Starting phenix.real_space_refine
on Fri Aug 22 14:32:34 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1b_36791/08_2025/8k1b_36791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1b_36791/08_2025/8k1b_36791.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.47
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1b_36791/08_2025/8k1b_36791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1b_36791/08_2025/8k1b_36791.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1b_36791/08_2025/8k1b_36791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1b_36791/08_2025/8k1b_36791.map"
  }
  resolution = 3.47
  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=   0.007 sd=   0.121
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      16      5.16       5
     C    2694      2.51       5
     N     666      2.21       5
     O     800      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 6 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 4176
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 2046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 2046
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 239}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "B"
      Number of atoms: 2046
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 254, 2046
          Classifications: {'peptide': 254}
          Incomplete info: {'truncation_to_alanine': 1}
          Link IDs: {'PCIS': 3, 'PTRANS': 11, 'TRANS': 239}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 7
          Unresolved non-hydrogen dihedrals: 5
          Planarities with less than four sites: {'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 5
    Chain: "A"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
    Chain: "B"
      Number of atoms: 42
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 42
          Unusual residues: {'NAG': 3}
          Classifications: {'undetermined': 3}
          Link IDs: {None: 2}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 1.40, per 1000 atoms: 0.34
  Number of scatterers: 4176
  At special positions: 0
  Unit cell: (74.25, 81, 60.75, 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      16     16.00
     O     800      8.00
     N     666      7.00
     C    2694      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=4, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 130 " - pdb=" SG  CYS A 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 212 " - pdb=" SG  CYS A 271 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 130 " - pdb=" SG  CYS B 222 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B 212 " - pdb=" SG  CYS B 271 " 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 A 401 " - " ASN A  67 "
      " NAG A 402 " - " ASN A  83 "
      " NAG A 403 " - " ASN A 136 "
      " NAG B 401 " - " ASN B  67 "
      " NAG B 402 " - " ASN B  83 "
      " NAG B 403 " - " ASN B 136 "
  Time building additional restraints: 0.39
  Conformation dependent library (CDL) restraints added in 169.2 milliseconds
  
  Enol-peptide restraints added in 953.7 nanoseconds
  

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  984

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 10 sheets defined
      2.4% alpha, 40.6% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 115 through 117
      No H-bonds generated for 'chain 'A' and resid 115 through 117'
    Processing helix  chain 'A' and resid 251 through 253
      No H-bonds generated for 'chain 'A' and resid 251 through 253'
    Processing helix  chain 'B' and resid 115 through 117
      No H-bonds generated for 'chain 'B' and resid 115 through 117'
    Processing helix  chain 'B' and resid 251 through 253
      No H-bonds generated for 'chain 'B' and resid 251 through 253'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 50 through 56
      removed outlier: 4.217A  pdb=" N   HIS A  50 " --> pdb=" O   VAL A 163 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   VAL A 163 " --> pdb=" O   HIS A  50 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 62 through 70
      removed outlier: 3.811A  pdb=" N   SER A  70 " --> pdb=" O   LEU A 141 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   LEU A 141 " --> pdb=" O   SER A  70 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 110 through 113
      removed outlier: 7.367A  pdb=" N   SER A 119 " --> pdb=" O   GLN A 283 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'A' and resid 177 through 181
    Processing sheet with id=AA5, first strand: chain 'A' and resid 187 through 192
    Processing sheet with id=AA6, first strand: chain 'B' and resid 50 through 56
      removed outlier: 4.216A  pdb=" N   HIS B  50 " --> pdb=" O   VAL B 163 " (cutoff:3.500A)
      removed outlier: 3.903A  pdb=" N   VAL B 163 " --> pdb=" O   HIS B  50 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'B' and resid 62 through 70
      removed outlier: 3.812A  pdb=" N   SER B  70 " --> pdb=" O   LEU B 141 " (cutoff:3.500A)
      removed outlier: 4.390A  pdb=" N   LEU B 141 " --> pdb=" O   SER B  70 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'B' and resid 110 through 113
      removed outlier: 7.367A  pdb=" N   SER B 119 " --> pdb=" O   GLN B 283 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'B' and resid 177 through 181
    Processing sheet with id=AB1, first strand: chain 'B' and resid 187 through 192

    152 hydrogen bonds defined for protein.
    402 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: 0.62

