Starting phenix.real_space_refine
on Fri Aug 22 16:44:45 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8jva_36672/08_2025/8jva_36672.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8jva_36672/08_2025/8jva_36672.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.81
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8jva_36672/08_2025/8jva_36672.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8jva_36672/08_2025/8jva_36672.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8jva_36672/08_2025/8jva_36672.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8jva_36672/08_2025/8jva_36672.cif"
  }
  resolution = 2.81
  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=  -0.002 sd=   0.015
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      20      5.16       5
     C    3862      2.51       5
     N    1002      2.21       5
     O    1187      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6071
  Number of models: 1
  Model: ""
    Number of chains: 5
    Chain: "D"
      Number of atoms: 922
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 922
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 7, 'TRANS': 112}
    Chain: "A"
      Number of atoms: 1652
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 213, 1652
          Classifications: {'peptide': 213}
          Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200}
    Chain: "B"
      Number of atoms: 1455
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 193, 1455
          Classifications: {'peptide': 193}
          Link IDs: {'PTRANS': 9, 'TRANS': 183}
          Chain breaks: 1
    Chain: "F"
      Number of atoms: 1972
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 243, 1972
          Classifications: {'peptide': 243}
          Link IDs: {'PTRANS': 15, 'TRANS': 227}
          Chain breaks: 6
    Chain: "F"
      Number of atoms: 70
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 5, 70
          Unusual residues: {'NAG': 5}
          Classifications: {'undetermined': 5}
          Link IDs: {None: 4}
          Unresolved non-hydrogen bonds: 5
          Unresolved non-hydrogen angles: 10
          Unresolved non-hydrogen dihedrals: 15
          Unresolved non-hydrogen chiralities: 5
  Time building chain proxies: 1.53, per 1000 atoms: 0.25
  Number of scatterers: 6071
  At special positions: 0
  Unit cell: (76.68, 73.44, 147.96, 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      20     16.00
     O    1187      8.00
     N    1002      7.00
     C    3862      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS D  22 " - pdb=" SG  CYS D  96 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  23 " - pdb=" SG  CYS A  88 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 134 " - pdb=" SG  CYS A 194 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 131 " - pdb=" SG  CYS F 166 " distance=2.03
    Simple disulfide: pdb=" SG  CYS F 291 " - pdb=" SG  CYS F 301 " 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 F 401 " - " ASN F 122 "
      " NAG F 402 " - " ASN F 165 "
      " NAG F 403 " - " ASN F 282 "
      " NAG F 404 " - " ASN F 234 "
      " NAG F 405 " - " ASN F  61 "
  Time building additional restraints: 0.48
  Conformation dependent library (CDL) restraints added in 236.4 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1430

  Finding SS restraints...
    Secondary structure from input PDB file:
      8 helices and 16 sheets defined
      5.9% alpha, 38.1% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.17
  Creating SS restraints...
    Processing helix  chain 'D' and resid 28 through 32
    Processing helix  chain 'D' and resid 61 through 65
      removed outlier: 3.929A  pdb=" N   LYS D  65 " --> pdb=" O   ASP D  62 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 87 through 91
      removed outlier: 3.676A  pdb=" N   THR D  91 " --> pdb=" O   PRO D  88 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 100 through 103
      removed outlier: 4.016A  pdb=" N   GLN D 103 " --> pdb=" O   PRO D 100 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'D' and resid 100 through 103'
    Processing helix  chain 'A' and resid 121 through 126
    Processing helix  chain 'B' and resid 28 through 32
      removed outlier: 3.904A  pdb=" N   SER B  31 " --> pdb=" O   THR B  28 " (cutoff:3.500A)
      removed outlier: 3.726A  pdb=" N   TYR B  32 " --> pdb=" O   PHE B  29 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'B' and resid 28 through 32'
    Processing helix  chain 'B' and resid 86 through 90
      removed outlier: 3.689A  pdb=" N   THR B  90 " --> pdb=" O   ALA B  87 " (cutoff:3.500A)
    Processing helix  chain 'F' and resid 294 through 303
      removed outlier: 3.635A  pdb=" N   LYS F 300 " --> pdb=" O   LEU F 296 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'D' and resid 3 through 7
    Processing sheet with id=AA2, first strand: chain 'D' and resid 11 through 12
      removed outlier: 3.548A  pdb=" N   ASN D  97 " --> pdb=" O   SER D  35 " (cutoff:3.500A)
      removed outlier: 3.652A  pdb=" N   MET D  34 " --> pdb=" O   THR D  51 " (cutoff:3.500A)
      removed outlier: 5.983A  pdb=" N   ARG D  38 " --> pdb=" O   LEU D  47 " (cutoff:3.500A)
      removed outlier: 5.346A  pdb=" N   LEU D  47 " --> pdb=" O   ARG D  38 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 4 through 7
      removed outlier: 3.613A  pdb=" N   ASP A  70 " --> pdb=" O   SER A  67 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 10 through 13
    Processing sheet with id=AA5, first strand: chain 'A' and resid 45 through 49
      removed outlier: 6.665A  pdb=" N   TRP A  35 " --> pdb=" O   LEU A  47 " (cutoff:3.500A)
      removed outlier: 4.749A  pdb=" N   SER A  49 " --> pdb=" O   LEU A  33 " (cutoff:3.500A)
      removed outlier: 6.720A  pdb=" N   LEU A  33 " --> pdb=" O   SER A  49 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 114 through 118
      removed outlier: 3.935A  pdb=" N   ASN A 137 " --> pdb=" O   SER A 114 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 145 through 150
      removed outlier: 4.066A  pdb=" N   TYR A 192 " --> pdb=" O   PHE A 209 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA9, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.177A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
      removed outlier: 6.665A  pdb=" N   MET B  34 " --> pdb=" O   PHE B  50 " (cutoff:3.500A)
      removed outlier: 4.397A  pdb=" N   PHE B  50 " --> pdb=" O   MET B  34 " (cutoff:3.500A)
      removed outlier: 6.507A  pdb=" N   TRP B  36 " --> pdb=" O   VAL B  48 " (cutoff:3.500A)
      removed outlier: 3.738A  pdb=" N   ARG B  52 " --> pdb=" O   ASN B  56 " (cutoff:3.500A)
      removed outlier: 7.131A  pdb=" N   ASN B  56 " --> pdb=" O   ARG B  52 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.177A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 118 " (cutoff:3.500A)
    Processing sheet with id=AB2, first strand: chain 'B' and resid 128 through 129
      removed outlier: 3.821A  pdb=" N   VAL B 152 " --> pdb=" O   LEU B 188 " (cutoff:3.500A)
    Processing sheet with id=AB3, first strand: chain 'F' and resid 27 through 30
      removed outlier: 4.097A  pdb=" N   ALA F  27 " --> pdb=" O   TRP F  64 " (cutoff:3.500A)
      removed outlier: 8.647A  pdb=" N   ASN F  61 " --> pdb=" O   TYR F 269 " (cutoff:3.500A)
      removed outlier: 6.787A  pdb=" N   TYR F 269 " --> pdb=" O   ASN F  61 " (cutoff:3.500A)
      removed outlier: 3.529A  pdb=" N   THR F  63 " --> pdb=" O   VAL F 267 " (cutoff:3.500A)
      removed outlier: 3.511A  pdb=" N   VAL F 227 " --> pdb=" O   ILE F 203 " (cutoff:3.500A)
      removed outlier: 5.703A  pdb=" N   SER F 205 " --> pdb=" O   PRO F 225 " (cutoff:3.500A)
    Processing sheet with id=AB4, first strand: chain 'F' and resid 47 through 55
      removed outlier: 3.561A  pdb=" N   VAL F  47 " --> pdb=" O   TYR F 279 " (cutoff:3.500A)
      removed outlier: 4.017A  pdb=" N   ASP F 287 " --> pdb=" O   LYS F 278 " (cutoff:3.500A)
    Processing sheet with id=AB5, first strand: chain 'F' and resid 84 through 85
      removed outlier: 3.994A  pdb=" N   SER F 162 " --> pdb=" O   GLN F 134 " (cutoff:3.500A)
    Processing sheet with id=AB6, first strand: chain 'F' and resid 84 through 85
      removed outlier: 3.547A  pdb=" N   SER F 172 " --> pdb=" O   VAL F 126 " (cutoff:3.500A)
    Processing sheet with id=AB7, first strand: chain 'F' and resid 141 through 145
      removed outlier: 5.924A  pdb=" N   LEU F 141 " --> pdb=" O   LEU F 244 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AB7

