Starting phenix.real_space_refine
on Fri May  9 23:17:27 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8k1b_36791/05_2025/8k1b_36791.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8k1b_36791/05_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 {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8k1b_36791/05_2025/8k1b_36791.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8k1b_36791/05_2025/8k1b_36791.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8k1b_36791/05_2025/8k1b_36791.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8k1b_36791/05_2025/8k1b_36791.cif"
  }
  resolution = 3.47
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.007 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): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/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: 2.73, per 1000 atoms: 0.65
  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: 0.85
  Conformation dependent library (CDL) restraints added in 437.6 milliseconds
  

  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: 0.46
  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: 0.97

  Time building geometry restraints manager: 1.02 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: 0.02
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:             0.190
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.140
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     12.620
  Find NCS groups from input model:        0.060
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.550
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   15.660
-------------------------------------------------------------------------------
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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.31 (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
 TRP   0.006   0.001   TRP B 106 
 HIS   0.001   0.000   HIS A 229 
 PHE   0.007   0.001   PHE A 193 
 TYR   0.038   0.002   TYR A  91 
 ARG   0.002   0.001   ARG A 127 

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

*********************** 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  : 0.639 
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: 0.2308
  time to fit residues: 37.0886
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  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 42 optimal weight:    0.7980
   chunk 37 optimal weight:    9.9990
   chunk 21 optimal weight:    1.9990
   chunk 12 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 20 optimal weight:    0.4980
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    0.9980
   chunk 23 optimal weight:   30.0000
   chunk 29 optimal weight:    0.2980
   chunk 45 optimal weight:    0.4980
   overall best weight:    0.6180

-------------------------------------------------------------------------------
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 = 0.188316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3704 r_free = 0.3704 target = 0.134769 restraints weight = 5631.385|
|-----------------------------------------------------------------------------|
r_work (start): 0.3687 rms_B_bonded: 4.63
r_work (final): 0.3687
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6968
moved from start:          0.2557

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4290  Z= 0.128
  Angle     :  0.631   7.492   5856  Z= 0.327
  Chirality :  0.050   0.173    672
  Planarity :  0.004   0.032    742
  Dihedral  :  7.049  57.264    672
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.66
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.98 %
    Favored  : 98.02 %
  Rotamer:
    Outliers :  3.63 %
    Allowed  : 28.21 %
    Favored  : 68.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.90 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.17 (0.29), residues: 268
  loop : -1.52 (0.38), residues: 236

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 106 
 HIS   0.004   0.001   HIS B 178 
 PHE   0.010   0.001   PHE B 177 
 TYR   0.017   0.001   TYR A 188 
 ARG   0.001   0.000   ARG A 289 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00349 (    6)
  link_NAG-ASN         : angle       2.14278 (   18)
  hydrogen bonds       : bond        0.03627 (  152)
  hydrogen bonds       : angle       6.36120 (  402)
  SS BOND              : bond        0.00121 (    4)
  SS BOND              : angle       0.46349 (    8)
  covalent geometry    : bond        0.00306 ( 4280)
  covalent geometry    : angle       0.62092 ( 5830)

*********************** 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
  103 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 86
  time to evaluate  : 0.494 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  100 GLN cc_start: 0.8195 (pp30) cc_final: 0.7992 (pp30)
REVERT: A  224 VAL cc_start: 0.8540 (t) cc_final: 0.8202 (p)
REVERT: B   48 PHE cc_start: 0.7658 (m-80) cc_final: 0.7425 (m-80)
REVERT: B  208 MET cc_start: 0.7121 (mmm) cc_final: 0.6521 (mmm)
  outliers start: 17
  outliers final: 9
  residues processed: 98
  average time/residue: 0.1542
  time to fit residues: 19.2588
Evaluate side-chains
  87 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 78
  time to evaluate  : 0.426 
-------------------------------------------------------------------------------
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  145 ILE
Chi-restraints excluded: chain B residue  147 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 19 optimal weight:    4.9990
   chunk 6 optimal weight:    3.9990
   chunk 29 optimal weight:    5.9990
   chunk 24 optimal weight:    6.9990
   chunk 39 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 17 optimal weight:    1.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.9980
   chunk 15 optimal weight:    2.9990
   chunk 43 optimal weight:    1.9990
   overall best weight:    1.5988

