Starting phenix.real_space_refine
on Tue Aug  4 15:37:28 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9z12_73730/08_2026/9z12_73730.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9z12_73730/08_2026/9z12_73730.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9z12_73730/08_2026/9z12_73730.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9z12_73730/08_2026/9z12_73730.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9z12_73730/08_2026/9z12_73730.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9z12_73730/08_2026/9z12_73730.map"
  }
  resolution = 3.2
  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=   0.013
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      24      5.16       5
     C    2760      2.51       5
     N     735      2.21       5
     O     851      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4370
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "H"
      Number of atoms: 921
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 921
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
    Chain: "L"
      Number of atoms: 816
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 816
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
    Chain: "A"
      Number of atoms: 2619
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 343, 2619
          Classifications: {'peptide': 343}
          Link IDs: {'PTRANS': 17, 'TRANS': 325}
          Chain breaks: 1
    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: 1.19, per 1000 atoms: 0.27
  Number of scatterers: 4370
  At special positions: 0
  Unit cell: (62.37, 82.62, 106.92, 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      24     16.00
     O     851      8.00
     N     735      7.00
     C    2760      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  92 " distance=2.03
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 738 " - pdb=" SG  CYS A 760 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 743 " - pdb=" SG  CYS A 749 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 840 " - pdb=" SG  CYS A 851 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A1032 " - pdb=" SG  CYS A1043 " distance=2.03

  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
    NAG-ASN
      " NAG A1301 " - " ASN A 801 "
  Time building additional restraints: 0.35
  Conformation dependent library (CDL) restraints added in 163.9 milliseconds
  

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1050

  Finding SS restraints...
    Secondary structure from input PDB file:
      20 helices and 8 sheets defined
      43.3% alpha, 22.5% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.13
  Creating SS restraints...
    Processing helix  chain 'H' and resid 83 through 87
    Processing helix  chain 'H' and resid 97 through 100B
      removed outlier: 6.373A  pdb=" N   TYR H 100 " --> pdb=" O   GLY H  97 " (cutoff:3.500A)
      removed outlier: 6.714A  pdb=" N   TYR H 100A" --> pdb=" O   GLY H  98 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   TYR H 100B" --> pdb=" O   SER H  99 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'H' and resid 97 through 100B'
    Processing helix  chain 'L' and resid 79 through 83
      removed outlier: 3.936A  pdb=" N   PHE L  83 " --> pdb=" O   PRO L  80 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 737 through 742
    Processing helix  chain 'A' and resid 748 through 783
      removed outlier: 3.806A  pdb=" N   LEU A 752 " --> pdb=" O   GLU A 748 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   GLN A 755 " --> pdb=" O   ASN A 751 " (cutoff:3.500A)
      removed outlier: 6.194A  pdb=" N   SER A 758 " --> pdb=" O   LEU A 754 " (cutoff:3.500A)
      removed outlier: 6.147A  pdb=" N   PHE A 759 " --> pdb=" O   GLN A 755 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 802 through 806
      removed outlier: 3.657A  pdb=" N   LEU A 806 " --> pdb=" O   SER A 803 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 816 through 826
    Processing helix  chain 'A' and resid 831 through 842
      removed outlier: 3.539A  pdb=" N   LYS A 835 " --> pdb=" O   ALA A 831 " (cutoff:3.500A)
      removed outlier: 4.119A  pdb=" N   CYS A 840 " --> pdb=" O   GLN A 836 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   LEU A 841 " --> pdb=" O   TYR A 837 " (cutoff:3.500A)
      removed outlier: 3.766A  pdb=" N   GLY A 842 " --> pdb=" O   GLY A 838 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 844 through 846
      No H-bonds generated for 'chain 'A' and resid 844 through 846'
    Processing helix  chain 'A' and resid 847 through 855
    Processing helix  chain 'A' and resid 866 through 884
    Processing helix  chain 'A' and resid 897 through 907
    Processing helix  chain 'A' and resid 908 through 910
      No H-bonds generated for 'chain 'A' and resid 908 through 910'
    Processing helix  chain 'A' and resid 913 through 919
      removed outlier: 3.679A  pdb=" N   TYR A 917 " --> pdb=" O   GLN A 913 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 919 through 929
    Processing helix  chain 'A' and resid 929 through 941
    Processing helix  chain 'A' and resid 942 through 944
      No H-bonds generated for 'chain 'A' and resid 942 through 944'
    Processing helix  chain 'A' and resid 945 through 968
      removed outlier: 3.669A  pdb=" N   SER A 967 " --> pdb=" O   VAL A 963 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 976 through 984
      removed outlier: 3.748A  pdb=" N   LEU A 984 " --> pdb=" O   ILE A 980 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 985 through 1032
      removed outlier: 4.079A  pdb=" N   VAL A 991 " --> pdb=" O   PRO A 987 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.515A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
      removed outlier: 7.091A  pdb=" N   CYS H  92 " --> pdb=" O   TRP H 103 " (cutoff:3.500A)
      removed outlier: 4.786A  pdb=" N   TRP H 103 " --> pdb=" O   CYS H  92 " (cutoff:3.500A)
      removed outlier: 6.648A  pdb=" N   ARG H  94 " --> pdb=" O   ASP H 101 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'H' and resid 57 through 59
      removed outlier: 6.515A  pdb=" N   TRP H  36 " --> pdb=" O   VAL H  48 " (cutoff:3.500A)
      removed outlier: 4.333A  pdb=" N   VAL H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.587A  pdb=" N   MET H  34 " --> pdb=" O   VAL H  50 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'L' and resid 5 through 7
    Processing sheet with id=AA5, first strand: chain 'L' and resid 45 through 46
      removed outlier: 3.699A  pdb=" N   THR L  97 " --> pdb=" O   GLN L  90 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'L' and resid 45 through 46
    Processing sheet with id=AA7, first strand: chain 'A' and resid 720 through 727
      removed outlier: 5.979A  pdb=" N   TYR A1067 " --> pdb=" O   HIS A1048 " (cutoff:3.500A)
      removed outlier: 5.488A  pdb=" N   HIS A1048 " --> pdb=" O   TYR A1067 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'A' and resid 734 through 736

    246 hydrogen bonds defined for protein.
    690 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: 0.70