    215 hydrogen bonds defined for protein.
    531 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: 0.65 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: 1923
        1.34 -     1.46: 1599
        1.46 -     1.58: 2671
        1.58 -     1.70: 0
        1.70 -     1.82: 26
  Bond restraints: 6219
  Sorted by residual:
  bond pdb=" C1  NAG F 402 "
       pdb=" O5  NAG F 402 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.17e+00
  bond pdb=" C1  NAG F 405 "
       pdb=" O5  NAG F 405 "
    ideal  model  delta    sigma   weight residual
    1.406  1.435 -0.029 2.00e-02 2.50e+03 2.11e+00
  bond pdb=" C1  NAG F 403 "
       pdb=" O5  NAG F 403 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.97e+00
  bond pdb=" C5  NAG F 405 "
       pdb=" O5  NAG F 405 "
    ideal  model  delta    sigma   weight residual
    1.413  1.436 -0.023 2.00e-02 2.50e+03 1.33e+00
  bond pdb=" C5  NAG F 403 "
       pdb=" O5  NAG F 403 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.20e+00
  ... (remaining 6214 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.69: 8234
        1.69 -     3.37: 193
        3.37 -     5.06: 21
        5.06 -     6.75: 3
        6.75 -     8.44: 1
  Bond angle restraints: 8452
  Sorted by residual:
  angle pdb=" N   ILE F 100 "
        pdb=" CA  ILE F 100 "
        pdb=" C   ILE F 100 "
      ideal   model   delta    sigma   weight residual
     112.96  108.70    4.26 1.00e+00 1.00e+00 1.81e+01
  angle pdb=" C   TYR B 103 "
        pdb=" CA  TYR B 103 "
        pdb=" CB  TYR B 103 "
      ideal   model   delta    sigma   weight residual
     117.23  111.53    5.70 1.36e+00 5.41e-01 1.76e+01
  angle pdb=" C   PHE F  32 "
        pdb=" CA  PHE F  32 "
        pdb=" CB  PHE F  32 "
      ideal   model   delta    sigma   weight residual
     115.89  110.98    4.91 1.32e+00 5.74e-01 1.38e+01
  angle pdb=" N   GLY B 149 "
        pdb=" CA  GLY B 149 "
        pdb=" C   GLY B 149 "
      ideal   model   delta    sigma   weight residual
     110.87  115.91   -5.04 1.54e+00 4.22e-01 1.07e+01
  angle pdb=" CA  GLY A  66 "
        pdb=" C   GLY A  66 "
        pdb=" O   GLY A  66 "
      ideal   model   delta    sigma   weight residual
     122.45  120.16    2.29 7.20e-01 1.93e+00 1.01e+01
  ... (remaining 8447 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.77: 3391
       16.77 -    33.54: 290
       33.54 -    50.32: 53
       50.32 -    67.09: 8
       67.09 -    83.86: 4
  Dihedral angle restraints: 3746
    sinusoidal: 1516
      harmonic: 2230
  Sorted by residual:
  dihedral pdb=" CB  CYS A 134 "
           pdb=" SG  CYS A 134 "
           pdb=" SG  CYS A 194 "
           pdb=" CB  CYS A 194 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  169.35  -76.35     1      1.00e+01 1.00e-02 7.34e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  95 "
           pdb=" CB  CYS B  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  134.15  -41.15     1      1.00e+01 1.00e-02 2.37e+01
  dihedral pdb=" CA  ASP A 167 "
           pdb=" C   ASP A 167 "
           pdb=" N   SER A 168 "
           pdb=" CA  SER A 168 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.52  -17.48     0      5.00e+00 4.00e-02 1.22e+01
  ... (remaining 3743 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.036: 627
       0.036 -    0.071: 207
       0.071 -    0.107: 78
       0.107 -    0.142: 32
       0.142 -    0.178: 2
  Chirality restraints: 946
  Sorted by residual:
  chirality pdb=" C1  NAG F 403 "
            pdb=" ND2 ASN F 282 "
            pdb=" C2  NAG F 403 "
            pdb=" O5  NAG F 403 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.22   -0.18 2.00e-01 2.50e+01 7.92e-01
  chirality pdb=" CA  GLU B 158 "
            pdb=" N   GLU B 158 "
            pdb=" C   GLU B 158 "
            pdb=" CB  GLU B 158 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.34    0.17 2.00e-01 2.50e+01 7.62e-01
  chirality pdb=" C1  NAG F 402 "
            pdb=" ND2 ASN F 165 "
            pdb=" C2  NAG F 402 "
            pdb=" O5  NAG F 402 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.26   -0.14 2.00e-01 2.50e+01 4.95e-01
  ... (remaining 943 not shown)