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4220 r_free = 0.4220 target = 0.182326 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.128590 restraints weight = 5616.828|
|-----------------------------------------------------------------------------|
r_work (start): 0.3628 rms_B_bonded: 4.55
r_work (final): 0.3628
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7106
moved from start:          0.3170

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   4290  Z= 0.168
  Angle     :  0.685   8.024   5856  Z= 0.338
  Chirality :  0.050   0.169    672
  Planarity :  0.004   0.033    742
  Dihedral  :  6.648  59.954    672
  Min Nonbonded Distance : 2.422

Molprobity Statistics.
  All-atom Clashscore : 11.26
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.17 %
    Favored  : 96.83 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 27.99 %
    Favored  : 66.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.92 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.03 (0.30), residues: 260
  loop : -1.30 (0.38), residues: 244

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP B 106 
 HIS   0.006   0.002   HIS B 168 
 PHE   0.013   0.002   PHE A 253 
 TYR   0.021   0.002   TYR A 188 
 ARG   0.001   0.000   ARG A  79 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00242 (    6)
  link_NAG-ASN         : angle       2.20881 (   18)
  hydrogen bonds       : bond        0.03498 (  152)
  hydrogen bonds       : angle       6.36873 (  402)
  SS BOND              : bond        0.00202 (    4)
  SS BOND              : angle       0.89291 (    8)
  covalent geometry    : bond        0.00421 ( 4280)
  covalent geometry    : angle       0.67426 ( 5830)

*********************** 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
  102 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 76
  time to evaluate  : 0.482 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 PHE cc_start: 0.7239 (m-80) cc_final: 0.6961 (m-80)
REVERT: A  155 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7257 (tp)
REVERT: A  207 GLU cc_start: 0.7808 (tp30) cc_final: 0.7517 (tp30)
REVERT: A  208 MET cc_start: 0.7164 (mmm) cc_final: 0.6494 (mmm)
REVERT: A  224 VAL cc_start: 0.8674 (t) cc_final: 0.8371 (p)
REVERT: B  106 TRP cc_start: 0.8227 (p90) cc_final: 0.7905 (p90)
REVERT: B  117 GLN cc_start: 0.7537 (pp30) cc_final: 0.7290 (pp30)
REVERT: B  207 GLU cc_start: 0.7375 (tp30) cc_final: 0.6982 (tp30)
REVERT: B  208 MET cc_start: 0.7229 (mmm) cc_final: 0.6983 (mmm)
REVERT: B  252 ASP cc_start: 0.8842 (m-30) cc_final: 0.8558 (m-30)
  outliers start: 26
  outliers final: 14
  residues processed: 101
  average time/residue: 0.1510
  time to fit residues: 19.5091
Evaluate side-chains
  84 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 69
  time to evaluate  : 0.423 
-------------------------------------------------------------------------------
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  158 GLN
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 25 optimal weight:   10.0000
   chunk 27 optimal weight:    7.9990
   chunk 4 optimal weight:    5.9990
   chunk 17 optimal weight:    0.8980
   chunk 39 optimal weight:    2.9990
   chunk 3 optimal weight:   10.0000
   chunk 40 optimal weight:    1.9990
   chunk 34 optimal weight:    9.9990
   chunk 20 optimal weight:    0.1980
   chunk 32 optimal weight:    7.9990
   chunk 30 optimal weight:    0.0050
   overall best weight:    1.2198

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4237 r_free = 0.4237 target = 0.183630 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.130012 restraints weight = 5590.662|
|-----------------------------------------------------------------------------|
r_work (start): 0.3643 rms_B_bonded: 4.55
r_work (final): 0.3643
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7091
moved from start:          0.3449