  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:
        1.20 -     1.33: 732
        1.33 -     1.45: 1152
        1.45 -     1.57: 2372
        1.57 -     1.69: 0
        1.69 -     1.81: 24
  Bond restraints: 4280
  Sorted by residual:
  bond pdb=" N   MET B 152 "
       pdb=" CA  MET B 152 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.08e-02 8.57e+03 7.17e+00
  bond pdb=" N   MET A 152 "
       pdb=" CA  MET A 152 "
    ideal  model  delta    sigma   weight residual
    1.458  1.487 -0.029 1.08e-02 8.57e+03 7.03e+00
  bond pdb=" N   ASN B 230 "
       pdb=" CA  ASN B 230 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.29e-02 6.01e+03 6.66e+00
  bond pdb=" C   PRO B 183 "
       pdb=" O   PRO B 183 "
    ideal  model  delta    sigma   weight residual
    1.237  1.204  0.033 1.29e-02 6.01e+03 6.65e+00
  bond pdb=" N   ASN A 230 "
       pdb=" CA  ASN A 230 "
    ideal  model  delta    sigma   weight residual
    1.457  1.491 -0.033 1.29e-02 6.01e+03 6.62e+00
  ... (remaining 4275 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.05: 5276
        1.05 -     2.10: 399
        2.10 -     3.16: 114
        3.16 -     4.21: 35
        4.21 -     5.26: 6
  Bond angle restraints: 5830
  Sorted by residual:
  angle pdb=" CA  ARG A 127 "
        pdb=" C   ARG A 127 "
        pdb=" O   ARG A 127 "
      ideal   model   delta    sigma   weight residual
     121.23  117.74    3.49 1.07e+00 8.73e-01 1.06e+01
  angle pdb=" CA  ARG B 127 "
        pdb=" C   ARG B 127 "
        pdb=" O   ARG B 127 "
      ideal   model   delta    sigma   weight residual
     121.23  117.88    3.35 1.07e+00 8.73e-01 9.78e+00
  angle pdb=" N   GLN A 100 "
        pdb=" CA  GLN A 100 "
        pdb=" C   GLN A 100 "
      ideal   model   delta    sigma   weight residual
     112.54  108.92    3.62 1.22e+00 6.72e-01 8.79e+00
  angle pdb=" CA  ASN B 219 "
        pdb=" C   ASN B 219 "
        pdb=" O   ASN B 219 "
      ideal   model   delta    sigma   weight residual
     121.94  118.54    3.40 1.15e+00 7.56e-01 8.74e+00
  angle pdb=" CA  ASN A 219 "
        pdb=" C   ASN A 219 "
        pdb=" O   ASN A 219 "
      ideal   model   delta    sigma   weight residual
     121.94  118.54    3.40 1.15e+00 7.56e-01 8.73e+00
  ... (remaining 5825 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.82: 2216
       16.82 -    33.65: 336
       33.65 -    50.47: 66
       50.47 -    67.30: 22
       67.30 -    84.12: 6
  Dihedral angle restraints: 2646
    sinusoidal: 1126
      harmonic: 1520
  Sorted by residual:
  dihedral pdb=" CB  CYS B 212 "
           pdb=" SG  CYS B 212 "
           pdb=" SG  CYS B 271 "
           pdb=" CB  CYS B 271 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.29   38.71     1      1.00e+01 1.00e-02 2.11e+01
  dihedral pdb=" CB  CYS A 212 "
           pdb=" SG  CYS A 212 "
           pdb=" SG  CYS A 271 "
           pdb=" CB  CYS A 271 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   54.30   38.70     1      1.00e+01 1.00e-02 2.11e+01
  dihedral pdb=" CA  ASN B 136 "
           pdb=" C   ASN B 136 "
           pdb=" N   GLU B 137 "
           pdb=" CA  GLU B 137 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  162.88   17.12     0      5.00e+00 4.00e-02 1.17e+01
  ... (remaining 2643 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.031: 356
       0.031 -    0.062: 168
       0.062 -    0.092: 64
       0.092 -    0.123: 71
       0.123 -    0.154: 13
  Chirality restraints: 672
  Sorted by residual:
  chirality pdb=" CA  MET A 152 "
            pdb=" N   MET A 152 "
            pdb=" C   MET A 152 "
            pdb=" CB  MET A 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.91e-01
  chirality pdb=" CA  MET B 152 "
            pdb=" N   MET B 152 "
            pdb=" C   MET B 152 "
            pdb=" CB  MET B 152 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.82e-01
  chirality pdb=" CA  LEU A  94 "
            pdb=" N   LEU A  94 "
            pdb=" C   LEU A  94 "
            pdb=" CB  LEU A  94 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.66   -0.15 2.00e-01 2.50e+01 5.36e-01
  ... (remaining 669 not shown)

  Planarity restraints: 748
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR A  91 "   -0.012 2.00e-02 2.50e+03   1.52e-02 4.60e+00
        pdb=" CG  TYR A  91 "    0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR A  91 "   -0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR A  91 "   -0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR A  91 "   -0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR A  91 "   -0.002 2.00e-02 2.50e+03
        pdb=" CZ  TYR A  91 "   -0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR A  91 "    0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  TYR B  91 "    0.012 2.00e-02 2.50e+03   1.51e-02 4.59e+00
        pdb=" CG  TYR B  91 "   -0.038 2.00e-02 2.50e+03
        pdb=" CD1 TYR B  91 "    0.012 2.00e-02 2.50e+03
        pdb=" CD2 TYR B  91 "    0.010 2.00e-02 2.50e+03
        pdb=" CE1 TYR B  91 "    0.001 2.00e-02 2.50e+03
        pdb=" CE2 TYR B  91 "    0.003 2.00e-02 2.50e+03
        pdb=" CZ  TYR B  91 "    0.004 2.00e-02 2.50e+03
        pdb=" OH  TYR B  91 "   -0.004 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS B 222 "   -0.031 5.00e-02 4.00e+02   4.66e-02 3.47e+00
        pdb=" N   PRO B 223 "    0.081 5.00e-02 4.00e+02
        pdb=" CA  PRO B 223 "   -0.026 5.00e-02 4.00e+02
        pdb=" CD  PRO B 223 "   -0.023 5.00e-02 4.00e+02
  ... (remaining 745 not shown)

  Histogram of nonbonded interaction distances:
        2.36 -     2.87: 1558
        2.87 -     3.37: 3514
        3.37 -     3.88: 6502
        3.88 -     4.39: 6905
        4.39 -     4.90: 12590
  Nonbonded interactions: 31069
  Sorted by model distance:
  nonbonded pdb=" NH2 ARG B  79 "
            pdb=" OE1 GLN B 187 "
     model   vdw
     2.357 3.120
  nonbonded pdb=" NH2 ARG A  79 "
            pdb=" OE1 GLN A 187 "
     model   vdw
     2.358 3.120
  nonbonded pdb=" NH2 ARG A  79 "
            pdb=" O   PRO A 186 "
     model   vdw
     2.380 3.120
  nonbonded pdb=" NH2 ARG B  79 "
            pdb=" O   PRO B 186 "
     model   vdw
     2.381 3.120
  nonbonded pdb=" O   PRO A 266 "
            pdb=" NH2 ARG A 289 "
     model   vdw
     2.389 3.120
  ... (remaining 31064 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: 0.01
Found NCS groups:
ncs_group {
  reference = chain 'A'
  selection = chain 'B'
}

