Starting phenix.real_space_refine
on Fri Aug 22 15:17:31 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8vti_43523/08_2025/8vti_43523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8vti_43523/08_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_43523/08_2025/8vti_43523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8vti_43523/08_2025/8vti_43523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8vti_43523/08_2025/8vti_43523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8vti_43523/08_2025/8vti_43523.cif"
  }
  resolution = 3.9
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.000 sd=   0.007
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 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: 1.14, per 1000 atoms: 0.24
  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: 0.34
  Conformation dependent library (CDL) restraints added in 177.5 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  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: 0.11
  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: 0.63

  Time building geometry restraints manager: 0.47 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:             12.890
  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:             0.010
  Extract box with map and model:          0.130
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.400
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.050
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.530
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -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
 ARG   0.003   0.000   ARG C  62 
 TYR   0.017   0.002   TYR D  36 
 PHE   0.015   0.002   PHE A 745 
 TRP   0.020   0.002   TRP A 554 
 HIS   0.004   0.001   HIS A 846 

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

*********************** 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  : 0.128 
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: 0.7354 (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: 0.7744 (m-10)
REVERT: B  860 LEU cc_start: 0.8420 (OUTLIER) cc_final: 0.8146 (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: 0.5853 (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: 0.7204 (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: 0.0741
  time to fit residues: 19.7199
Evaluate side-chains
  143 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 136
  time to evaluate  : 0.137 
-------------------------------------------------------------------------------
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 54 optimal weight:    0.9990
   chunk 24 optimal weight:    2.9990
   chunk 48 optimal weight:    0.6980
   chunk 56 optimal weight:    0.8980
   chunk 26 optimal weight:    3.9990
   chunk 2 optimal weight:    0.4980
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.6980
   chunk 50 optimal weight:    3.9990
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 644 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 662 GLN
A 773 HIS
** A 813 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3828 r_free = 0.3828 target = 0.125590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3627 r_free = 0.3627 target = 0.111766 restraints weight = 12265.803|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.116358 restraints weight = 10733.675|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3728 r_free = 0.3728 target = 0.119041 restraints weight = 4617.322|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.119243 restraints weight = 2886.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.119862 restraints weight = 2443.816|
|-----------------------------------------------------------------------------|
r_work (final): 0.3741
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7480
moved from start:          0.3379

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= 0.169
  Angle     :  0.698   7.228   6496  Z= 0.360
  Chirality :  0.043   0.185    743
  Planarity :  0.005   0.047    825
  Dihedral  :  8.786  80.003    737
  Min Nonbonded Distance : 2.569

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.08 %
    Favored  : 95.92 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 15.75 %
    Favored  : 79.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.46 (0.34), residues: 588
  helix:  1.77 (0.43), residues: 129
  sheet: -2.07 (0.34), residues: 189
  loop : -1.42 (0.38), residues: 270

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 593 
 TYR   0.029   0.003   TYR C  56 
 PHE   0.019   0.002   PHE A 745 
 TRP   0.015   0.002   TRP A 554 
 HIS   0.003   0.001   HIS A 773 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 4762)
  covalent geometry    : angle       0.68777 ( 6472)
  SS BOND              : bond        0.00474 (    6)
  SS BOND              : angle       0.93839 (   12)
  hydrogen bonds       : bond        0.04595 (  181)
  hydrogen bonds       : angle       5.82059 (  561)
  link_BETA1-4         : bond        0.00567 (    2)
  link_BETA1-4         : angle       2.08364 (    6)
  link_NAG-ASN         : bond        0.00103 (    2)
  link_NAG-ASN         : angle       3.36046 (    6)

*********************** 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
  151 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 127
  time to evaluate  : 0.127 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  688 ASP cc_start: 0.8237 (t0) cc_final: 0.7923 (m-30)
REVERT: A  782 ILE cc_start: 0.8987 (tp) cc_final: 0.8780 (tt)
REVERT: A  790 PHE cc_start: 0.7648 (m-80) cc_final: 0.7413 (m-80)
REVERT: B  865 GLU cc_start: 0.7384 (mm-30) cc_final: 0.7116 (mm-30)
REVERT: C   36 TRP cc_start: 0.9280 (m100) cc_final: 0.8427 (m100)
REVERT: C   90 GLN cc_start: 0.9371 (tm-30) cc_final: 0.8982 (tm-30)
REVERT: C   94 GLN cc_start: 0.8724 (OUTLIER) cc_final: 0.7594 (pp30)
REVERT: C  104 LYS cc_start: 0.7489 (mtpt) cc_final: 0.7250 (mtpp)
REVERT: D   39 TRP cc_start: 0.8176 (m100) cc_final: 0.7845 (m100)
REVERT: D   87 ASN cc_start: 0.8081 (m-40) cc_final: 0.7593 (m-40)
REVERT: D   92 GLU cc_start: 0.8361 (mp0) cc_final: 0.8148 (mp0)
REVERT: D   93 ASP cc_start: 0.8035 (m-30) cc_final: 0.7736 (m-30)
REVERT: D  101 ARG cc_start: 0.7721 (tmm160) cc_final: 0.6881 (tmm-80)
  outliers start: 24
  outliers final: 16
  residues processed: 141
  average time/residue: 0.0699
  time to fit residues: 12.4083
Evaluate side-chains
  119 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
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 6 optimal weight:    1.9990
   chunk 13 optimal weight:    2.9990
   chunk 54 optimal weight:    0.0270
   chunk 47 optimal weight:    0.8980
   chunk 57 optimal weight:    1.9990
   chunk 19 optimal weight:    3.9990
   chunk 52 optimal weight:    2.9990
   chunk 25 optimal weight:    1.9990
   chunk 11 optimal weight:    0.8980
   chunk 33 optimal weight:    0.2980
   chunk 28 optimal weight:    0.0770
   overall best weight:    0.4396