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.048   4290  Z= 0.147
  Angle     :  0.657   7.486   5856  Z= 0.326
  Chirality :  0.049   0.161    672
  Planarity :  0.004   0.031    742
  Dihedral  :  6.363  59.818    672
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.78
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.78 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 28.42 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.75 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.27 (0.31), residues: 252
  loop : -1.32 (0.37), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 106 
 HIS   0.005   0.001   HIS B 178 
 PHE   0.009   0.001   PHE A 253 
 TYR   0.019   0.001   TYR A 188 
 ARG   0.001   0.000   ARG A 127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00230 (    6)
  link_NAG-ASN         : angle       2.18902 (   18)
  hydrogen bonds       : bond        0.03388 (  152)
  hydrogen bonds       : angle       6.24336 (  402)
  SS BOND              : bond        0.00151 (    4)
  SS BOND              : angle       0.50271 (    8)
  covalent geometry    : bond        0.00365 ( 4280)
  covalent geometry    : angle       0.64700 ( 5830)

*********************** 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
  98 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 75
  time to evaluate  : 0.444 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 PHE cc_start: 0.7246 (m-80) cc_final: 0.6994 (m-80)
REVERT: A  207 GLU cc_start: 0.7777 (tp30) cc_final: 0.7492 (tp30)
REVERT: A  208 MET cc_start: 0.7052 (mmm) cc_final: 0.6463 (mmm)
REVERT: A  224 VAL cc_start: 0.8689 (t) cc_final: 0.8397 (p)
REVERT: B  106 TRP cc_start: 0.8268 (p90) cc_final: 0.7824 (p90)
REVERT: B  117 GLN cc_start: 0.7457 (pp30) cc_final: 0.7204 (pp30)
REVERT: B  161 LEU cc_start: 0.3909 (OUTLIER) cc_final: 0.3656 (tp)
REVERT: B  207 GLU cc_start: 0.7483 (tp30) cc_final: 0.6873 (tp30)
REVERT: B  208 MET cc_start: 0.7311 (mmm) cc_final: 0.6912 (mmm)
  outliers start: 23
  outliers final: 13
  residues processed: 97
  average time/residue: 0.1320
  time to fit residues: 16.7779
Evaluate side-chains
  82 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.556 
-------------------------------------------------------------------------------
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  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  161 LEU
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=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 3 optimal weight:   10.0000
   chunk 18 optimal weight:    4.9990
   chunk 12 optimal weight:    6.9990
   chunk 45 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9990
   chunk 41 optimal weight:    0.0770
   chunk 5 optimal weight:    6.9990
   chunk 46 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0030
   chunk 33 optimal weight:    2.9990
   overall best weight:    0.5352

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4252 r_free = 0.4252 target = 0.186139 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3685 r_free = 0.3685 target = 0.133210 restraints weight = 5656.269|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 4.55
r_work (final): 0.3682
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7036
moved from start:          0.3671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4290  Z= 0.113
  Angle     :  0.653   9.651   5856  Z= 0.315
  Chirality :  0.049   0.224    672
  Planarity :  0.004   0.028    742
  Dihedral  :  5.793  55.619    672
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 9.81
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  5.77 %
    Allowed  : 26.71 %
    Favored  : 67.52 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.67 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.39 (0.31), residues: 248
  loop : -1.32 (0.36), residues: 256

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 106 
 HIS   0.008   0.002   HIS B 168 
 PHE   0.010   0.001   PHE B 112 
 TYR   0.015   0.001   TYR B  91 
 ARG   0.001   0.000   ARG A  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00271 (    6)
  link_NAG-ASN         : angle       2.10245 (   18)
  hydrogen bonds       : bond        0.03243 (  152)
  hydrogen bonds       : angle       5.89386 (  402)
  SS BOND              : bond        0.00165 (    4)
  SS BOND              : angle       0.58620 (    8)
  covalent geometry    : bond        0.00273 ( 4280)
  covalent geometry    : angle       0.64385 ( 5830)

