Starting phenix.real_space_refine
on Wed Sep 17 03:30:21 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgs_50420/09_2025/9fgs_50420.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgs_50420/09_2025/9fgs_50420.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.0
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fgs_50420/09_2025/9fgs_50420.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgs_50420/09_2025/9fgs_50420.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgs_50420/09_2025/9fgs_50420.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgs_50420/09_2025/9fgs_50420.cif"
  }
  resolution = 4.0
  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=  -0.003 sd=   0.047
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      14      5.16       5
     C    2025      2.51       5
     N     532      2.21       5
     O     616      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3187
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1513
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 11, 'TRANS': 178}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1660
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 8, 'TRANS': 213}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 1.03, per 1000 atoms: 0.32
  Number of scatterers: 3187
  At special positions: 0
  Unit cell: (83.566, 63.119, 88.011, 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      14     16.00
     O     616      8.00
     N     532      7.00
     C    2025      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.04
    Simple disulfide: pdb=" SG  CYS E  22 " - pdb=" SG  CYS E  95 " distance=2.03
    Simple disulfide: pdb=" SG  CYS E 156 " - pdb=" SG  CYS E 222 " distance=2.04

  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 C1301 " - " ASN C 343 "
  Time building additional restraints: 0.25
  Conformation dependent library (CDL) restraints added in 124.1 milliseconds
  
  Enol-peptide restraints added in 476.8 nanoseconds
  

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  750

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 6 sheets defined
      7.3% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.12
  Creating SS restraints...
    Processing helix  chain 'C' and resid 364 through 368
      removed outlier: 4.472A  pdb=" N   VAL C 367 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 411
      removed outlier: 4.192A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA C 411 " --> pdb=" O   ARG C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
      removed outlier: 3.640A  pdb=" N   TYR C 421 " --> pdb=" O   LYS C 417 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 90
      removed outlier: 3.801A  pdb=" N   THR E  90 " --> pdb=" O   VAL E  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 213 through 217
      removed outlier: 3.972A  pdb=" N   LEU E 217 " --> pdb=" O   ALA E 214 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 355 through 358
      removed outlier: 4.253A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP C 398 " --> pdb=" O   VAL C 512 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL C 512 " --> pdb=" O   ASP C 398 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY C 431 " --> pdb=" O   TYR C 380 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.591A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU E  18 " --> pdb=" O   MET E  82 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.799A  pdb=" N   THR E 115 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL E  12 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL E 114 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA E  91 " --> pdb=" O   VAL E 114 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   MET E  34 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   VAL E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL E  50 " --> pdb=" O   PHE E  58 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139
      removed outlier: 3.539A  pdb=" N   ALA E 152 " --> pdb=" O   ILE E 209 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR E 206 " --> pdb=" O   SER E 199 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188
      removed outlier: 7.038A  pdb=" N   TRP E 169 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   TYR E 183 " --> pdb=" O   LEU E 167 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   LEU E 167 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN E 223 " --> pdb=" O   ALA E 168 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR E 236 " --> pdb=" O   TYR E 220 " (cutoff:3.500A)

    71 hydrogen bonds defined for protein.
    165 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: 0.43