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

Flipped N/Q/H residues before XYZ refinement:
A 644 ASN
** C   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C  94 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3806 r_free = 0.3806 target = 0.124119 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.110211 restraints weight = 12225.896|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3666 r_free = 0.3666 target = 0.114778 restraints weight = 10675.990|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3703 r_free = 0.3703 target = 0.117491 restraints weight = 4584.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3706 r_free = 0.3706 target = 0.117734 restraints weight = 2812.762|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.117969 restraints weight = 2403.771|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7529
moved from start:          0.4056

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4772  Z= 0.134
  Angle     :  0.631   7.942   6496  Z= 0.324
  Chirality :  0.042   0.145    743
  Planarity :  0.005   0.047    825
  Dihedral  :  6.408  77.550    728
  Min Nonbonded Distance : 2.532

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.25 %
    Favored  : 95.75 %
  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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.35), residues: 588
  helix:  2.66 (0.46), residues: 123
  sheet: -1.83 (0.35), residues: 191
  loop : -1.29 (0.38), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG A 593 
 TYR   0.030   0.002   TYR A 634 
 PHE   0.014   0.001   PHE A 745 
 TRP   0.032   0.002   TRP A 554 
 HIS   0.003   0.001   HIS A 806 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4762)
  covalent geometry    : angle       0.61670 ( 6472)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       1.16978 (   12)
  hydrogen bonds       : bond        0.04201 (  181)
  hydrogen bonds       : angle       5.31070 (  561)
  link_BETA1-4         : bond        0.00445 (    2)
  link_BETA1-4         : angle       1.73952 (    6)
  link_NAG-ASN         : bond        0.01259 (    2)
  link_NAG-ASN         : angle       3.81367 (    6)

*********************** 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
  138 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 113
  time to evaluate  : 0.123 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  531 TYR cc_start: 0.4467 (t80) cc_final: 0.4242 (t80)
REVERT: A  592 VAL cc_start: 0.9130 (OUTLIER) cc_final: 0.8839 (t)
REVERT: A  638 MET cc_start: 0.8411 (OUTLIER) cc_final: 0.8194 (tpp)
REVERT: A  651 LEU cc_start: 0.8152 (pp) cc_final: 0.7877 (pp)
REVERT: A  688 ASP cc_start: 0.8222 (t0) cc_final: 0.7919 (m-30)
REVERT: A  715 PHE cc_start: 0.8623 (t80) cc_final: 0.8255 (t80)
REVERT: A  743 VAL cc_start: 0.9612 (t) cc_final: 0.9284 (m)
REVERT: A  790 PHE cc_start: 0.7716 (m-80) cc_final: 0.6851 (m-10)
REVERT: B  865 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7144 (mm-30)
REVERT: C   36 TRP cc_start: 0.9435 (m100) cc_final: 0.8575 (m100)
REVERT: C   90 GLN cc_start: 0.9395 (tm-30) cc_final: 0.8794 (tm-30)
REVERT: D   22 ARG cc_start: 0.7669 (ttt-90) cc_final: 0.7042 (mmm-85)
REVERT: D   39 TRP cc_start: 0.8492 (m100) cc_final: 0.8064 (m100)
REVERT: D   87 ASN cc_start: 0.7999 (m-40) cc_final: 0.7493 (m-40)
REVERT: D   92 GLU cc_start: 0.8346 (mp0) cc_final: 0.8088 (mp0)
REVERT: D   98 TYR cc_start: 0.8493 (m-80) cc_final: 0.8037 (m-80)
REVERT: D  101 ARG cc_start: 0.7815 (tmm160) cc_final: 0.6970 (tmm-80)
  outliers start: 25
  outliers final: 15
  residues processed: 128
  average time/residue: 0.0602
  time to fit residues: 9.8287
Evaluate side-chains
  116 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 99
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  529 SER
Chi-restraints excluded: chain A residue  532 LEU
Chi-restraints excluded: chain A residue  540 TRP
Chi-restraints excluded: chain A residue  592 VAL
Chi-restraints excluded: chain A residue  627 ARG
Chi-restraints excluded: chain A residue  638 MET
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   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 45 optimal weight:    0.4980
   chunk 14 optimal weight:    0.9980
   chunk 30 optimal weight:    1.9990
   chunk 39 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 22 optimal weight:    2.9990
   chunk 10 optimal weight:    0.6980
   chunk 47 optimal weight:    2.9990
   chunk 53 optimal weight:    1.9990
   chunk 46 optimal weight:    2.9990
   overall best weight:    1.0382