  Planarity restraints: 1085
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ILE D  53 "   -0.042 5.00e-02 4.00e+02   6.32e-02 6.40e+00
        pdb=" N   PRO D  54 "    0.109 5.00e-02 4.00e+02
        pdb=" CA  PRO D  54 "   -0.033 5.00e-02 4.00e+02
        pdb=" CD  PRO D  54 "   -0.035 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLY B 126 "   -0.034 5.00e-02 4.00e+02   5.28e-02 4.46e+00
        pdb=" N   PRO B 127 "    0.091 5.00e-02 4.00e+02
        pdb=" CA  PRO B 127 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO B 127 "   -0.029 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   VAL A  58 "    0.028 5.00e-02 4.00e+02   4.26e-02 2.90e+00
        pdb=" N   PRO A  59 "   -0.074 5.00e-02 4.00e+02
        pdb=" CA  PRO A  59 "    0.022 5.00e-02 4.00e+02
        pdb=" CD  PRO A  59 "    0.024 5.00e-02 4.00e+02
  ... (remaining 1082 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.75: 700
        2.75 -     3.29: 5199
        3.29 -     3.83: 8847
        3.83 -     4.36: 10352
        4.36 -     4.90: 19171
  Nonbonded interactions: 44269
  Sorted by model distance:
  nonbonded pdb=" OG  SER F  94 "
            pdb=" OE1 GLU F  96 "
     model   vdw
     2.217 3.040
  nonbonded pdb=" OG  SER D  35 "
            pdb=" O   ALA D  49 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OD2 ASP F  40 "
            pdb=" NH2 ARG F  44 "
     model   vdw
     2.304 3.120
  nonbonded pdb=" O   ARG B  52 "
            pdb=" NH1 ARG B  71 "
     model   vdw
     2.310 3.120
  nonbonded pdb=" O   SER A 114 "
            pdb=" OG  SER A 114 "
     model   vdw
     2.321 3.040
  ... (remaining 44264 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:             11.160
  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:          0.160
  Check model and map are aligned:         0.020
  Set scattering table:                    0.020
  Process input model:                     6.670
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:6.580
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   24.670
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8074
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   0.038   6230  Z= 0.172
  Angle     :  0.636   8.436   8479  Z= 0.350
  Chirality :  0.044   0.178    946
  Planarity :  0.005   0.063   1080
  Dihedral  : 12.608  83.859   2298
  Min Nonbonded Distance : 2.217

Molprobity Statistics.
  All-atom Clashscore : 5.62
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.55 %
    Favored  : 95.45 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.15 %
    Favored  : 99.85 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.47 (0.30), residues: 747
  helix:  0.33 (1.21), residues: 16
  sheet:  0.87 (0.32), residues: 283
  loop : -1.18 (0.27), residues: 448

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D  31 
 TYR   0.016   0.001   TYR A 140 
 PHE   0.016   0.001   PHE F 220 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00376 ( 6219)
  covalent geometry    : angle       0.62979 ( 8452)
  SS BOND              : bond        0.00436 (    6)
  SS BOND              : angle       1.00306 (   12)
  hydrogen bonds       : bond        0.16763 (  195)
  hydrogen bonds       : angle       5.89823 (  531)
  link_NAG-ASN         : bond        0.00366 (    5)
  link_NAG-ASN         : angle       2.03959 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  145 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 145
  time to evaluate  : 0.239 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   90 ASP cc_start: 0.6254 (m-30) cc_final: 0.5410 (m-30)
REVERT: F  158 ARG cc_start: 0.8370 (mtt-85) cc_final: 0.7841 (tmt170)
  outliers start: 0
  outliers final: 0
  residues processed: 145
  average time/residue: 0.6291
  time to fit residues: 94.6818
Evaluate side-chains
  78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.198 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 49 optimal weight:    0.0270
   chunk 53 optimal weight:    3.9990
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    5.9990
   chunk 65 optimal weight:    5.9990
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    6.9990
   chunk 38 optimal weight:    1.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    2.9990
   chunk 74 optimal weight:    0.9980
   overall best weight:    0.9240

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

Flipped N/Q/H residues before XYZ refinement:
F  23 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3778 r_free = 0.3778 target = 0.090386 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3166 r_free = 0.3166 target = 0.060314 restraints weight = 16822.309|
|-----------------------------------------------------------------------------|
r_work (start): 0.3092 rms_B_bonded: 4.07
r_work: 0.2961 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2961
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8410
moved from start:          0.2414

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   6230  Z= 0.139
  Angle     :  0.645   8.268   8479  Z= 0.331
  Chirality :  0.045   0.180    946
  Planarity :  0.005   0.054   1080
  Dihedral  :  5.849  54.430    934
  Min Nonbonded Distance : 2.410

