Starting phenix.real_space_refine
on Tue Feb  3 15:56:53 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9ntq_49761/02_2026/9ntq_49761_neut.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9ntq_49761/02_2026/9ntq_49761.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.04
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9ntq_49761/02_2026/9ntq_49761.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9ntq_49761/02_2026/9ntq_49761.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9ntq_49761/02_2026/9ntq_49761_neut.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9ntq_49761/02_2026/9ntq_49761_neut.cif"
  }
  resolution = 4.04
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.000 sd=   0.027
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: 5
    Type Number    sf(0)   Gaussians
     S      33      5.16       5
     C    2308      2.51       5
     N     611      2.21       5
     O     695      1.98       5
     H     866      0.53       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4513
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 2754
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 352, 2754
          Classifications: {'peptide': 352}
          Incomplete info: {'truncation_to_alanine': 10}
          Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 340}
          Chain breaks: 13
          Unresolved non-hydrogen bonds: 44
          Unresolved non-hydrogen angles: 49
          Unresolved non-hydrogen dihedrals: 39
          Unresolved non-hydrogen chiralities: 1
          Planarities with less than four sites: {'ARG:plan': 3, 'ASP:plan': 1}
          Unresolved non-hydrogen planarities: 18
    Chain: "B"
      Number of atoms: 1745
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 118, 1745
          Classifications: {'peptide': 118}
          Modifications used: {'COO': 1, 'NH3': 1}
          Link IDs: {'PTRANS': 5, 'TRANS': 112}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.14, per 1000 atoms: 0.25
  Number of scatterers: 4513
  At special positions: 0
  Unit cell: (53.1, 80.535, 125.67, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     S      33     16.00
     O     695      8.00
     N     611      7.00
     C    2308      6.00
     H     866      1.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=8, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  35 " - pdb=" SG  CYS A  72 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  65 " - pdb=" SG  CYS A 262 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  73 " - pdb=" SG  CYS A 265 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 197 " - pdb=" SG  CYS A 349 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 252 " - pdb=" SG  CYS A 285 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 274 " - pdb=" SG  CYS A 422 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 278 " - pdb=" SG  CYS A 410 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B 103 " distance=2.02

  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=1, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 501 " - " ASN A 124 "
  Number of additional bonds: simple=1, symmetry=0
  Coordination:
  Other bonds:
  Time building additional restraints: 0.40
  Conformation dependent library (CDL) restraints added in 258.3 milliseconds
  

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  870

  Finding SS restraints...
    Secondary structure from input PDB file:
      27 helices and 3 sheets defined
      61.7% alpha, 10.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 74 through 114
      removed outlier: 4.756A  pdb=" N   GLU A  99 " --> pdb=" O   SER A  95 " (cutoff:3.500A)
      removed outlier: 5.268A  pdb=" N   LEU A 100 " --> pdb=" O   ALA A  96 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 115 through 134
    Processing helix  chain 'A' and resid 135 through 138
    Processing helix  chain 'A' and resid 139 through 157
      removed outlier: 3.601A  pdb=" N   GLY A 146 " --> pdb=" O   PHE A 142 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 162 through 182
      removed outlier: 3.567A  pdb=" N   MET A 166 " --> pdb=" O   ASN A 162 " (cutoff:3.500A)
      Proline residue:  A 176  - end of helix
    Processing helix  chain 'A' and resid 194 through 205
      removed outlier: 3.554A  pdb=" N   LEU A 198 " --> pdb=" O   ILE A 194 " (cutoff:3.500A)
      removed outlier: 4.174A  pdb=" N   ARG A 203 " --> pdb=" O   ARG A 199 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 210 through 227
      removed outlier: 3.794A  pdb=" N   SER A 222 " --> pdb=" O   GLN A 218 " (cutoff:3.500A)
      removed outlier: 3.528A  pdb=" N   VAL A 225 " --> pdb=" O   LYS A 221 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 231 through 244
      removed outlier: 4.014A  pdb=" N   ASP A 244 " --> pdb=" O   ILE A 240 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 249 through 261
    Processing helix  chain 'A' and resid 261 through 266
      removed outlier: 3.822A  pdb=" N   CYS A 265 " --> pdb=" O   TYR A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 274 through 286
    Processing helix  chain 'A' and resid 286 through 291
      removed outlier: 4.050A  pdb=" N   GLU A 291 " --> pdb=" O   ALA A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 291 through 298
      removed outlier: 4.528A  pdb=" N   TYR A 295 " --> pdb=" O   GLU A 291 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 301 through 307
    Processing helix  chain 'A' and resid 316 through 322
    Processing helix  chain 'A' and resid 322 through 329
    Processing helix  chain 'A' and resid 332 through 336
    Processing helix  chain 'A' and resid 337 through 349
      removed outlier: 3.795A  pdb=" N   THR A 343 " --> pdb=" O   GLY A 339 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 384 through 397
      removed outlier: 3.550A  pdb=" N   SER A 397 " --> pdb=" O   GLN A 393 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 404 through 412
    Processing helix  chain 'A' and resid 457 through 466
    Processing helix  chain 'A' and resid 468 through 470
      No H-bonds generated for 'chain 'A' and resid 468 through 470'
    Processing helix  chain 'B' and resid 26 through 27
      No H-bonds generated for 'chain 'B' and resid 26 through 27'
    Processing helix  chain 'B' and resid 29 through 31
      No H-bonds generated for 'chain 'B' and resid 29 through 31'
    Processing helix  chain 'B' and resid 32 through 36
    Processing helix  chain 'B' and resid 69 through 72
    Processing helix  chain 'B' and resid 94 through 98
    Processing sheet with id=AA1, first strand: chain 'A' and resid 420 through 423
      removed outlier: 6.997A  pdb=" N   THR A 420 " --> pdb=" O   ARG A 431 " (cutoff:3.500A)
      removed outlier: 6.627A  pdb=" N   ARG A 431 " --> pdb=" O   THR A 420 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'B' and resid 3 through 7
    Processing sheet with id=AA3, first strand: chain 'B' and resid 10 through 12
      removed outlier: 6.225A  pdb=" N   GLY B  10 " --> pdb=" O   THR B 116 " (cutoff:3.500A)
      removed outlier: 5.794A  pdb=" N   ARG B  42 " --> pdb=" O   LEU B  51 " (cutoff:3.500A)
      removed outlier: 5.350A  pdb=" N   LEU B  51 " --> pdb=" O   ARG B  42 " (cutoff:3.500A)