-------------------------------------------------------------------------------
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 671 HIS
** C   7 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 = 0.3726 r_free = 0.3726 target = 0.119182 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3499 r_free = 0.3499 target = 0.104122 restraints weight = 12211.313|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3572 r_free = 0.3572 target = 0.109173 restraints weight = 11654.528|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.111589 restraints weight = 4783.549|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3610 r_free = 0.3610 target = 0.111898 restraints weight = 3247.393|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.112307 restraints weight = 2776.202|
|-----------------------------------------------------------------------------|
r_work (final): 0.3618
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7706
moved from start:          0.4855

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4772  Z= 0.195
  Angle     :  0.684   8.660   6496  Z= 0.353
  Chirality :  0.043   0.163    743
  Planarity :  0.005   0.069    825
  Dihedral  :  5.969  74.228    728
  Min Nonbonded Distance : 2.454

Molprobity Statistics.
  All-atom Clashscore : 9.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 18.11 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.00 (0.35), residues: 588
  helix:  2.67 (0.47), residues: 123
  sheet: -1.73 (0.35), residues: 198
  loop : -1.35 (0.38), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG A 593 
 TYR   0.027   0.002   TYR A 634 
 PHE   0.018   0.002   PHE A 509 
 TRP   0.025   0.002   TRP A 554 
 HIS   0.004   0.001   HIS A 671 

Details of bonding type rmsd
  covalent geometry    : bond        0.00448 ( 4762)
  covalent geometry    : angle       0.67356 ( 6472)
  SS BOND              : bond        0.00543 (    6)
  SS BOND              : angle       1.38813 (   12)
  hydrogen bonds       : bond        0.04333 (  181)
  hydrogen bonds       : angle       5.17868 (  561)
  link_BETA1-4         : bond        0.00224 (    2)
  link_BETA1-4         : angle       1.47132 (    6)
  link_NAG-ASN         : bond        0.00489 (    2)
  link_NAG-ASN         : angle       3.34721 (    6)

*********************** 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
  131 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 104
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  634 TYR cc_start: 0.8334 (t80) cc_final: 0.7919 (t80)
REVERT: A  675 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7579 (mt-10)
REVERT: A  688 ASP cc_start: 0.8209 (t0) cc_final: 0.7915 (m-30)
REVERT: A  715 PHE cc_start: 0.8778 (t80) cc_final: 0.8388 (t80)
REVERT: A  743 VAL cc_start: 0.9650 (t) cc_final: 0.9356 (m)
REVERT: A  790 PHE cc_start: 0.7841 (m-80) cc_final: 0.7421 (m-10)
REVERT: C   36 TRP cc_start: 0.9503 (m100) cc_final: 0.8575 (m100)
REVERT: C   90 GLN cc_start: 0.9402 (tm-30) cc_final: 0.8789 (tm-30)
REVERT: D   22 ARG cc_start: 0.7709 (ttt-90) cc_final: 0.7499 (mtp-110)
REVERT: D   41 ARG cc_start: 0.8587 (ptt180) cc_final: 0.8222 (ptm160)
REVERT: D   54 ILE cc_start: 0.9224 (mt) cc_final: 0.8476 (tp)
REVERT: D   92 GLU cc_start: 0.8155 (mp0) cc_final: 0.7950 (mp0)
REVERT: D  101 ARG cc_start: 0.8176 (tmm160) cc_final: 0.7274 (tmm-80)
REVERT: D  103 ASN cc_start: 0.8593 (t0) cc_final: 0.8372 (t0)
  outliers start: 27
  outliers final: 19
  residues processed: 122
  average time/residue: 0.0682
  time to fit residues: 10.5505
Evaluate side-chains
  110 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 91
  time to evaluate  : 0.196 
-------------------------------------------------------------------------------
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  658 THR
Chi-restraints excluded: chain A residue  672 THR
Chi-restraints excluded: chain A residue  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   98 THR
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  110 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 40 optimal weight:    0.4980
   chunk 53 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 48 optimal weight:    1.9990
   chunk 39 optimal weight:    1.9990
   chunk 45 optimal weight:    0.3980
   chunk 18 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 29 optimal weight:    2.9990
   chunk 13 optimal weight:    0.7980
   chunk 3 optimal weight:    0.7980
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 605 GLN
A 608 ASN
A 644 ASN
** A 787 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.119991 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3514 r_free = 0.3514 target = 0.104983 restraints weight = 12079.552|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3586 r_free = 0.3586 target = 0.110081 restraints weight = 11136.480|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3622 r_free = 0.3622 target = 0.112512 restraints weight = 4587.646|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3624 r_free = 0.3624 target = 0.112743 restraints weight = 3100.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.113265 restraints weight = 2657.675|
|-----------------------------------------------------------------------------|
r_work (final): 0.3637
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7678
moved from start:          0.5231

