Starting phenix.real_space_refine
on Sat May 10 04:55:59 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8epa_28523/05_2025/8epa_28523.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8epa_28523/05_2025/8epa_28523.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.4
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8epa_28523/05_2025/8epa_28523.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8epa_28523/05_2025/8epa_28523.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8epa_28523/05_2025/8epa_28523.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8epa_28523/05_2025/8epa_28523.cif"
  }
  resolution = 3.4
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.012
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    3179      2.51       5
     N     872      2.21       5
     O     970      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 5045
  Number of models: 1
  Model: ""
    Number of chains: 6
    Chain: "I"
      Number of atoms: 1580
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 185, 1580
          Classifications: {'peptide': 185}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 173}
          Chain breaks: 1
    Chain: "H"
      Number of atoms: 918
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 119, 918
          Classifications: {'peptide': 119}
          Link IDs: {'PTRANS': 2, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "L"
      Number of atoms: 818
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 106, 818
          Classifications: {'peptide': 106}
          Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 99}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "A"
      Number of atoms: 897
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 897
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 3, 'TRANS': 116}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen chiralities: 2
    Chain: "B"
      Number of atoms: 804
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 804
          Classifications: {'peptide': 107}
          Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen chiralities: 1
    Chain: "C"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
  Time building chain proxies: 3.71, per 1000 atoms: 0.74
  Number of scatterers: 5045
  At special positions: 0
  Unit cell: (73.1, 63.64, 128.14, 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     970      8.00
     N     872      7.00
     C    3179      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS I  40 " - pdb=" SG  CYS I  50 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I  80 " - pdb=" SG  CYS I  93 " distance=2.03
    Simple disulfide: pdb=" SG  CYS I 160 " - pdb=" SG  CYS I 209 " distance=2.03
    Simple disulfide: pdb=" SG  CYS H  22 " - pdb=" SG  CYS H  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS L  23 " - pdb=" SG  CYS L  88 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  96 " distance=2.04
    Simple disulfide: pdb=" SG  CYS B  23 " - pdb=" SG  CYS B  88 " 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
    BETA1-4
      " NAG C   1 " - " NAG C   2 "
    NAG-ASN
      " NAG C   1 " - " ASN I  49 "
  Time building additional restraints: 1.28
  Conformation dependent library (CDL) restraints added in 578.6 milliseconds
  

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1174

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 16 sheets defined
      2.5% alpha, 34.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.80
  Creating SS restraints...
    Processing helix  chain 'I' and resid 98 through 100
      No H-bonds generated for 'chain 'I' and resid 98 through 100'
    Processing helix  chain 'I' and resid 127 through 129
      No H-bonds generated for 'chain 'I' and resid 127 through 129'
    Processing helix  chain 'A' and resid 28 through 32
      removed outlier: 3.567A  pdb=" N   PHE A  32 " --> pdb=" O   PHE A  29 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 87 through 91
      removed outlier: 4.103A  pdb=" N   THR A  91 " --> pdb=" O   ALA A  88 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'I' and resid 39 through 43
      removed outlier: 3.799A  pdb=" N   GLN I  39 " --> pdb=" O   THR I  51 " (cutoff:3.500A)
      removed outlier: 4.102A  pdb=" N   TYR I  47 " --> pdb=" O   PHE I  43 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'I' and resid 78 through 79
      removed outlier: 3.752A  pdb=" N   TYR I  67 " --> pdb=" O   GLN I  78 " (cutoff:3.500A)
      removed outlier: 3.534A  pdb=" N   GLN I 109 " --> pdb=" O   HIS I  66 " (cutoff:3.500A)
      removed outlier: 3.548A  pdb=" N   PHE I 106 " --> pdb=" O   LEU I 124 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'I' and resid 136 through 141
      removed outlier: 5.613A  pdb=" N   ASN I 137 " --> pdb=" O   ASN I 153 " (cutoff:3.500A)
      removed outlier: 4.917A  pdb=" N   ASN I 153 " --> pdb=" O   ASN I 137 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'I' and resid 176 through 180
    Processing sheet with id=AA5, first strand: chain 'H' and resid 3 through 8
      removed outlier: 3.945A  pdb=" N   THR H  69 " --> pdb=" O   HIS H  82 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.513A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 3.831A  pdb=" N   GLU H  33 " --> pdb=" O   ALA H  99 " (cutoff:3.500A)
      removed outlier: 6.586A  pdb=" N   MET H  34 " --> pdb=" O   TYR H  50 " (cutoff:3.500A)
      removed outlier: 4.467A  pdb=" N   TYR H  50 " --> pdb=" O   MET H  34 " (cutoff:3.500A)
      removed outlier: 6.731A  pdb=" N   TRP H  36 " --> pdb=" O   ILE H  48 " (cutoff:3.500A)
      removed outlier: 3.758A  pdb=" N   THR H  56 " --> pdb=" O   SER H  52 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12
      removed outlier: 3.513A  pdb=" N   VAL H  12 " --> pdb=" O   THR H 118 " (cutoff:3.500A)
      removed outlier: 6.281A  pdb=" N   CYS H  96 " --> pdb=" O   TRP H 111 " (cutoff:3.500A)
      removed outlier: 4.811A  pdb=" N   TRP H 111 " --> pdb=" O   CYS H  96 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 22
      removed outlier: 3.718A  pdb=" N   VAL L  19 " --> pdb=" O   ILE L  75 " (cutoff:3.500A)
      removed outlier: 3.747A  pdb=" N   ILE L  75 " --> pdb=" O   VAL L  19 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'L' and resid 34 through 38
      removed outlier: 3.659A  pdb=" N   THR L  85 " --> pdb=" O   GLN L  38 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 3 through 7
      removed outlier: 3.673A  pdb=" N   SER A  21 " --> pdb=" O   SER A   7 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'A' and resid 11 through 12
      removed outlier: 3.872A  pdb=" N   VAL A  12 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
      removed outlier: 7.527A  pdb=" N   MET A  34 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 5.250A  pdb=" N   GLY A  50 " --> pdb=" O   MET A  34 " (cutoff:3.500A)
      removed outlier: 6.812A  pdb=" N   TRP A  36 " --> pdb=" O   VAL A  48 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'A' and resid 11 through 12
      removed outlier: 3.872A  pdb=" N   VAL A  12 " --> pdb=" O   THR A 119 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'B' and resid 4 through 5
    Processing sheet with id=AB5, first strand: chain 'B' and resid 10 through 11
    Processing sheet with id=AB6, first strand: chain 'B' and resid 21 through 22
    Processing sheet with id=AB7, first strand: chain 'B' and resid 35 through 37
      removed outlier: 6.533A  pdb=" N   TRP B  35 " --> pdb=" O   LEU B  47 " (cutoff:3.500A)