*********************** 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
  108 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 27
    poor density    : 81
  time to evaluate  : 0.474 
Fit side-chains
   revert: symmetry clash
REVERT: A  155 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7150 (tp)
REVERT: A  183 PRO cc_start: 0.8342 (Cg_exo) cc_final: 0.8107 (Cg_endo)
REVERT: A  190 LEU cc_start: 0.7518 (OUTLIER) cc_final: 0.6963 (tp)
REVERT: A  207 GLU cc_start: 0.7788 (tp30) cc_final: 0.7297 (tp30)
REVERT: A  208 MET cc_start: 0.6839 (mmm) cc_final: 0.6321 (mmm)
REVERT: A  224 VAL cc_start: 0.8650 (t) cc_final: 0.8374 (p)
REVERT: A  252 ASP cc_start: 0.8690 (m-30) cc_final: 0.8488 (m-30)
REVERT: B  106 TRP cc_start: 0.8320 (p90) cc_final: 0.7982 (p90)
REVERT: B  183 PRO cc_start: 0.8366 (Cg_exo) cc_final: 0.8158 (Cg_endo)
REVERT: B  190 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7006 (tp)
REVERT: B  207 GLU cc_start: 0.7537 (tp30) cc_final: 0.6878 (tp30)
REVERT: B  208 MET cc_start: 0.7236 (mmm) cc_final: 0.6822 (mmm)
  outliers start: 27
  outliers final: 16
  residues processed: 106
  average time/residue: 0.1211
  time to fit residues: 17.3933
Evaluate side-chains
  89 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 70
  time to evaluate  : 0.384 
-------------------------------------------------------------------------------
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  173 THR
Chi-restraints excluded: chain A residue  190 LEU
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  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  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 14 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 28 optimal weight:   10.0000
   chunk 18 optimal weight:    3.9990
   chunk 44 optimal weight:    1.9990
   chunk 46 optimal weight:    0.9990
   chunk 0 optimal weight:   10.0000
   chunk 9 optimal weight:    0.9990
   chunk 26 optimal weight:   10.0000
   chunk 38 optimal weight:    1.9990
   chunk 6 optimal weight:    2.9990
   overall best weight:    1.3988

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4217 r_free = 0.4217 target = 0.182141 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.129625 restraints weight = 5595.064|
|-----------------------------------------------------------------------------|
r_work (start): 0.3638 rms_B_bonded: 4.50
r_work (final): 0.3638
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7107
moved from start:          0.3915

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.060   4290  Z= 0.159
  Angle     :  0.663   9.093   5856  Z= 0.326
  Chirality :  0.049   0.193    672
  Planarity :  0.004   0.034    742
  Dihedral  :  5.427  45.178    672
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  5.56 %
    Allowed  : 28.21 %
    Favored  : 66.24 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.82 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.11 (0.30), residues: 258
  loop : -1.25 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 106 
 HIS   0.006   0.001   HIS B 168 
 PHE   0.010   0.001   PHE A 253 
 TYR   0.020   0.001   TYR A 188 
 ARG   0.002   0.000   ARG A  79 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00215 (    6)
  link_NAG-ASN         : angle       2.24392 (   18)
  hydrogen bonds       : bond        0.03445 (  152)
  hydrogen bonds       : angle       6.02424 (  402)
  SS BOND              : bond        0.00293 (    4)
  SS BOND              : angle       0.50297 (    8)
  covalent geometry    : bond        0.00406 ( 4280)
  covalent geometry    : angle       0.65202 ( 5830)