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4772  Z= 0.150
  Angle     :  0.629   8.825   6496  Z= 0.323
  Chirality :  0.042   0.149    743
  Planarity :  0.005   0.053    825
  Dihedral  :  5.676  71.065    728
  Min Nonbonded Distance : 2.493

Molprobity Statistics.
  All-atom Clashscore : 9.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 19.88 %
    Favored  : 75.20 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.86 (0.35), residues: 588
  helix:  2.88 (0.48), residues: 123
  sheet: -1.63 (0.36), residues: 179
  loop : -1.39 (0.36), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 737 
 TYR   0.028   0.002   TYR A 634 
 PHE   0.013   0.001   PHE A 745 
 TRP   0.034   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00341 ( 4762)
  covalent geometry    : angle       0.61348 ( 6472)
  SS BOND              : bond        0.00393 (    6)
  SS BOND              : angle       1.20794 (   12)
  hydrogen bonds       : bond        0.04135 (  181)
  hydrogen bonds       : angle       4.96964 (  561)
  link_BETA1-4         : bond        0.00487 (    2)
  link_BETA1-4         : angle       1.15918 (    6)
  link_NAG-ASN         : bond        0.00628 (    2)
  link_NAG-ASN         : angle       4.26271 (    6)

*********************** 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
  128 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 103
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8666 (OUTLIER) cc_final: 0.8327 (p90)
REVERT: A  634 TYR cc_start: 0.8459 (t80) cc_final: 0.7895 (t80)
REVERT: A  675 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7861 (mt-10)
REVERT: A  688 ASP cc_start: 0.8140 (t0) cc_final: 0.7869 (m-30)
REVERT: A  700 GLU cc_start: 0.8365 (tp30) cc_final: 0.8004 (tp30)
REVERT: A  715 PHE cc_start: 0.8775 (t80) cc_final: 0.8351 (t80)
REVERT: A  846 HIS cc_start: 0.8209 (m-70) cc_final: 0.7990 (m-70)
REVERT: C   36 TRP cc_start: 0.9489 (m100) cc_final: 0.8564 (m100)
REVERT: C   90 GLN cc_start: 0.9366 (tm-30) cc_final: 0.9089 (tm-30)
REVERT: D   22 ARG cc_start: 0.7752 (ttt-90) cc_final: 0.7493 (mtp-110)
REVERT: D   41 ARG cc_start: 0.8643 (ptt180) cc_final: 0.8201 (ptm160)
REVERT: D   54 ILE cc_start: 0.9243 (mt) cc_final: 0.8520 (tp)
REVERT: D   83 TYR cc_start: 0.8709 (m-80) cc_final: 0.8326 (m-80)
REVERT: D  101 ARG cc_start: 0.8240 (tmm160) cc_final: 0.7370 (tmm-80)
  outliers start: 25
  outliers final: 16
  residues processed: 118
  average time/residue: 0.0540
  time to fit residues: 8.4085
Evaluate side-chains
  112 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 95
  time to evaluate  : 0.118 
-------------------------------------------------------------------------------
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  746 VAL
Chi-restraints excluded: chain A residue  762 MET
Chi-restraints excluded: chain C residue   59 VAL
Chi-restraints excluded: chain C residue   70 THR
Chi-restraints excluded: chain C residue   79 LEU
Chi-restraints excluded: chain C residue   98 THR
Chi-restraints excluded: chain D residue   10 SER
Chi-restraints excluded: chain D residue   25 CYS
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 6 optimal weight:    3.9990
   chunk 40 optimal weight:    1.9990
   chunk 57 optimal weight:    0.8980
   chunk 9 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 49 optimal weight:    2.9990
   chunk 50 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 41 optimal weight:    0.9990
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
A 813 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.118653 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.103435 restraints weight = 12419.934|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.108581 restraints weight = 11695.193|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.110972 restraints weight = 4770.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3601 r_free = 0.3601 target = 0.111221 restraints weight = 3281.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.111740 restraints weight = 2735.124|
|-----------------------------------------------------------------------------|
r_work (final): 0.3611
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7729
moved from start:          0.5572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4772  Z= 0.174
  Angle     :  0.661   8.021   6496  Z= 0.335
  Chirality :  0.042   0.145    743
  Planarity :  0.004   0.050    825
  Dihedral  :  5.630  68.117    728
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.12 %
    Favored  : 93.88 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 21.06 %
    Favored  : 73.62 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.95 (0.36), residues: 588
  helix:  2.78 (0.47), residues: 123
  sheet: -1.72 (0.35), residues: 196
  loop : -1.36 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 655 
 TYR   0.025   0.002   TYR C  56 
 PHE   0.013   0.001   PHE A 745 
 TRP   0.022   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00396 ( 4762)
  covalent geometry    : angle       0.64705 ( 6472)
  SS BOND              : bond        0.00470 (    6)
  SS BOND              : angle       1.20991 (   12)
  hydrogen bonds       : bond        0.04178 (  181)
  hydrogen bonds       : angle       4.94618 (  561)
  link_BETA1-4         : bond        0.00335 (    2)
  link_BETA1-4         : angle       1.24603 (    6)
  link_NAG-ASN         : bond        0.00451 (    2)
  link_NAG-ASN         : angle       4.05709 (    6)