    138 hydrogen bonds defined for protein.
    339 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 1.50 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1627
        1.34 -     1.46: 1328
        1.46 -     1.58: 2184
        1.58 -     1.70: 0
        1.70 -     1.81: 34
  Bond restraints: 5173
  Sorted by residual:
  bond pdb=" C5  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.15e+00
  bond pdb=" C5  NAG C   2 "
       pdb=" O5  NAG C   2 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.11e+00
  bond pdb=" C1  NAG C   1 "
       pdb=" O5  NAG C   1 "
    ideal  model  delta    sigma   weight residual
    1.406  1.427 -0.021 2.00e-02 2.50e+03 1.07e+00
  bond pdb=" CG1 ILE H  70 "
       pdb=" CD1 ILE H  70 "
    ideal  model  delta    sigma   weight residual
    1.513  1.473  0.040 3.90e-02 6.57e+02 1.04e+00
  bond pdb=" CB  PRO L   8 "
       pdb=" CG  PRO L   8 "
    ideal  model  delta    sigma   weight residual
    1.492  1.543 -0.051 5.00e-02 4.00e+02 1.03e+00
  ... (remaining 5168 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.46: 6919
        2.46 -     4.91: 93
        4.91 -     7.37: 4
        7.37 -     9.82: 1
        9.82 -    12.28: 1
  Bond angle restraints: 7018
  Sorted by residual:
  angle pdb=" CB  LYS L  45 "
        pdb=" CG  LYS L  45 "
        pdb=" CD  LYS L  45 "
      ideal   model   delta    sigma   weight residual
     111.30  118.72   -7.42 2.30e+00 1.89e-01 1.04e+01
  angle pdb=" N   SER L  52 "
        pdb=" CA  SER L  52 "
        pdb=" C   SER L  52 "
      ideal   model   delta    sigma   weight residual
     114.62  111.13    3.49 1.14e+00 7.69e-01 9.38e+00
  angle pdb=" C   ILE H  48 "
        pdb=" N   SER H  49 "
        pdb=" CA  SER H  49 "
      ideal   model   delta    sigma   weight residual
     121.75  116.65    5.10 1.73e+00 3.34e-01 8.70e+00
  angle pdb=" C   ASP H 109 "
        pdb=" N   ILE H 110 "
        pdb=" CA  ILE H 110 "
      ideal   model   delta    sigma   weight residual
     121.97  127.21   -5.24 1.80e+00 3.09e-01 8.47e+00
  angle pdb=" CA  SER L  52 "
        pdb=" C   SER L  52 "
        pdb=" N   ASN L  53 "
      ideal   model   delta    sigma   weight residual
     119.71  116.73    2.98 1.17e+00 7.31e-01 6.47e+00
  ... (remaining 7013 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.44: 2829
       21.44 -    42.88: 207
       42.88 -    64.33: 19
       64.33 -    85.77: 16
       85.77 -   107.21: 4
  Dihedral angle restraints: 3075
    sinusoidal: 1240
      harmonic: 1835
  Sorted by residual:
  dihedral pdb=" CB  CYS L  23 "
           pdb=" SG  CYS L  23 "
           pdb=" SG  CYS L  88 "
           pdb=" CB  CYS L  88 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  168.78  -75.78     1      1.00e+01 1.00e-02 7.24e+01
  dihedral pdb=" CA  HIS I 141 "
           pdb=" C   HIS I 141 "
           pdb=" N   LYS I 142 "
           pdb=" CA  LYS I 142 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -160.26  -19.74     0      5.00e+00 4.00e-02 1.56e+01
  dihedral pdb=" CB  CYS I 160 "
           pdb=" SG  CYS I 160 "
           pdb=" SG  CYS I 209 "
           pdb=" CB  CYS I 209 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -53.76  -32.24     1      1.00e+01 1.00e-02 1.48e+01
  ... (remaining 3072 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.047: 570
       0.047 -    0.093: 136
       0.093 -    0.140: 47
       0.140 -    0.186: 3
       0.186 -    0.233: 1
  Chirality restraints: 757
  Sorted by residual:
  chirality pdb=" C1  NAG C   1 "
            pdb=" ND2 ASN I  49 "
            pdb=" C2  NAG C   1 "
            pdb=" O5  NAG C   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.17   -0.23 2.00e-01 2.50e+01 1.35e+00
  chirality pdb=" CA  ILE H  51 "
            pdb=" N   ILE H  51 "
            pdb=" C   ILE H  51 "
            pdb=" CB  ILE H  51 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.58   -0.15 2.00e-01 2.50e+01 5.58e-01
  chirality pdb=" CA  ASN I 137 "
            pdb=" N   ASN I 137 "
            pdb=" C   ASN I 137 "
            pdb=" CB  ASN I 137 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.36    0.15 2.00e-01 2.50e+01 5.40e-01
  ... (remaining 754 not shown)