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:             0.260
  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:             0.000
  Extract box with map and model:          0.040
  Check model and map are aligned:         0.000
  Set scattering table:                    0.020
  Process input model:                     6.980
  Find NCS groups from input model:        0.030
  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:             0.010
  Load rotamer database and sin/cos tables:1.140
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.490
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6941
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   4290  Z= 0.265
  Angle     :  0.719   5.260   5856  Z= 0.411
  Chirality :  0.052   0.154    672
  Planarity :  0.005   0.056    742
  Dihedral  : 16.501  84.119   1650
  Min Nonbonded Distance : 2.357

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  0.85 %
    Allowed  : 28.42 %
    Favored  : 70.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.31 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet: -0.04 (0.29), residues: 278
  loop : -1.97 (0.39), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A 127 
 TYR   0.038   0.002   TYR A  91 
 PHE   0.007   0.001   PHE A 193 
 TRP   0.006   0.001   TRP B 106 
 HIS   0.001   0.000   HIS A 229 

Details of bonding type rmsd
  covalent geometry    : bond        0.00460 ( 4280)
  covalent geometry    : angle       0.70975 ( 5830)
  SS BOND              : bond        0.00056 (    4)
  SS BOND              : angle       1.36785 (    8)
  hydrogen bonds       : bond        0.17323 (  152)
  hydrogen bonds       : angle       7.38141 (  402)
  link_NAG-ASN         : bond        0.00279 (    6)
  link_NAG-ASN         : angle       2.02701 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  136 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 132
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
  outliers start: 4
  outliers final: 0
  residues processed: 132
  average time/residue: 0.0830
  time to fit residues: 13.1959
Evaluate side-chains
  75 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 75
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 24 optimal weight:    0.9990
   chunk 48 optimal weight:   40.0000
   chunk 26 optimal weight:   10.0000
   chunk 2 optimal weight:    6.9990
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 19 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9980
   chunk 22 optimal weight:    0.0970
   overall best weight:    0.6780

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

Flipped N/Q/H residues before XYZ refinement:
A 158 GLN
B 178 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4271 r_free = 0.4271 target = 0.188412 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3691 r_free = 0.3691 target = 0.134097 restraints weight = 5716.715|
|-----------------------------------------------------------------------------|
r_work (start): 0.3681 rms_B_bonded: 4.71
r_work (final): 0.3681
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6913
moved from start:          0.2604

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4290  Z= 0.130
  Angle     :  0.628   7.652   5856  Z= 0.325
  Chirality :  0.050   0.175    672
  Planarity :  0.004   0.031    742
  Dihedral  :  7.048  57.371    672
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  4.06 %
    Allowed  : 27.99 %
    Favored  : 67.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.92 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.15 (0.29), residues: 268
  loop : -1.52 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 127 
 TYR   0.018   0.001   TYR A 188 
 PHE   0.010   0.001   PHE B 177 
 TRP   0.010   0.001   TRP B 106 
 HIS   0.004   0.001   HIS B 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00308 ( 4280)
  covalent geometry    : angle       0.61851 ( 5830)
  SS BOND              : bond        0.00120 (    4)
  SS BOND              : angle       0.57582 (    8)
  hydrogen bonds       : bond        0.03667 (  152)
  hydrogen bonds       : angle       6.34812 (  402)
  link_NAG-ASN         : bond        0.00344 (    6)
  link_NAG-ASN         : angle       2.10855 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  102 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 83
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  224 VAL cc_start: 0.8535 (t) cc_final: 0.8191 (p)
REVERT: B  208 MET cc_start: 0.7055 (mmm) cc_final: 0.6404 (mmm)
  outliers start: 19
  outliers final: 9
  residues processed: 97
  average time/residue: 0.0680
  time to fit residues: 8.3609
Evaluate side-chains
  85 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 76
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  147 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  205 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 5 optimal weight:    0.7980
   chunk 23 optimal weight:   20.0000
   chunk 0 optimal weight:   10.0000
   chunk 18 optimal weight:    0.4980
   chunk 19 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 2 optimal weight:    1.9990
   chunk 39 optimal weight:    0.8980
   chunk 9 optimal weight:    5.9990
   chunk 38 optimal weight:    3.9990
   chunk 10 optimal weight:   10.0000
   overall best weight:    1.4384

-------------------------------------------------------------------------------
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 = 0.4224 r_free = 0.4224 target = 0.183018 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.129442 restraints weight = 5669.710|
|-----------------------------------------------------------------------------|
r_work (start): 0.3635 rms_B_bonded: 4.55
r_work (final): 0.3635
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7075
moved from start:          0.3150