    209 hydrogen bonds defined for protein.
    591 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: 0.78

  Time building geometry restraints manager: 0.55 seconds

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

  Histogram of bond lengths:
        0.96 -     1.20: 866
        1.20 -     1.45: 1560
        1.45 -     1.69: 2089
        1.69 -     1.94: 50
        1.94 -     2.18: 1
  Bond restraints: 4566
  Sorted by residual:
  bond pdb=" C   ALA A 114 "
       pdb=" N   PHE A 115 "
    ideal  model  delta    sigma   weight residual
    1.332  2.184 -0.851 1.40e-02 5.10e+03 3.70e+03
  bond pdb=" N   GLY B 112 "
       pdb=" H   GLY B 112 "
    ideal  model  delta    sigma   weight residual
    0.860  1.012 -0.152 2.00e-02 2.50e+03 5.79e+01
  bond pdb=" NE2 GLN B 111 "
       pdb="HE22 GLN B 111 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.74e+01
  bond pdb=" N   ASP B  97 "
       pdb=" H   ASP B  97 "
    ideal  model  delta    sigma   weight residual
    0.860  1.011 -0.151 2.00e-02 2.50e+03 5.73e+01
  bond pdb=" CE3 TRP B 109 "
       pdb=" HE3 TRP B 109 "
    ideal  model  delta    sigma   weight residual
    0.930  1.081 -0.151 2.00e-02 2.50e+03 5.72e+01
  ... (remaining 4561 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -    15.74: 6944
       15.74 -    31.49: 0
       31.49 -    47.23: 2
       47.23 -    62.98: 0
       62.98 -    78.72: 1
  Bond angle restraints: 6947
  Sorted by residual:
  angle pdb=" O   ALA A 114 "
        pdb=" C   ALA A 114 "
        pdb=" N   PHE A 115 "
      ideal   model   delta    sigma   weight residual
     122.59   43.87   78.72 1.33e+00 5.65e-01 3.50e+03
  angle pdb=" CA  ALA A 114 "
        pdb=" C   ALA A 114 "
        pdb=" N   PHE A 115 "
      ideal   model   delta    sigma   weight residual
     116.84  151.19  -34.35 1.71e+00 3.42e-01 4.04e+02
  angle pdb=" C   ALA A 114 "
        pdb=" N   PHE A 115 "
        pdb=" CA  PHE A 115 "
      ideal   model   delta    sigma   weight residual
     121.54  155.87  -34.33 1.91e+00 2.74e-01 3.23e+02
  angle pdb=" OE1 GLN B   3 "
        pdb=" CD  GLN B   3 "
        pdb=" NE2 GLN B   3 "
      ideal   model   delta    sigma   weight residual
     122.60  118.30    4.30 1.00e+00 1.00e+00 1.85e+01
  angle pdb=" OE1 GLN B 111 "
        pdb=" CD  GLN B 111 "
        pdb=" NE2 GLN B 111 "
      ideal   model   delta    sigma   weight residual
     122.60  118.60    4.00 1.00e+00 1.00e+00 1.60e+01
  ... (remaining 6942 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.54: 2215
       17.54 -    35.08: 227
       35.08 -    52.62: 71
       52.62 -    70.16: 33
       70.16 -    87.70: 8
  Dihedral angle restraints: 2554
    sinusoidal: 1165
      harmonic: 1389
  Sorted by residual:
  dihedral pdb=" CA  GLN B   3 "
           pdb=" C   GLN B   3 "
           pdb=" N   LEU B   4 "
           pdb=" CA  LEU B   4 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.11   23.89     0      5.00e+00 4.00e-02 2.28e+01
  dihedral pdb=" CA  ALA B  56 "
           pdb=" C   ALA B  56 "
           pdb=" N   PRO B  57 "
           pdb=" CA  PRO B  57 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.76   22.24     0      5.00e+00 4.00e-02 1.98e+01
  dihedral pdb=" CA  PHE B 102 "
           pdb=" C   PHE B 102 "
           pdb=" N   CYS B 103 "
           pdb=" CA  CYS B 103 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  161.07   18.93     0      5.00e+00 4.00e-02 1.43e+01
  ... (remaining 2551 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.052: 426
       0.052 -    0.103: 107
       0.103 -    0.155: 34
       0.155 -    0.207: 7
       0.207 -    0.259: 2
  Chirality restraints: 576
  Sorted by residual:
  chirality pdb=" CA  ASP B  97 "
            pdb=" N   ASP B  97 "
            pdb=" C   ASP B  97 "
            pdb=" CB  ASP B  97 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.25    0.26 2.00e-01 2.50e+01 1.67e+00
  chirality pdb=" CA  SER B 119 "
            pdb=" N   SER B 119 "
            pdb=" C   SER B 119 "
            pdb=" CB  SER B 119 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.29    0.23 2.00e-01 2.50e+01 1.27e+00
  chirality pdb=" CA  VAL B   2 "
            pdb=" N   VAL B   2 "
            pdb=" C   VAL B   2 "
            pdb=" CB  VAL B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.63   -0.19 2.00e-01 2.50e+01 9.36e-01
  ... (remaining 573 not shown)