  Planarity restraints: 897
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER L   7 "    0.050 5.00e-02 4.00e+02   7.45e-02 8.89e+00
        pdb=" N   PRO L   8 "   -0.129 5.00e-02 4.00e+02
        pdb=" CA  PRO L   8 "    0.038 5.00e-02 4.00e+02
        pdb=" CD  PRO L   8 "    0.041 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ASN I 206 "    0.031 5.00e-02 4.00e+02   4.67e-02 3.49e+00
        pdb=" N   PRO I 207 "   -0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO I 207 "    0.027 5.00e-02 4.00e+02
        pdb=" CD  PRO I 207 "    0.023 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN B  79 "   -0.031 5.00e-02 4.00e+02   4.62e-02 3.41e+00
        pdb=" N   PRO B  80 "    0.080 5.00e-02 4.00e+02
        pdb=" CA  PRO B  80 "   -0.024 5.00e-02 4.00e+02
        pdb=" CD  PRO B  80 "   -0.026 5.00e-02 4.00e+02
  ... (remaining 894 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.73: 360
        2.73 -     3.27: 5009
        3.27 -     3.81: 8017
        3.81 -     4.36: 9185
        4.36 -     4.90: 16263
  Nonbonded interactions: 38834
  Sorted by model distance:
  nonbonded pdb=" OG1 THR L  20 "
            pdb=" OG1 THR L  72 "
     model   vdw
     2.184 3.040
  nonbonded pdb=" O   PHE H  29 "
            pdb=" NH2 ARG H  72 "
     model   vdw
     2.189 3.120
  nonbonded pdb=" OE2 GLU A   6 "
            pdb=" OG1 THR A 116 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OD1 ASP L  82 "
            pdb=" OH  TYR L  86 "
     model   vdw
     2.238 3.040
  nonbonded pdb=" OG  SER H  52 "
            pdb=" OG1 THR H  56 "
     model   vdw
     2.240 3.040
  ... (remaining 38829 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:             1.480
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     15.230
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.010
  Load rotamer database and sin/cos tables:2.690
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7358
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   5182  Z= 0.172
  Angle     :  0.698  12.281   7038  Z= 0.360
  Chirality :  0.046   0.233    757
  Planarity :  0.005   0.075    896
  Dihedral  : 15.759 107.211   1880
  Min Nonbonded Distance : 2.184

Molprobity Statistics.
  All-atom Clashscore : 14.18
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.28 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  0.18 %
    Allowed  :  1.08 %
    Favored  : 98.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.32), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.53 (0.35), residues: 228
  loop : -2.10 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP I 175 
 HIS   0.003   0.001   HIS A  95 
 PHE   0.012   0.002   PHE A  29 
 TYR   0.018   0.001   TYR H  50 
 ARG   0.003   0.000   ARG I 196 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00604 (    1)
  link_NAG-ASN         : angle       2.47397 (    3)
  link_BETA1-4         : bond        0.00466 (    1)
  link_BETA1-4         : angle       2.90765 (    3)
  hydrogen bonds       : bond        0.25297 (  130)
  hydrogen bonds       : angle       9.40427 (  339)
  SS BOND              : bond        0.00435 (    7)
  SS BOND              : angle       1.17423 (   14)
  covalent geometry    : bond        0.00387 ( 5173)
  covalent geometry    : angle       0.69262 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.529 
Fit side-chains
   revert: symmetry clash
REVERT: I   39 GLN cc_start: 0.7979 (mp10) cc_final: 0.7687 (mp10)
  outliers start: 1
  outliers final: 0
  residues processed: 86
  average time/residue: 0.1972
  time to fit residues: 21.1828
Evaluate side-chains
  74 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 51 optimal weight:    3.9990
   chunk 46 optimal weight:    0.8980
   chunk 25 optimal weight:    4.9990
   chunk 15 optimal weight:    4.9990
   chunk 31 optimal weight:    0.5980
   chunk 24 optimal weight:    6.9990
   chunk 47 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 29 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 55 optimal weight:    5.9990
   overall best weight:    1.8584

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

Flipped N/Q/H residues before XYZ refinement:
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3775 r_free = 0.3775 target = 0.094958 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3554 r_free = 0.3554 target = 0.083715 restraints weight = 15562.581|
|-----------------------------------------------------------------------------|
r_work (start): 0.3554 rms_B_bonded: 3.87
r_work: 0.3429 rms_B_bonded: 4.32 restraints_weight: 0.5000
r_work (final): 0.3429
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7627
moved from start:          0.1322

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   5182  Z= 0.203
  Angle     :  0.742  11.995   7038  Z= 0.376
  Chirality :  0.049   0.179    757
  Planarity :  0.005   0.053    896
  Dihedral  :  8.606  59.884    735
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 12.06
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.12 %
    Favored  : 90.56 %
  Rotamer:
    Outliers :  0.54 %
    Allowed  : 10.22 %
    Favored  : 89.25 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.20 (0.33), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.87 (0.33), residues: 242
  loop : -1.92 (0.30), residues: 383