  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:
        1.22 -     1.34: 1415
        1.34 -     1.46: 1003
        1.46 -     1.58: 2002
        1.58 -     1.70: 0
        1.70 -     1.82: 35
  Bond restraints: 4455
  Sorted by residual:
  bond pdb=" N   ILE A 931 "
       pdb=" CA  ILE A 931 "
    ideal  model  delta    sigma   weight residual
    1.458  1.493 -0.036 1.41e-02 5.03e+03 6.46e+00
  bond pdb=" CE  LYS A 733 "
       pdb=" NZ  LYS A 733 "
    ideal  model  delta    sigma   weight residual
    1.489  1.451  0.038 3.00e-02 1.11e+03 1.62e+00
  bond pdb=" CG  MET A1050 "
       pdb=" SD  MET A1050 "
    ideal  model  delta    sigma   weight residual
    1.803  1.771  0.032 2.50e-02 1.60e+03 1.59e+00
  bond pdb=" CG  LEU A 916 "
       pdb=" CD2 LEU A 916 "
    ideal  model  delta    sigma   weight residual
    1.521  1.480  0.041 3.30e-02 9.18e+02 1.55e+00
  bond pdb=" CB  LYS A 733 "
       pdb=" CG  LYS A 733 "
    ideal  model  delta    sigma   weight residual
    1.520  1.483  0.037 3.00e-02 1.11e+03 1.50e+00
  ... (remaining 4450 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.63: 5735
        1.63 -     3.27: 253
        3.27 -     4.90: 41
        4.90 -     6.54: 12
        6.54 -     8.17: 5
  Bond angle restraints: 6046
  Sorted by residual:
  angle pdb=" C   ASN A 801 "
        pdb=" N   PHE A 802 "
        pdb=" CA  PHE A 802 "
      ideal   model   delta    sigma   weight residual
     122.65  116.63    6.02 1.60e+00 3.91e-01 1.41e+01
  angle pdb=" N   TYR L  94 "
        pdb=" CA  TYR L  94 "
        pdb=" C   TYR L  94 "
      ideal   model   delta    sigma   weight residual
     113.18  108.19    4.99 1.33e+00 5.65e-01 1.41e+01
  angle pdb=" CA  ASN A 801 "
        pdb=" CB  ASN A 801 "
        pdb=" CG  ASN A 801 "
      ideal   model   delta    sigma   weight residual
     112.60  116.18   -3.58 1.00e+00 1.00e+00 1.28e+01
  angle pdb=" N   ILE A 931 "
        pdb=" CA  ILE A 931 "
        pdb=" C   ILE A 931 "
      ideal   model   delta    sigma   weight residual
     112.04  107.21    4.83 1.40e+00 5.10e-01 1.19e+01
  angle pdb=" N   GLY H 100C"
        pdb=" CA  GLY H 100C"
        pdb=" C   GLY H 100C"
      ideal   model   delta    sigma   weight residual
     112.22  117.85   -5.63 1.74e+00 3.30e-01 1.05e+01
  ... (remaining 6041 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.10: 2391
       17.10 -    34.20: 213
       34.20 -    51.31: 66
       51.31 -    68.41: 21
       68.41 -    85.51: 9
  Dihedral angle restraints: 2700
    sinusoidal: 1060
      harmonic: 1640
  Sorted by residual:
  dihedral pdb=" CB  CYS H  22 "
           pdb=" SG  CYS H  22 "
           pdb=" SG  CYS H  92 "
           pdb=" CB  CYS H  92 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   38.31   54.69     1      1.00e+01 1.00e-02 4.05e+01
  dihedral pdb=" CB  CYS A 840 "
           pdb=" SG  CYS A 840 "
           pdb=" SG  CYS A 851 "
           pdb=" CB  CYS A 851 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   55.42   37.58     1      1.00e+01 1.00e-02 1.99e+01
  dihedral pdb=" CA  GLN H 105 "
           pdb=" C   GLN H 105 "
           pdb=" N   GLY H 106 "
           pdb=" CA  GLY H 106 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.77  -19.23     0      5.00e+00 4.00e-02 1.48e+01
  ... (remaining 2697 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.139: 681
       0.139 -    0.278: 11
       0.278 -    0.417: 0
       0.417 -    0.556: 0
       0.556 -    0.695: 1
  Chirality restraints: 693
  Sorted by residual:
  chirality pdb=" C1  NAG A1301 "
            pdb=" ND2 ASN A 801 "
            pdb=" C2  NAG A1301 "
            pdb=" O5  NAG A1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.71   -0.69 2.00e-01 2.50e+01 1.21e+01
  chirality pdb=" CG  LEU A 916 "
            pdb=" CB  LEU A 916 "
            pdb=" CD1 LEU A 916 "
            pdb=" CD2 LEU A 916 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.59   -2.32   -0.27 2.00e-01 2.50e+01 1.76e+00
  chirality pdb=" CA  ASN A 801 "
            pdb=" N   ASN A 801 "
            pdb=" C   ASN A 801 "
            pdb=" CB  ASN A 801 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.74   -0.23 2.00e-01 2.50e+01 1.34e+00
  ... (remaining 690 not shown)

  Planarity restraints: 777
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 801 "    0.035 2.00e-02 2.50e+03   3.32e-02 1.38e+01
        pdb=" CG  ASN A 801 "   -0.046 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 801 "    0.011 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 801 "   -0.032 2.00e-02 2.50e+03
        pdb=" C1  NAG A1301 "    0.032 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  SER A 884 "   -0.011 2.00e-02 2.50e+03   2.16e-02 4.65e+00
        pdb=" C   SER A 884 "    0.037 2.00e-02 2.50e+03
        pdb=" O   SER A 884 "   -0.014 2.00e-02 2.50e+03
        pdb=" N   GLY A 885 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN A 801 "    0.011 2.00e-02 2.50e+03   2.13e-02 4.53e+00
        pdb=" CG  ASN A 801 "   -0.037 2.00e-02 2.50e+03
        pdb=" OD1 ASN A 801 "    0.014 2.00e-02 2.50e+03
        pdb=" ND2 ASN A 801 "    0.013 2.00e-02 2.50e+03
  ... (remaining 774 not shown)