  Time building geometry restraints manager: 0.35 seconds

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

  Histogram of bond lengths:
        1.23 -     1.34: 1021
        1.34 -     1.46: 850
        1.46 -     1.58: 1376
        1.58 -     1.70: 0
        1.70 -     1.81: 16
  Bond restraints: 3263
  Sorted by residual:
  bond pdb=" C   ALA C 520 "
       pdb=" N   PRO C 521 "
    ideal  model  delta    sigma   weight residual
    1.332  1.356 -0.024 1.12e-02 7.97e+03 4.66e+00
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.442 -0.036 2.00e-02 2.50e+03 3.16e+00
  bond pdb=" C5  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.08e+00
  bond pdb=" C3  NAG C1301 "
       pdb=" O3  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.403  1.422 -0.019 2.00e-02 2.50e+03 9.26e-01
  bond pdb=" CB  GLU E 215 "
       pdb=" CG  GLU E 215 "
    ideal  model  delta    sigma   weight residual
    1.520  1.545 -0.025 3.00e-02 1.11e+03 6.94e-01
  ... (remaining 3258 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.04: 4074
        1.04 -     2.08: 277
        2.08 -     3.13: 61
        3.13 -     4.17: 21
        4.17 -     5.21: 7
  Bond angle restraints: 4440
  Sorted by residual:
  angle pdb=" CA  ALA C 520 "
        pdb=" C   ALA C 520 "
        pdb=" N   PRO C 521 "
      ideal   model   delta    sigma   weight residual
     117.67  120.55   -2.88 1.09e+00 8.42e-01 6.98e+00
  angle pdb=" CA  ARG E 211 "
        pdb=" CB  ARG E 211 "
        pdb=" CG  ARG E 211 "
      ideal   model   delta    sigma   weight residual
     114.10  119.31   -5.21 2.00e+00 2.50e-01 6.79e+00
  angle pdb=" CA  ALA C 520 "
        pdb=" C   ALA C 520 "
        pdb=" O   ALA C 520 "
      ideal   model   delta    sigma   weight residual
     121.08  118.83    2.25 8.90e-01 1.26e+00 6.38e+00
  angle pdb=" N   ALA E  91 "
        pdb=" CA  ALA E  91 "
        pdb=" C   ALA E  91 "
      ideal   model   delta    sigma   weight residual
     107.73  111.65   -3.92 1.61e+00 3.86e-01 5.92e+00
  angle pdb=" N   SER C 438 "
        pdb=" CA  SER C 438 "
        pdb=" C   SER C 438 "
      ideal   model   delta    sigma   weight residual
     108.17  112.64   -4.47 1.85e+00 2.92e-01 5.83e+00
  ... (remaining 4435 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.91: 1747
       17.91 -    35.82: 153
       35.82 -    53.73: 22
       53.73 -    71.64: 6
       71.64 -    89.55: 2
  Dihedral angle restraints: 1930
    sinusoidal: 744
      harmonic: 1186
  Sorted by residual:
  dihedral pdb=" CB  CYS C 480 "
           pdb=" SG  CYS C 480 "
           pdb=" SG  CYS C 488 "
           pdb=" CB  CYS C 488 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  152.82  -59.82     1      1.00e+01 1.00e-02 4.77e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  128.68  -35.68     1      1.00e+01 1.00e-02 1.80e+01
  dihedral pdb=" CB  CYS E 156 "
           pdb=" SG  CYS E 156 "
           pdb=" SG  CYS E 222 "
           pdb=" CB  CYS E 222 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   59.90   33.10     1      1.00e+01 1.00e-02 1.56e+01
  ... (remaining 1927 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.044: 373
       0.044 -    0.087: 87
       0.087 -    0.131: 28
       0.131 -    0.175: 0
       0.175 -    0.218: 1
  Chirality restraints: 489
  Sorted by residual:
  chirality pdb=" CB  ILE C 468 "
            pdb=" CA  ILE C 468 "
            pdb=" CG1 ILE C 468 "
            pdb=" CG2 ILE C 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.43    0.22 2.00e-01 2.50e+01 1.19e+00
  chirality pdb=" CA  VAL C 401 "
            pdb=" N   VAL C 401 "
            pdb=" C   VAL C 401 "
            pdb=" CB  VAL C 401 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.44    2.57   -0.13 2.00e-01 2.50e+01 4.12e-01
  chirality pdb=" CA  ASP E 216 "
            pdb=" N   ASP E 216 "
            pdb=" C   ASP E 216 "
            pdb=" CB  ASP E 216 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.09e-01
  ... (remaining 486 not shown)