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I  52 
 HIS   0.006   0.001   HIS A  95 
 PHE   0.015   0.002   PHE I 106 
 TYR   0.010   0.002   TYR I 167 
 ARG   0.003   0.000   ARG I 196 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00647 (    1)
  link_NAG-ASN         : angle       2.90571 (    3)
  link_BETA1-4         : bond        0.00122 (    1)
  link_BETA1-4         : angle       2.42506 (    3)
  hydrogen bonds       : bond        0.04710 (  130)
  hydrogen bonds       : angle       7.37846 (  339)
  SS BOND              : bond        0.00499 (    7)
  SS BOND              : angle       0.86022 (   14)
  covalent geometry    : bond        0.00465 ( 5173)
  covalent geometry    : angle       0.73773 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.567 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 3
  outliers final: 3
  residues processed: 88
  average time/residue: 0.2236
  time to fit residues: 24.3955
Evaluate side-chains
  78 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 75
  time to evaluate  : 0.581 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain L residue  104 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 28 optimal weight:    3.9990
   chunk 47 optimal weight:    0.0060
   chunk 33 optimal weight:    0.3980
   chunk 25 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9990
   chunk 59 optimal weight:    6.9990
   chunk 52 optimal weight:    0.5980
   chunk 20 optimal weight:    4.9990
   chunk 32 optimal weight:    0.9980
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    9.9990
   overall best weight:    0.5596

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** 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 = 0.3837 r_free = 0.3837 target = 0.098039 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3616 r_free = 0.3616 target = 0.086818 restraints weight = 15543.129|
|-----------------------------------------------------------------------------|
r_work (start): 0.3611 rms_B_bonded: 3.93
r_work: 0.3491 rms_B_bonded: 4.31 restraints_weight: 0.5000
r_work (final): 0.3491
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7507
moved from start:          0.1705

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   5182  Z= 0.116
  Angle     :  0.652  10.226   7038  Z= 0.329
  Chirality :  0.046   0.205    757
  Planarity :  0.005   0.048    896
  Dihedral  :  6.493  59.233    735
  Min Nonbonded Distance : 2.434

Molprobity Statistics.
  All-atom Clashscore : 9.93
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  7.52 %
    Favored  : 92.16 %
  Rotamer:
    Outliers :  1.08 %
    Allowed  : 14.34 %
    Favored  : 84.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.03 (0.32), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.48 (0.35), residues: 227
  loop : -1.98 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  52 
 HIS   0.005   0.001   HIS H  82 
 PHE   0.012   0.001   PHE I 106 
 TYR   0.014   0.001   TYR I 182 
 ARG   0.002   0.000   ARG L  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01014 (    1)
  link_NAG-ASN         : angle       3.03970 (    3)
  link_BETA1-4         : bond        0.00507 (    1)
  link_BETA1-4         : angle       1.96239 (    3)
  hydrogen bonds       : bond        0.03626 (  130)
  hydrogen bonds       : angle       6.71279 (  339)
  SS BOND              : bond        0.00391 (    7)
  SS BOND              : angle       0.83875 (   14)
  covalent geometry    : bond        0.00254 ( 5173)
  covalent geometry    : angle       0.64756 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 92
  time to evaluate  : 0.601 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I  142 LYS cc_start: 0.7907 (tttm) cc_final: 0.7575 (tptt)
REVERT: A   34 MET cc_start: 0.8579 (mmm) cc_final: 0.8323 (mmm)
  outliers start: 6
  outliers final: 5
  residues processed: 96
  average time/residue: 0.2122
  time to fit residues: 25.2146
Evaluate side-chains
  84 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 79
  time to evaluate  : 0.585 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   22 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 10 optimal weight:    3.9990
   chunk 5 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 16 optimal weight:    5.9990
   chunk 11 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 36 optimal weight:    6.9990
   chunk 42 optimal weight:    3.9990
   chunk 56 optimal weight:    6.9990
   chunk 38 optimal weight:    5.9990
   chunk 52 optimal weight:    0.7980
   overall best weight:    1.7584

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3765 r_free = 0.3765 target = 0.094740 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3547 r_free = 0.3547 target = 0.083326 restraints weight = 15821.977|
|-----------------------------------------------------------------------------|
r_work (start): 0.3546 rms_B_bonded: 3.95
r_work: 0.3419 rms_B_bonded: 4.37 restraints_weight: 0.5000
r_work (final): 0.3419
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7635
moved from start:          0.1856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   5182  Z= 0.190
  Angle     :  0.699  11.528   7038  Z= 0.357
  Chirality :  0.047   0.199    757
  Planarity :  0.005   0.048    896
  Dihedral  :  6.459  59.552    735
  Min Nonbonded Distance : 2.394