  Histogram of nonbonded interaction distances:
        2.44 -     2.93: 1871
        2.93 -     3.42: 4499
        3.42 -     3.91: 7197
        3.91 -     4.41: 8195
        4.41 -     4.90: 13825
  Nonbonded interactions: 35587
  Sorted by model distance:
  nonbonded pdb=" O   GLY A 880 "
            pdb=" O   SER A 884 "
     model   vdw
     2.436 3.040
  nonbonded pdb=" OD1 ASN A 801 "
            pdb=" N2  NAG A1301 "
     model   vdw
     2.573 3.120
  nonbonded pdb=" OD1 ASP H 101 "
            pdb=" N   VAL H 102 "
     model   vdw
     2.589 3.120
  nonbonded pdb=" OE1 GLN A 804 "
            pdb=" OE1 GLN A 935 "
     model   vdw
     2.589 3.040
  nonbonded pdb=" N   VAL A1033 "
            pdb=" O   VAL A1033 "
     model   vdw
     2.594 2.496
  ... (remaining 35582 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 individual isotropic
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:             4.180
  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:          0.090
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.110
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.200
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7724
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      :  0.005   0.041   4462  Z= 0.225
  Angle     :  0.841  11.030   6061  Z= 0.468
  Chirality :  0.058   0.695    693
  Planarity :  0.005   0.035    776
  Dihedral  : 15.770  85.510   1632
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 4.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.46 %
    Favored  : 95.54 %
  Rotamer:
    Outliers :  0.83 %
    Allowed  : 15.11 %
    Favored  : 84.06 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.79 (0.35), residues: 560
  helix:  0.32 (0.34), residues: 196
  sheet: -0.45 (0.51), residues: 105
  loop : -1.16 (0.40), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG H  96 
 TYR   0.018   0.004   TYR A 756 
 PHE   0.027   0.003   PHE A 898 
 TRP   0.009   0.002   TRP L  96 
 HIS   0.004   0.002   HIS A1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00498 /  0.22 ( 4455)
  covalent geometry    : angle       0.81338 /  0.46 ( 6046)
  SS BOND              : bond        0.00485 /  0.24 (    6)
  SS BOND              : angle       2.30240 /  1.31 (   12)
  hydrogen bonds       : bond        0.15044 / 10.01 (  227)
  hydrogen bonds       : angle       8.10964 /  6.04 (  690)
  link_NAG-ASN         : bond        0.03256 /  1.71 (    1)
  link_NAG-ASN         : angle       8.52933 /  4.37 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 97
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: L   86 TYR cc_start: 0.7908 (m-80) cc_final: 0.7521 (m-80)
REVERT: L   88 CYS cc_start: 0.7460 (p) cc_final: 0.7217 (p)
REVERT: A  804 GLN cc_start: 0.8398 (mt0) cc_final: 0.8011 (mm-40)
REVERT: A  835 LYS cc_start: 0.7777 (tttm) cc_final: 0.7425 (tttm)
REVERT: A  921 LYS cc_start: 0.7935 (mmtt) cc_final: 0.7733 (mmtt)
REVERT: A  933 LYS cc_start: 0.7391 (tttp) cc_final: 0.6998 (tttp)
REVERT: A  949 GLN cc_start: 0.7849 (tp40) cc_final: 0.7594 (tp-100)
REVERT: A  953 ASN cc_start: 0.8045 (m-40) cc_final: 0.7791 (m110)
REVERT: A  954 GLN cc_start: 0.7957 (mt0) cc_final: 0.7739 (mt0)
REVERT: A  965 GLN cc_start: 0.7496 (mt0) cc_final: 0.7225 (mt0)
REVERT: A  969 ASN cc_start: 0.7400 (m-40) cc_final: 0.7193 (m-40)
REVERT: A  993 ILE cc_start: 0.7768 (mt) cc_final: 0.7518 (mt)
REVERT: A 1017 GLU cc_start: 0.7916 (tm-30) cc_final: 0.7626 (tm-30)
REVERT: A 1031 GLU cc_start: 0.7307 (mt-10) cc_final: 0.7000 (mt-10)
  outliers start: 4
  outliers final: 3
  residues processed: 99
  average time/residue: 0.0636
  time to fit residues: 8.2200
Evaluate side-chains
  97 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 94
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  801 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 54 optimal weight:    0.5980
   chunk 24 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 2 optimal weight:    0.5980
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9980
   chunk 53 optimal weight:    0.1980
   overall best weight:    0.4780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
A 824 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3856 r_free = 0.3856 target = 0.148282 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.128201 restraints weight = 6073.848|
|-----------------------------------------------------------------------------|
r_work (start): 0.3581 rms_B_bonded: 2.03
r_work: 0.3452 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3274 rms_B_bonded: 4.48 restraints_weight: 0.2500
r_work (final): 0.3274
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7721
moved from start:          0.0980

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.035   4462  Z= 0.198
  Angle     :  0.621   8.209   6061  Z= 0.325
  Chirality :  0.046   0.292    693
  Planarity :  0.004   0.039    776
  Dihedral  :  6.191  51.832    639
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 5.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.04 %
    Favored  : 96.96 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 13.87 %
    Favored  : 83.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.28 (0.36), residues: 560
  helix:  0.94 (0.36), residues: 198
  sheet: -0.34 (0.48), residues: 105
  loop : -0.96 (0.41), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  96 
 TYR   0.012   0.002   TYR H  91 
 PHE   0.014   0.002   PHE H  27 
 TRP   0.004   0.001   TRP L  96 
 HIS   0.005   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00451 /  0.20 ( 4455)
  covalent geometry    : angle       0.60526 /  0.32 ( 6046)
  SS BOND              : bond        0.00410 /  0.21 (    6)
  SS BOND              : angle       1.48837 /  0.93 (   12)
  hydrogen bonds       : bond        0.04624 /  3.03 (  227)
  hydrogen bonds       : angle       5.66162 /  4.19 (  690)
  link_NAG-ASN         : bond        0.00985 /  0.52 (    1)
  link_NAG-ASN         : angle       5.67039 /  2.95 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 104
  time to evaluate  : 0.195 
Fit side-chains
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.8452 (mt) cc_final: 0.7952 (mt)
REVERT: H   66 ARG cc_start: 0.8114 (ttp80) cc_final: 0.7797 (mtp180)
REVERT: L   89 GLN cc_start: 0.8198 (tt0) cc_final: 0.7952 (tt0)
REVERT: A  804 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.7965 (mm-40)
REVERT: A  835 LYS cc_start: 0.7749 (tttm) cc_final: 0.7370 (tttm)
REVERT: A  921 LYS cc_start: 0.7975 (mmtt) cc_final: 0.7770 (mmtt)
REVERT: A  933 LYS cc_start: 0.7395 (tttp) cc_final: 0.6972 (tttp)
REVERT: A  945 LEU cc_start: 0.7544 (OUTLIER) cc_final: 0.7330 (mp)
REVERT: A  951 VAL cc_start: 0.8386 (OUTLIER) cc_final: 0.8138 (t)
REVERT: A  993 ILE cc_start: 0.7690 (mt) cc_final: 0.7417 (pt)
REVERT: A 1017 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7627 (tm-30)
REVERT: A 1031 GLU cc_start: 0.7314 (mt-10) cc_final: 0.6987 (mt-10)
  outliers start: 13
  outliers final: 5
  residues processed: 111
  average time/residue: 0.0713
  time to fit residues: 10.2742
Evaluate side-chains
  109 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 101
  time to evaluate  : 0.208 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  945 LEU
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    0.0980
   chunk 42 optimal weight:    0.9990
   chunk 28 optimal weight:    0.0070
   chunk 37 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 52 optimal weight:    0.3980
   chunk 22 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9990
   chunk 49 optimal weight:    0.9980
   overall best weight:    0.4198