  Planarity restraints: 574
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN C 343 "    0.001 2.00e-02 2.50e+03   1.93e-02 4.66e+00
        pdb=" CG  ASN C 343 "   -0.024 2.00e-02 2.50e+03
        pdb=" OD1 ASN C 343 "    0.023 2.00e-02 2.50e+03
        pdb=" ND2 ASN C 343 "   -0.019 2.00e-02 2.50e+03
        pdb=" C1  NAG C1301 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   CYS C 336 "    0.026 5.00e-02 4.00e+02   4.05e-02 2.63e+00
        pdb=" N   PRO C 337 "   -0.070 5.00e-02 4.00e+02
        pdb=" CA  PRO C 337 "    0.021 5.00e-02 4.00e+02
        pdb=" CD  PRO C 337 "    0.022 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER C 383 "   -0.026 5.00e-02 4.00e+02   3.90e-02 2.43e+00
        pdb=" N   PRO C 384 "    0.067 5.00e-02 4.00e+02
        pdb=" CA  PRO C 384 "   -0.020 5.00e-02 4.00e+02
        pdb=" CD  PRO C 384 "   -0.022 5.00e-02 4.00e+02
  ... (remaining 571 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 716
        2.78 -     3.31: 2841
        3.31 -     3.84: 4747
        3.84 -     4.37: 5344
        4.37 -     4.90: 9350
  Nonbonded interactions: 22998
  Sorted by model distance:
  nonbonded pdb=" OD2 ASP C 442 "
            pdb=" OH  TYR C 451 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OD1 ASP C 427 "
            pdb=" N   ASP C 428 "
     model   vdw
     2.290 3.120
  nonbonded pdb=" OG  SER C 349 "
            pdb=" O   LEU C 452 "
     model   vdw
     2.294 3.040
  nonbonded pdb=" O   SER C 359 "
            pdb=" OG1 THR C 523 "
     model   vdw
     2.313 3.040
  nonbonded pdb=" NH1 ARG E  38 "
            pdb=" OD1 ASP E  89 "
     model   vdw
     2.319 3.120
  ... (remaining 22993 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             4.280
  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:          0.070
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     5.260
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.000
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.210
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   10.860
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
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      :  0.003   0.036   3270  Z= 0.156
  Angle     :  0.666   6.316   4455  Z= 0.362
  Chirality :  0.043   0.218    489
  Planarity :  0.004   0.041    573
  Dihedral  : 13.377  89.545   1162
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.99 (0.39), residues: 404
  helix: -4.31 (0.76), residues: 12
  sheet: -0.72 (0.47), residues: 124
  loop : -1.53 (0.35), residues: 268

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG E 188 
 TYR   0.016   0.001   TYR C 473 
 PHE   0.019   0.002   PHE C 392 
 TRP   0.011   0.002   TRP C 436 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00329 ( 3263)
  covalent geometry    : angle       0.65724 ( 4440)
  SS BOND              : bond        0.00295 (    6)
  SS BOND              : angle       0.70418 (   12)
  hydrogen bonds       : bond        0.25377 (   71)
  hydrogen bonds       : angle      10.87525 (  165)
  link_NAG-ASN         : bond        0.00209 (    1)
  link_NAG-ASN         : angle       4.18427 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.130 
Fit side-chains
REVERT: C  368 LEU cc_start: 0.8618 (mm) cc_final: 0.8229 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.0678
  time to fit residues: 5.3420
Evaluate side-chains
  45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.125 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 24 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 2 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0270
   chunk 32 optimal weight:    3.9990
   chunk 31 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9980
   chunk 19 optimal weight:    1.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9990
   chunk 37 optimal weight:    4.9990
   overall best weight:    0.7238

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

Flipped N/Q/H residues before XYZ refinement:
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 519 HIS
E 234 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3455 r_free = 0.3455 target = 0.112699 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3291 r_free = 0.3291 target = 0.101438 restraints weight = 7599.931|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 38)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.103502 restraints weight = 4585.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 21)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.104901 restraints weight = 3120.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.106022 restraints weight = 2342.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3366 r_free = 0.3366 target = 0.106591 restraints weight = 1853.468|
|-----------------------------------------------------------------------------|
r_work (final): 0.3364
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.1387

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   3270  Z= 0.161
  Angle     :  0.635   5.609   4455  Z= 0.325
  Chirality :  0.044   0.142    489
  Planarity :  0.005   0.038    573
  Dihedral  :  6.942  58.398    476
  Min Nonbonded Distance : 2.392