Molprobity Statistics.
  All-atom Clashscore : 12.76
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.44 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  1.25 %
    Allowed  : 17.38 %
    Favored  : 81.36 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.05 (0.32), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.49 (0.35), residues: 227
  loop : -1.99 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.002   TRP I  52 
 HIS   0.006   0.001   HIS I 141 
 PHE   0.009   0.001   PHE I 106 
 TYR   0.012   0.001   TYR I 182 
 ARG   0.003   0.000   ARG I 196 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00780 (    1)
  link_NAG-ASN         : angle       2.92873 (    3)
  link_BETA1-4         : bond        0.00420 (    1)
  link_BETA1-4         : angle       2.39155 (    3)
  hydrogen bonds       : bond        0.04162 (  130)
  hydrogen bonds       : angle       6.71886 (  339)
  SS BOND              : bond        0.00528 (    7)
  SS BOND              : angle       0.96272 (   14)
  covalent geometry    : bond        0.00431 ( 5173)
  covalent geometry    : angle       0.69403 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 84
  time to evaluate  : 0.636 
Fit side-chains
   revert: symmetry clash
REVERT: I  142 LYS cc_start: 0.7994 (tttm) cc_final: 0.7674 (tptt)
REVERT: L   17 ASP cc_start: 0.7023 (m-30) cc_final: 0.6760 (m-30)
REVERT: L   66 ARG cc_start: 0.9193 (tmm-80) cc_final: 0.8978 (tmm-80)
REVERT: A   38 ARG cc_start: 0.8560 (ttp-170) cc_final: 0.8225 (ttp80)
  outliers start: 7
  outliers final: 6
  residues processed: 89
  average time/residue: 0.2030
  time to fit residues: 22.5781
Evaluate side-chains
  85 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 79
  time to evaluate  : 0.586 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  141 HIS
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   96 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 9 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 60 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 59 optimal weight:    6.9990
   chunk 57 optimal weight:    7.9990
   chunk 22 optimal weight:    0.6980
   chunk 21 optimal weight:    0.7980
   chunk 31 optimal weight:    2.9990
   chunk 39 optimal weight:    5.9990
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 ASN ** 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 = 0.3807 r_free = 0.3807 target = 0.096810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3594 r_free = 0.3594 target = 0.085490 restraints weight = 15724.858|
|-----------------------------------------------------------------------------|
r_work (start): 0.3596 rms_B_bonded: 3.95
r_work: 0.3473 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7564
moved from start:          0.2046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5182  Z= 0.125
  Angle     :  0.655  10.772   7038  Z= 0.330
  Chirality :  0.046   0.207    757
  Planarity :  0.004   0.049    896
  Dihedral  :  5.907  57.757    735
  Min Nonbonded Distance : 2.412

Molprobity Statistics.
  All-atom Clashscore : 10.94
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.16 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 17.74 %
    Favored  : 79.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.98 (0.32), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.45 (0.35), residues: 227
  loop : -1.94 (0.29), residues: 398

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I  52 
 HIS   0.005   0.001   HIS H  82 
 PHE   0.010   0.001   PHE I 106 
 TYR   0.015   0.001   TYR I 182 
 ARG   0.002   0.000   ARG L  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00894 (    1)
  link_NAG-ASN         : angle       2.97427 (    3)
  link_BETA1-4         : bond        0.00498 (    1)
  link_BETA1-4         : angle       2.25993 (    3)
  hydrogen bonds       : bond        0.03508 (  130)
  hydrogen bonds       : angle       6.39014 (  339)
  SS BOND              : bond        0.00396 (    7)
  SS BOND              : angle       0.82881 (   14)
  covalent geometry    : bond        0.00281 ( 5173)
  covalent geometry    : angle       0.65038 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  105 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 92
  time to evaluate  : 0.664 
Fit side-chains
   revert: symmetry clash
REVERT: I   74 ASN cc_start: 0.8582 (t0) cc_final: 0.8289 (t0)
REVERT: I  118 ARG cc_start: 0.7202 (mtp180) cc_final: 0.6922 (mtp180)
REVERT: I  142 LYS cc_start: 0.7877 (tttm) cc_final: 0.7469 (tttp)
REVERT: L   66 ARG cc_start: 0.9170 (tmm-80) cc_final: 0.8948 (tmm-80)
REVERT: A   34 MET cc_start: 0.8614 (mmm) cc_final: 0.8339 (mmm)
  outliers start: 13
  outliers final: 10
  residues processed: 101
  average time/residue: 0.2086
  time to fit residues: 26.2858
Evaluate side-chains
  94 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 84
  time to evaluate  : 0.539 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  141 HIS
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   22 CYS
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   96 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 2 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0980
   chunk 54 optimal weight:    3.9990
   chunk 7 optimal weight:    0.9980
   chunk 50 optimal weight:    2.9990
   chunk 46 optimal weight:    0.5980
   chunk 5 optimal weight:    0.9980
   chunk 60 optimal weight:    2.9990
   chunk 34 optimal weight:    5.9990
   chunk 27 optimal weight:    3.9990
   chunk 10 optimal weight:    4.9990
   overall best weight:    1.1382

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
** A  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3789 r_free = 0.3789 target = 0.095843 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3576 r_free = 0.3576 target = 0.084580 restraints weight = 15839.708|
|-----------------------------------------------------------------------------|
r_work (start): 0.3577 rms_B_bonded: 3.93
r_work: 0.3451 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3451
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7589
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   5182  Z= 0.146
  Angle     :  0.684  11.574   7038  Z= 0.346
  Chirality :  0.046   0.206    757
  Planarity :  0.005   0.051    896
  Dihedral  :  5.899  58.824    735
  Min Nonbonded Distance : 2.403

Molprobity Statistics.
  All-atom Clashscore : 11.45
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.28 %
    Favored  : 90.40 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 19.53 %
    Favored  : 78.14 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.95 (0.33), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.46 (0.35), residues: 228
  loop : -1.91 (0.29), residues: 397