  Planarity restraints: 743
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 114 "    0.175 2.00e-02 2.50e+03   1.75e-01 3.05e+02
        pdb=" C   ALA A 114 "   -0.266 2.00e-02 2.50e+03
        pdb=" O   ALA A 114 "   -0.046 2.00e-02 2.50e+03
        pdb=" N   PHE A 115 "    0.136 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  54 "    0.122 9.50e-02 1.11e+02   1.05e-01 2.13e+02
        pdb=" NE  ARG B  54 "   -0.081 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  54 "   -0.086 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  54 "   -0.086 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  54 "   -0.056 2.00e-02 2.50e+03
        pdb="HH11 ARG B  54 "    0.154 2.00e-02 2.50e+03
        pdb="HH12 ARG B  54 "    0.021 2.00e-02 2.50e+03
        pdb="HH21 ARG B  54 "   -0.054 2.00e-02 2.50e+03
        pdb="HH22 ARG B  54 "    0.181 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CD  ARG B  79 "    0.297 9.50e-02 1.11e+02   1.20e-01 1.15e+02
        pdb=" NE  ARG B  79 "    0.079 2.00e-02 2.50e+03
        pdb=" CZ  ARG B  79 "    0.037 2.00e-02 2.50e+03
        pdb=" NH1 ARG B  79 "    0.017 2.00e-02 2.50e+03
        pdb=" NH2 ARG B  79 "    0.018 2.00e-02 2.50e+03
        pdb="HH11 ARG B  79 "    0.037 2.00e-02 2.50e+03
        pdb="HH12 ARG B  79 "   -0.122 2.00e-02 2.50e+03
        pdb="HH21 ARG B  79 "   -0.125 2.00e-02 2.50e+03
        pdb="HH22 ARG B  79 "    0.045 2.00e-02 2.50e+03
  ... (remaining 740 not shown)

  Histogram of nonbonded interaction distances:
        1.32 -     1.97: 43
        1.97 -     2.63: 1999
        2.63 -     3.29: 8345
        3.29 -     3.94: 12422
        3.94 -     4.60: 18125
  Nonbonded interactions: 40934
  Sorted by model distance:
  nonbonded pdb=" NE2 GLN A 218 "
            pdb=" HA  VAL B 107 "
     model   vdw
     1.317 2.216
  nonbonded pdb=" CD2 LEU A 214 "
            pdb="HG11 VAL B 107 "
     model   vdw
     1.647 2.920
  nonbonded pdb=" HG  SER B  21 "
            pdb=" OD1 ASP B  87 "
     model   vdw
     1.648 2.450
  nonbonded pdb=" NE2 GLN A 218 "
            pdb="HG12 VAL B 107 "
     model   vdw
     1.655 2.216
  nonbonded pdb="HH21 ARG B  19 "
            pdb=" OD2 ASP B  87 "
     model   vdw
     1.675 2.450
  ... (remaining 40929 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== WARNING! ============

  No NCS relation were found !!!

================================

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.240
  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:             0.040
  Extract box with map and model:          0.100
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.450
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.320
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   12.210
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.3974
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      :  0.016   0.851   3710  Z= 1.168
  Angle     :  1.627  78.721   5005  Z= 1.081
  Chirality :  0.054   0.259    576
  Planarity :  0.011   0.175    631
  Dihedral  : 16.417  87.705   1361
  Min Nonbonded Distance : 2.296

Molprobity Statistics.
  All-atom Clashscore : 8.04
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.20 %
    Favored  : 96.80 %
  Rotamer:
    Outliers :  1.24 %
    Allowed  : 20.10 %
    Favored  : 78.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.43 (0.38), residues: 438
  helix: -0.23 (0.30), residues: 238
  sheet: -0.02 (0.63), residues: 64
  loop : -0.14 (0.56), residues: 136

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.011   0.002   ARG B  74 
 TYR   0.037   0.003   TYR B 101 
 PHE   0.058   0.005   PHE B  29 
 TRP   0.033   0.008   TRP B  40 
 HIS   0.013   0.003   HIS A 245 

Details of bonding type rmsd
  covalent geometry    : bond        0.01549 ( 3700)
  covalent geometry    : angle       1.62909 ( 4986)
  SS BOND              : bond        0.00454 (    8)
  SS BOND              : angle       1.07240 (   16)
  hydrogen bonds       : bond        0.17631 (  209)
  hydrogen bonds       : angle       6.89570 (  591)
  Misc. bond           : bond        0.29673 (    1)
  link_NAG-ASN         : bond        0.00401 (    1)
  link_NAG-ASN         : angle       1.07401 (    3)

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

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

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  876 Ramachandran restraints generated.
    438 Oldfield, 0 Emsley, 438 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  119 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 114
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 5
  outliers final: 0
  residues processed: 119
  average time/residue: 0.1059
  time to fit residues: 15.0501
Evaluate side-chains
  62 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 24 optimal weight:    5.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    8.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    7.9990
   chunk 30 optimal weight:    0.4980
   chunk 22 optimal weight:    5.9990
   chunk 37 optimal weight:    1.9990
   overall best weight:    1.0584

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 283 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4439 r_free = 0.4439 target = 0.100226 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4227 r_free = 0.4227 target = 0.084977 restraints weight = 42186.676|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.085733 restraints weight = 35273.987|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4256 r_free = 0.4256 target = 0.086708 restraints weight = 32957.246|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.4263 r_free = 0.4263 target = 0.087281 restraints weight = 29083.693|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.4268 r_free = 0.4268 target = 0.087599 restraints weight = 26869.830|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5422
moved from start:          0.5220

