: 101
  average time/residue: 0.1581
  time to fit residues: 20.5989
Evaluate side-chains
  101 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 84
  time to evaluate  : 0.507 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  554 TRP
Chi-restraints excluded: chain A residue  609 LEU
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  644 ASN
Chi-restraints excluded: chain A residue  697 ILE
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   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:    0.9990
   chunk 41 optimal weight:    0.0470
   chunk 5 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9990
   chunk 3 optimal weight:    0.5980
   chunk 0 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 28 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9980
   chunk 55 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9980
   overall best weight:    0.6678

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3737 r_free = 0.3737 target = 0.119438 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3496 r_free = 0.3496 target = 0.104133 restraints weight = 12318.306|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3573 r_free = 0.3573 target = 0.109467 restraints weight = 11464.386|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.110641 restraints weight = 4756.189|
|-----------------------------------------------------------------------------|
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7741
moved from start:          0.6294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4772  Z= 0.148
  Angle     :  0.656   8.373   6496  Z= 0.331
  Chirality :  0.041   0.142    743
  Planarity :  0.004   0.053    825
  Dihedral  :  5.528  66.560    728
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  3.94 %
    Allowed  : 24.41 %
    Favored  : 71.65 %
  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: -0.72 (0.36), residues: 588
  helix:  2.76 (0.47), residues: 123
  sheet: -1.36 (0.36), residues: 186
  loop : -1.31 (0.38), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.041   0.002   TRP A 654 
 HIS   0.004   0.001   HIS D 102 
 PHE   0.010   0.001   PHE A 745 
 TYR   0.026   0.002   TYR C  56 
 ARG   0.002   0.000   ARG D 101 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00195 (    2)
  link_NAG-ASN         : angle       4.53941 (    6)
  link_BETA1-4         : bond        0.00519 (    2)
  link_BETA1-4         : angle       1.21313 (    6)
  hydrogen bonds       : bond        0.03950 (  181)
  hydrogen bonds       : angle       4.88993 (  561)
  SS BOND              : bond        0.00424 (    6)
  SS BOND              : angle       1.05993 (   12)
  covalent geometry    : bond        0.00340 ( 4762)
  covalent geometry    : angle       0.64001 ( 6472)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2252.37 seconds
wall clock time: 41 minutes 9.23 seconds (2469.23 seconds total)