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   4290  Z= 0.157
  Angle     :  0.672   7.846   5856  Z= 0.331
  Chirality :  0.050   0.165    672
  Planarity :  0.004   0.034    742
  Dihedral  :  6.589  59.856    672
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.50
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.13 %
    Allowed  : 28.21 %
    Favored  : 66.67 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    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: -0.89 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.04 (0.30), residues: 260
  loop : -1.28 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 127 
 TYR   0.020   0.001   TYR A 188 
 PHE   0.011   0.001   PHE B 253 
 TRP   0.006   0.001   TRP A 106 
 HIS   0.007   0.001   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00394 ( 4280)
  covalent geometry    : angle       0.66159 ( 5830)
  SS BOND              : bond        0.00112 (    4)
  SS BOND              : angle       0.86805 (    8)
  hydrogen bonds       : bond        0.03454 (  152)
  hydrogen bonds       : angle       6.28315 (  402)
  link_NAG-ASN         : bond        0.00239 (    6)
  link_NAG-ASN         : angle       2.17576 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 24
    poor density    : 77
  time to evaluate  : 0.174 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 PHE cc_start: 0.7294 (m-80) cc_final: 0.7062 (m-80)
REVERT: A  100 GLN cc_start: 0.7945 (pp30) cc_final: 0.7538 (tt0)
REVERT: A  155 LEU cc_start: 0.7890 (OUTLIER) cc_final: 0.7253 (tp)
REVERT: A  207 GLU cc_start: 0.7789 (tp30) cc_final: 0.7389 (tp30)
REVERT: A  208 MET cc_start: 0.7103 (mmm) cc_final: 0.6538 (mmm)
REVERT: A  224 VAL cc_start: 0.8610 (t) cc_final: 0.8279 (p)
REVERT: B   48 PHE cc_start: 0.7304 (m-80) cc_final: 0.7045 (m-80)
REVERT: B  106 TRP cc_start: 0.8191 (p90) cc_final: 0.7970 (p90)
REVERT: B  117 GLN cc_start: 0.7482 (pp30) cc_final: 0.7212 (pp30)
REVERT: B  207 GLU cc_start: 0.7252 (tp30) cc_final: 0.6856 (tp30)
REVERT: B  208 MET cc_start: 0.7191 (mmm) cc_final: 0.6959 (mmm)
  outliers start: 24
  outliers final: 13
  residues processed: 99
  average time/residue: 0.0535
  time to fit residues: 6.9860
Evaluate side-chains
  87 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 73
  time to evaluate  : 0.133 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 31 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 11 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9980
   chunk 29 optimal weight:    0.7980
   chunk 33 optimal weight:    8.9990
   chunk 47 optimal weight:    3.9990
   chunk 30 optimal weight:    2.9990
   chunk 8 optimal weight:    4.9990
   chunk 1 optimal weight:   10.0000
   chunk 15 optimal weight:    3.9990
   overall best weight:    2.3586

-------------------------------------------------------------------------------
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 = 0.4195 r_free = 0.4195 target = 0.179467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3598 r_free = 0.3598 target = 0.125745 restraints weight = 5751.371|
|-----------------------------------------------------------------------------|
r_work (start): 0.3594 rms_B_bonded: 4.56
r_work (final): 0.3594
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
moved from start:          0.3742

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.073   4290  Z= 0.219
  Angle     :  0.715   8.169   5856  Z= 0.356
  Chirality :  0.051   0.165    672
  Planarity :  0.004   0.033    742
  Dihedral  :  6.672  59.936    672
  Min Nonbonded Distance : 2.417

Molprobity Statistics.
  All-atom Clashscore : 12.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.97 %
    Favored  : 96.03 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 28.21 %
    Favored  : 65.38 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    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: -0.97 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.06 (0.30), residues: 252
  loop : -1.39 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.001   ARG A  79 
 TYR   0.026   0.002   TYR A 188 
 PHE   0.016   0.002   PHE A 253 
 TRP   0.008   0.001   TRP A 106 
 HIS   0.004   0.001   HIS B 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00549 ( 4280)
  covalent geometry    : angle       0.70260 ( 5830)
  SS BOND              : bond        0.00295 (    4)
  SS BOND              : angle       0.64445 (    8)
  hydrogen bonds       : bond        0.03583 (  152)
  hydrogen bonds       : angle       6.72332 (  402)
  link_NAG-ASN         : bond        0.00231 (    6)
  link_NAG-ASN         : angle       2.48490 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  103 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 73
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 PHE cc_start: 0.7341 (m-80) cc_final: 0.6987 (m-80)
REVERT: A  117 GLN cc_start: 0.7545 (pp30) cc_final: 0.7303 (pp30)
REVERT: A  207 GLU cc_start: 0.7928 (tp30) cc_final: 0.7227 (tp30)
REVERT: A  208 MET cc_start: 0.7408 (mmm) cc_final: 0.6701 (mmm)
REVERT: A  224 VAL cc_start: 0.8533 (t) cc_final: 0.8254 (p)
REVERT: B   48 PHE cc_start: 0.7327 (m-80) cc_final: 0.6999 (m-80)
REVERT: B  106 TRP cc_start: 0.8428 (p90) cc_final: 0.8019 (p90)
REVERT: B  155 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7377 (tp)
REVERT: B  190 LEU cc_start: 0.7605 (OUTLIER) cc_final: 0.6975 (tp)
REVERT: B  207 GLU cc_start: 0.7445 (tp30) cc_final: 0.6752 (tp30)
REVERT: B  208 MET cc_start: 0.7457 (mmm) cc_final: 0.7019 (mmm)
  outliers start: 30
  outliers final: 20
  residues processed: 101
  average time/residue: 0.0485
  time to fit residues: 6.5334
Evaluate side-chains
  85 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 63
  time to evaluate  : 0.153 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  103 VAL
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  163 VAL
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 VAL
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 25 optimal weight:   10.0000
   chunk 26 optimal weight:   10.0000
   chunk 6 optimal weight:    1.9990
   chunk 22 optimal weight:    3.9990
   chunk 13 optimal weight:    1.9990
   chunk 42 optimal weight:    0.9990
   chunk 48 optimal weight:   20.0000
   chunk 31 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 11 optimal weight:    5.9990
   chunk 2 optimal weight:    0.7980
   overall best weight:    1.3186

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4223 r_free = 0.4223 target = 0.182521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3650 r_free = 0.3650 target = 0.129508 restraints weight = 5529.464|
|-----------------------------------------------------------------------------|
r_work (start): 0.3639 rms_B_bonded: 4.45
r_work (final): 0.3639
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.3887

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.049   4290  Z= 0.149
  Angle     :  0.692   8.883   5856  Z= 0.330
  Chirality :  0.049   0.159    672
  Planarity :  0.004   0.031    742
  Dihedral  :  6.103  55.071    672
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  6.41 %
    Allowed  : 29.49 %
    Favored  : 64.10 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    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: -0.90 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.12 (0.30), residues: 252
  loop : -1.36 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG B 127 
 TYR   0.019   0.001   TYR A 188 
 PHE   0.009   0.001   PHE B 253 
 TRP   0.003   0.001   TRP A 106 
 HIS   0.004   0.001   HIS B 178 