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.044   3710  Z= 0.148
  Angle     :  0.603   6.625   5005  Z= 0.315
  Chirality :  0.039   0.137    576
  Planarity :  0.005   0.050    631
  Dihedral  :  4.836  20.761    512
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 35.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.18 %
    Favored  : 96.82 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.36), residues: 440
  helix:  1.41 (0.30), residues: 243
  sheet:  0.69 (0.63), residues: 57
  loop : -0.41 (0.47), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  86 
 TYR   0.015   0.002   TYR A 432 
 PHE   0.019   0.002   PHE A 324 
 TRP   0.012   0.002   TRP A 296 
 HIS   0.005   0.002   HIS A 121 

Details of bonding type rmsd
  covalent geometry    : bond        0.00322 ( 3700)
  covalent geometry    : angle       0.59325 ( 4986)
  SS BOND              : bond        0.00301 (    8)
  SS BOND              : angle       1.34021 (   16)
  hydrogen bonds       : bond        0.03912 (  209)
  hydrogen bonds       : angle       4.42476 (  591)
  Misc. bond           : bond        0.00139 (    1)
  link_NAG-ASN         : bond        0.01028 (    1)
  link_NAG-ASN         : angle       3.41290 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  77 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 77
  time to evaluate  : 0.102 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 GLU cc_start: 0.8077 (pt0) cc_final: 0.7761 (pt0)
REVERT: A  152 VAL cc_start: 0.8985 (t) cc_final: 0.8743 (t)
REVERT: A  216 MET cc_start: 0.6417 (ptt) cc_final: 0.5499 (ptt)
REVERT: A  255 MET cc_start: 0.8684 (mmp) cc_final: 0.8459 (mmp)
REVERT: A  269 MET cc_start: 0.5830 (mpp) cc_final: 0.4869 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 77
  average time/residue: 0.0823
  time to fit residues: 7.7066
Evaluate side-chains
  59 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    6.9990
   chunk 41 optimal weight:    7.9990
   chunk 38 optimal weight:    4.9990
   chunk 6 optimal weight:    0.9990
   chunk 19 optimal weight:    0.5980
   chunk 8 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    0.1980
   chunk 4 optimal weight:    6.9990
   chunk 21 optimal weight:    4.9990
   overall best weight:    0.6982

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 393 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4417 r_free = 0.4417 target = 0.097838 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.4216 r_free = 0.4216 target = 0.084052 restraints weight = 45704.792|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.4238 r_free = 0.4238 target = 0.085341 restraints weight = 36810.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4254 r_free = 0.4254 target = 0.086215 restraints weight = 31292.057|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.4266 r_free = 0.4266 target = 0.086897 restraints weight = 27718.838|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4275 r_free = 0.4275 target = 0.087429 restraints weight = 25057.426|
|-----------------------------------------------------------------------------|
r_work (final): 0.4252
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5496
moved from start:          0.6219

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.037   3710  Z= 0.101
  Angle     :  0.457   5.287   5005  Z= 0.246
  Chirality :  0.036   0.138    576
  Planarity :  0.004   0.038    631
  Dihedral  :  4.013  17.206    512
  Min Nonbonded Distance : 2.464

Molprobity Statistics.
  All-atom Clashscore : 36.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.73 %
    Favored  : 97.27 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.24 %
    Favored  : 98.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  2.10 (0.39), residues: 440
  helix:  2.36 (0.32), residues: 244
  sheet:  1.10 (0.65), residues: 57
  loop : -0.22 (0.52), residues: 139

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  86 
 TYR   0.011   0.001   TYR A 408 
 PHE   0.017   0.002   PHE A 324 
 TRP   0.007   0.001   TRP A 296 
 HIS   0.003   0.001   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00215 ( 3700)
  covalent geometry    : angle       0.45210 ( 4986)
  SS BOND              : bond        0.00522 (    8)
  SS BOND              : angle       0.89758 (   16)
  hydrogen bonds       : bond        0.03291 (  209)
  hydrogen bonds       : angle       3.92860 (  591)
  Misc. bond           : bond        0.00088 (    1)
  link_NAG-ASN         : bond        0.00547 (    1)
  link_NAG-ASN         : angle       2.13385 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  72 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 72
  time to evaluate  : 0.097 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 GLU cc_start: 0.7917 (pt0) cc_final: 0.7614 (pt0)
REVERT: A  216 MET cc_start: 0.6715 (ptt) cc_final: 0.5754 (ptt)
REVERT: A  255 MET cc_start: 0.8803 (mmp) cc_final: 0.8545 (mmp)
REVERT: A  257 THR cc_start: 0.8845 (p) cc_final: 0.8549 (p)
REVERT: A  269 MET cc_start: 0.6058 (mpp) cc_final: 0.5031 (mmp)
REVERT: B   41 TYR cc_start: 0.7053 (m-80) cc_final: 0.6470 (m-80)
  outliers start: 0
  outliers final: 0
  residues processed: 72
  average time/residue: 0.0735
  time to fit residues: 6.6558
Evaluate side-chains
  60 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 60
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 42 optimal weight:    4.9990
   chunk 26 optimal weight:    2.9990
   chunk 35 optimal weight:    4.9990
   chunk 43 optimal weight:    0.7980
   chunk 21 optimal weight:    4.9990
   chunk 10 optimal weight:    4.9990
   chunk 44 optimal weight:    3.9990
   chunk 15 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 25 optimal weight:    0.9990
   chunk 6 optimal weight:    6.9990
   overall best weight:    2.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 106 GLN
** A 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 184 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 = 0.4198 r_free = 0.4198 target = 0.084283 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3974 r_free = 0.3974 target = 0.070665 restraints weight = 58363.596|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 33)----------------|
| r_work = 0.4003 r_free = 0.4003 target = 0.072205 restraints weight = 44003.885|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.073412 restraints weight = 35345.201|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4042 r_free = 0.4042 target = 0.074310 restraints weight = 29606.457|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.074951 restraints weight = 25657.824|
|-----------------------------------------------------------------------------|
r_work (final): 0.4037
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5443
moved from start:          0.9328