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  1.05 %
    Allowed  : 12.72 %
    Favored  : 86.23 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.26 (0.30), residues: 747
  helix:  0.42 (1.24), residues: 16
  sheet:  1.22 (0.32), residues: 280
  loop : -1.19 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG D  57 
 TYR   0.014   0.001   TYR A 140 
 PHE   0.017   0.001   PHE A 118 
 TRP   0.008   0.001   TRP B  47 
 HIS   0.003   0.001   HIS F  66 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 6219)
  covalent geometry    : angle       0.63893 ( 8452)
  SS BOND              : bond        0.00420 (    6)
  SS BOND              : angle       1.07909 (   12)
  hydrogen bonds       : bond        0.03782 (  195)
  hydrogen bonds       : angle       4.95099 (  531)
  link_NAG-ASN         : bond        0.00417 (    5)
  link_NAG-ASN         : angle       1.96832 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 93
  time to evaluate  : 0.186 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D    1 GLN cc_start: 0.8381 (pt0) cc_final: 0.7803 (pp30)
REVERT: D   73 ASP cc_start: 0.8452 (t0) cc_final: 0.8126 (t0)
REVERT: A   54 MET cc_start: 0.8792 (mmm) cc_final: 0.8186 (mpp)
REVERT: A  105 ASP cc_start: 0.8118 (m-30) cc_final: 0.7805 (p0)
REVERT: A  195 GLU cc_start: 0.8129 (tt0) cc_final: 0.7907 (tm-30)
REVERT: F  158 ARG cc_start: 0.8832 (mtt-85) cc_final: 0.7511 (tmt170)
REVERT: F  169 GLU cc_start: 0.8789 (OUTLIER) cc_final: 0.8356 (tp30)
REVERT: F  298 GLU cc_start: 0.8144 (tp30) cc_final: 0.7922 (tp30)
  outliers start: 7
  outliers final: 4
  residues processed: 96
  average time/residue: 0.6030
  time to fit residues: 60.3982
Evaluate side-chains
  78 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 73
  time to evaluate  : 0.291 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   33 ASP
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain F residue  169 GLU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 71 optimal weight:    4.9990
   chunk 67 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0670
   chunk 7 optimal weight:    0.8980
   chunk 3 optimal weight:    4.9990
   chunk 43 optimal weight:    2.9990
   chunk 54 optimal weight:    0.6980
   chunk 61 optimal weight:    1.9990
   chunk 40 optimal weight:    4.9990
   chunk 75 optimal weight:    7.9990
   overall best weight:    1.3322

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

Flipped N/Q/H residues before XYZ refinement:
A 166 GLN
B 113 GLN
F  23 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3742 r_free = 0.3742 target = 0.089163 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.058939 restraints weight = 16875.765|
|-----------------------------------------------------------------------------|
r_work (start): 0.3046 rms_B_bonded: 4.09
r_work: 0.2918 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2918
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.2866

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   6230  Z= 0.161
  Angle     :  0.638   8.020   8479  Z= 0.325
  Chirality :  0.045   0.183    946
  Planarity :  0.005   0.051   1080
  Dihedral  :  5.266  35.346    934
  Min Nonbonded Distance : 2.508

Molprobity Statistics.
  All-atom Clashscore : 7.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 14.07 %
    Favored  : 83.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.30), residues: 747
  helix:  1.07 (1.42), residues: 16
  sheet:  1.18 (0.32), residues: 280
  loop : -1.10 (0.27), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 142 
 TYR   0.014   0.001   TYR B  94 
 PHE   0.014   0.001   PHE A 118 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00391 ( 6219)
  covalent geometry    : angle       0.63216 ( 8452)
  SS BOND              : bond        0.00369 (    6)
  SS BOND              : angle       1.09448 (   12)
  hydrogen bonds       : bond        0.03517 (  195)
  hydrogen bonds       : angle       4.81216 (  531)
  link_NAG-ASN         : bond        0.00346 (    5)
  link_NAG-ASN         : angle       1.94868 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 81
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   73 ASP cc_start: 0.8510 (t0) cc_final: 0.8051 (t0)
REVERT: D   90 ASP cc_start: 0.8268 (t70) cc_final: 0.8027 (t70)
REVERT: A   54 MET cc_start: 0.8809 (mmm) cc_final: 0.8106 (mpp)
REVERT: A  108 ARG cc_start: 0.8277 (tmm-80) cc_final: 0.7897 (tpt-90)
REVERT: A  147 GLN cc_start: 0.7723 (tp40) cc_final: 0.7451 (tp-100)
REVERT: B   89 ASP cc_start: 0.8896 (m-30) cc_final: 0.8535 (m-30)
REVERT: F  100 ILE cc_start: 0.8759 (OUTLIER) cc_final: 0.8393 (mp)
REVERT: F  158 ARG cc_start: 0.8797 (mtt-85) cc_final: 0.7477 (tmt170)
REVERT: F  169 GLU cc_start: 0.8848 (OUTLIER) cc_final: 0.8399 (tp30)
REVERT: F  298 GLU cc_start: 0.8171 (tp30) cc_final: 0.7931 (tp30)
  outliers start: 17
  outliers final: 9
  residues processed: 91
  average time/residue: 0.5991
  time to fit residues: 56.9188
Evaluate side-chains
  86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.211 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   33 ASP
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  131 SER
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain F residue  100 ILE
Chi-restraints excluded: chain F residue  169 GLU
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 66 optimal weight:    1.9990
   chunk 63 optimal weight:    0.4980
   chunk 64 optimal weight:    5.9990
   chunk 3 optimal weight:    4.9990
   chunk 9 optimal weight:    2.9990
   chunk 22 optimal weight:    0.3980
   chunk 46 optimal weight:   20.0000
   chunk 58 optimal weight:    3.9990
   chunk 12 optimal weight:    3.9990
   overall best weight:    1.3784

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

Flipped N/Q/H residues before XYZ refinement:
B  13 GLN
F  23 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.088549 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3102 r_free = 0.3102 target = 0.058558 restraints weight = 16790.856|
|-----------------------------------------------------------------------------|
r_work (start): 0.3042 rms_B_bonded: 4.02
r_work: 0.2916 rms_B_bonded: 4.00 restraints_weight: 0.5000
r_work (final): 0.2916
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   6230  Z= 0.166
  Angle     :  0.645  10.314   8479  Z= 0.328
  Chirality :  0.044   0.185    946
  Planarity :  0.005   0.051   1080
  Dihedral  :  5.052  34.594    934
  Min Nonbonded Distance : 2.461

Molprobity Statistics.
  All-atom Clashscore : 7.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.02 %
    Favored  : 95.98 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 14.82 %
    Favored  : 82.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.30), residues: 747
  helix:  0.97 (1.43), residues: 16
  sheet:  1.16 (0.32), residues: 280
  loop : -1.06 (0.28), residues: 451