Details of bonding type rmsd
  covalent geometry    : bond        0.00370 ( 4280)
  covalent geometry    : angle       0.67993 ( 5830)
  SS BOND              : bond        0.00153 (    4)
  SS BOND              : angle       0.49213 (    8)
  hydrogen bonds       : bond        0.03271 (  152)
  hydrogen bonds       : angle       6.27913 (  402)
  link_NAG-ASN         : bond        0.00212 (    6)
  link_NAG-ASN         : angle       2.40904 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 30
    poor density    : 70
  time to evaluate  : 0.090 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLN cc_start: 0.7555 (pp30) cc_final: 0.7339 (pp30)
REVERT: A  190 LEU cc_start: 0.7556 (OUTLIER) cc_final: 0.6967 (tp)
REVERT: A  207 GLU cc_start: 0.7769 (tp30) cc_final: 0.7014 (tp30)
REVERT: A  208 MET cc_start: 0.7190 (mmm) cc_final: 0.6645 (mmm)
REVERT: A  224 VAL cc_start: 0.8551 (t) cc_final: 0.8300 (p)
REVERT: B   48 PHE cc_start: 0.7386 (m-80) cc_final: 0.7161 (m-80)
REVERT: B  106 TRP cc_start: 0.8489 (p90) cc_final: 0.8065 (p90)
REVERT: B  155 LEU cc_start: 0.7971 (OUTLIER) cc_final: 0.7359 (tp)
REVERT: B  207 GLU cc_start: 0.7533 (tp30) cc_final: 0.6656 (tp30)
REVERT: B  208 MET cc_start: 0.7351 (mmm) cc_final: 0.6758 (mmm)
  outliers start: 30
  outliers final: 13
  residues processed: 95
  average time/residue: 0.0466
  time to fit residues: 5.9716
Evaluate side-chains
  77 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 62
  time to evaluate  : 0.143 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 19 optimal weight:    3.9990
   chunk 49 optimal weight:    4.9990
   chunk 44 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 15 optimal weight:    2.9990
   chunk 33 optimal weight:    6.9990
   chunk 38 optimal weight:    0.9980
   chunk 0 optimal weight:    8.9990
   chunk 43 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 41 optimal weight:    4.9990
   overall best weight:    2.9988

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4143 r_free = 0.4143 target = 0.174747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3557 r_free = 0.3557 target = 0.121995 restraints weight = 5809.952|
|-----------------------------------------------------------------------------|
r_work (start): 0.3562 rms_B_bonded: 4.46
r_work (final): 0.3562
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7245
moved from start:          0.4368

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.090   4290  Z= 0.275
  Angle     :  0.775   8.721   5856  Z= 0.382
  Chirality :  0.055   0.371    672
  Planarity :  0.005   0.038    742
  Dihedral  :  6.869  47.410    672
  Min Nonbonded Distance : 2.439

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.16 %
    Favored  : 94.84 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 30.13 %
    Favored  : 63.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.22 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet: -0.23 (0.29), residues: 262
  loop : -1.42 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG A  79 
 TYR   0.029   0.002   TYR A 188 
 PHE   0.016   0.002   PHE B 253 
 TRP   0.009   0.002   TRP A 106 
 HIS   0.007   0.002   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00686 ( 4280)
  covalent geometry    : angle       0.76108 ( 5830)
  SS BOND              : bond        0.00274 (    4)
  SS BOND              : angle       0.45890 (    8)
  hydrogen bonds       : bond        0.03870 (  152)
  hydrogen bonds       : angle       6.77632 (  402)
  link_NAG-ASN         : bond        0.00277 (    6)
  link_NAG-ASN         : angle       2.73645 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  100 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 71
  time to evaluate  : 0.191 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLN cc_start: 0.7603 (pp30) cc_final: 0.7391 (pp30)
REVERT: A  190 LEU cc_start: 0.7583 (OUTLIER) cc_final: 0.7007 (tp)
REVERT: A  198 ASP cc_start: 0.8735 (t0) cc_final: 0.8395 (t0)
REVERT: A  207 GLU cc_start: 0.7737 (tp30) cc_final: 0.6763 (tp30)
REVERT: A  208 MET cc_start: 0.7540 (mmm) cc_final: 0.6832 (mmm)
REVERT: A  250 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8272 (ptmt)
REVERT: B   48 PHE cc_start: 0.7369 (m-80) cc_final: 0.7060 (m-80)
REVERT: B  106 TRP cc_start: 0.8507 (p90) cc_final: 0.8126 (p90)
REVERT: B  190 LEU cc_start: 0.7515 (OUTLIER) cc_final: 0.6929 (tp)
REVERT: B  198 ASP cc_start: 0.8726 (t0) cc_final: 0.8427 (t0)
REVERT: B  207 GLU cc_start: 0.7541 (tp30) cc_final: 0.6576 (tp30)
REVERT: B  208 MET cc_start: 0.7673 (mmm) cc_final: 0.6974 (mmm)
REVERT: B  250 LYS cc_start: 0.8637 (OUTLIER) cc_final: 0.8260 (ptmt)
  outliers start: 29
  outliers final: 22
  residues processed: 94
  average time/residue: 0.0604
  time to fit residues: 7.3486
Evaluate side-chains
  93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 67
  time to evaluate  : 0.148 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  190 LEU
Chi-restraints excluded: chain A residue  222 CYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   56 VAL
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  100 GLN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  190 LEU
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 44 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 9 optimal weight:    0.7980
   chunk 17 optimal weight:    0.8980
   chunk 20 optimal weight:    0.4980
   chunk 8 optimal weight:    9.9990
   chunk 4 optimal weight:    0.9980
   chunk 43 optimal weight:    0.8980
   chunk 37 optimal weight:    0.8980
   chunk 10 optimal weight:    1.9990
   chunk 6 optimal weight:    0.0470
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
A 185 GLN
B  50 HIS
B 100 GLN
B 185 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4230 r_free = 0.4230 target = 0.185425 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3721 r_free = 0.3721 target = 0.136185 restraints weight = 5606.657|
|-----------------------------------------------------------------------------|
r_work (start): 0.3693 rms_B_bonded: 4.36
r_work: 0.3542 rms_B_bonded: 4.83 restraints_weight: 0.5000
r_work (final): 0.3542
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7018
moved from start:          0.4398