Molprobity Statistics.
  All-atom Clashscore : 11.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  9.36 %
    Favored  : 88.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.88 (0.40), residues: 404
  helix: -4.55 (0.69), residues: 12
  sheet: -0.59 (0.45), residues: 134
  loop : -1.50 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E  66 
 TYR   0.018   0.001   TYR C 380 
 PHE   0.019   0.002   PHE C 392 
 TRP   0.007   0.001   TRP C 353 
 HIS   0.001   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00382 ( 3263)
  covalent geometry    : angle       0.62822 ( 4440)
  SS BOND              : bond        0.00718 (    6)
  SS BOND              : angle       1.43177 (   12)
  hydrogen bonds       : bond        0.04025 (   71)
  hydrogen bonds       : angle       7.32254 (  165)
  link_NAG-ASN         : bond        0.00019 (    1)
  link_NAG-ASN         : angle       2.43610 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 52
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: C  368 LEU cc_start: 0.8735 (mm) cc_final: 0.8233 (mt)
REVERT: E   75 LYS cc_start: 0.7635 (mmtt) cc_final: 0.7081 (tptm)
  outliers start: 7
  outliers final: 5
  residues processed: 56
  average time/residue: 0.0666
  time to fit residues: 4.6029
Evaluate side-chains
  51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 46
  time to evaluate  : 0.102 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  512 VAL
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 25 optimal weight:    0.8980
   chunk 37 optimal weight:    4.9990
   chunk 20 optimal weight:    0.5980
   chunk 39 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 22 optimal weight:    0.9990
   chunk 14 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 24 optimal weight:    0.5980
   overall best weight:    0.7380

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

Flipped N/Q/H residues before XYZ refinement:
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 519 HIS
E 234 GLN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3443 r_free = 0.3443 target = 0.112819 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3284 r_free = 0.3284 target = 0.101411 restraints weight = 7428.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.103559 restraints weight = 4518.720|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3334 r_free = 0.3334 target = 0.104969 restraints weight = 3092.725|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.106101 restraints weight = 2332.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3359 r_free = 0.3359 target = 0.106775 restraints weight = 1848.793|
|-----------------------------------------------------------------------------|
r_work (final): 0.3358
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8030
moved from start:          0.1689

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3270  Z= 0.159
  Angle     :  0.612   4.853   4455  Z= 0.319
  Chirality :  0.044   0.137    489
  Planarity :  0.004   0.039    573
  Dihedral  :  6.673  51.055    476
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 9.61
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.15 %
    Favored  : 89.85 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 12.87 %
    Favored  : 84.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.99 (0.40), residues: 404
  helix: -4.54 (0.69), residues: 12
  sheet: -0.59 (0.45), residues: 134
  loop : -1.62 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG C 357 
 TYR   0.015   0.001   TYR C 380 
 PHE   0.011   0.002   PHE C 429 
 TRP   0.009   0.001   TRP C 353 
 HIS   0.003   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00381 ( 3263)
  covalent geometry    : angle       0.60534 ( 4440)
  SS BOND              : bond        0.00507 (    6)
  SS BOND              : angle       1.42041 (   12)
  hydrogen bonds       : bond        0.03332 (   71)
  hydrogen bonds       : angle       6.71694 (  165)
  link_NAG-ASN         : bond        0.00052 (    1)
  link_NAG-ASN         : angle       2.29343 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 52
  time to evaluate  : 0.147 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: E   75 LYS cc_start: 0.7633 (mmtt) cc_final: 0.7056 (tptm)
  outliers start: 9
  outliers final: 7
  residues processed: 57
  average time/residue: 0.0651
  time to fit residues: 4.6147
Evaluate side-chains
  53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.117 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.8980
   chunk 6 optimal weight:    0.0870
   chunk 19 optimal weight:    0.8980
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    0.9980
   chunk 10 optimal weight:    0.0570
   chunk 20 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5476

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

Flipped N/Q/H residues before XYZ refinement:
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
C 519 HIS
E  39 GLN
E 172 GLN
E 234 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3465 r_free = 0.3465 target = 0.114077 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.102681 restraints weight = 7273.124|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.104834 restraints weight = 4414.973|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3355 r_free = 0.3355 target = 0.106214 restraints weight = 3008.157|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.107351 restraints weight = 2274.579|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108014 restraints weight = 1803.319|
|-----------------------------------------------------------------------------|
r_work (final): 0.3377
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8000
moved from start:          0.2012

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3270  Z= 0.134
  Angle     :  0.609   5.798   4455  Z= 0.317
  Chirality :  0.044   0.217    489
  Planarity :  0.004   0.042    573
  Dihedral  :  6.326  51.858    476
  Min Nonbonded Distance : 2.448