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  57 
 TYR   0.014   0.001   TYR B  94 
 PHE   0.018   0.002   PHE B 130 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00404 ( 6219)
  covalent geometry    : angle       0.63982 ( 8452)
  SS BOND              : bond        0.00367 (    6)
  SS BOND              : angle       0.99548 (   12)
  hydrogen bonds       : bond        0.03398 (  195)
  hydrogen bonds       : angle       4.74335 (  531)
  link_NAG-ASN         : bond        0.00328 (    5)
  link_NAG-ASN         : angle       1.91203 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 72
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   34 MET cc_start: 0.8548 (OUTLIER) cc_final: 0.7763 (mmm)
REVERT: D   73 ASP cc_start: 0.8722 (t0) cc_final: 0.8115 (t0)
REVERT: D   76 LYS cc_start: 0.9299 (mtmt) cc_final: 0.8896 (pttp)
REVERT: A   54 MET cc_start: 0.8829 (mmm) cc_final: 0.8161 (mpp)
REVERT: A  147 GLN cc_start: 0.7720 (tp40) cc_final: 0.7424 (tp-100)
REVERT: B   89 ASP cc_start: 0.8947 (m-30) cc_final: 0.8537 (m-30)
REVERT: F  158 ARG cc_start: 0.8786 (mtt-85) cc_final: 0.7476 (tmt170)
REVERT: F  169 GLU cc_start: 0.8862 (OUTLIER) cc_final: 0.8431 (tp30)
REVERT: F  298 GLU cc_start: 0.8142 (tp30) cc_final: 0.7894 (tp30)
  outliers start: 18
  outliers final: 7
  residues processed: 83
  average time/residue: 0.5209
  time to fit residues: 45.2999
Evaluate side-chains
  77 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 68
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   33 ASP
Chi-restraints excluded: chain D residue   34 MET
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain F residue  169 GLU
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 69 optimal weight:    0.8980
   chunk 60 optimal weight:    3.9990
   chunk 62 optimal weight:    0.8980
   chunk 65 optimal weight:    4.9990
   chunk 12 optimal weight:    1.9990
   chunk 45 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 25 optimal weight:    5.9990
   chunk 57 optimal weight:    0.7980
   chunk 11 optimal weight:    7.9990
   chunk 15 optimal weight:    4.9990
   overall best weight:    1.5184

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

Flipped N/Q/H residues before XYZ refinement:
D   1 GLN
A 124 GLN
F  23 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3732 r_free = 0.3732 target = 0.088131 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3095 r_free = 0.3095 target = 0.057907 restraints weight = 17074.374|
|-----------------------------------------------------------------------------|
r_work (start): 0.3032 rms_B_bonded: 4.06
r_work: 0.2907 rms_B_bonded: 4.04 restraints_weight: 0.5000
r_work (final): 0.2907
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8343
moved from start:          0.3298

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6230  Z= 0.176
  Angle     :  0.647   8.146   8479  Z= 0.331
  Chirality :  0.044   0.185    946
  Planarity :  0.005   0.050   1080
  Dihedral  :  4.960  34.435    934
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  2.69 %
    Allowed  : 15.87 %
    Favored  : 81.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.15 (0.31), residues: 747
  helix:  0.90 (1.43), residues: 16
  sheet:  1.00 (0.31), residues: 300
  loop : -0.99 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG D  57 
 TYR   0.014   0.001   TYR B  94 
 PHE   0.016   0.002   PHE B 130 
 TRP   0.010   0.001   TRP B  47 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00429 ( 6219)
  covalent geometry    : angle       0.64150 ( 8452)
  SS BOND              : bond        0.00389 (    6)
  SS BOND              : angle       1.09090 (   12)
  hydrogen bonds       : bond        0.03402 (  195)
  hydrogen bonds       : angle       4.69456 (  531)
  link_NAG-ASN         : bond        0.00315 (    5)
  link_NAG-ASN         : angle       1.87454 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.237 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   73 ASP cc_start: 0.8752 (t0) cc_final: 0.8269 (t0)
REVERT: A   54 MET cc_start: 0.8805 (mmm) cc_final: 0.8179 (mpp)
REVERT: A  108 ARG cc_start: 0.8172 (tmm-80) cc_final: 0.7757 (tpt-90)
REVERT: A  147 GLN cc_start: 0.7753 (tp40) cc_final: 0.7447 (tp-100)
REVERT: B   89 ASP cc_start: 0.8984 (m-30) cc_final: 0.8581 (m-30)
REVERT: F   24 LEU cc_start: 0.8516 (OUTLIER) cc_final: 0.8111 (mp)
REVERT: F  158 ARG cc_start: 0.8790 (mtt-85) cc_final: 0.7493 (tmt170)
REVERT: F  169 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8469 (tp30)
REVERT: F  298 GLU cc_start: 0.8080 (tp30) cc_final: 0.7843 (tp30)
  outliers start: 18
  outliers final: 8
  residues processed: 86
  average time/residue: 0.5661
  time to fit residues: 50.7904
Evaluate side-chains
  76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 66
  time to evaluate  : 0.177 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   33 ASP
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue  169 GLU
Chi-restraints excluded: chain F residue  197 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    1.9990
   chunk 46 optimal weight:    9.9990
   chunk 45 optimal weight:    7.9990
   chunk 65 optimal weight:    0.5980
   chunk 64 optimal weight:    2.9990
   chunk 24 optimal weight:    0.5980
   chunk 74 optimal weight:    0.9990
   chunk 68 optimal weight:    2.9990
   chunk 52 optimal weight:    0.6980
   chunk 29 optimal weight:    1.9990
   chunk 28 optimal weight:    3.9990
   overall best weight:    0.9784

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

Flipped N/Q/H residues before XYZ refinement:
D   1 GLN
D   3 GLN
F  23 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3740 r_free = 0.3740 target = 0.088570 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3107 r_free = 0.3107 target = 0.058435 restraints weight = 16729.772|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 4.03
r_work: 0.2914 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.2914
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8333
moved from start:          0.3459

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   6230  Z= 0.139
  Angle     :  0.649  10.472   8479  Z= 0.330
  Chirality :  0.044   0.182    946
  Planarity :  0.005   0.050   1080
  Dihedral  :  4.782  33.117    934
  Min Nonbonded Distance : 2.408