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4290  Z= 0.124
  Angle     :  0.696   9.922   5856  Z= 0.330
  Chirality :  0.051   0.307    672
  Planarity :  0.004   0.033    742
  Dihedral  :  5.282  33.795    672
  Min Nonbonded Distance : 2.497

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 29.91 %
    Favored  : 64.53 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    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: -0.90 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.10 (0.30), residues: 252
  loop : -1.33 (0.38), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.015   0.001   TYR B 188 
 PHE   0.014   0.001   PHE B 177 
 TRP   0.009   0.001   TRP A 106 
 HIS   0.006   0.001   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00304 ( 4280)
  covalent geometry    : angle       0.68263 ( 5830)
  SS BOND              : bond        0.00101 (    4)
  SS BOND              : angle       0.40652 (    8)
  hydrogen bonds       : bond        0.03263 (  152)
  hydrogen bonds       : angle       6.20362 (  402)
  link_NAG-ASN         : bond        0.00218 (    6)
  link_NAG-ASN         : angle       2.55315 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  98 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.093 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLN cc_start: 0.7563 (OUTLIER) cc_final: 0.7239 (pt0)
REVERT: A  187 GLN cc_start: 0.8088 (OUTLIER) cc_final: 0.7677 (mm-40)
REVERT: A  207 GLU cc_start: 0.8186 (tp30) cc_final: 0.7425 (tp30)
REVERT: A  208 MET cc_start: 0.7421 (mmm) cc_final: 0.7015 (mmm)
REVERT: A  243 LYS cc_start: 0.4870 (pttm) cc_final: 0.4635 (pttt)
REVERT: B   48 PHE cc_start: 0.7408 (m-80) cc_final: 0.7018 (m-80)
REVERT: B  106 TRP cc_start: 0.8545 (p90) cc_final: 0.8120 (p90)
REVERT: B  155 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7137 (tp)
REVERT: B  187 GLN cc_start: 0.8091 (OUTLIER) cc_final: 0.7688 (mm-40)
REVERT: B  207 GLU cc_start: 0.8002 (tp30) cc_final: 0.7788 (tp30)
REVERT: B  208 MET cc_start: 0.7493 (mmm) cc_final: 0.7051 (mmm)
  outliers start: 26
  outliers final: 21
  residues processed: 90
  average time/residue: 0.0586
  time to fit residues: 6.8027
Evaluate side-chains
  90 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 25
    poor density    : 65
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  173 THR
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  222 CYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  100 GLN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  173 THR
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 29 optimal weight:    9.9990
   chunk 0 optimal weight:   10.0000
   chunk 40 optimal weight:    4.9990
   chunk 36 optimal weight:    6.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    3.9990
   chunk 33 optimal weight:    6.9990
   chunk 49 optimal weight:    3.9990
   chunk 22 optimal weight:    4.9990
   chunk 8 optimal weight:    4.9990
   chunk 13 optimal weight:    0.7980
   overall best weight:    3.1588

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4138 r_free = 0.4138 target = 0.174457 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3553 r_free = 0.3553 target = 0.122003 restraints weight = 5669.427|
|-----------------------------------------------------------------------------|
r_work (start): 0.3559 rms_B_bonded: 4.36
r_work (final): 0.3559
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7244
moved from start:          0.4629

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.007   0.097   4290  Z= 0.283
  Angle     :  0.779  10.550   5856  Z= 0.382
  Chirality :  0.054   0.307    672
  Planarity :  0.005   0.037    742
  Dihedral  :  5.909  34.586    672
  Min Nonbonded Distance : 2.426

Molprobity Statistics.
  All-atom Clashscore : 14.29
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.96 %
    Favored  : 95.04 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 30.13 %
    Favored  : 63.68 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.18 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet: -0.25 (0.29), residues: 262
  loop : -1.34 (0.40), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG B 127 
 TYR   0.027   0.002   TYR B 188 
 PHE   0.018   0.003   PHE A 146 
 TRP   0.007   0.002   TRP A 106 
 HIS   0.006   0.002   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00713 ( 4280)
  covalent geometry    : angle       0.76533 ( 5830)
  SS BOND              : bond        0.00520 (    4)
  SS BOND              : angle       0.64982 (    8)
  hydrogen bonds       : bond        0.03877 (  152)
  hydrogen bonds       : angle       6.64093 (  402)
  link_NAG-ASN         : bond        0.00226 (    6)
  link_NAG-ASN         : angle       2.76651 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 65
  time to evaluate  : 0.161 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 PHE cc_start: 0.8068 (t80) cc_final: 0.7815 (t80)
REVERT: A  198 ASP cc_start: 0.8681 (t0) cc_final: 0.8341 (t0)
REVERT: A  207 GLU cc_start: 0.7724 (tp30) cc_final: 0.6757 (tp30)
REVERT: A  208 MET cc_start: 0.7651 (mmm) cc_final: 0.7106 (mmm)
REVERT: A  250 LYS cc_start: 0.8664 (OUTLIER) cc_final: 0.8296 (ptmt)
REVERT: A  300 SER cc_start: 0.8708 (t) cc_final: 0.8043 (m)
REVERT: B   48 PHE cc_start: 0.7200 (m-80) cc_final: 0.6912 (m-80)
REVERT: B  106 TRP cc_start: 0.8487 (p90) cc_final: 0.8230 (p90)
REVERT: B  177 PHE cc_start: 0.7792 (t80) cc_final: 0.7375 (t80)
REVERT: B  187 GLN cc_start: 0.8018 (OUTLIER) cc_final: 0.7542 (mm-40)
REVERT: B  198 ASP cc_start: 0.8688 (t0) cc_final: 0.8354 (t0)
REVERT: B  207 GLU cc_start: 0.7695 (tp30) cc_final: 0.6715 (tp30)
REVERT: B  208 MET cc_start: 0.7642 (mmm) cc_final: 0.6918 (mmm)
REVERT: B  250 LYS cc_start: 0.8645 (OUTLIER) cc_final: 0.8286 (ptmt)
REVERT: B  300 SER cc_start: 0.8697 (t) cc_final: 0.8032 (m)
  outliers start: 29
  outliers final: 24
  residues processed: 87
  average time/residue: 0.0578
  time to fit residues: 6.4638
Evaluate side-chains
  88 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 61
  time to evaluate  : 0.096 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  222 CYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  100 GLN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  163 VAL
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  236 VAL
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    0.0010
   chunk 17 optimal weight:    3.9990
   chunk 20 optimal weight:    0.8980
   chunk 47 optimal weight:    3.9990
   chunk 8 optimal weight:    2.9990
   chunk 11 optimal weight:    7.9990
   chunk 3 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 32 optimal weight:    3.9990
   chunk 4 optimal weight:    0.5980
   chunk 33 optimal weight:    2.9990
   overall best weight:    1.0990