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.070   3710  Z= 0.236
  Angle     :  0.814  11.243   5005  Z= 0.428
  Chirality :  0.046   0.210    576
  Planarity :  0.006   0.067    631
  Dihedral  :  6.092  21.368    512
  Min Nonbonded Distance : 2.371

Molprobity Statistics.
  All-atom Clashscore : 67.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.77 %
    Favored  : 95.23 %
  Rotamer:
    Outliers :  0.25 %
    Allowed  :  2.98 %
    Favored  : 96.77 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.37 (0.37), residues: 440
  helix: -0.09 (0.30), residues: 244
  sheet:  1.46 (0.63), residues: 62
  loop : -1.17 (0.48), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG B  42 
 TYR   0.026   0.003   TYR A 277 
 PHE   0.024   0.003   PHE A 324 
 TRP   0.013   0.003   TRP B 109 
 HIS   0.014   0.003   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00495 ( 3700)
  covalent geometry    : angle       0.80302 ( 4986)
  SS BOND              : bond        0.00770 (    8)
  SS BOND              : angle       1.55735 (   16)
  hydrogen bonds       : bond        0.05306 (  209)
  hydrogen bonds       : angle       5.04208 (  591)
  Misc. bond           : bond        0.00307 (    1)
  link_NAG-ASN         : bond        0.01526 (    1)
  link_NAG-ASN         : angle       4.55811 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 57
  time to evaluate  : 0.230 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  257 THR cc_start: 0.9119 (p) cc_final: 0.8693 (p)
REVERT: A  269 MET cc_start: 0.6870 (mpp) cc_final: 0.6610 (mmm)
REVERT: A  282 MET cc_start: 0.6198 (mtt) cc_final: 0.5985 (mtt)
REVERT: B   40 TRP cc_start: 0.8510 (m100) cc_final: 0.7883 (m100)
  outliers start: 1
  outliers final: 0
  residues processed: 58
  average time/residue: 0.0892
  time to fit residues: 6.4855
Evaluate side-chains
  45 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 35 optimal weight:    4.9990
   chunk 23 optimal weight:    2.9990
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 5 optimal weight:    0.8980
   chunk 39 optimal weight:    0.7980
   chunk 32 optimal weight:    0.8980
   chunk 21 optimal weight:   20.0000
   chunk 34 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9980
   chunk 27 optimal weight:    0.8980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** A 132 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 393 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4249 r_free = 0.4249 target = 0.086433 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.076159 restraints weight = 56686.035|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 46)----------------|
| r_work = 0.4068 r_free = 0.4068 target = 0.077530 restraints weight = 42073.938|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4087 r_free = 0.4087 target = 0.078501 restraints weight = 33454.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4102 r_free = 0.4102 target = 0.079260 restraints weight = 27812.833|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.079796 restraints weight = 23820.951|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5811
moved from start:          0.9390

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.032   3710  Z= 0.117
  Angle     :  0.521   7.582   5005  Z= 0.279
  Chirality :  0.037   0.167    576
  Planarity :  0.003   0.035    631
  Dihedral  :  4.660  17.944    512
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 54.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.99 %
    Favored  : 98.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.79 (0.39), residues: 440
  helix:  1.06 (0.32), residues: 244
  sheet:  1.65 (0.63), residues: 62
  loop : -0.97 (0.52), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.008   0.001   ARG A 297 
 TYR   0.012   0.001   TYR A 277 
 PHE   0.014   0.002   PHE A 324 
 TRP   0.009   0.001   TRP B  40 
 HIS   0.005   0.001   HIS A  36 

Details of bonding type rmsd
  covalent geometry    : bond        0.00249 ( 3700)
  covalent geometry    : angle       0.51547 ( 4986)
  SS BOND              : bond        0.00315 (    8)
  SS BOND              : angle       1.09059 (   16)
  hydrogen bonds       : bond        0.03704 (  209)
  hydrogen bonds       : angle       4.35557 (  591)
  Misc. bond           : bond        0.00089 (    1)
  link_NAG-ASN         : bond        0.00579 (    1)
  link_NAG-ASN         : angle       2.34099 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 59
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  118 VAL cc_start: 0.8329 (t) cc_final: 0.7955 (t)
REVERT: A  143 GLU cc_start: 0.7919 (pt0) cc_final: 0.7538 (pt0)
REVERT: A  216 MET cc_start: 0.6991 (ptt) cc_final: 0.5836 (ptt)
REVERT: A  255 MET cc_start: 0.9126 (mmp) cc_final: 0.8702 (mmp)
REVERT: A  269 MET cc_start: 0.6818 (mpp) cc_final: 0.6101 (mmt)
  outliers start: 0
  outliers final: 0
  residues processed: 59
  average time/residue: 0.0916
  time to fit residues: 6.8254
Evaluate side-chains
  49 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 2 optimal weight:    0.8980
   chunk 7 optimal weight:    2.9990
   chunk 20 optimal weight:    0.9980
   chunk 14 optimal weight:    5.9990
   chunk 13 optimal weight:    0.0060
   chunk 16 optimal weight:    0.8980
   chunk 37 optimal weight:    5.9990
   chunk 25 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   chunk 44 optimal weight:    1.9990
   chunk 22 optimal weight:    5.9990
   overall best weight:    0.7598