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
A 784 GLN
A 824 ASN
A 853 GLN
A 907 ASN
A 953 ASN
A1054 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3863 r_free = 0.3863 target = 0.148836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3596 r_free = 0.3596 target = 0.128315 restraints weight = 6083.234|
|-----------------------------------------------------------------------------|
r_work (start): 0.3590 rms_B_bonded: 2.10
r_work: 0.3464 rms_B_bonded: 2.65 restraints_weight: 0.5000
r_work: 0.3287 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3287
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7718
moved from start:          0.1294

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   4462  Z= 0.179
  Angle     :  0.573   7.565   6061  Z= 0.302
  Chirality :  0.044   0.272    693
  Planarity :  0.004   0.041    776
  Dihedral  :  5.329  39.641    634
  Min Nonbonded Distance : 2.563

Molprobity Statistics.
  All-atom Clashscore : 6.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.21 %
    Favored  : 96.79 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 17.18 %
    Favored  : 80.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.17 (0.36), residues: 560
  helix:  1.19 (0.36), residues: 198
  sheet: -0.31 (0.47), residues: 105
  loop : -1.04 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.010   0.001   TYR H  91 
 PHE   0.012   0.002   PHE H  27 
 TRP   0.005   0.001   TRP H  47 
 HIS   0.005   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00407 /  0.18 ( 4455)
  covalent geometry    : angle       0.56365 /  0.30 ( 6046)
  SS BOND              : bond        0.00432 /  0.22 (    6)
  SS BOND              : angle       1.25492 /  0.80 (   12)
  hydrogen bonds       : bond        0.04301 /  2.84 (  227)
  hydrogen bonds       : angle       5.37744 /  3.96 (  690)
  link_NAG-ASN         : bond        0.00924 /  0.49 (    1)
  link_NAG-ASN         : angle       4.19376 /  2.17 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 102
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.8422 (mt) cc_final: 0.7986 (mt)
REVERT: H   66 ARG cc_start: 0.8036 (ttp80) cc_final: 0.7803 (ttp-170)
REVERT: A  751 ASN cc_start: 0.7929 (m110) cc_final: 0.7680 (m110)
REVERT: A  801 ASN cc_start: 0.8287 (t0) cc_final: 0.8050 (m-40)
REVERT: A  804 GLN cc_start: 0.8351 (OUTLIER) cc_final: 0.7936 (mm-40)
REVERT: A  921 LYS cc_start: 0.8003 (mmtt) cc_final: 0.7800 (mmtt)
REVERT: A  933 LYS cc_start: 0.7402 (tttp) cc_final: 0.7021 (tttp)
REVERT: A  951 VAL cc_start: 0.8398 (p) cc_final: 0.8106 (t)
REVERT: A  953 ASN cc_start: 0.7944 (m110) cc_final: 0.7529 (m110)
REVERT: A  954 GLN cc_start: 0.7909 (mt0) cc_final: 0.7680 (mt0)
REVERT: A  993 ILE cc_start: 0.7723 (mt) cc_final: 0.7452 (pt)
REVERT: A 1017 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7637 (tm-30)
REVERT: A 1031 GLU cc_start: 0.7316 (mt-10) cc_final: 0.7000 (mt-10)
  outliers start: 13
  outliers final: 6
  residues processed: 109
  average time/residue: 0.0582
  time to fit residues: 8.1995
Evaluate side-chains
  105 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 98
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  945 LEU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 52 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 41 optimal weight:    0.9980
   chunk 36 optimal weight:    0.6980
   chunk 15 optimal weight:    0.3980
   chunk 42 optimal weight:    1.9990
   chunk 47 optimal weight:    1.9990
   chunk 1 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9990
   chunk 43 optimal weight:    1.9990
   chunk 4 optimal weight:    0.0470
   overall best weight:    0.5678

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
L  89 GLN
A 824 ASN
A 907 ASN
A1054 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3852 r_free = 0.3852 target = 0.148186 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3574 r_free = 0.3574 target = 0.127003 restraints weight = 5975.065|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 2.16
r_work: 0.3431 rms_B_bonded: 2.71 restraints_weight: 0.5000
r_work: 0.3250 rms_B_bonded: 4.64 restraints_weight: 0.2500
r_work (final): 0.3250
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7746
moved from start:          0.1491

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.036   4462  Z= 0.219
  Angle     :  0.580   6.864   6061  Z= 0.307
  Chirality :  0.044   0.253    693
  Planarity :  0.005   0.043    776
  Dihedral  :  5.384  38.622    634
  Min Nonbonded Distance : 2.562

Molprobity Statistics.
  All-atom Clashscore : 7.60
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 18.43 %
    Favored  : 78.47 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.19 (0.36), residues: 560
  helix:  1.29 (0.36), residues: 198
  sheet: -0.29 (0.47), residues: 105
  loop : -1.18 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  96 
 TYR   0.011   0.002   TYR H  91 
 PHE   0.014   0.002   PHE H  27 
 TRP   0.008   0.001   TRP L  96 
 HIS   0.005   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00502 /  0.22 ( 4455)
  covalent geometry    : angle       0.57414 /  0.31 ( 6046)
  SS BOND              : bond        0.00467 /  0.24 (    6)
  SS BOND              : angle       1.16877 /  0.76 (   12)
  hydrogen bonds       : bond        0.04329 /  2.86 (  227)
  hydrogen bonds       : angle       5.27519 /  3.87 (  690)
  link_NAG-ASN         : bond        0.00682 /  0.36 (    1)
  link_NAG-ASN         : angle       3.31444 /  1.72 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  115 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 100
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.8422 (mt) cc_final: 0.7967 (mt)
REVERT: A  751 ASN cc_start: 0.8044 (m110) cc_final: 0.7776 (m110)
REVERT: A  801 ASN cc_start: 0.8296 (t0) cc_final: 0.8070 (m-40)
REVERT: A  804 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7963 (mm-40)
REVERT: A  902 MET cc_start: 0.7643 (mmm) cc_final: 0.6948 (mmm)
REVERT: A  933 LYS cc_start: 0.7367 (tttp) cc_final: 0.6979 (tttp)
REVERT: A  951 VAL cc_start: 0.8438 (OUTLIER) cc_final: 0.8173 (t)
REVERT: A  954 GLN cc_start: 0.7922 (mt0) cc_final: 0.7668 (mt0)
REVERT: A  990 GLU cc_start: 0.6649 (pm20) cc_final: 0.6229 (pm20)
REVERT: A  993 ILE cc_start: 0.7742 (mt) cc_final: 0.7480 (mt)
REVERT: A 1014 ARG cc_start: 0.7923 (ttm-80) cc_final: 0.7119 (mtm-85)
REVERT: A 1017 GLU cc_start: 0.7875 (tm-30) cc_final: 0.7564 (tm-30)
REVERT: A 1031 GLU cc_start: 0.7323 (mt-10) cc_final: 0.7033 (mt-10)
  outliers start: 15
  outliers final: 5
  residues processed: 109
  average time/residue: 0.0578
  time to fit residues: 8.3570
Evaluate side-chains
  104 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 97
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 51 optimal weight:    0.9990
   chunk 43 optimal weight:    0.7980
   chunk 9 optimal weight:    0.6980
   chunk 47 optimal weight:    0.9990
   chunk 5 optimal weight:    0.5980
   chunk 41 optimal weight:    0.9990
   chunk 7 optimal weight:    0.7980
   chunk 39 optimal weight:    0.3980
   chunk 27 optimal weight:    0.9990
   chunk 37 optimal weight:    0.0770
   chunk 15 optimal weight:    0.9980
   overall best weight:    0.5138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
L  89 GLN
A 784 GLN
A 824 ASN
A 907 ASN
A 953 ASN
A1054 GLN