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP I  52 
 HIS   0.005   0.001   HIS I 141 
 PHE   0.008   0.001   PHE I 106 
 TYR   0.015   0.001   TYR I 182 
 ARG   0.005   0.000   ARG B  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00836 (    1)
  link_NAG-ASN         : angle       2.96757 (    3)
  link_BETA1-4         : bond        0.00518 (    1)
  link_BETA1-4         : angle       2.37032 (    3)
  hydrogen bonds       : bond        0.03665 (  130)
  hydrogen bonds       : angle       6.39344 (  339)
  SS BOND              : bond        0.00427 (    7)
  SS BOND              : angle       0.87988 (   14)
  covalent geometry    : bond        0.00328 ( 5173)
  covalent geometry    : angle       0.67972 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  99 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 86
  time to evaluate  : 0.544 
Fit side-chains
   revert: symmetry clash
REVERT: I   74 ASN cc_start: 0.8576 (t0) cc_final: 0.8282 (t0)
REVERT: I  118 ARG cc_start: 0.7199 (mtp180) cc_final: 0.6749 (mtp180)
REVERT: I  142 LYS cc_start: 0.7927 (tttm) cc_final: 0.7601 (tttp)
REVERT: H   76 LYS cc_start: 0.8790 (mmmt) cc_final: 0.8209 (tptp)
  outliers start: 13
  outliers final: 10
  residues processed: 94
  average time/residue: 0.2020
  time to fit residues: 23.5361
Evaluate side-chains
  92 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 82
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  141 HIS
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   28 THR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 41 optimal weight:    7.9990
   chunk 1 optimal weight:    4.9990
   chunk 54 optimal weight:    3.9990
   chunk 17 optimal weight:    5.9990
   chunk 16 optimal weight:    0.0570
   chunk 39 optimal weight:    0.8980
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    0.9980
   chunk 23 optimal weight:    4.9990
   chunk 58 optimal weight:    8.9990
   overall best weight:    1.3700

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
** A  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3776 r_free = 0.3776 target = 0.095005 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3559 r_free = 0.3559 target = 0.083566 restraints weight = 15533.303|
|-----------------------------------------------------------------------------|
r_work (start): 0.3560 rms_B_bonded: 3.93
r_work: 0.3434 rms_B_bonded: 4.35 restraints_weight: 0.5000
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7610
moved from start:          0.2220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   5182  Z= 0.161
  Angle     :  0.699  12.248   7038  Z= 0.352
  Chirality :  0.047   0.204    757
  Planarity :  0.005   0.050    896
  Dihedral  :  5.975  59.509    735
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 11.35
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.64 %
    Favored  : 91.04 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 20.61 %
    Favored  : 76.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.32), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.57 (0.34), residues: 239
  loop : -1.93 (0.30), residues: 386

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP I  52 
 HIS   0.005   0.001   HIS I 141 
 PHE   0.008   0.001   PHE I 106 
 TYR   0.013   0.001   TYR I 182 
 ARG   0.007   0.000   ARG B  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00845 (    1)
  link_NAG-ASN         : angle       2.99107 (    3)
  link_BETA1-4         : bond        0.00444 (    1)
  link_BETA1-4         : angle       2.37437 (    3)
  hydrogen bonds       : bond        0.03788 (  130)
  hydrogen bonds       : angle       6.47431 (  339)
  SS BOND              : bond        0.00444 (    7)
  SS BOND              : angle       0.86995 (   14)
  covalent geometry    : bond        0.00368 ( 5173)
  covalent geometry    : angle       0.69432 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 86
  time to evaluate  : 0.542 
Fit side-chains
   revert: symmetry clash
REVERT: I   74 ASN cc_start: 0.8576 (t0) cc_final: 0.8289 (t0)
REVERT: I  118 ARG cc_start: 0.7083 (mtp180) cc_final: 0.6809 (mtp180)
REVERT: I  142 LYS cc_start: 0.7886 (tttm) cc_final: 0.7457 (tttp)
REVERT: H   76 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8201 (tptp)
REVERT: L    3 GLN cc_start: 0.8421 (tm-30) cc_final: 0.8197 (tm-30)
REVERT: A   34 MET cc_start: 0.8650 (mmm) cc_final: 0.8354 (mmm)
  outliers start: 15
  outliers final: 12
  residues processed: 95
  average time/residue: 0.2027
  time to fit residues: 23.8563
Evaluate side-chains
  90 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 78
  time to evaluate  : 0.589 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  121 THR
Chi-restraints excluded: chain I residue  141 HIS
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   28 THR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 0 optimal weight:    4.9990
   chunk 17 optimal weight:    0.6980
   chunk 49 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 28 optimal weight:    3.9990
   chunk 14 optimal weight:    0.7980
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    0.0470
   chunk 41 optimal weight:    3.9990
   chunk 26 optimal weight:    0.8980
   chunk 52 optimal weight:    2.9990
   overall best weight:    0.6678

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
** L  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A  52 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3819 r_free = 0.3819 target = 0.097205 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.085799 restraints weight = 15846.191|
|-----------------------------------------------------------------------------|
r_work (start): 0.3598 rms_B_bonded: 4.00
r_work: 0.3474 rms_B_bonded: 4.41 restraints_weight: 0.5000
r_work (final): 0.3474
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7540
moved from start:          0.2363

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   5182  Z= 0.120
  Angle     :  0.676  11.221   7038  Z= 0.337
  Chirality :  0.046   0.212    757
  Planarity :  0.004   0.049    896
  Dihedral  :  5.659  56.882    735
  Min Nonbonded Distance : 2.397

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.16 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  : 21.86 %
    Favored  : 75.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.97 (0.33), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.55 (0.34), residues: 235
  loop : -1.88 (0.30), residues: 390