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

Flipped N/Q/H residues before XYZ refinement:
** A  36 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
A 132 ASN
A 181 GLN
A 393 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4260 r_free = 0.4260 target = 0.086151 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.075868 restraints weight = 57503.452|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.4073 r_free = 0.4073 target = 0.077226 restraints weight = 42569.691|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.4093 r_free = 0.4093 target = 0.078265 restraints weight = 33586.111|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 39)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.079016 restraints weight = 27579.572|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.4118 r_free = 0.4118 target = 0.079612 restraints weight = 23542.157|
|-----------------------------------------------------------------------------|
r_work (final): 0.4104
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5784
moved from start:          0.9747

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   3710  Z= 0.103
  Angle     :  0.478   6.557   5005  Z= 0.256
  Chirality :  0.037   0.163    576
  Planarity :  0.003   0.028    631
  Dihedral  :  4.226  16.341    512
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 52.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.64 %
    Favored  : 96.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.99 %
    Favored  : 99.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.44 (0.40), residues: 440
  helix:  1.80 (0.33), residues: 244
  sheet:  1.54 (0.63), residues: 62
  loop : -0.92 (0.53), residues: 134

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 297 
 TYR   0.008   0.001   TYR B  63 
 PHE   0.014   0.002   PHE A 149 
 TRP   0.023   0.002   TRP B  40 
 HIS   0.001   0.000   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00209 ( 3700)
  covalent geometry    : angle       0.47106 ( 4986)
  SS BOND              : bond        0.00562 (    8)
  SS BOND              : angle       1.25761 (   16)
  hydrogen bonds       : bond        0.03234 (  209)
  hydrogen bonds       : angle       4.04989 (  591)
  Misc. bond           : bond        0.00044 (    1)
  link_NAG-ASN         : bond        0.00495 (    1)
  link_NAG-ASN         : angle       2.13846 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.154 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 GLU cc_start: 0.7862 (pt0) cc_final: 0.7568 (pt0)
REVERT: A  216 MET cc_start: 0.7043 (ptt) cc_final: 0.6013 (ptt)
REVERT: A  255 MET cc_start: 0.9137 (mmp) cc_final: 0.8734 (mmp)
REVERT: A  269 MET cc_start: 0.6784 (mpp) cc_final: 0.5981 (mmp)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0877
  time to fit residues: 6.1622
Evaluate side-chains
  49 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 49
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 41 optimal weight:    0.6980
   chunk 3 optimal weight:    0.8980
   chunk 32 optimal weight:    4.9990
   chunk 30 optimal weight:    1.9990
   chunk 44 optimal weight:    3.9990
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:    1.9990
   chunk 23 optimal weight:    1.9990
   chunk 35 optimal weight:    4.9990
   overall best weight:    1.5186

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

Flipped N/Q/H residues before XYZ refinement:
A 181 GLN
A 279 ASN
A 393 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4164 r_free = 0.4164 target = 0.080608 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.071038 restraints weight = 58883.206|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3973 r_free = 0.3973 target = 0.072337 restraints weight = 42754.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3991 r_free = 0.3991 target = 0.073243 restraints weight = 33360.809|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 40)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.073938 restraints weight = 27479.368|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4016 r_free = 0.4016 target = 0.074429 restraints weight = 23583.610|
|-----------------------------------------------------------------------------|
r_work (final): 0.4000
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5960
moved from start:          1.0972

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3710  Z= 0.162
  Angle     :  0.647   7.704   5005  Z= 0.342
  Chirality :  0.041   0.223    576
  Planarity :  0.004   0.036    631
  Dihedral  :  5.204  20.655    512
  Min Nonbonded Distance : 2.360

Molprobity Statistics.
  All-atom Clashscore : 69.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.14 %
    Favored  : 93.86 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.74 %
    Favored  : 98.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.39 (0.39), residues: 440
  helix:  0.77 (0.32), residues: 245
  sheet:  1.50 (0.68), residues: 55
  loop : -1.10 (0.51), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A  86 
 TYR   0.024   0.002   TYR A 277 
 PHE   0.017   0.002   PHE A 324 
 TRP   0.018   0.003   TRP B  40 
 HIS   0.003   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00338 ( 3700)
  covalent geometry    : angle       0.63656 ( 4986)
  SS BOND              : bond        0.00631 (    8)
  SS BOND              : angle       1.61133 (   16)
  hydrogen bonds       : bond        0.04322 (  209)
  hydrogen bonds       : angle       4.59759 (  591)
  Misc. bond           : bond        0.00064 (    1)
  link_NAG-ASN         : bond        0.01273 (    1)
  link_NAG-ASN         : angle       3.17737 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 52
  time to evaluate  : 0.108 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 GLU cc_start: 0.7851 (pt0) cc_final: 0.7426 (pt0)
REVERT: A  255 MET cc_start: 0.9213 (mmp) cc_final: 0.8833 (mmp)
REVERT: A  269 MET cc_start: 0.6707 (mpp) cc_final: 0.5971 (mmt)
REVERT: A  289 VAL cc_start: 0.8678 (t) cc_final: 0.8430 (t)
REVERT: A  316 MET cc_start: 0.7707 (ppp) cc_final: 0.7447 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 52
  average time/residue: 0.0614
  time to fit residues: 4.1430
Evaluate side-chains
  46 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 10 optimal weight:    5.9990
   chunk 8 optimal weight:    8.9990
   chunk 19 optimal weight:    4.9990
   chunk 3 optimal weight:    0.9980
   chunk 36 optimal weight:    0.3980
   chunk 44 optimal weight:    4.9990
   chunk 20 optimal weight:    0.3980
   chunk 24 optimal weight:   10.0000
   chunk 16 optimal weight:    0.9990
   chunk 35 optimal weight:    3.9990
   chunk 45 optimal weight:    0.9980
   overall best weight:    0.7582