Molprobity Statistics.
  All-atom Clashscore : 7.63
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.62 %
    Favored  : 80.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.09 (0.31), residues: 747
  helix:  0.83 (1.43), residues: 16
  sheet:  1.10 (0.31), residues: 298
  loop : -1.00 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG D  57 
 TYR   0.013   0.001   TYR B  94 
 PHE   0.010   0.001   PHE F 220 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 6219)
  covalent geometry    : angle       0.64496 ( 8452)
  SS BOND              : bond        0.00323 (    6)
  SS BOND              : angle       0.97655 (   12)
  hydrogen bonds       : bond        0.03085 (  195)
  hydrogen bonds       : angle       4.61151 (  531)
  link_NAG-ASN         : bond        0.00323 (    5)
  link_NAG-ASN         : angle       1.75577 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  91 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 69
  time to evaluate  : 0.157 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: D   34 MET cc_start: 0.8574 (OUTLIER) cc_final: 0.7817 (mmm)
REVERT: D   73 ASP cc_start: 0.8821 (t0) cc_final: 0.8368 (t0)
REVERT: A   54 MET cc_start: 0.8802 (mmm) cc_final: 0.8198 (mpp)
REVERT: A  105 ASP cc_start: 0.8044 (m-30) cc_final: 0.7804 (p0)
REVERT: A  108 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7825 (tpt-90)
REVERT: A  147 GLN cc_start: 0.7783 (tp40) cc_final: 0.7469 (tp-100)
REVERT: B   89 ASP cc_start: 0.8986 (m-30) cc_final: 0.8560 (m-30)
REVERT: B  125 LYS cc_start: 0.9064 (OUTLIER) cc_final: 0.8338 (tmmm)
REVERT: B  154 ASP cc_start: 0.8472 (m-30) cc_final: 0.7906 (m-30)
REVERT: F   24 LEU cc_start: 0.8527 (OUTLIER) cc_final: 0.8132 (mp)
REVERT: F  158 ARG cc_start: 0.8771 (mtt-85) cc_final: 0.7489 (tmt170)
REVERT: F  298 GLU cc_start: 0.8031 (tp30) cc_final: 0.7797 (tp30)
  outliers start: 22
  outliers final: 11
  residues processed: 84
  average time/residue: 0.5496
  time to fit residues: 48.0767
Evaluate side-chains
  82 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 67
  time to evaluate  : 0.144 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   33 ASP
Chi-restraints excluded: chain D residue   34 MET
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  183 LYS
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain B residue  130 PHE
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain F residue   24 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   chunk 39 optimal weight:    0.8980
   chunk 28 optimal weight:    5.9990
   chunk 5 optimal weight:    0.9980
   chunk 53 optimal weight:    3.9990
   chunk 61 optimal weight:    0.7980
   chunk 21 optimal weight:    3.9990
   chunk 74 optimal weight:    0.9980
   chunk 26 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0030
   overall best weight:    0.7390

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

Flipped N/Q/H residues before XYZ refinement:
** D   1 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
F  23 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3748 r_free = 0.3748 target = 0.089053 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.058881 restraints weight = 16974.102|
|-----------------------------------------------------------------------------|
r_work (start): 0.3052 rms_B_bonded: 4.06
r_work: 0.2925 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.2925
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8329
moved from start:          0.3587

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   6230  Z= 0.130
  Angle     :  0.654   9.633   8479  Z= 0.335
  Chirality :  0.045   0.181    946
  Planarity :  0.005   0.049   1080
  Dihedral  :  4.617  31.972    934
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 7.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.48 %
    Favored  : 96.52 %
  Rotamer:
    Outliers :  2.54 %
    Allowed  : 18.11 %
    Favored  : 79.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.04 (0.31), residues: 747
  helix:  1.06 (1.41), residues: 16
  sheet:  1.13 (0.31), residues: 300
  loop : -0.97 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.012   0.001   ARG D  57 
 TYR   0.013   0.001   TYR B  94 
 PHE   0.019   0.001   PHE B 130 
 TRP   0.009   0.001   TRP B  47 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6219)
  covalent geometry    : angle       0.64989 ( 8452)
  SS BOND              : bond        0.00307 (    6)
  SS BOND              : angle       1.11223 (   12)
  hydrogen bonds       : bond        0.02871 (  195)
  hydrogen bonds       : angle       4.54410 (  531)
  link_NAG-ASN         : bond        0.00346 (    5)
  link_NAG-ASN         : angle       1.68761 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 72
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: D   73 ASP cc_start: 0.8873 (t0) cc_final: 0.8505 (t0)
REVERT: D  112 GLN cc_start: 0.8317 (mp10) cc_final: 0.8047 (pm20)
REVERT: A   54 MET cc_start: 0.8817 (mmm) cc_final: 0.8206 (mpp)
REVERT: A  105 ASP cc_start: 0.8051 (m-30) cc_final: 0.7794 (p0)
REVERT: A  108 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.7854 (tpt-90)
REVERT: A  147 GLN cc_start: 0.7857 (tp40) cc_final: 0.7523 (tp-100)
REVERT: B   89 ASP cc_start: 0.8987 (m-30) cc_final: 0.8540 (m-30)
REVERT: B  125 LYS cc_start: 0.9060 (OUTLIER) cc_final: 0.8339 (tmmm)
REVERT: B  154 ASP cc_start: 0.8381 (m-30) cc_final: 0.7784 (m-30)
REVERT: F   24 LEU cc_start: 0.8508 (OUTLIER) cc_final: 0.8124 (mp)
REVERT: F  158 ARG cc_start: 0.8729 (mtt-85) cc_final: 0.7404 (tpt170)
REVERT: F  298 GLU cc_start: 0.7998 (tp30) cc_final: 0.7768 (tp30)
  outliers start: 17
  outliers final: 10
  residues processed: 85
  average time/residue: 0.6055
  time to fit residues: 53.6468
Evaluate side-chains
  81 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.227 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   33 ASP
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain B residue  194 VAL
Chi-restraints excluded: chain F residue   24 LEU
Chi-restraints excluded: chain F residue  197 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 3 optimal weight:    4.9990
   chunk 11 optimal weight:    5.9990
   chunk 52 optimal weight:    7.9990
   chunk 27 optimal weight:    0.0270
   chunk 28 optimal weight:    9.9990
   chunk 63 optimal weight:    0.0870
   chunk 60 optimal weight:    4.9990
   chunk 58 optimal weight:    4.9990
   chunk 33 optimal weight:    5.9990
   chunk 70 optimal weight:    0.9980
   chunk 48 optimal weight:    2.9990
   overall best weight:    1.8220

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

Flipped N/Q/H residues before XYZ refinement:
F  23 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3719 r_free = 0.3719 target = 0.087379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.057311 restraints weight = 17032.492|
|-----------------------------------------------------------------------------|
r_work (start): 0.3018 rms_B_bonded: 4.00
r_work: 0.2890 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2890
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8337
moved from start:          0.3713