*********************** 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
  98 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 72
  time to evaluate  : 0.446 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  117 GLN cc_start: 0.7600 (pp30) cc_final: 0.7337 (pp30)
REVERT: A  155 LEU cc_start: 0.7862 (OUTLIER) cc_final: 0.7100 (tp)
REVERT: A  183 PRO cc_start: 0.8267 (Cg_exo) cc_final: 0.8023 (Cg_endo)
REVERT: A  190 LEU cc_start: 0.7567 (OUTLIER) cc_final: 0.6956 (tp)
REVERT: A  207 GLU cc_start: 0.7720 (tp30) cc_final: 0.7162 (tp30)
REVERT: A  208 MET cc_start: 0.7103 (mmm) cc_final: 0.6585 (mmm)
REVERT: A  224 VAL cc_start: 0.8666 (t) cc_final: 0.8413 (p)
REVERT: A  252 ASP cc_start: 0.8760 (m-30) cc_final: 0.8488 (m-30)
REVERT: B  106 TRP cc_start: 0.8479 (p90) cc_final: 0.8015 (p90)
REVERT: B  183 PRO cc_start: 0.8260 (Cg_exo) cc_final: 0.8036 (Cg_endo)
REVERT: B  190 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.6977 (tp)
REVERT: B  207 GLU cc_start: 0.7417 (tp30) cc_final: 0.6683 (tp30)
REVERT: B  208 MET cc_start: 0.7384 (mmm) cc_final: 0.6893 (mmm)
  outliers start: 26
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1292
  time to fit residues: 16.1642
Evaluate side-chains
  92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 72
  time to evaluate  : 0.436 
-------------------------------------------------------------------------------
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  173 THR
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  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  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=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 22 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0970
   chunk 27 optimal weight:    7.9990
   chunk 40 optimal weight:    3.9990
   chunk 11 optimal weight:   10.0000
   chunk 29 optimal weight:    7.9990
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 25 optimal weight:   10.0000
   chunk 13 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.7382

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4242 r_free = 0.4242 target = 0.185098 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3687 r_free = 0.3687 target = 0.133021 restraints weight = 5723.894|
|-----------------------------------------------------------------------------|
r_work (start): 0.3679 rms_B_bonded: 4.55
r_work (final): 0.3679
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7058
moved from start:          0.4079

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   4290  Z= 0.121
  Angle     :  0.662   9.441   5856  Z= 0.317
  Chirality :  0.049   0.180    672
  Planarity :  0.004   0.032    742
  Dihedral  :  4.455  26.333    672
  Min Nonbonded Distance : 2.451

Molprobity Statistics.
  All-atom Clashscore : 9.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.38 %
    Favored  : 97.62 %
  Rotamer:
    Outliers :  4.70 %
    Allowed  : 29.27 %
    Favored  : 66.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.68 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.22 (0.30), residues: 258
  loop : -1.17 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.003   0.001   TRP B 106 
 HIS   0.003   0.001   HIS B 178 
 PHE   0.007   0.001   PHE B 112 
 TYR   0.019   0.001   TYR B  91 
 ARG   0.001   0.000   ARG B 127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00236 (    6)
  link_NAG-ASN         : angle       2.17158 (   18)
  hydrogen bonds       : bond        0.03221 (  152)
  hydrogen bonds       : angle       5.81061 (  402)
  SS BOND              : bond        0.00185 (    4)
  SS BOND              : angle       0.49632 (    8)
  covalent geometry    : bond        0.00303 ( 4280)
  covalent geometry    : angle       0.65262 ( 5830)

*********************** 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: 22
    poor density    : 76
  time to evaluate  : 0.478 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 GLN cc_start: 0.7582 (pp30) cc_final: 0.7348 (pp30)
REVERT: A  155 LEU cc_start: 0.7885 (OUTLIER) cc_final: 0.7141 (tp)
REVERT: A  207 GLU cc_start: 0.7681 (tp30) cc_final: 0.7267 (tp30)
REVERT: A  208 MET cc_start: 0.7026 (mmm) cc_final: 0.6696 (mmm)
REVERT: A  224 VAL cc_start: 0.8650 (t) cc_final: 0.8413 (p)
REVERT: B  106 TRP cc_start: 0.8417 (p90) cc_final: 0.7988 (p90)
REVERT: B  208 MET cc_start: 0.7385 (mmm) cc_final: 0.6938 (mmm)
  outliers start: 22
  outliers final: 17
  residues processed: 95
  average time/residue: 0.1343
  time to fit residues: 16.7892
Evaluate side-chains
  91 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.478 
-------------------------------------------------------------------------------
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  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  100 GLN
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  147 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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 12 optimal weight:    7.9990
   chunk 25 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 27 optimal weight:    8.9990
   chunk 34 optimal weight:   10.0000
   chunk 47 optimal weight:    0.0060
   chunk 36 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 43 optimal weight:    4.9990
   chunk 11 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   overall best weight:    1.9202