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

Flipped N/Q/H residues before XYZ refinement:
A 279 ASN
A 393 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4209 r_free = 0.4209 target = 0.083049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3985 r_free = 0.3985 target = 0.072923 restraints weight = 57894.718|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4011 r_free = 0.4011 target = 0.074247 restraints weight = 43469.857|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.075161 restraints weight = 34445.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.075859 restraints weight = 28671.769|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.4055 r_free = 0.4055 target = 0.076421 restraints weight = 24820.063|
|-----------------------------------------------------------------------------|
r_work (final): 0.4040
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5874
moved from start:          1.0975

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   3710  Z= 0.104
  Angle     :  0.486   5.630   5005  Z= 0.262
  Chirality :  0.037   0.153    576
  Planarity :  0.003   0.026    631
  Dihedral  :  4.418  17.610    512
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 58.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.45 %
    Favored  : 94.55 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.74 %
    Favored  : 99.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.07 (0.40), residues: 440
  helix:  1.42 (0.33), residues: 245
  sheet:  1.52 (0.64), residues: 55
  loop : -0.86 (0.54), residues: 140

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 297 
 TYR   0.010   0.001   TYR A 277 
 PHE   0.014   0.002   PHE A 324 
 TRP   0.015   0.002   TRP B  40 
 HIS   0.002   0.001   HIS A 412 

Details of bonding type rmsd
  covalent geometry    : bond        0.00216 ( 3700)
  covalent geometry    : angle       0.47876 ( 4986)
  SS BOND              : bond        0.00377 (    8)
  SS BOND              : angle       1.37089 (   16)
  hydrogen bonds       : bond        0.03321 (  209)
  hydrogen bonds       : angle       4.24010 (  591)
  Misc. bond           : bond        0.00012 (    1)
  link_NAG-ASN         : bond        0.00444 (    1)
  link_NAG-ASN         : angle       1.81290 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 56
  time to evaluate  : 0.136 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 GLU cc_start: 0.8086 (pt0) cc_final: 0.7865 (pt0)
REVERT: A  255 MET cc_start: 0.9198 (mmp) cc_final: 0.8862 (mmp)
REVERT: A  269 MET cc_start: 0.6864 (mpp) cc_final: 0.6123 (mmt)
REVERT: A  289 VAL cc_start: 0.8442 (t) cc_final: 0.8088 (p)
REVERT: A  316 MET cc_start: 0.7579 (ppp) cc_final: 0.7370 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 56
  average time/residue: 0.0624
  time to fit residues: 4.5848
Evaluate side-chains
  46 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 32 optimal weight:    7.9990
   chunk 6 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 38 optimal weight:    4.9990
   chunk 21 optimal weight:    0.8980
   chunk 20 optimal weight:    0.2980
   chunk 39 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 8 optimal weight:    8.9990
   chunk 45 optimal weight:    0.6980
   chunk 0 optimal weight:    3.9990
   overall best weight:    0.7780

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

Flipped N/Q/H residues before XYZ refinement:
A 393 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4211 r_free = 0.4211 target = 0.083237 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3989 r_free = 0.3989 target = 0.073222 restraints weight = 56169.181|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4015 r_free = 0.4015 target = 0.074455 restraints weight = 42743.968|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.075357 restraints weight = 34156.777|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.076018 restraints weight = 28673.854|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.4058 r_free = 0.4058 target = 0.076543 restraints weight = 24914.261|
|-----------------------------------------------------------------------------|
r_work (final): 0.4043
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5891
moved from start:          1.1236

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.026   3710  Z= 0.103
  Angle     :  0.495   7.012   5005  Z= 0.261
  Chirality :  0.037   0.153    576
  Planarity :  0.003   0.028    631
  Dihedral  :  4.254  17.342    512
  Min Nonbonded Distance : 2.435

Molprobity Statistics.
  All-atom Clashscore : 60.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.68 %
    Favored  : 94.32 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.27 (0.41), residues: 440
  helix:  1.69 (0.33), residues: 244
  sheet:  1.47 (0.64), residues: 55
  loop : -0.93 (0.54), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 297 
 TYR   0.011   0.001   TYR A 277 
 PHE   0.013   0.002   PHE A 324 
 TRP   0.013   0.002   TRP A 296 
 HIS   0.002   0.000   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00220 ( 3700)
  covalent geometry    : angle       0.48870 ( 4986)
  SS BOND              : bond        0.00377 (    8)
  SS BOND              : angle       1.23940 (   16)
  hydrogen bonds       : bond        0.03242 (  209)
  hydrogen bonds       : angle       4.09042 (  591)
  Misc. bond           : bond        0.00008 (    1)
  link_NAG-ASN         : bond        0.00491 (    1)
  link_NAG-ASN         : angle       1.88432 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.106 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  255 MET cc_start: 0.9184 (mmp) cc_final: 0.8849 (mmp)
REVERT: A  269 MET cc_start: 0.6777 (mpp) cc_final: 0.6137 (mmp)
REVERT: A  289 VAL cc_start: 0.8427 (t) cc_final: 0.8083 (t)
REVERT: A  316 MET cc_start: 0.7792 (ppp) cc_final: 0.7517 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0722
  time to fit residues: 5.0090
Evaluate side-chains
  46 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 46
  time to evaluate  : 0.162 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 8 optimal weight:    7.9990
   chunk 45 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.9990
   chunk 15 optimal weight:    0.9980
   chunk 41 optimal weight:    8.9990
   chunk 35 optimal weight:    0.9990
   chunk 44 optimal weight:    3.9990
   chunk 37 optimal weight:    0.8980
   chunk 43 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.8580