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4178 r_free = 0.4178 target = 0.178723 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3604 r_free = 0.3604 target = 0.126183 restraints weight = 5701.170|
|-----------------------------------------------------------------------------|
r_work (start): 0.3613 rms_B_bonded: 4.43
r_work (final): 0.3613
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.4643

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.061   4290  Z= 0.149
  Angle     :  0.725  10.110   5856  Z= 0.345
  Chirality :  0.051   0.272    672
  Planarity :  0.004   0.034    742
  Dihedral  :  5.128  25.397    672
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 12.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 30.34 %
    Favored  : 63.46 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    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: -0.94 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.06 (0.30), residues: 248
  loop : -1.31 (0.38), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  98 
 TYR   0.018   0.001   TYR B 188 
 PHE   0.011   0.001   PHE B 146 
 TRP   0.009   0.002   TRP B 106 
 HIS   0.007   0.001   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 4280)
  covalent geometry    : angle       0.71032 ( 5830)
  SS BOND              : bond        0.00364 (    4)
  SS BOND              : angle       0.55950 (    8)
  hydrogen bonds       : bond        0.03515 (  152)
  hydrogen bonds       : angle       6.28439 (  402)
  link_NAG-ASN         : bond        0.00184 (    6)
  link_NAG-ASN         : angle       2.70776 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 64
  time to evaluate  : 0.115 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 PHE cc_start: 0.8032 (t80) cc_final: 0.7764 (t80)
REVERT: A  187 GLN cc_start: 0.8034 (OUTLIER) cc_final: 0.7532 (mm-40)
REVERT: A  207 GLU cc_start: 0.8052 (tp30) cc_final: 0.7113 (tp30)
REVERT: A  208 MET cc_start: 0.7186 (mmm) cc_final: 0.6756 (mmm)
REVERT: A  249 GLN cc_start: 0.7099 (OUTLIER) cc_final: 0.5434 (mm110)
REVERT: A  250 LYS cc_start: 0.8647 (OUTLIER) cc_final: 0.8348 (ptpt)
REVERT: A  300 SER cc_start: 0.8601 (t) cc_final: 0.7902 (m)
REVERT: B   48 PHE cc_start: 0.7216 (m-80) cc_final: 0.6851 (m-80)
REVERT: B  106 TRP cc_start: 0.8537 (p90) cc_final: 0.8165 (p90)
REVERT: B  155 LEU cc_start: 0.7858 (OUTLIER) cc_final: 0.7080 (tp)
REVERT: B  183 PRO cc_start: 0.8189 (Cg_exo) cc_final: 0.7948 (Cg_endo)
REVERT: B  187 GLN cc_start: 0.7985 (OUTLIER) cc_final: 0.7524 (mm-40)
REVERT: B  208 MET cc_start: 0.7314 (mmm) cc_final: 0.6915 (mmm)
REVERT: B  249 GLN cc_start: 0.7148 (OUTLIER) cc_final: 0.5416 (mm110)
REVERT: B  250 LYS cc_start: 0.8667 (OUTLIER) cc_final: 0.8370 (ptpt)
REVERT: B  300 SER cc_start: 0.8605 (t) cc_final: 0.7903 (m)
  outliers start: 29
  outliers final: 22
  residues processed: 87
  average time/residue: 0.0610
  time to fit residues: 6.7140
Evaluate side-chains
  92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.145 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  222 CYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  249 GLN
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  265 LYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  100 GLN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  249 GLN
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    4.9990
   chunk 20 optimal weight:    1.9990
   chunk 11 optimal weight:    3.9990
   chunk 4 optimal weight:    0.9980
   chunk 13 optimal weight:    0.7980
   chunk 38 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9990
   chunk 0 optimal weight:    0.8980
   chunk 21 optimal weight:    0.4980
   overall best weight:    0.8382

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4185 r_free = 0.4185 target = 0.179313 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.127571 restraints weight = 5642.361|
|-----------------------------------------------------------------------------|
r_work (start): 0.3633 rms_B_bonded: 4.39
r_work (final): 0.3633
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7137
moved from start:          0.4666

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   4290  Z= 0.133
  Angle     :  0.695  10.231   5856  Z= 0.336
  Chirality :  0.050   0.265    672
  Planarity :  0.004   0.035    742
  Dihedral  :  4.831  22.644    672
  Min Nonbonded Distance : 2.495