*********************** 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
  125 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 98
  time to evaluate  : 0.110 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8303 (p90)
REVERT: A  596 ASP cc_start: 0.8386 (t0) cc_final: 0.8177 (t0)
REVERT: A  634 TYR cc_start: 0.8547 (t80) cc_final: 0.8115 (t80)
REVERT: A  668 MET cc_start: 0.8675 (tpt) cc_final: 0.8212 (tpp)
REVERT: A  688 ASP cc_start: 0.8057 (t0) cc_final: 0.7810 (m-30)
REVERT: A  700 GLU cc_start: 0.8311 (tp30) cc_final: 0.7826 (tp30)
REVERT: A  715 PHE cc_start: 0.8847 (t80) cc_final: 0.8448 (t80)
REVERT: A  846 HIS cc_start: 0.8164 (m-70) cc_final: 0.7962 (m-70)
REVERT: C   36 TRP cc_start: 0.9516 (m100) cc_final: 0.8622 (m100)
REVERT: C   90 GLN cc_start: 0.9358 (tm-30) cc_final: 0.8715 (tm-30)
REVERT: D   41 ARG cc_start: 0.8784 (ptt180) cc_final: 0.8467 (ptm160)
REVERT: D   54 ILE cc_start: 0.9312 (mt) cc_final: 0.8608 (tp)
REVERT: D   83 TYR cc_start: 0.8780 (m-80) cc_final: 0.8444 (m-80)
REVERT: D  101 ARG cc_start: 0.8381 (tmm160) cc_final: 0.7545 (tmm-80)
  outliers start: 27
  outliers final: 23
  residues processed: 117
  average time/residue: 0.0530
  time to fit residues: 8.1506
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 91
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
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  635 VAL
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  847 THR
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   25 CYS
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   61 THR
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue   66 SER
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 20 optimal weight:    0.9980
   chunk 57 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 53 optimal weight:    0.8980
   chunk 32 optimal weight:    0.7980
   chunk 33 optimal weight:    0.9980
   chunk 5 optimal weight:    0.9990
   chunk 37 optimal weight:    1.9990
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.8780

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

Flipped N/Q/H residues before XYZ refinement:
A 605 GLN
A 773 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3717 r_free = 0.3717 target = 0.118305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3479 r_free = 0.3479 target = 0.102702 restraints weight = 12482.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3552 r_free = 0.3552 target = 0.108025 restraints weight = 11738.898|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3578 r_free = 0.3578 target = 0.109855 restraints weight = 5095.865|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.110946 restraints weight = 3623.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.111169 restraints weight = 2672.523|
|-----------------------------------------------------------------------------|
r_work (final): 0.3601
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7742
moved from start:          0.5787

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.057   4772  Z= 0.169
  Angle     :  0.666   9.011   6496  Z= 0.335
  Chirality :  0.042   0.143    743
  Planarity :  0.005   0.054    825
  Dihedral  :  5.664  69.255    728
  Min Nonbonded Distance : 2.488

Molprobity Statistics.
  All-atom Clashscore : 9.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.78 %
    Favored  : 94.22 %
  Rotamer:
    Outliers :  5.31 %
    Allowed  : 21.65 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.36), residues: 588
  helix:  2.75 (0.47), residues: 123
  sheet: -1.71 (0.35), residues: 196
  loop : -1.30 (0.38), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  22 
 TYR   0.026   0.002   TYR C  56 
 PHE   0.012   0.001   PHE A 745 
 TRP   0.030   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00389 ( 4762)
  covalent geometry    : angle       0.64778 ( 6472)
  SS BOND              : bond        0.00462 (    6)
  SS BOND              : angle       1.15632 (   12)
  hydrogen bonds       : bond        0.04065 (  181)
  hydrogen bonds       : angle       5.00238 (  561)
  link_BETA1-4         : bond        0.00456 (    2)
  link_BETA1-4         : angle       1.14347 (    6)
  link_NAG-ASN         : bond        0.00176 (    2)
  link_NAG-ASN         : angle       4.84602 (    6)