Total number of N/Q/H flips: 7

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3855 r_free = 0.3855 target = 0.148589 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3592 r_free = 0.3592 target = 0.128347 restraints weight = 6061.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 2.03
r_work: 0.3435 rms_B_bonded: 2.61 restraints_weight: 0.5000
r_work: 0.3259 rms_B_bonded: 4.44 restraints_weight: 0.2500
r_work (final): 0.3259
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7730
moved from start:          0.1612

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.030   4462  Z= 0.202
  Angle     :  0.573   8.244   6061  Z= 0.301
  Chirality :  0.044   0.240    693
  Planarity :  0.004   0.044    776
  Dihedral  :  5.304  37.407    634
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.57 %
    Favored  : 96.43 %
  Rotamer:
    Outliers :  3.31 %
    Allowed  : 18.84 %
    Favored  : 77.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.16 (0.35), residues: 560
  helix:  1.39 (0.36), residues: 198
  sheet: -0.37 (0.47), residues: 105
  loop : -1.19 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG H  96 
 TYR   0.011   0.002   TYR H  91 
 PHE   0.013   0.002   PHE A 797 
 TRP   0.006   0.001   TRP H  47 
 HIS   0.005   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00459 /  0.20 ( 4455)
  covalent geometry    : angle       0.56789 /  0.30 ( 6046)
  SS BOND              : bond        0.00442 /  0.22 (    6)
  SS BOND              : angle       1.16976 /  0.76 (   12)
  hydrogen bonds       : bond        0.04229 /  2.79 (  227)
  hydrogen bonds       : angle       5.16649 /  3.78 (  690)
  link_NAG-ASN         : bond        0.00656 /  0.35 (    1)
  link_NAG-ASN         : angle       2.71707 /  1.41 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  118 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 102
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.8402 (mt) cc_final: 0.7975 (mt)
REVERT: A  751 ASN cc_start: 0.7989 (m110) cc_final: 0.7712 (m110)
REVERT: A  752 LEU cc_start: 0.8533 (mp) cc_final: 0.8327 (mp)
REVERT: A  780 GLU cc_start: 0.7401 (mt-10) cc_final: 0.6988 (mt-10)
REVERT: A  801 ASN cc_start: 0.8308 (t0) cc_final: 0.8056 (m-40)
REVERT: A  804 GLN cc_start: 0.8330 (OUTLIER) cc_final: 0.7946 (mm-40)
REVERT: A  933 LYS cc_start: 0.7316 (tttp) cc_final: 0.6955 (tttp)
REVERT: A  951 VAL cc_start: 0.8462 (OUTLIER) cc_final: 0.8194 (t)
REVERT: A  954 GLN cc_start: 0.7934 (mt0) cc_final: 0.7699 (mt0)
REVERT: A  990 GLU cc_start: 0.6593 (pm20) cc_final: 0.6172 (pm20)
REVERT: A  993 ILE cc_start: 0.7753 (mt) cc_final: 0.7493 (mt)
REVERT: A 1014 ARG cc_start: 0.7932 (ttm-80) cc_final: 0.7226 (mtm-85)
REVERT: A 1017 GLU cc_start: 0.7933 (tm-30) cc_final: 0.7633 (tm-30)
REVERT: A 1031 GLU cc_start: 0.7284 (mt-10) cc_final: 0.7022 (mt-10)
  outliers start: 16
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0474
  time to fit residues: 6.8721
Evaluate side-chains
  108 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 97
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   21 SER
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 11 optimal weight:    1.9990
   chunk 54 optimal weight:    0.9980
   chunk 50 optimal weight:    0.5980
   chunk 43 optimal weight:    0.9980
   chunk 47 optimal weight:    1.9990
   chunk 36 optimal weight:    0.2980
   chunk 38 optimal weight:    0.0980
   chunk 23 optimal weight:    0.0770
   chunk 53 optimal weight:    0.4980
   chunk 33 optimal weight:    3.9990
   chunk 3 optimal weight:    0.1980
   overall best weight:    0.2338

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
A 784 GLN
A 824 ASN
A 907 ASN
A 953 ASN
A1054 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.150112 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.129298 restraints weight = 6171.452|
|-----------------------------------------------------------------------------|
r_work (start): 0.3605 rms_B_bonded: 2.18
r_work: 0.3475 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3292 rms_B_bonded: 4.71 restraints_weight: 0.2500
r_work (final): 0.3292
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7702
moved from start:          0.1777

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4462  Z= 0.126
  Angle     :  0.531   7.087   6061  Z= 0.277
  Chirality :  0.042   0.211    693
  Planarity :  0.004   0.039    776
  Dihedral  :  5.010  36.598    634
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 19.67 %
    Favored  : 76.81 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.09 (0.36), residues: 560
  helix:  1.79 (0.37), residues: 198
  sheet: -0.37 (0.47), residues: 105
  loop : -1.15 (0.40), residues: 257