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.042   6230  Z= 0.207
  Angle     :  0.700   9.290   8479  Z= 0.360
  Chirality :  0.045   0.187    946
  Planarity :  0.005   0.050   1080
  Dihedral  :  4.869  33.939    934
  Min Nonbonded Distance : 2.469

Molprobity Statistics.
  All-atom Clashscore : 8.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  2.40 %
    Allowed  : 18.86 %
    Favored  : 78.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.31), residues: 747
  helix:  0.82 (1.36), residues: 16
  sheet:  1.07 (0.31), residues: 300
  loop : -1.04 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.009   0.001   ARG D  57 
 TYR   0.015   0.001   TYR B  94 
 PHE   0.015   0.002   PHE A 118 
 TRP   0.011   0.001   TRP B  47 
 HIS   0.005   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00507 ( 6219)
  covalent geometry    : angle       0.69565 ( 8452)
  SS BOND              : bond        0.00421 (    6)
  SS BOND              : angle       1.26707 (   12)
  hydrogen bonds       : bond        0.03485 (  195)
  hydrogen bonds       : angle       4.74898 (  531)
  link_NAG-ASN         : bond        0.00314 (    5)
  link_NAG-ASN         : angle       1.78458 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 70
  time to evaluate  : 0.242 
Fit side-chains
   revert: symmetry clash
REVERT: D   73 ASP cc_start: 0.8862 (t0) cc_final: 0.8482 (t0)
REVERT: A   54 MET cc_start: 0.8820 (mmm) cc_final: 0.8606 (mpp)
REVERT: A  105 ASP cc_start: 0.8019 (m-30) cc_final: 0.7687 (p0)
REVERT: A  108 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.7806 (tpt-90)
REVERT: A  147 GLN cc_start: 0.7904 (tp40) cc_final: 0.7563 (tp-100)
REVERT: B   89 ASP cc_start: 0.9034 (m-30) cc_final: 0.8603 (m-30)
REVERT: B  125 LYS cc_start: 0.9069 (OUTLIER) cc_final: 0.8325 (tmmm)
REVERT: B  154 ASP cc_start: 0.8436 (m-30) cc_final: 0.7878 (m-30)
REVERT: F   24 LEU cc_start: 0.8523 (OUTLIER) cc_final: 0.8147 (mp)
REVERT: F  158 ARG cc_start: 0.8739 (mtt-85) cc_final: 0.7445 (tmt170)
REVERT: F  298 GLU cc_start: 0.7978 (tp30) cc_final: 0.7756 (tp30)
  outliers start: 16
  outliers final: 8
  residues processed: 81
  average time/residue: 0.6321
  time to fit residues: 53.3837
Evaluate side-chains
  76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.172 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   64 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  192 TYR
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain F residue   24 LEU
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 48 optimal weight:    2.9990
   chunk 22 optimal weight:    3.9990
   chunk 11 optimal weight:    6.9990
   chunk 16 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   chunk 71 optimal weight:    0.0370
   chunk 33 optimal weight:    1.9990
   chunk 70 optimal weight:    1.9990
   chunk 75 optimal weight:    0.6980
   chunk 31 optimal weight:   10.0000
   chunk 51 optimal weight:    1.9990
   overall best weight:    1.3464

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

Flipped N/Q/H residues before XYZ refinement:
F  23 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3725 r_free = 0.3725 target = 0.087628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.057495 restraints weight = 17116.318|
|-----------------------------------------------------------------------------|
r_work (start): 0.3024 rms_B_bonded: 4.03
r_work: 0.2896 rms_B_bonded: 4.05 restraints_weight: 0.5000
r_work (final): 0.2896
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8332
moved from start:          0.3809

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   6230  Z= 0.170
  Angle     :  0.695   9.706   8479  Z= 0.355
  Chirality :  0.045   0.195    946
  Planarity :  0.005   0.053   1080
  Dihedral  :  4.829  33.392    934
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 8.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  2.25 %
    Allowed  : 19.16 %
    Favored  : 78.59 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.14 (0.31), residues: 747
  helix:  0.71 (1.37), residues: 16
  sheet:  1.07 (0.31), residues: 300
  loop : -1.03 (0.29), residues: 431

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.014   0.001   ARG D  57 
 TYR   0.031   0.001   TYR A 186 
 PHE   0.012   0.001   PHE B 156 
 TRP   0.011   0.001   TRP B  47 
 HIS   0.004   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00421 ( 6219)
  covalent geometry    : angle       0.69101 ( 8452)
  SS BOND              : bond        0.00365 (    6)
  SS BOND              : angle       1.14751 (   12)
  hydrogen bonds       : bond        0.03213 (  195)
  hydrogen bonds       : angle       4.66709 (  531)
  link_NAG-ASN         : bond        0.00287 (    5)
  link_NAG-ASN         : angle       1.61327 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  83 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 68
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: D   73 ASP cc_start: 0.8852 (t0) cc_final: 0.8460 (t0)
REVERT: D  112 GLN cc_start: 0.8387 (mp10) cc_final: 0.8107 (pm20)
REVERT: A   54 MET cc_start: 0.8800 (mmm) cc_final: 0.8589 (mpp)
REVERT: A  105 ASP cc_start: 0.7970 (m-30) cc_final: 0.7685 (p0)
REVERT: A  108 ARG cc_start: 0.8236 (OUTLIER) cc_final: 0.7895 (tpt-90)
REVERT: A  147 GLN cc_start: 0.7912 (tp40) cc_final: 0.7552 (tp-100)
REVERT: A  211 ARG cc_start: 0.9059 (ptm-80) cc_final: 0.8859 (mtp-110)
REVERT: B   89 ASP cc_start: 0.9022 (m-30) cc_final: 0.8582 (m-30)
REVERT: B  125 LYS cc_start: 0.9086 (OUTLIER) cc_final: 0.8344 (tmmm)
REVERT: B  154 ASP cc_start: 0.8382 (m-30) cc_final: 0.7784 (m-30)
REVERT: F   24 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8125 (mp)
REVERT: F  158 ARG cc_start: 0.8727 (mtt-85) cc_final: 0.7425 (tpt170)
  outliers start: 15
  outliers final: 8
  residues processed: 79
  average time/residue: 0.6636
  time to fit residues: 54.5254
Evaluate side-chains
  76 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 65
  time to evaluate  : 0.239 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   53 ILE
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  192 TYR
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain F residue   24 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 70 optimal weight:    2.9990
   chunk 68 optimal weight:    5.9990
   chunk 64 optimal weight:    2.9990
   chunk 33 optimal weight:    5.9990
   chunk 2 optimal weight:    2.9990
   chunk 40 optimal weight:    2.9990
   chunk 61 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 43 optimal weight:    0.7980
   chunk 66 optimal weight:    2.9990
   overall best weight:    1.6584