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.67 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  1.75 %
    Allowed  : 16.08 %
    Favored  : 82.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.91 (0.40), residues: 404
  helix: -4.68 (0.56), residues: 12
  sheet: -0.48 (0.48), residues: 125
  loop : -1.57 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG C 454 
 TYR   0.012   0.001   TYR C 380 
 PHE   0.009   0.001   PHE C 429 
 TRP   0.008   0.001   TRP C 353 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00320 ( 3263)
  covalent geometry    : angle       0.59839 ( 4440)
  SS BOND              : bond        0.00661 (    6)
  SS BOND              : angle       1.97705 (   12)
  hydrogen bonds       : bond        0.02870 (   71)
  hydrogen bonds       : angle       6.47705 (  165)
  link_NAG-ASN         : bond        0.00108 (    1)
  link_NAG-ASN         : angle       2.14687 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 50
  time to evaluate  : 0.135 
Fit side-chains
   revert: symmetry clash
REVERT: E   75 LYS cc_start: 0.7675 (mmtt) cc_final: 0.7065 (tptm)
  outliers start: 6
  outliers final: 5
  residues processed: 53
  average time/residue: 0.0615
  time to fit residues: 4.0344
Evaluate side-chains
  48 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 43
  time to evaluate  : 0.120 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 1 optimal weight:    0.0970
   chunk 22 optimal weight:    2.9990
   chunk 6 optimal weight:    0.9980
   chunk 36 optimal weight:    0.0070
   chunk 23 optimal weight:    0.5980
   chunk 21 optimal weight:    0.9980
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    0.1980
   chunk 38 optimal weight:    0.0570
   chunk 14 optimal weight:    0.2980
   overall best weight:    0.1314

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 506 GLN
C 519 HIS
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 234 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3512 r_free = 0.3512 target = 0.117477 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.105819 restraints weight = 7259.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108066 restraints weight = 4364.195|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3403 r_free = 0.3403 target = 0.109631 restraints weight = 2950.538|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.110695 restraints weight = 2196.921|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3429 r_free = 0.3429 target = 0.111433 restraints weight = 1737.894|
|-----------------------------------------------------------------------------|
r_work (final): 0.3424
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7910
moved from start:          0.2287

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   3270  Z= 0.101
  Angle     :  0.565   4.538   4455  Z= 0.295
  Chirality :  0.043   0.130    489
  Planarity :  0.004   0.042    573
  Dihedral  :  5.682  53.842    476
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.18 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 18.42 %
    Favored  : 78.95 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.77 (0.40), residues: 404
  helix: -4.87 (0.38), residues: 12
  sheet: -0.35 (0.48), residues: 125
  loop : -1.47 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG E 195 
 TYR   0.012   0.001   TYR E  79 
 PHE   0.011   0.001   PHE C 429 
 TRP   0.007   0.001   TRP E  47 
 HIS   0.002   0.001   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00224 ( 3263)
  covalent geometry    : angle       0.56029 ( 4440)
  SS BOND              : bond        0.00328 (    6)
  SS BOND              : angle       1.24444 (   12)
  hydrogen bonds       : bond        0.02607 (   71)
  hydrogen bonds       : angle       6.10235 (  165)
  link_NAG-ASN         : bond        0.00167 (    1)
  link_NAG-ASN         : angle       1.78149 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 50
  time to evaluate  : 0.125 
Fit side-chains
REVERT: C  452 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8130 (pp)
REVERT: E   75 LYS cc_start: 0.7435 (mmtt) cc_final: 0.6949 (tptm)
REVERT: E  216 ASP cc_start: 0.7898 (p0) cc_final: 0.7682 (p0)
  outliers start: 9
  outliers final: 6
  residues processed: 55
  average time/residue: 0.0698
  time to fit residues: 4.7282
Evaluate side-chains
  51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.123 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.0370
   chunk 18 optimal weight:    2.9990
   chunk 29 optimal weight:    2.9990
   chunk 8 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 32 optimal weight:    4.9990
   chunk 36 optimal weight:    0.0770
   chunk 5 optimal weight:    1.9990
   chunk 9 optimal weight:    0.8980
   chunk 24 optimal weight:    0.0030
   overall best weight:    0.3626