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP I  52 
 HIS   0.004   0.001   HIS I 141 
 PHE   0.008   0.001   PHE I 106 
 TYR   0.013   0.001   TYR I 182 
 ARG   0.003   0.000   ARG L  66 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00888 (    1)
  link_NAG-ASN         : angle       2.98546 (    3)
  link_BETA1-4         : bond        0.00565 (    1)
  link_BETA1-4         : angle       2.20413 (    3)
  hydrogen bonds       : bond        0.03338 (  130)
  hydrogen bonds       : angle       6.38090 (  339)
  SS BOND              : bond        0.00322 (    7)
  SS BOND              : angle       0.80080 (   14)
  covalent geometry    : bond        0.00268 ( 5173)
  covalent geometry    : angle       0.67162 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.553 
Fit side-chains
   revert: symmetry clash
REVERT: I   74 ASN cc_start: 0.8549 (t0) cc_final: 0.8275 (t0)
REVERT: I  118 ARG cc_start: 0.7066 (mtp180) cc_final: 0.6792 (mtp180)
REVERT: I  142 LYS cc_start: 0.7914 (tttm) cc_final: 0.7519 (tttp)
REVERT: I  149 GLU cc_start: 0.6784 (tm-30) cc_final: 0.6523 (tm-30)
REVERT: H   76 LYS cc_start: 0.8767 (mmmt) cc_final: 0.8320 (tptp)
REVERT: L    3 GLN cc_start: 0.8375 (tm-30) cc_final: 0.8126 (tm-30)
REVERT: A   34 MET cc_start: 0.8679 (mmm) cc_final: 0.8413 (mmm)
  outliers start: 12
  outliers final: 11
  residues processed: 99
  average time/residue: 0.1901
  time to fit residues: 23.6701
Evaluate side-chains
  92 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 81
  time to evaluate  : 0.533 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  141 HIS
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   85 THR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 35 optimal weight:    8.9990
   chunk 30 optimal weight:    9.9990
   chunk 37 optimal weight:    3.9990
   chunk 1 optimal weight:    3.9990
   chunk 15 optimal weight:    0.3980
   chunk 50 optimal weight:    2.9990
   chunk 51 optimal weight:    0.7980
   chunk 49 optimal weight:    0.1980
   chunk 34 optimal weight:    4.9990
   chunk 14 optimal weight:    1.9990
   overall best weight:    1.2784

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3786 r_free = 0.3786 target = 0.095886 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3568 r_free = 0.3568 target = 0.084409 restraints weight = 15629.084|
|-----------------------------------------------------------------------------|
r_work (start): 0.3563 rms_B_bonded: 3.96
r_work: 0.3436 rms_B_bonded: 4.40 restraints_weight: 0.5000
r_work (final): 0.3436
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7595
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.032   5182  Z= 0.158
  Angle     :  0.719  11.994   7038  Z= 0.361
  Chirality :  0.047   0.225    757
  Planarity :  0.004   0.048    896
  Dihedral  :  5.890  59.348    735
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  9.44 %
    Favored  : 90.24 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 21.51 %
    Favored  : 75.63 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.02 (0.32), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.52 (0.34), residues: 238
  loop : -1.97 (0.30), residues: 387

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP B  35 
 HIS   0.005   0.001   HIS I 141 
 PHE   0.017   0.001   PHE A  68 
 TYR   0.012   0.001   TYR B  86 
 ARG   0.003   0.000   ARG B  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00836 (    1)
  link_NAG-ASN         : angle       3.00883 (    3)
  link_BETA1-4         : bond        0.00406 (    1)
  link_BETA1-4         : angle       2.28033 (    3)
  hydrogen bonds       : bond        0.03752 (  130)
  hydrogen bonds       : angle       6.50204 (  339)
  SS BOND              : bond        0.00473 (    7)
  SS BOND              : angle       0.87817 (   14)
  covalent geometry    : bond        0.00360 ( 5173)
  covalent geometry    : angle       0.71462 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 87
  time to evaluate  : 0.628 
Fit side-chains
   revert: symmetry clash
REVERT: I   74 ASN cc_start: 0.8600 (t0) cc_final: 0.8328 (t0)
REVERT: I  118 ARG cc_start: 0.7074 (mtp180) cc_final: 0.6801 (mtp180)
REVERT: I  142 LYS cc_start: 0.7873 (tttm) cc_final: 0.7458 (tttp)
REVERT: H   76 LYS cc_start: 0.8787 (mmmt) cc_final: 0.8324 (tptp)
REVERT: L    3 GLN cc_start: 0.8450 (tm-30) cc_final: 0.8217 (tm-30)
REVERT: L    4 MET cc_start: 0.7174 (OUTLIER) cc_final: 0.6846 (ppp)
REVERT: A   34 MET cc_start: 0.8767 (mmm) cc_final: 0.8515 (mmm)
REVERT: B   38 GLN cc_start: 0.8038 (tp40) cc_final: 0.7495 (tp40)
  outliers start: 16
  outliers final: 14
  residues processed: 98
  average time/residue: 0.2033
  time to fit residues: 24.9987
Evaluate side-chains
  97 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 82
  time to evaluate  : 0.637 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  121 THR
Chi-restraints excluded: chain I residue  141 HIS
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain L residue    4 MET
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 48 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 35 optimal weight:    8.9990
   chunk 5 optimal weight:    1.9990
   chunk 16 optimal weight:    4.9990
   chunk 23 optimal weight:    0.6980
   chunk 49 optimal weight:    0.9990
   chunk 9 optimal weight:    0.0670
   chunk 29 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 32 optimal weight:    0.7980
   overall best weight:    0.6918

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS
** L  34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3825 r_free = 0.3825 target = 0.097635 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.086111 restraints weight = 15600.349|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 4.00
r_work: 0.3481 rms_B_bonded: 4.43 restraints_weight: 0.5000
r_work (final): 0.3481
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7534
moved from start:          0.2550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   5182  Z= 0.128
  Angle     :  0.720   9.272   7038  Z= 0.359
  Chirality :  0.047   0.212    757
  Planarity :  0.005   0.052    896
  Dihedral  :  5.685  57.065    735
  Min Nonbonded Distance : 2.390