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

Flipped N/Q/H residues before XYZ refinement:
F  23 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3705 r_free = 0.3705 target = 0.086899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3061 r_free = 0.3061 target = 0.056599 restraints weight = 17061.989|
|-----------------------------------------------------------------------------|
r_work (start): 0.3002 rms_B_bonded: 4.00
r_work: 0.2879 rms_B_bonded: 3.98 restraints_weight: 0.5000
r_work (final): 0.2879
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8366
moved from start:          0.3985

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.047   6230  Z= 0.198
  Angle     :  0.737   9.794   8479  Z= 0.377
  Chirality :  0.046   0.205    946
  Planarity :  0.005   0.063   1080
  Dihedral  :  4.980  34.264    934
  Min Nonbonded Distance : 2.486

Molprobity Statistics.
  All-atom Clashscore : 9.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.42 %
    Favored  : 95.58 %
  Rotamer:
    Outliers :  1.95 %
    Allowed  : 20.06 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.19 (0.31), residues: 747
  helix:  0.84 (1.42), residues: 16
  sheet:  0.89 (0.31), residues: 306
  loop : -0.98 (0.29), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.015   0.001   ARG D  57 
 TYR   0.015   0.001   TYR B  94 
 PHE   0.014   0.002   PHE F 220 
 TRP   0.010   0.001   TRP B  47 
 HIS   0.005   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00487 ( 6219)
  covalent geometry    : angle       0.73282 ( 8452)
  SS BOND              : bond        0.00432 (    6)
  SS BOND              : angle       1.28687 (   12)
  hydrogen bonds       : bond        0.03494 (  195)
  hydrogen bonds       : angle       4.76710 (  531)
  link_NAG-ASN         : bond        0.00301 (    5)
  link_NAG-ASN         : angle       1.64440 (   15)

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

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

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1494 Ramachandran restraints generated.
    747 Oldfield, 0 Emsley, 747 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.340 
Fit side-chains
   revert: symmetry clash
REVERT: D   73 ASP cc_start: 0.8839 (t0) cc_final: 0.8524 (t0)
REVERT: A   54 MET cc_start: 0.8808 (mmm) cc_final: 0.8581 (mpp)
REVERT: A  108 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7878 (tpt-90)
REVERT: A  147 GLN cc_start: 0.7970 (tp40) cc_final: 0.7582 (tp-100)
REVERT: B   89 ASP cc_start: 0.9044 (m-30) cc_final: 0.8612 (m-30)
REVERT: B  125 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8358 (tmmm)
REVERT: B  154 ASP cc_start: 0.8433 (m-30) cc_final: 0.7901 (m-30)
REVERT: F   24 LEU cc_start: 0.8507 (OUTLIER) cc_final: 0.8100 (mp)
REVERT: F  158 ARG cc_start: 0.8760 (mtt-85) cc_final: 0.7466 (tmt170)
  outliers start: 13
  outliers final: 8
  residues processed: 76
  average time/residue: 0.6290
  time to fit residues: 49.8550
Evaluate side-chains
  73 residues out of total 668 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 62
  time to evaluate  : 0.269 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue    2 VAL
Chi-restraints excluded: chain D residue   33 ASP
Chi-restraints excluded: chain D residue   93 VAL
Chi-restraints excluded: chain D residue   96 CYS
Chi-restraints excluded: chain D residue  117 THR
Chi-restraints excluded: chain A residue  108 ARG
Chi-restraints excluded: chain A residue  180 THR
Chi-restraints excluded: chain A residue  192 TYR
Chi-restraints excluded: chain B residue  125 LYS
Chi-restraints excluded: chain B residue  179 VAL
Chi-restraints excluded: chain F residue   24 LEU
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 76
   random chunks:
   chunk 17 optimal weight:    0.2980
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    8.9990
   chunk 22 optimal weight:    3.9990
   chunk 26 optimal weight:    4.9990
   chunk 37 optimal weight:    0.0170
   chunk 67 optimal weight:    0.9990
   chunk 40 optimal weight:    5.9990
   chunk 16 optimal weight:    1.9990
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   overall best weight:    0.6020

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3735 r_free = 0.3735 target = 0.088366 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.058244 restraints weight = 17038.831|
|-----------------------------------------------------------------------------|
r_work (start): 0.3041 rms_B_bonded: 4.00
r_work: 0.2920 rms_B_bonded: 3.99 restraints_weight: 0.5000
r_work (final): 0.2920
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8328
moved from start:          0.4000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   6230  Z= 0.134
  Angle     :  0.721  10.444   8479  Z= 0.366
  Chirality :  0.045   0.181    946
  Planarity :  0.005   0.087   1080
  Dihedral  :  4.699  32.373    934
  Min Nonbonded Distance : 2.504

Molprobity Statistics.
  All-atom Clashscore : 7.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.95 %
    Favored  : 97.05 %
  Rotamer:
    Outliers :  1.80 %
    Allowed  : 20.21 %
    Favored  : 77.99 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 4.65 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.07 (0.31), residues: 747
  helix:  0.82 (1.38), residues: 16
  sheet:  1.13 (0.31), residues: 298
  loop : -0.99 (0.29), residues: 433

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.021   0.001   ARG D  57 
 TYR   0.032   0.001   TYR A 186 
 PHE   0.012   0.001   PHE A 118 
 TRP   0.009   0.001   TRP A 148 
 HIS   0.003   0.001   HIS B  35 

Details of bonding type rmsd
  covalent geometry    : bond        0.00339 ( 6219)
  covalent geometry    : angle       0.71839 ( 8452)
  SS BOND              : bond        0.00276 (    6)
  SS BOND              : angle       1.03914 (   12)
  hydrogen bonds       : bond        0.02808 (  195)
  hydrogen bonds       : angle       4.59163 (  531)
  link_NAG-ASN         : bond        0.00369 (    5)
  link_NAG-ASN         : angle       1.42592 (   15)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2542.41 seconds
wall clock time: 44 minutes 2.49 seconds (2642.49 seconds total)