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.007   0.001   TYR H  32 
 PHE   0.009   0.001   PHE A 898 
 TRP   0.005   0.001   TRP H  47 
 HIS   0.003   0.001   HIS A1048 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00278 /  0.13 ( 4455)
  covalent geometry    : angle       0.52729 /  0.28 ( 6046)
  SS BOND              : bond        0.00331 /  0.17 (    6)
  SS BOND              : angle       1.04038 /  0.67 (   12)
  hydrogen bonds       : bond        0.03903 /  2.56 (  227)
  hydrogen bonds       : angle       4.92518 /  3.59 (  690)
  link_NAG-ASN         : bond        0.00609 /  0.32 (    1)
  link_NAG-ASN         : angle       2.08725 /  1.09 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  125 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 108
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.8331 (mt) cc_final: 0.8021 (mt)
REVERT: H   66 ARG cc_start: 0.7972 (ttp80) cc_final: 0.7711 (mtp180)
REVERT: A  751 ASN cc_start: 0.7938 (m110) cc_final: 0.7649 (m110)
REVERT: A  754 LEU cc_start: 0.8244 (mt) cc_final: 0.8031 (tt)
REVERT: A  776 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7466 (tttm)
REVERT: A  780 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7002 (mt-10)
REVERT: A  801 ASN cc_start: 0.8321 (t0) cc_final: 0.8048 (m-40)
REVERT: A  804 GLN cc_start: 0.8336 (OUTLIER) cc_final: 0.7919 (mm-40)
REVERT: A  933 LYS cc_start: 0.7294 (tttp) cc_final: 0.6915 (tttp)
REVERT: A  954 GLN cc_start: 0.7899 (mt0) cc_final: 0.7636 (mt0)
REVERT: A  990 GLU cc_start: 0.6679 (pm20) cc_final: 0.6125 (pm20)
REVERT: A  993 ILE cc_start: 0.7661 (mt) cc_final: 0.7397 (mt)
REVERT: A 1014 ARG cc_start: 0.7924 (ttm-80) cc_final: 0.7145 (mtm-85)
REVERT: A 1017 GLU cc_start: 0.7924 (tm-30) cc_final: 0.7654 (tm-30)
REVERT: A 1031 GLU cc_start: 0.7249 (mt-10) cc_final: 0.6980 (mt-10)
  outliers start: 17
  outliers final: 10
  residues processed: 117
  average time/residue: 0.0546
  time to fit residues: 8.4579
Evaluate side-chains
  113 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 101
  time to evaluate  : 0.128 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   70 SER
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   33 LEU
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain A residue  726 ILE
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  776 LYS
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 23 optimal weight:    0.0980
   chunk 47 optimal weight:    0.3980
   chunk 30 optimal weight:    0.0170
   chunk 5 optimal weight:    0.5980
   chunk 24 optimal weight:    0.0970
   chunk 3 optimal weight:    0.3980
   chunk 25 optimal weight:    0.2980
   chunk 2 optimal weight:    0.6980
   chunk 29 optimal weight:    0.0570
   chunk 35 optimal weight:    0.9990
   overall best weight:    0.1134

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
A 824 ASN
A 907 ASN
A 953 ASN
A1054 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3923 r_free = 0.3923 target = 0.153374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3670 r_free = 0.3670 target = 0.133609 restraints weight = 5979.025|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 2.04
r_work: 0.3539 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3359 rms_B_bonded: 4.60 restraints_weight: 0.2500
r_work (final): 0.3359
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7644
moved from start:          0.2074

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   4462  Z= 0.102
  Angle     :  0.509   6.547   6061  Z= 0.265
  Chirality :  0.041   0.195    693
  Planarity :  0.004   0.038    776
  Dihedral  :  4.757  36.626    634
  Min Nonbonded Distance : 2.627

Molprobity Statistics.
  All-atom Clashscore : 6.10
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.75 %
    Favored  : 96.25 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 19.88 %
    Favored  : 76.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.34 (0.36), residues: 560
  helix:  2.07 (0.37), residues: 198
  sheet: -0.13 (0.49), residues: 99
  loop : -1.11 (0.39), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.011   0.001   TYR A 917 
 PHE   0.012   0.001   PHE A 898 
 TRP   0.004   0.001   TRP H  47 
 HIS   0.004   0.001   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00218 /  0.10 ( 4455)
  covalent geometry    : angle       0.50614 /  0.26 ( 6046)
  SS BOND              : bond        0.00309 /  0.15 (    6)
  SS BOND              : angle       1.00448 /  0.65 (   12)
  hydrogen bonds       : bond        0.03653 /  2.39 (  227)
  hydrogen bonds       : angle       4.74354 /  3.45 (  690)
  link_NAG-ASN         : bond        0.00591 /  0.31 (    1)
  link_NAG-ASN         : angle       1.70540 /  0.89 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  111 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 92
  time to evaluate  : 0.155 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: H    4 LEU cc_start: 0.8271 (mt) cc_final: 0.8032 (mt)
REVERT: H   66 ARG cc_start: 0.7933 (ttp80) cc_final: 0.7657 (mtp180)
REVERT: L   90 GLN cc_start: 0.7736 (OUTLIER) cc_final: 0.7374 (pp30)
REVERT: A  801 ASN cc_start: 0.8347 (t0) cc_final: 0.8081 (m-40)
REVERT: A  804 GLN cc_start: 0.8387 (OUTLIER) cc_final: 0.7994 (mm-40)
REVERT: A  902 MET cc_start: 0.7249 (mmm) cc_final: 0.7039 (tmm)
REVERT: A  933 LYS cc_start: 0.7323 (tttp) cc_final: 0.6936 (tttp)
REVERT: A  951 VAL cc_start: 0.8320 (OUTLIER) cc_final: 0.8076 (t)
REVERT: A  954 GLN cc_start: 0.7871 (mt0) cc_final: 0.7594 (mt0)
REVERT: A 1014 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7116 (mtm-85)
REVERT: A 1017 GLU cc_start: 0.7915 (tm-30) cc_final: 0.7674 (tm-30)
REVERT: A 1034 LEU cc_start: 0.7333 (mp) cc_final: 0.7083 (mt)
  outliers start: 19
  outliers final: 9
  residues processed: 103
  average time/residue: 0.0642
  time to fit residues: 8.5633
Evaluate side-chains
  102 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 90
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  753 LEU
Chi-restraints excluded: chain A residue  772 VAL
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 46 optimal weight:    0.9980
   chunk 43 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9990
   chunk 33 optimal weight:    0.7980
   chunk 8 optimal weight:    0.9980
   chunk 35 optimal weight:    0.3980
   chunk 20 optimal weight:    0.9990
   chunk 42 optimal weight:    0.1980
   chunk 18 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   overall best weight:    0.6180