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

Flipped N/Q/H residues before XYZ refinement:
A 393 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4202 r_free = 0.4202 target = 0.083019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3984 r_free = 0.3984 target = 0.073085 restraints weight = 57294.340|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 42)----------------|
| r_work = 0.4008 r_free = 0.4008 target = 0.074255 restraints weight = 43821.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.075158 restraints weight = 35460.743|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4041 r_free = 0.4041 target = 0.075820 restraints weight = 29729.121|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4050 r_free = 0.4050 target = 0.076302 restraints weight = 25800.853|
|-----------------------------------------------------------------------------|
r_work (final): 0.4033
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.5925
moved from start:          1.1501

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.025   3710  Z= 0.105
  Angle     :  0.499   6.976   5005  Z= 0.260
  Chirality :  0.037   0.145    576
  Planarity :  0.003   0.029    631
  Dihedral  :  4.314  17.239    512
  Min Nonbonded Distance : 2.432

Molprobity Statistics.
  All-atom Clashscore : 59.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.91 %
    Favored  : 94.09 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.25 %
    Favored  : 99.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  1.28 (0.40), residues: 440
  helix:  1.70 (0.33), residues: 244
  sheet:  1.55 (0.63), residues: 55
  loop : -0.96 (0.54), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 297 
 TYR   0.012   0.001   TYR A 277 
 PHE   0.013   0.002   PHE A 324 
 TRP   0.014   0.002   TRP B  40 
 HIS   0.002   0.000   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00225 ( 3700)
  covalent geometry    : angle       0.49331 ( 4986)
  SS BOND              : bond        0.00389 (    8)
  SS BOND              : angle       1.17611 (   16)
  hydrogen bonds       : bond        0.03174 (  209)
  hydrogen bonds       : angle       4.11411 (  591)
  Misc. bond           : bond        0.00017 (    1)
  link_NAG-ASN         : bond        0.00510 (    1)
  link_NAG-ASN         : angle       1.85826 (    3)

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

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

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  880 Ramachandran restraints generated.
    440 Oldfield, 0 Emsley, 440 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 55
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  143 GLU cc_start: 0.8224 (pt0) cc_final: 0.7930 (pt0)
REVERT: A  174 LEU cc_start: 0.7370 (mt) cc_final: 0.7155 (mt)
REVERT: A  255 MET cc_start: 0.9180 (mmp) cc_final: 0.8842 (mmp)
REVERT: A  269 MET cc_start: 0.6722 (mpp) cc_final: 0.6091 (mmp)
REVERT: A  289 VAL cc_start: 0.8477 (t) cc_final: 0.8216 (t)
REVERT: A  316 MET cc_start: 0.7852 (ppp) cc_final: 0.7569 (ppp)
  outliers start: 0
  outliers final: 0
  residues processed: 55
  average time/residue: 0.0763
  time to fit residues: 5.4768
Evaluate side-chains
  47 residues out of total 413 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 47
  time to evaluate  : 0.154 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 46
   random chunks:
   chunk 16 optimal weight:    5.9990
   chunk 33 optimal weight:    6.9990
   chunk 11 optimal weight:    3.9990
   chunk 21 optimal weight:    6.9990
   chunk 25 optimal weight:    4.9990
   chunk 31 optimal weight:    1.9990
   chunk 45 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0010
   chunk 18 optimal weight:    3.9990
   overall best weight:    1.3992

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

Flipped N/Q/H residues before XYZ refinement:
** A 184 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 279 ASN
A 393 GLN
** A 470 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4121 r_free = 0.4121 target = 0.079234 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3912 r_free = 0.3912 target = 0.069832 restraints weight = 59172.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3937 r_free = 0.3937 target = 0.071007 restraints weight = 43963.078|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3955 r_free = 0.3955 target = 0.071788 restraints weight = 34972.370|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3968 r_free = 0.3968 target = 0.072442 restraints weight = 29362.180|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3977 r_free = 0.3977 target = 0.072959 restraints weight = 25346.434|
|-----------------------------------------------------------------------------|
r_work (final): 0.3962
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6029
moved from start:          1.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3710  Z= 0.153
  Angle     :  0.619   8.736   5005  Z= 0.322
  Chirality :  0.041   0.205    576
  Planarity :  0.004   0.034    631
  Dihedral  :  5.060  17.630    512
  Min Nonbonded Distance : 2.407

Molprobity Statistics.
  All-atom Clashscore : 68.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.50 %
    Favored  : 92.50 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.50 %
    Favored  : 99.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 6.25 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.50 (0.40), residues: 440
  helix:  1.05 (0.33), residues: 244
  sheet:  1.16 (0.62), residues: 55
  loop : -1.23 (0.51), residues: 141

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG A  86 
 TYR   0.023   0.002   TYR A 277 
 PHE   0.021   0.002   PHE A 144 
 TRP   0.017   0.003   TRP A 296 
 HIS   0.002   0.001   HIS A 468 

Details of bonding type rmsd
  covalent geometry    : bond        0.00327 ( 3700)
  covalent geometry    : angle       0.61098 ( 4986)
  SS BOND              : bond        0.00548 (    8)
  SS BOND              : angle       1.50673 (   16)
  hydrogen bonds       : bond        0.04018 (  209)
  hydrogen bonds       : angle       4.56016 (  591)
  Misc. bond           : bond        0.00042 (    1)
  link_NAG-ASN         : bond        0.00972 (    1)
  link_NAG-ASN         : angle       2.47653 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1327.69 seconds
wall clock time: 23 minutes 27.71 seconds (1407.71 seconds total)