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4199 r_free = 0.4199 target = 0.180288 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3628 r_free = 0.3628 target = 0.127987 restraints weight = 5689.918|
|-----------------------------------------------------------------------------|
r_work (start): 0.3627 rms_B_bonded: 4.51
r_work (final): 0.3627
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7171
moved from start:          0.4257

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.065   4290  Z= 0.191
  Angle     :  0.699  11.460   5856  Z= 0.341
  Chirality :  0.050   0.160    672
  Planarity :  0.004   0.033    742
  Dihedral  :  5.016  29.582    672
  Min Nonbonded Distance : 2.473

Molprobity Statistics.
  All-atom Clashscore : 11.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.91 %
    Allowed  : 29.49 %
    Favored  : 65.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 21.43 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.69 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.16 (0.30), residues: 262
  loop : -1.13 (0.39), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 106 
 HIS   0.004   0.001   HIS B 168 
 PHE   0.011   0.002   PHE A 253 
 TYR   0.023   0.002   TYR A 188 
 ARG   0.002   0.000   ARG A 127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    6)
  link_NAG-ASN         : angle       2.37587 (   18)
  hydrogen bonds       : bond        0.03430 (  152)
  hydrogen bonds       : angle       6.13754 (  402)
  SS BOND              : bond        0.00549 (    4)
  SS BOND              : angle       0.90164 (    8)
  covalent geometry    : bond        0.00484 ( 4280)
  covalent geometry    : angle       0.68732 ( 5830)

*********************** 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
  92 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 69
  time to evaluate  : 0.517 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.8459 (tt) cc_final: 0.8258 (tt)
REVERT: A  117 GLN cc_start: 0.7665 (pp30) cc_final: 0.7451 (pp30)
REVERT: A  177 PHE cc_start: 0.8033 (t80) cc_final: 0.7602 (t80)
REVERT: A  207 GLU cc_start: 0.7648 (tp30) cc_final: 0.6976 (tp30)
REVERT: A  208 MET cc_start: 0.7194 (mmm) cc_final: 0.6649 (mmm)
REVERT: A  224 VAL cc_start: 0.8560 (t) cc_final: 0.8359 (p)
REVERT: B  100 GLN cc_start: 0.7839 (OUTLIER) cc_final: 0.7591 (pp30)
REVERT: B  106 TRP cc_start: 0.8496 (p90) cc_final: 0.8112 (p90)
REVERT: B  207 GLU cc_start: 0.7589 (tp30) cc_final: 0.7015 (tp30)
REVERT: B  208 MET cc_start: 0.7440 (mmm) cc_final: 0.6960 (mmm)
  outliers start: 23
  outliers final: 18
  residues processed: 87
  average time/residue: 0.1249
  time to fit residues: 14.5592
Evaluate side-chains
  83 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 64
  time to evaluate  : 0.472 
-------------------------------------------------------------------------------
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  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  110 LEU
Chi-restraints excluded: chain B residue  145 ILE
Chi-restraints excluded: chain B residue  166 LEU
Chi-restraints excluded: chain B residue  202 ILE
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 18 optimal weight:    0.0670
   chunk 36 optimal weight:   10.0000
   chunk 17 optimal weight:    3.9990
   chunk 47 optimal weight:    1.9990
   chunk 14 optimal weight:    0.8980
   chunk 8 optimal weight:    0.0020
   chunk 20 optimal weight:    0.5980
   chunk 19 optimal weight:    1.9990
   chunk 41 optimal weight:   20.0000
   chunk 43 optimal weight:    0.9990
   chunk 33 optimal weight:    5.9990
   overall best weight:    0.5128

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4222 r_free = 0.4222 target = 0.183075 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.131497 restraints weight = 5658.885|
|-----------------------------------------------------------------------------|
r_work (start): 0.3680 rms_B_bonded: 4.48
r_work (final): 0.3680
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7071
moved from start:          0.4332

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4290  Z= 0.119
  Angle     :  0.676  10.721   5856  Z= 0.324
  Chirality :  0.049   0.179    672
  Planarity :  0.003   0.030    742
  Dihedral  :  4.360  18.485    672
  Min Nonbonded Distance : 2.478