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 519 HIS
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 234 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.116055 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.104104 restraints weight = 7255.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3358 r_free = 0.3358 target = 0.106469 restraints weight = 4224.492|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.108058 restraints weight = 2806.962|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3395 r_free = 0.3395 target = 0.109086 restraints weight = 2072.721|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.109935 restraints weight = 1650.889|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7942
moved from start:          0.2423

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.023   3270  Z= 0.110
  Angle     :  0.596   9.382   4455  Z= 0.302
  Chirality :  0.043   0.128    489
  Planarity :  0.004   0.044    573
  Dihedral  :  6.252  53.219    476
  Min Nonbonded Distance : 2.399

Molprobity Statistics.
  All-atom Clashscore : 9.45
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.67 %
    Favored  : 92.08 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 19.88 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.74 (0.40), residues: 404
  helix: -4.85 (0.37), residues: 12
  sheet: -0.32 (0.48), residues: 125
  loop : -1.46 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG E 211 
 TYR   0.011   0.001   TYR C 380 
 PHE   0.014   0.001   PHE C 374 
 TRP   0.006   0.001   TRP E  47 
 HIS   0.003   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 3263)
  covalent geometry    : angle       0.57653 ( 4440)
  SS BOND              : bond        0.00414 (    6)
  SS BOND              : angle       1.29727 (   12)
  hydrogen bonds       : bond        0.02623 (   71)
  hydrogen bonds       : angle       5.98953 (  165)
  link_NAG-ASN         : bond        0.00102 (    1)
  link_NAG-ASN         : angle       5.43211 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 47
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8492 (t0) cc_final: 0.8213 (t0)
REVERT: C  452 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8137 (pp)
REVERT: E   75 LYS cc_start: 0.7486 (mmtt) cc_final: 0.6944 (tptm)
  outliers start: 9
  outliers final: 6
  residues processed: 53
  average time/residue: 0.0587
  time to fit residues: 3.7565
Evaluate side-chains
  51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 29 optimal weight:    1.9990
   chunk 2 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 20 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 9 optimal weight:    0.5980
   chunk 34 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 15 optimal weight:    3.9990
   chunk 26 optimal weight:    0.0370
   overall best weight:    0.8660

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 519 HIS
** E   6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 234 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112400 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3273 r_free = 0.3273 target = 0.100727 restraints weight = 7563.651|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3304 r_free = 0.3304 target = 0.102856 restraints weight = 4707.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.104269 restraints weight = 3245.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 31)----------------|
| r_work = 0.3338 r_free = 0.3338 target = 0.105324 restraints weight = 2461.349|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3348 r_free = 0.3348 target = 0.106018 restraints weight = 1973.369|
|-----------------------------------------------------------------------------|
r_work (final): 0.3345
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8044
moved from start:          0.2458

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.033   3270  Z= 0.181
  Angle     :  0.640   6.507   4455  Z= 0.331
  Chirality :  0.045   0.174    489
  Planarity :  0.005   0.046    573
  Dihedral  :  6.491  51.081    476
  Min Nonbonded Distance : 2.395

Molprobity Statistics.
  All-atom Clashscore : 10.41
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  9.41 %
    Favored  : 90.35 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 19.59 %
    Favored  : 76.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -2.00 (0.39), residues: 404
  helix: -4.72 (0.47), residues: 12
  sheet: -0.47 (0.47), residues: 130
  loop : -1.69 (0.35), residues: 262

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 211 
 TYR   0.012   0.001   TYR C 380 
 PHE   0.017   0.002   PHE C 374 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.004   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00422 ( 3263)
  covalent geometry    : angle       0.62720 ( 4440)
  SS BOND              : bond        0.00483 (    6)
  SS BOND              : angle       1.63473 (   12)
  hydrogen bonds       : bond        0.02914 (   71)
  hydrogen bonds       : angle       6.17129 (  165)
  link_NAG-ASN         : bond        0.00268 (    1)
  link_NAG-ASN         : angle       4.00682 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 49
  time to evaluate  : 0.073 
Fit side-chains
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8563 (t0) cc_final: 0.8328 (t0)
REVERT: C  452 LEU cc_start: 0.8433 (OUTLIER) cc_final: 0.8199 (pp)
REVERT: E   75 LYS cc_start: 0.7675 (OUTLIER) cc_final: 0.7087 (tptm)
  outliers start: 13
  outliers final: 9
  residues processed: 57
  average time/residue: 0.0656
  time to fit residues: 4.5892
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    2.9990
   chunk 18 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9980
   chunk 2 optimal weight:    0.8980
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 12 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9990
   chunk 10 optimal weight:    0.0870
   overall best weight:    0.7760