*********************** 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
  126 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 99
  time to evaluate  : 0.139 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8627 (OUTLIER) cc_final: 0.8315 (p90)
REVERT: A  596 ASP cc_start: 0.8427 (t0) cc_final: 0.8186 (t0)
REVERT: A  634 TYR cc_start: 0.8598 (t80) cc_final: 0.7997 (t80)
REVERT: A  638 MET cc_start: 0.8387 (tpp) cc_final: 0.7985 (ttm)
REVERT: A  688 ASP cc_start: 0.8033 (t0) cc_final: 0.7806 (m-30)
REVERT: A  700 GLU cc_start: 0.8309 (tp30) cc_final: 0.7825 (tp30)
REVERT: A  715 PHE cc_start: 0.8884 (t80) cc_final: 0.8444 (t80)
REVERT: C   28 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8913 (tm-30)
REVERT: C   36 TRP cc_start: 0.9531 (m100) cc_final: 0.8633 (m100)
REVERT: C   90 GLN cc_start: 0.9333 (tm-30) cc_final: 0.9101 (tm-30)
REVERT: D   41 ARG cc_start: 0.8825 (ptt180) cc_final: 0.8426 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9329 (mt) cc_final: 0.8667 (tp)
REVERT: D  101 ARG cc_start: 0.8459 (tmm160) cc_final: 0.7599 (tmm-80)
  outliers start: 27
  outliers final: 21
  residues processed: 116
  average time/residue: 0.0506
  time to fit residues: 7.8962
Evaluate side-chains
  115 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 93
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
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  658 THR
Chi-restraints excluded: chain A residue  684 LEU
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  817 ASN
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   25 CYS
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 0 optimal weight:    6.9990
   chunk 43 optimal weight:    0.9990
   chunk 50 optimal weight:    0.6980
   chunk 13 optimal weight:    1.9990
   chunk 30 optimal weight:    0.9980
   chunk 19 optimal weight:    4.9990
   chunk 33 optimal weight:    0.8980
   chunk 15 optimal weight:    0.5980
   chunk 2 optimal weight:    0.2980
   chunk 31 optimal weight:    0.7980
   chunk 9 optimal weight:    1.9990
   overall best weight:    0.6580

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3723 r_free = 0.3723 target = 0.118839 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3487 r_free = 0.3487 target = 0.103596 restraints weight = 12531.236|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3563 r_free = 0.3563 target = 0.108884 restraints weight = 11405.136|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3580 r_free = 0.3580 target = 0.110148 restraints weight = 4665.843|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3591 r_free = 0.3591 target = 0.110851 restraints weight = 3722.318|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3595 r_free = 0.3595 target = 0.111118 restraints weight = 3298.702|
|-----------------------------------------------------------------------------|
r_work (final): 0.3600
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7736
moved from start:          0.5956

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= 0.145
  Angle     :  0.647   7.888   6496  Z= 0.329
  Chirality :  0.042   0.140    743
  Planarity :  0.004   0.052    825
  Dihedral  :  5.485  63.985    728
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 10.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 22.05 %
    Favored  : 73.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 13.64 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.87 (0.35), residues: 588
  helix:  2.73 (0.47), residues: 123
  sheet: -1.45 (0.36), residues: 182
  loop : -1.46 (0.37), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 504 
 TYR   0.028   0.002   TYR C  56 
 PHE   0.011   0.001   PHE A 745 
 TRP   0.022   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00330 ( 4762)
  covalent geometry    : angle       0.63041 ( 6472)
  SS BOND              : bond        0.00400 (    6)
  SS BOND              : angle       1.10493 (   12)
  hydrogen bonds       : bond        0.03876 (  181)
  hydrogen bonds       : angle       4.89449 (  561)
  link_BETA1-4         : bond        0.00600 (    2)
  link_BETA1-4         : angle       1.12478 (    6)
  link_NAG-ASN         : bond        0.00129 (    2)
  link_NAG-ASN         : angle       4.53534 (    6)

*********************** 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
  119 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 94
  time to evaluate  : 0.137 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8600 (OUTLIER) cc_final: 0.8301 (p90)
REVERT: A  596 ASP cc_start: 0.8396 (t0) cc_final: 0.8140 (t0)
REVERT: A  634 TYR cc_start: 0.8592 (t80) cc_final: 0.7975 (t80)
REVERT: A  638 MET cc_start: 0.8392 (tpp) cc_final: 0.7960 (ttm)
REVERT: A  688 ASP cc_start: 0.8047 (t0) cc_final: 0.7803 (m-30)
REVERT: A  700 GLU cc_start: 0.8282 (tp30) cc_final: 0.7802 (tp30)
REVERT: A  715 PHE cc_start: 0.8885 (t80) cc_final: 0.8447 (t80)
REVERT: A  790 PHE cc_start: 0.7694 (m-80) cc_final: 0.7447 (m-80)
REVERT: B  861 MET cc_start: 0.6670 (OUTLIER) cc_final: 0.6390 (tmm)
REVERT: C   36 TRP cc_start: 0.9511 (m100) cc_final: 0.8633 (m100)
REVERT: C   90 GLN cc_start: 0.9323 (tm-30) cc_final: 0.9040 (tm-30)
REVERT: D   41 ARG cc_start: 0.8913 (ptt180) cc_final: 0.8549 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9351 (mt) cc_final: 0.8700 (tp)
  outliers start: 25
  outliers final: 20
  residues processed: 110
  average time/residue: 0.0490
  time to fit residues: 7.2769
Evaluate side-chains
  111 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 89
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
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  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  817 ASN
Chi-restraints excluded: chain B residue  861 MET
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   25 CYS
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 26 optimal weight:    9.9990
   chunk 33 optimal weight:    1.9990
   chunk 51 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0970
   chunk 14 optimal weight:    0.7980
   chunk 29 optimal weight:    1.9990
   chunk 34 optimal weight:    0.5980
   chunk 4 optimal weight:    0.0030
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.4988