Molprobity Statistics.
  All-atom Clashscore : 11.65
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  :  8.16 %
    Favored  : 91.52 %
  Rotamer:
    Outliers :  2.33 %
    Allowed  : 22.40 %
    Favored  : 75.27 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.01 (0.32), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.51 (0.34), residues: 241
  loop : -1.98 (0.30), residues: 384

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.002   TRP B  35 
 HIS   0.005   0.001   HIS I 141 
 PHE   0.012   0.001   PHE A  68 
 TYR   0.016   0.001   TYR B  86 
 ARG   0.009   0.000   ARG B  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00871 (    1)
  link_NAG-ASN         : angle       2.98553 (    3)
  link_BETA1-4         : bond        0.00594 (    1)
  link_BETA1-4         : angle       2.17299 (    3)
  hydrogen bonds       : bond        0.03399 (  130)
  hydrogen bonds       : angle       6.37450 (  339)
  SS BOND              : bond        0.00488 (    7)
  SS BOND              : angle       0.86210 (   14)
  covalent geometry    : bond        0.00290 ( 5173)
  covalent geometry    : angle       0.71547 ( 7018)

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

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

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1250 Ramachandran restraints generated.
    625 Oldfield, 0 Emsley, 625 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 89
  time to evaluate  : 0.537 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: I   74 ASN cc_start: 0.8520 (t0) cc_final: 0.8212 (t0)
REVERT: I  118 ARG cc_start: 0.7089 (mtp180) cc_final: 0.6816 (mtp180)
REVERT: I  142 LYS cc_start: 0.7789 (tttm) cc_final: 0.7332 (tttp)
REVERT: H   76 LYS cc_start: 0.8753 (mmmt) cc_final: 0.8275 (tptp)
REVERT: L    3 GLN cc_start: 0.8397 (tm-30) cc_final: 0.8153 (tm-30)
REVERT: A   34 MET cc_start: 0.8703 (mmm) cc_final: 0.8449 (mmm)
  outliers start: 13
  outliers final: 13
  residues processed: 97
  average time/residue: 0.1904
  time to fit residues: 23.1843
Evaluate side-chains
  96 residues out of total 558 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 83
  time to evaluate  : 0.572 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain I residue  141 HIS
Chi-restraints excluded: chain H residue   50 TYR
Chi-restraints excluded: chain H residue   70 ILE
Chi-restraints excluded: chain H residue   80 TYR
Chi-restraints excluded: chain H residue   81 LEU
Chi-restraints excluded: chain H residue   96 CYS
Chi-restraints excluded: chain L residue   11 LEU
Chi-restraints excluded: chain L residue   19 VAL
Chi-restraints excluded: chain L residue  102 THR
Chi-restraints excluded: chain A residue   32 PHE
Chi-restraints excluded: chain A residue   96 CYS
Chi-restraints excluded: chain B residue   28 THR
Chi-restraints excluded: chain B residue   85 THR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 61
   random chunks:
   chunk 45 optimal weight:    2.9990
   chunk 57 optimal weight:    2.9990
   chunk 17 optimal weight:    6.9990
   chunk 43 optimal weight:    4.9990
   chunk 4 optimal weight:    4.9990
   chunk 35 optimal weight:    6.9990
   chunk 15 optimal weight:    0.9980
   chunk 55 optimal weight:    0.7980
   chunk 18 optimal weight:    5.9990
   chunk 12 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   overall best weight:    1.7586

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

Flipped N/Q/H residues before XYZ refinement:
** I  66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
H  82 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3758 r_free = 0.3758 target = 0.094204 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3532 r_free = 0.3532 target = 0.082312 restraints weight = 16087.636|
|-----------------------------------------------------------------------------|
r_work (start): 0.3531 rms_B_bonded: 4.07
r_work: 0.3402 rms_B_bonded: 4.46 restraints_weight: 0.5000
r_work (final): 0.3402
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7639
moved from start:          0.2522

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   5182  Z= 0.198
  Angle     :  0.776   9.733   7038  Z= 0.391
  Chirality :  0.049   0.244    757
  Planarity :  0.005   0.049    896
  Dihedral  :  6.147  59.743    735
  Min Nonbonded Distance : 2.368

Molprobity Statistics.
  All-atom Clashscore : 13.58
  Ramachandran Plot:
    Outliers :  0.32 %
    Allowed  : 10.40 %
    Favored  : 89.28 %
  Rotamer:
    Outliers :  2.87 %
    Allowed  : 22.40 %
    Favored  : 74.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 14.81 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.16 (0.32), residues: 625
  helix:  None (None), residues: 0
  sheet: -0.70 (0.33), residues: 248
  loop : -2.03 (0.30), residues: 377

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP B  35 
 HIS   0.006   0.001   HIS A  95 
 PHE   0.010   0.002   PHE A  68 
 TYR   0.016   0.001   TYR B  86 
 ARG   0.008   0.001   ARG B  61 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00790 (    1)
  link_NAG-ASN         : angle       3.04980 (    3)
  link_BETA1-4         : bond        0.00294 (    1)
  link_BETA1-4         : angle       2.31392 (    3)
  hydrogen bonds       : bond        0.04033 (  130)
  hydrogen bonds       : angle       6.58308 (  339)
  SS BOND              : bond        0.00554 (    7)
  SS BOND              : angle       0.93156 (   14)
  covalent geometry    : bond        0.00454 ( 5173)
  covalent geometry    : angle       0.77202 ( 7018)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2565.82 seconds
wall clock time: 45 minutes 26.37 seconds (2726.37 seconds total)