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.77 %
    Favored  : 96.23 %
  Rotamer:
    Outliers :  6.20 %
    Allowed  : 30.98 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    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: -0.83 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.15 (0.31), residues: 248
  loop : -1.26 (0.37), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A  98 
 TYR   0.016   0.001   TYR B 188 
 PHE   0.013   0.001   PHE B 146 
 TRP   0.009   0.001   TRP B 106 
 HIS   0.007   0.001   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00335 ( 4280)
  covalent geometry    : angle       0.68061 ( 5830)
  SS BOND              : bond        0.00328 (    4)
  SS BOND              : angle       0.41657 (    8)
  hydrogen bonds       : bond        0.03460 (  152)
  hydrogen bonds       : angle       6.08278 (  402)
  link_NAG-ASN         : bond        0.00193 (    6)
  link_NAG-ASN         : angle       2.67238 (   18)

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

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

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1008 Ramachandran restraints generated.
    504 Oldfield, 0 Emsley, 504 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 63
  time to evaluate  : 0.094 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  177 PHE cc_start: 0.8048 (t80) cc_final: 0.7800 (t80)
REVERT: A  183 PRO cc_start: 0.7981 (Cg_exo) cc_final: 0.7739 (Cg_endo)
REVERT: A  187 GLN cc_start: 0.7966 (OUTLIER) cc_final: 0.7521 (mm-40)
REVERT: A  207 GLU cc_start: 0.7918 (tp30) cc_final: 0.7055 (tp30)
REVERT: A  208 MET cc_start: 0.7119 (mmm) cc_final: 0.6707 (mmm)
REVERT: A  249 GLN cc_start: 0.7191 (OUTLIER) cc_final: 0.5499 (mm110)
REVERT: A  250 LYS cc_start: 0.8661 (OUTLIER) cc_final: 0.8387 (ptpt)
REVERT: A  300 SER cc_start: 0.8590 (t) cc_final: 0.7932 (m)
REVERT: B  106 TRP cc_start: 0.8451 (p90) cc_final: 0.8065 (p90)
REVERT: B  145 ILE cc_start: 0.2568 (OUTLIER) cc_final: 0.2336 (tt)
REVERT: B  155 LEU cc_start: 0.7907 (OUTLIER) cc_final: 0.7164 (tp)
REVERT: B  187 GLN cc_start: 0.7882 (OUTLIER) cc_final: 0.7418 (mm-40)
REVERT: B  208 MET cc_start: 0.7318 (mmm) cc_final: 0.6841 (mmm)
REVERT: B  249 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.5480 (mm110)
REVERT: B  250 LYS cc_start: 0.8676 (OUTLIER) cc_final: 0.8399 (ptpt)
REVERT: B  300 SER cc_start: 0.8561 (t) cc_final: 0.7930 (m)
  outliers start: 29
  outliers final: 21
  residues processed: 86
  average time/residue: 0.0668
  time to fit residues: 7.2123
Evaluate side-chains
  91 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 29
    poor density    : 62
  time to evaluate  : 0.090 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   58 LEU
Chi-restraints excluded: chain A residue   96 VAL
Chi-restraints excluded: chain A residue  100 GLN
Chi-restraints excluded: chain A residue  145 ILE
Chi-restraints excluded: chain A residue  155 LEU
Chi-restraints excluded: chain A residue  166 LEU
Chi-restraints excluded: chain A residue  187 GLN
Chi-restraints excluded: chain A residue  202 ILE
Chi-restraints excluded: chain A residue  222 CYS
Chi-restraints excluded: chain A residue  236 VAL
Chi-restraints excluded: chain A residue  249 GLN
Chi-restraints excluded: chain A residue  250 LYS
Chi-restraints excluded: chain A residue  265 LYS
Chi-restraints excluded: chain A residue  293 LEU
Chi-restraints excluded: chain A residue  297 ILE
Chi-restraints excluded: chain B residue   58 LEU
Chi-restraints excluded: chain B residue   96 VAL
Chi-restraints excluded: chain B residue  100 GLN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  155 LEU
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  187 GLN
Chi-restraints excluded: chain B residue  202 ILE
Chi-restraints excluded: chain B residue  222 CYS
Chi-restraints excluded: chain B residue  224 VAL
Chi-restraints excluded: chain B residue  249 GLN
Chi-restraints excluded: chain B residue  250 LYS
Chi-restraints excluded: chain B residue  293 LEU
Chi-restraints excluded: chain B residue  297 ILE
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 41 optimal weight:    0.0170
   chunk 46 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 16 optimal weight:    0.1980
   chunk 18 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0020
   chunk 47 optimal weight:    0.6980
   chunk 15 optimal weight:    2.9990
   chunk 21 optimal weight:    0.6980
   overall best weight:    0.3226

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

Flipped N/Q/H residues before XYZ refinement:
A 100 GLN
B 100 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4214 r_free = 0.4214 target = 0.181971 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.130453 restraints weight = 5724.993|
|-----------------------------------------------------------------------------|
r_work (start): 0.3668 rms_B_bonded: 4.43
r_work (final): 0.3668
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7095
moved from start:          0.4688

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4290  Z= 0.119
  Angle     :  0.708   9.937   5856  Z= 0.335
  Chirality :  0.050   0.254    672
  Planarity :  0.004   0.033    742
  Dihedral  :  4.425  15.123    672
  Min Nonbonded Distance : 2.502

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 31.41 %
    Favored  : 62.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    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: -0.66 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.38 (0.32), residues: 236
  loop : -1.23 (0.36), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG B  79 
 TYR   0.013   0.001   TYR B 188 
 PHE   0.010   0.001   PHE B 146 
 TRP   0.010   0.001   TRP B 106 
 HIS   0.007   0.001   HIS B 168 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 4280)
  covalent geometry    : angle       0.69481 ( 5830)
  SS BOND              : bond        0.00288 (    4)
  SS BOND              : angle       0.43345 (    8)
  hydrogen bonds       : bond        0.03309 (  152)
  hydrogen bonds       : angle       5.89080 (  402)
  link_NAG-ASN         : bond        0.00226 (    6)
  link_NAG-ASN         : angle       2.58964 (   18)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 855.84 seconds
wall clock time: 15 minutes 27.58 seconds (927.58 seconds total)