-------------------------------------------------------------------------------
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 = 0.3740 r_free = 0.3740 target = 0.119820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.104745 restraints weight = 12246.949|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3582 r_free = 0.3582 target = 0.109984 restraints weight = 11173.455|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.111974 restraints weight = 4597.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.112296 restraints weight = 3394.699|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3626 r_free = 0.3626 target = 0.112949 restraints weight = 2878.132|
|-----------------------------------------------------------------------------|
r_work (final): 0.3630
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7694
moved from start:          0.6076

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4772  Z= 0.133
  Angle     :  0.636   7.797   6496  Z= 0.325
  Chirality :  0.041   0.142    743
  Planarity :  0.004   0.053    825
  Dihedral  :  5.446  64.570    728
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 9.23
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.44 %
    Favored  : 94.56 %
  Rotamer:
    Outliers :  4.92 %
    Allowed  : 22.83 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.82 (0.35), residues: 588
  helix:  2.78 (0.47), residues: 123
  sheet: -1.47 (0.36), residues: 186
  loop : -1.39 (0.37), residues: 279

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 580 
 TYR   0.028   0.002   TYR C  56 
 PHE   0.011   0.001   PHE A 745 
 TRP   0.026   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00302 ( 4762)
  covalent geometry    : angle       0.62102 ( 6472)
  SS BOND              : bond        0.00358 (    6)
  SS BOND              : angle       1.05030 (   12)
  hydrogen bonds       : bond        0.03777 (  181)
  hydrogen bonds       : angle       4.80347 (  561)
  link_BETA1-4         : bond        0.00511 (    2)
  link_BETA1-4         : angle       1.13335 (    6)
  link_NAG-ASN         : bond        0.00065 (    2)
  link_NAG-ASN         : angle       4.29182 (    6)

*********************** 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
  117 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 92
  time to evaluate  : 0.121 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8589 (OUTLIER) cc_final: 0.8330 (p90)
REVERT: A  634 TYR cc_start: 0.8573 (t80) cc_final: 0.7960 (t80)
REVERT: A  638 MET cc_start: 0.8428 (tpp) cc_final: 0.7974 (ttm)
REVERT: A  688 ASP cc_start: 0.8019 (t0) cc_final: 0.7807 (m-30)
REVERT: A  700 GLU cc_start: 0.8236 (tp30) cc_final: 0.7777 (tp30)
REVERT: A  715 PHE cc_start: 0.8872 (t80) cc_final: 0.8448 (t80)
REVERT: A  790 PHE cc_start: 0.7703 (m-80) cc_final: 0.7243 (m-80)
REVERT: B  861 MET cc_start: 0.6633 (OUTLIER) cc_final: 0.6334 (tmm)
REVERT: C   28 GLN cc_start: 0.9141 (tm-30) cc_final: 0.8894 (tm-30)
REVERT: C   36 TRP cc_start: 0.9487 (m100) cc_final: 0.8680 (m100)
REVERT: C   90 GLN cc_start: 0.9276 (tm-30) cc_final: 0.8993 (tm-30)
REVERT: D   41 ARG cc_start: 0.8910 (ptt180) cc_final: 0.8589 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9333 (mt) cc_final: 0.8708 (tp)
  outliers start: 25
  outliers final: 21
  residues processed: 109
  average time/residue: 0.0484
  time to fit residues: 7.0958
Evaluate side-chains
  112 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 89
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
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  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   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   25 CYS
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 49 optimal weight:    0.0980
   chunk 15 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 50 optimal weight:    1.9990
   chunk 18 optimal weight:    0.9990
   chunk 16 optimal weight:    0.7980
   chunk 3 optimal weight:    5.9990
   chunk 9 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 40 optimal weight:    0.0670
   chunk 2 optimal weight:    0.5980
   overall best weight:    0.5120

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

Flipped N/Q/H residues before XYZ refinement:
** C   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3747 r_free = 0.3747 target = 0.120205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.105070 restraints weight = 12416.562|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.110462 restraints weight = 11335.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3619 r_free = 0.3619 target = 0.112476 restraints weight = 4611.147|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3623 r_free = 0.3623 target = 0.112721 restraints weight = 3429.623|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.113168 restraints weight = 2872.323|
|-----------------------------------------------------------------------------|
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7695
moved from start:          0.6182

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4772  Z= 0.132
  Angle     :  0.628   7.934   6496  Z= 0.320
  Chirality :  0.042   0.147    743
  Planarity :  0.004   0.052    825
  Dihedral  :  5.446  64.681    728
  Min Nonbonded Distance : 2.483