Molprobity Statistics.
  All-atom Clashscore : 10.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.58 %
    Favored  : 97.42 %
  Rotamer:
    Outliers :  4.49 %
    Allowed  : 30.13 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.63 (0.35), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.21 (0.30), residues: 258
  loop : -1.09 (0.38), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B 106 
 HIS   0.005   0.001   HIS B 168 
 PHE   0.013   0.001   PHE A 146 
 TYR   0.017   0.001   TYR B  91 
 ARG   0.001   0.000   ARG B 127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00237 (    6)
  link_NAG-ASN         : angle       2.28594 (   18)
  hydrogen bonds       : bond        0.03166 (  152)
  hydrogen bonds       : angle       5.83721 (  402)
  SS BOND              : bond        0.00205 (    4)
  SS BOND              : angle       0.75167 (    8)
  covalent geometry    : bond        0.00292 ( 4280)
  covalent geometry    : angle       0.66489 ( 5830)

*********************** 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: 21
    poor density    : 72
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  111 LEU cc_start: 0.8393 (tt) cc_final: 0.8185 (tt)
REVERT: A  155 LEU cc_start: 0.7831 (OUTLIER) cc_final: 0.7103 (tp)
REVERT: A  177 PHE cc_start: 0.7975 (t80) cc_final: 0.7049 (t80)
REVERT: A  207 GLU cc_start: 0.7723 (tp30) cc_final: 0.6989 (tp30)
REVERT: A  208 MET cc_start: 0.7056 (mmm) cc_final: 0.6646 (mmm)
REVERT: A  224 VAL cc_start: 0.8656 (t) cc_final: 0.8440 (p)
REVERT: A  250 LYS cc_start: 0.8620 (OUTLIER) cc_final: 0.8342 (ptpt)
REVERT: B  106 TRP cc_start: 0.8361 (p90) cc_final: 0.8009 (p90)
REVERT: B  124 GLU cc_start: 0.7535 (mm-30) cc_final: 0.7243 (mm-30)
REVERT: B  207 GLU cc_start: 0.7800 (tp30) cc_final: 0.7187 (tp30)
REVERT: B  208 MET cc_start: 0.7373 (mmm) cc_final: 0.6848 (mmm)
REVERT: B  250 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8353 (ptpt)
  outliers start: 21
  outliers final: 16
  residues processed: 88
  average time/residue: 0.1384
  time to fit residues: 15.9323
Evaluate side-chains
  86 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 67
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
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  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  110 LEU
Chi-restraints excluded: chain B residue  145 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 1 optimal weight:    8.9990
   chunk 23 optimal weight:   20.0000
   chunk 42 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9980
   chunk 6 optimal weight:    2.9990
   chunk 11 optimal weight:    3.9990
   chunk 34 optimal weight:   10.0000
   chunk 40 optimal weight:    2.9990
   chunk 7 optimal weight:    0.7980
   chunk 35 optimal weight:    0.6980
   chunk 36 optimal weight:    2.9990
   overall best weight:    1.2782

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

Flipped N/Q/H residues before XYZ refinement:
** B 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4203 r_free = 0.4203 target = 0.181073 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3633 r_free = 0.3633 target = 0.128965 restraints weight = 5756.621|
|-----------------------------------------------------------------------------|
r_work (start): 0.3650 rms_B_bonded: 4.52
r_work (final): 0.3650
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7122
moved from start:          0.4410

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= 0.152
  Angle     :  0.684  10.273   5856  Z= 0.336
  Chirality :  0.050   0.181    672
  Planarity :  0.004   0.034    742
  Dihedral  :  4.607  24.210    672
  Min Nonbonded Distance : 2.402

Molprobity Statistics.
  All-atom Clashscore : 11.02
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.98 %
    Favored  : 97.02 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 30.34 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.60 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.24 (0.30), residues: 262
  loop : -1.09 (0.38), residues: 242