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
A 824 ASN
A 907 ASN
A 955 ASN
A1054 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3851 r_free = 0.3851 target = 0.148655 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3590 r_free = 0.3590 target = 0.128540 restraints weight = 5989.186|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.07
r_work: 0.3447 rms_B_bonded: 2.63 restraints_weight: 0.5000
r_work: 0.3266 rms_B_bonded: 4.54 restraints_weight: 0.2500
r_work (final): 0.3266
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7734
moved from start:          0.2000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.038   4462  Z= 0.232
  Angle     :  0.591   7.402   6061  Z= 0.307
  Chirality :  0.045   0.249    693
  Planarity :  0.004   0.040    776
  Dihedral  :  5.022  36.396    634
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.93 %
    Favored  : 96.07 %
  Rotamer:
    Outliers :  3.52 %
    Allowed  : 21.53 %
    Favored  : 74.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.01 (0.35), residues: 560
  helix:  1.69 (0.36), residues: 198
  sheet: -0.29 (0.49), residues: 98
  loop : -1.23 (0.38), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.013   0.002   TYR H  91 
 PHE   0.014   0.002   PHE A 797 
 TRP   0.009   0.002   TRP L  96 
 HIS   0.006   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00532 /  0.23 ( 4455)
  covalent geometry    : angle       0.58747 /  0.31 ( 6046)
  SS BOND              : bond        0.00497 /  0.25 (    6)
  SS BOND              : angle       1.25947 /  0.73 (   12)
  hydrogen bonds       : bond        0.04139 /  2.72 (  227)
  hydrogen bonds       : angle       4.99023 /  3.65 (  690)
  link_NAG-ASN         : bond        0.00520 /  0.27 (    1)
  link_NAG-ASN         : angle       1.90043 /  0.99 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  117 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 100
  time to evaluate  : 0.159 
Fit side-chains
REVERT: L    4 MET cc_start: 0.6279 (OUTLIER) cc_final: 0.5518 (tpt)
REVERT: L   90 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7344 (pp30)
REVERT: A  745 ASP cc_start: 0.7747 (t0) cc_final: 0.7387 (t0)
REVERT: A  751 ASN cc_start: 0.8062 (m110) cc_final: 0.7761 (m110)
REVERT: A  780 GLU cc_start: 0.7413 (mt-10) cc_final: 0.7034 (mt-10)
REVERT: A  801 ASN cc_start: 0.8311 (t0) cc_final: 0.8068 (m-40)
REVERT: A  804 GLN cc_start: 0.8350 (OUTLIER) cc_final: 0.7817 (mt0)
REVERT: A  835 LYS cc_start: 0.7706 (tttm) cc_final: 0.7239 (ttmt)
REVERT: A  933 LYS cc_start: 0.7308 (tttp) cc_final: 0.6931 (tttp)
REVERT: A  951 VAL cc_start: 0.8456 (OUTLIER) cc_final: 0.8189 (t)
REVERT: A  954 GLN cc_start: 0.7955 (mt0) cc_final: 0.7752 (mt0)
REVERT: A  990 GLU cc_start: 0.6545 (pm20) cc_final: 0.6137 (pm20)
REVERT: A 1014 ARG cc_start: 0.7973 (ttm-80) cc_final: 0.7325 (mtm-85)
REVERT: A 1017 GLU cc_start: 0.7900 (tm-30) cc_final: 0.7597 (tm-30)
REVERT: A 1031 GLU cc_start: 0.7385 (mt-10) cc_final: 0.7119 (mt-10)
  outliers start: 17
  outliers final: 9
  residues processed: 110
  average time/residue: 0.0580
  time to fit residues: 8.4189
Evaluate side-chains
  111 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 98
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  853 GLN
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 28 optimal weight:    0.1980
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9980
   chunk 9 optimal weight:    0.9980
   chunk 45 optimal weight:    0.9980
   chunk 11 optimal weight:    0.8980
   chunk 50 optimal weight:    0.6980
   chunk 52 optimal weight:    0.6980
   chunk 13 optimal weight:    0.6980
   chunk 26 optimal weight:    1.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
A 824 ASN
A 907 ASN
A1054 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3850 r_free = 0.3850 target = 0.148419 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3581 r_free = 0.3581 target = 0.127698 restraints weight = 6090.744|
|-----------------------------------------------------------------------------|
r_work (start): 0.3576 rms_B_bonded: 2.16
r_work: 0.3444 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3258 rms_B_bonded: 4.65 restraints_weight: 0.2500
r_work (final): 0.3258
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7748
moved from start:          0.2102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.039   4462  Z= 0.240
  Angle     :  0.604   7.059   6061  Z= 0.314
  Chirality :  0.047   0.304    693
  Planarity :  0.004   0.040    776
  Dihedral  :  5.114  36.380    634
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 21.33 %
    Favored  : 74.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.14 (0.35), residues: 560
  helix:  1.52 (0.36), residues: 199
  sheet: -0.31 (0.50), residues: 98
  loop : -1.30 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.013   0.002   TYR H  91 
 PHE   0.016   0.002   PHE A 906 
 TRP   0.009   0.002   TRP L  96 
 HIS   0.006   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00550 /  0.24 ( 4455)
  covalent geometry    : angle       0.60050 /  0.31 ( 6046)
  SS BOND              : bond        0.00539 /  0.27 (    6)
  SS BOND              : angle       1.39074 /  0.80 (   12)
  hydrogen bonds       : bond        0.04180 /  2.77 (  227)
  hydrogen bonds       : angle       5.08355 /  3.70 (  690)
  link_NAG-ASN         : bond        0.00469 /  0.25 (    1)
  link_NAG-ASN         : angle       1.77977 /  0.93 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 100
  time to evaluate  : 0.167 
Fit side-chains
REVERT: H    4 LEU cc_start: 0.8594 (mt) cc_final: 0.8319 (mt)
REVERT: L    4 MET cc_start: 0.6318 (OUTLIER) cc_final: 0.5606 (tpt)
REVERT: L   90 GLN cc_start: 0.7871 (OUTLIER) cc_final: 0.7335 (pp30)
REVERT: A  745 ASP cc_start: 0.7779 (t0) cc_final: 0.7411 (t0)
REVERT: A  751 ASN cc_start: 0.8067 (m110) cc_final: 0.7768 (m110)
REVERT: A  780 GLU cc_start: 0.7474 (mt-10) cc_final: 0.7082 (mt-10)
REVERT: A  801 ASN cc_start: 0.8297 (t0) cc_final: 0.8051 (m-40)
REVERT: A  804 GLN cc_start: 0.8327 (OUTLIER) cc_final: 0.7844 (mt0)
REVERT: A  835 LYS cc_start: 0.7700 (tttm) cc_final: 0.7220 (ttmt)
REVERT: A  933 LYS cc_start: 0.7439 (tttp) cc_final: 0.7051 (tttp)
REVERT: A  951 VAL cc_start: 0.8496 (OUTLIER) cc_final: 0.8256 (t)
REVERT: A  990 GLU cc_start: 0.6679 (pm20) cc_final: 0.6080 (pm20)
REVERT: A 1014 ARG cc_start: 0.8044 (ttm-80) cc_final: 0.7509 (mtm-85)
REVERT: A 1017 GLU cc_start: 0.7886 (tm-30) cc_final: 0.7565 (tm-30)
REVERT: A 1031 GLU cc_start: 0.7446 (mt-10) cc_final: 0.7205 (mt-10)
  outliers start: 19
  outliers final: 12
  residues processed: 110
  average time/residue: 0.0631
  time to fit residues: 9.2307
Evaluate side-chains
  113 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 97
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   11 VAL
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain H residue  110 THR
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   46 LEU
Chi-restraints excluded: chain L residue   47 LEU
Chi-restraints excluded: chain L residue   54 LEU
Chi-restraints excluded: chain L residue   72 THR
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  853 GLN
Chi-restraints excluded: chain A residue  916 LEU
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 29 optimal weight:    0.0970
   chunk 20 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 57.8905 > 50:)
   chunk 36 optimal weight:    0.8980
   chunk 32 optimal weight:    0.0770
   chunk 50 optimal weight:    0.5980
   chunk 35 optimal weight:    0.6980
   chunk 41 optimal weight:    0.5980
   chunk 3 optimal weight:    0.2980
   chunk 45 optimal weight:    1.9990
   chunk 37 optimal weight:    0.6980
   chunk 54 optimal weight:    0.0070
   overall best weight:    0.2154