Molprobity Statistics.
  All-atom Clashscore : 9.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.72 %
    Allowed  : 23.23 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.74 (0.36), residues: 588
  helix:  2.80 (0.46), residues: 123
  sheet: -1.39 (0.36), residues: 184
  loop : -1.34 (0.37), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 737 
 TYR   0.028   0.002   TYR C  56 
 PHE   0.011   0.001   PHE A 745 
 TRP   0.021   0.002   TRP A 654 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00300 ( 4762)
  covalent geometry    : angle       0.61371 ( 6472)
  SS BOND              : bond        0.00386 (    6)
  SS BOND              : angle       1.04592 (   12)
  hydrogen bonds       : bond        0.03748 (  181)
  hydrogen bonds       : angle       4.77535 (  561)
  link_BETA1-4         : bond        0.00585 (    2)
  link_BETA1-4         : angle       1.10795 (    6)
  link_NAG-ASN         : bond        0.00051 (    2)
  link_NAG-ASN         : angle       4.15486 (    6)

********************** 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
  112 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 88
  time to evaluate  : 0.180 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  554 TRP cc_start: 0.8568 (OUTLIER) cc_final: 0.8332 (p90)
REVERT: A  634 TYR cc_start: 0.8550 (t80) cc_final: 0.7908 (t80)
REVERT: A  638 MET cc_start: 0.8398 (tpp) cc_final: 0.7883 (ttm)
REVERT: A  656 ASP cc_start: 0.8320 (m-30) cc_final: 0.7953 (m-30)
REVERT: A  700 GLU cc_start: 0.8203 (tp30) cc_final: 0.7763 (tp30)
REVERT: A  715 PHE cc_start: 0.8893 (t80) cc_final: 0.8432 (t80)
REVERT: A  790 PHE cc_start: 0.7784 (m-80) cc_final: 0.7308 (m-80)
REVERT: B  861 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6287 (tmm)
REVERT: C   28 GLN cc_start: 0.9126 (tm-30) cc_final: 0.8851 (tm-30)
REVERT: C   90 GLN cc_start: 0.9253 (tm-30) cc_final: 0.9053 (tm-30)
REVERT: D   41 ARG cc_start: 0.8943 (ptt180) cc_final: 0.8617 (ptm-80)
REVERT: D   54 ILE cc_start: 0.9327 (mt) cc_final: 0.8732 (tp)
  outliers start: 24
  outliers final: 20
  residues processed: 103
  average time/residue: 0.0478
  time to fit residues: 6.7778
Evaluate side-chains
  108 residues out of total 508 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 86
  time to evaluate  : 0.247 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  526 ILE
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  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   21 THR
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   25 CYS
Chi-restraints excluded: chain D residue   32 ILE
Chi-restraints excluded: chain D residue   34 SER
Chi-restraints excluded: chain D residue   63 TYR
Chi-restraints excluded: chain D residue  110 TYR
Chi-restraints excluded: chain D residue  121 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 58
   random chunks:
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    0.6980
   chunk 10 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 21 optimal weight:    0.9980
   chunk 37 optimal weight:    1.9990
   chunk 27 optimal weight:    0.0040
   chunk 36 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    0.6992

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

Flipped N/Q/H residues before XYZ refinement:
** C   7 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.119188 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 28)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.103918 restraints weight = 12407.077|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.109352 restraints weight = 11555.608|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3609 r_free = 0.3609 target = 0.111545 restraints weight = 4645.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3615 r_free = 0.3615 target = 0.111913 restraints weight = 3269.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.112290 restraints weight = 2722.974|
|-----------------------------------------------------------------------------|
r_work (final): 0.3624
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7714
moved from start:          0.6276

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= 0.152
  Angle     :  0.643   7.652   6496  Z= 0.330
  Chirality :  0.042   0.146    743
  Planarity :  0.004   0.052    825
  Dihedral  :  5.550  67.429    728
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 10.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.61 %
    Favored  : 94.39 %
  Rotamer:
    Outliers :  4.53 %
    Allowed  : 23.62 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.71 (0.36), residues: 588
  helix:  2.81 (0.47), residues: 123
  sheet: -1.37 (0.36), residues: 184
  loop : -1.32 (0.38), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 573 
 TYR   0.028   0.002   TYR C  56 
 PHE   0.011   0.001   PHE A 745 
 TRP   0.020   0.002   TRP A 554 
 HIS   0.003   0.001   HIS D 102 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 4762)
  covalent geometry    : angle       0.62997 ( 6472)
  SS BOND              : bond        0.00441 (    6)
  SS BOND              : angle       1.11749 (   12)
  hydrogen bonds       : bond        0.03756 (  181)
  hydrogen bonds       : angle       4.82291 (  561)
  link_BETA1-4         : bond        0.00504 (    2)
  link_BETA1-4         : angle       1.10610 (    6)
  link_NAG-ASN         : bond        0.00137 (    2)
  link_NAG-ASN         : angle       4.05860 (    6)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1015.83 seconds
wall clock time: 18 minutes 13.90 seconds (1093.90 seconds total)