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B 106 
 HIS   0.005   0.001   HIS B 168 
 PHE   0.017   0.001   PHE B 146 
 TYR   0.019   0.001   TYR A 188 
 ARG   0.002   0.000   ARG B  98 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    6)
  link_NAG-ASN         : angle       2.32303 (   18)
  hydrogen bonds       : bond        0.03367 (  152)
  hydrogen bonds       : angle       5.94275 (  402)
  SS BOND              : bond        0.00258 (    4)
  SS BOND              : angle       0.70076 (    8)
  covalent geometry    : bond        0.00388 ( 4280)
  covalent geometry    : angle       0.67234 ( 5830)

********************** 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
  88 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 68
  time to evaluate  : 0.484 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  155 LEU cc_start: 0.7884 (OUTLIER) cc_final: 0.7137 (tp)
REVERT: A  168 HIS cc_start: 0.7638 (t-170) cc_final: 0.7331 (t-170)
REVERT: A  207 GLU cc_start: 0.7770 (tp30) cc_final: 0.7040 (tp30)
REVERT: A  208 MET cc_start: 0.7127 (mmm) cc_final: 0.6711 (mmm)
REVERT: A  250 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8365 (ptpt)
REVERT: B  106 TRP cc_start: 0.8498 (p90) cc_final: 0.7914 (p90)
REVERT: B  207 GLU cc_start: 0.7836 (tp30) cc_final: 0.7271 (tp30)
REVERT: B  208 MET cc_start: 0.7280 (mmm) cc_final: 0.6826 (mmm)
REVERT: B  250 LYS cc_start: 0.8593 (OUTLIER) cc_final: 0.8332 (ptpt)
  outliers start: 20
  outliers final: 15
  residues processed: 85
  average time/residue: 0.1365
  time to fit residues: 15.2081
Evaluate side-chains
  83 residues out of total 470 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 65
  time to evaluate  : 0.481 
-------------------------------------------------------------------------------
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  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  110 LEU
Chi-restraints excluded: chain B residue  145 ILE
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 50
   random chunks:
   chunk 30 optimal weight:    0.8980
   chunk 29 optimal weight:   10.0000
   chunk 34 optimal weight:   10.0000
   chunk 47 optimal weight:    4.9990
   chunk 21 optimal weight:    2.9990
   chunk 25 optimal weight:   10.0000
   chunk 44 optimal weight:    0.4980
   chunk 9 optimal weight:    7.9990
   chunk 13 optimal weight:   10.0000
   chunk 11 optimal weight:    7.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    2.0784

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

Flipped N/Q/H residues before XYZ refinement:
B 100 GLN
** B 168 HIS ** 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 = 0.4175 r_free = 0.4175 target = 0.178255 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3599 r_free = 0.3599 target = 0.126024 restraints weight = 5789.112|
|-----------------------------------------------------------------------------|
r_work (start): 0.3608 rms_B_bonded: 4.50
r_work (final): 0.3608
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7179
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.067   4290  Z= 0.208
  Angle     :  0.751   9.866   5856  Z= 0.366
  Chirality :  0.052   0.186    672
  Planarity :  0.004   0.035    742
  Dihedral  :  5.567  39.180    672
  Min Nonbonded Distance : 2.455

Molprobity Statistics.
  All-atom Clashscore : 13.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.37 %
    Favored  : 96.63 %
  Rotamer:
    Outliers :  4.27 %
    Allowed  : 31.62 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.73 (0.36), residues: 504
  helix:  None (None), residues: 0
  sheet:  0.16 (0.30), residues: 258
  loop : -1.18 (0.39), residues: 246

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 106 
 HIS   0.005   0.002   HIS B 178 
 PHE   0.014   0.002   PHE A 146 
 TYR   0.021   0.002   TYR B 188 
 ARG   0.002   0.000   ARG A 127 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00213 (    6)
  link_NAG-ASN         : angle       2.48445 (   18)
  hydrogen bonds       : bond        0.03602 (  152)
  hydrogen bonds       : angle       6.37223 (  402)
  SS BOND              : bond        0.00308 (    4)
  SS BOND              : angle       0.68470 (    8)
  covalent geometry    : bond        0.00529 ( 4280)
  covalent geometry    : angle       0.73931 ( 5830)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1825.08 seconds
wall clock time: 32 minutes 38.61 seconds (1958.61 seconds total)