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
A 824 ASN
A 836 GLN
A 907 ASN
A1011 GLN
A1054 GLN

Total number of N/Q/H flips: 6

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3875 r_free = 0.3875 target = 0.150009 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.129646 restraints weight = 6074.812|
|-----------------------------------------------------------------------------|
r_work (start): 0.3620 rms_B_bonded: 2.16
r_work: 0.3488 rms_B_bonded: 2.74 restraints_weight: 0.5000
r_work: 0.3304 rms_B_bonded: 4.73 restraints_weight: 0.2500
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7688
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4462  Z= 0.123
  Angle     :  0.538   6.595   6061  Z= 0.280
  Chirality :  0.043   0.222    693
  Planarity :  0.004   0.038    776
  Dihedral  :  4.833  36.853    634
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.11 %
    Favored  : 95.89 %
  Rotamer:
    Outliers :  3.11 %
    Allowed  : 22.36 %
    Favored  : 74.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.15 (0.36), residues: 560
  helix:  1.89 (0.37), residues: 199
  sheet: -0.23 (0.50), residues: 98
  loop : -1.21 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.014   0.001   TYR A1007 
 PHE   0.012   0.001   PHE A 898 
 TRP   0.006   0.001   TRP H  36 
 HIS   0.006   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00271 /  0.12 ( 4455)
  covalent geometry    : angle       0.53537 /  0.28 ( 6046)
  SS BOND              : bond        0.00361 /  0.18 (    6)
  SS BOND              : angle       1.05124 /  0.62 (   12)
  hydrogen bonds       : bond        0.03755 /  2.48 (  227)
  hydrogen bonds       : angle       4.86354 /  3.53 (  690)
  link_NAG-ASN         : bond        0.00521 /  0.27 (    1)
  link_NAG-ASN         : angle       1.31975 /  0.69 (    3)

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

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

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1120 Ramachandran restraints generated.
    560 Oldfield, 0 Emsley, 560 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 87
  time to evaluate  : 0.098 
Fit side-chains
   revert: symmetry clash
REVERT: H   66 ARG cc_start: 0.7986 (ttp80) cc_final: 0.7709 (mtp180)
REVERT: L   90 GLN cc_start: 0.7785 (OUTLIER) cc_final: 0.7293 (pp30)
REVERT: A  751 ASN cc_start: 0.7974 (m110) cc_final: 0.7665 (m110)
REVERT: A  804 GLN cc_start: 0.8310 (OUTLIER) cc_final: 0.7783 (mt0)
REVERT: A  835 LYS cc_start: 0.7666 (tttm) cc_final: 0.7191 (ttmt)
REVERT: A  902 MET cc_start: 0.7219 (tmm) cc_final: 0.6382 (tmm)
REVERT: A  933 LYS cc_start: 0.7347 (tttp) cc_final: 0.6933 (tttp)
REVERT: A  951 VAL cc_start: 0.8402 (OUTLIER) cc_final: 0.8146 (t)
REVERT: A 1014 ARG cc_start: 0.8055 (ttm-80) cc_final: 0.7705 (mtm-85)
REVERT: A 1017 GLU cc_start: 0.7913 (tm-30) cc_final: 0.7633 (tm-30)
REVERT: A 1034 LEU cc_start: 0.7551 (mp) cc_final: 0.7124 (mt)
  outliers start: 15
  outliers final: 6
  residues processed: 96
  average time/residue: 0.0668
  time to fit residues: 8.2247
Evaluate side-chains
  93 residues out of total 483 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 84
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue    2 VAL
Chi-restraints excluded: chain H residue   99 SER
Chi-restraints excluded: chain L residue   90 GLN
Chi-restraints excluded: chain A residue  747 THR
Chi-restraints excluded: chain A residue  785 VAL
Chi-restraints excluded: chain A residue  794 ILE
Chi-restraints excluded: chain A residue  804 GLN
Chi-restraints excluded: chain A residue  853 GLN
Chi-restraints excluded: chain A residue  951 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 55
   random chunks:
   chunk 32 optimal weight:    0.2980
   chunk 16 optimal weight:    0.2980
   chunk 50 optimal weight:    0.9990
   chunk 31 optimal weight:    0.7980
   chunk 54 optimal weight:    0.0370
   chunk 18 optimal weight:    1.9990
   chunk 7 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9980
   chunk 4 optimal weight:    0.6980
   chunk 26 optimal weight:    0.7980
   chunk 52 optimal weight:    0.0980
   overall best weight:    0.2858

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
H  39 GLN
A 824 ASN
A 907 ASN
A 925 ASN
A1054 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3882 r_free = 0.3882 target = 0.150916 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.130630 restraints weight = 6025.334|
|-----------------------------------------------------------------------------|
r_work (start): 0.3617 rms_B_bonded: 2.11
r_work: 0.3491 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3312 rms_B_bonded: 4.55 restraints_weight: 0.2500
r_work (final): 0.3312
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7683
moved from start:          0.2296

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   4462  Z= 0.139
  Angle     :  0.551   7.123   6061  Z= 0.285
  Chirality :  0.043   0.220    693
  Planarity :  0.004   0.039    776
  Dihedral  :  4.814  36.437    634
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.64 %
    Favored  : 95.36 %
  Rotamer:
    Outliers :  2.90 %
    Allowed  : 22.98 %
    Favored  : 74.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.12 (0.36), residues: 560
  helix:  1.90 (0.37), residues: 199
  sheet: -0.30 (0.50), residues: 98
  loop : -1.23 (0.38), residues: 263

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG H  96 
 TYR   0.013   0.001   TYR A1007 
 PHE   0.011   0.001   PHE A 898 
 TRP   0.008   0.001   TRP H  36 
 HIS   0.004   0.002   HIS H  35 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00315 /  0.14 ( 4455)
  covalent geometry    : angle       0.54878 /  0.28 ( 6046)
  SS BOND              : bond        0.00394 /  0.20 (    6)
  SS BOND              : angle       1.01586 /  0.61 (   12)
  hydrogen bonds       : bond        0.03729 /  2.46 (  227)
  hydrogen bonds       : angle       4.82364 /  3.49 (  690)
  link_NAG-ASN         : bond        0.00509 /  0.27 (    1)
  link_NAG-ASN         : angle       1.36547 /  0.72 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1371.51 seconds
wall clock time: 24 minutes 10.85 seconds (1450.85 seconds total)