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 519 HIS
E   6 GLN
** E  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 172 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E 234 GLN

Total number of N/Q/H flips: 4

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3442 r_free = 0.3442 target = 0.112897 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3263 r_free = 0.3263 target = 0.100490 restraints weight = 7469.772|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.102793 restraints weight = 4532.541|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.104372 restraints weight = 3096.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.105505 restraints weight = 2320.873|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3346 r_free = 0.3346 target = 0.106232 restraints weight = 1853.381|
|-----------------------------------------------------------------------------|
r_work (final): 0.3336
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8046
moved from start:          0.2628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   3270  Z= 0.165
  Angle     :  0.643   5.672   4455  Z= 0.336
  Chirality :  0.045   0.196    489
  Planarity :  0.005   0.045    573
  Dihedral  :  6.496  51.981    476
  Min Nonbonded Distance : 2.428

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.91 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  4.09 %
    Allowed  : 19.01 %
    Favored  : 76.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.97 (0.40), residues: 404
  helix: -4.82 (0.36), residues: 12
  sheet: -0.40 (0.46), residues: 131
  loop : -1.69 (0.37), residues: 261

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG C 408 
 TYR   0.013   0.001   TYR C 380 
 PHE   0.016   0.001   PHE C 374 
 TRP   0.011   0.001   TRP C 436 
 HIS   0.003   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00388 ( 3263)
  covalent geometry    : angle       0.63226 ( 4440)
  SS BOND              : bond        0.00515 (    6)
  SS BOND              : angle       1.61725 (   12)
  hydrogen bonds       : bond        0.02824 (   71)
  hydrogen bonds       : angle       6.23662 (  165)
  link_NAG-ASN         : bond        0.00106 (    1)
  link_NAG-ASN         : angle       3.52130 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  56 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 42
  time to evaluate  : 0.083 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8553 (t0) cc_final: 0.8243 (t0)
REVERT: C  452 LEU cc_start: 0.8473 (OUTLIER) cc_final: 0.8264 (pp)
REVERT: E   75 LYS cc_start: 0.7638 (OUTLIER) cc_final: 0.7030 (tptm)
  outliers start: 14
  outliers final: 10
  residues processed: 52
  average time/residue: 0.0736
  time to fit residues: 4.6515
Evaluate side-chains
  54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.135 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    0.0770
   chunk 32 optimal weight:    0.9980
   chunk 40 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9980
   chunk 10 optimal weight:    0.9990
   chunk 14 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    3.9990
   chunk 34 optimal weight:    0.5980
   chunk 5 optimal weight:    0.6980
   chunk 20 optimal weight:    0.0970
   overall best weight:    0.4936

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 519 HIS
E 234 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.113935 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3296 r_free = 0.3296 target = 0.102225 restraints weight = 7473.441|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.104398 restraints weight = 4612.677|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.105868 restraints weight = 3175.095|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3364 r_free = 0.3364 target = 0.106900 restraints weight = 2383.280|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3374 r_free = 0.3374 target = 0.107610 restraints weight = 1916.242|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.2725

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3270  Z= 0.133
  Angle     :  0.628   6.331   4455  Z= 0.331
  Chirality :  0.044   0.148    489
  Planarity :  0.004   0.044    573
  Dihedral  :  6.202  53.076    476
  Min Nonbonded Distance : 2.446

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.17 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 21.05 %
    Favored  : 76.32 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.86 (0.40), residues: 404
  helix: -4.83 (0.34), residues: 12
  sheet: -0.36 (0.47), residues: 126
  loop : -1.57 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.001   ARG E 195 
 TYR   0.012   0.001   TYR C 380 
 PHE   0.013   0.001   PHE C 374 
 TRP   0.008   0.001   TRP C 436 
 HIS   0.003   0.002   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00313 ( 3263)
  covalent geometry    : angle       0.61874 ( 4440)
  SS BOND              : bond        0.00426 (    6)
  SS BOND              : angle       1.40122 (   12)
  hydrogen bonds       : bond        0.02617 (   71)
  hydrogen bonds       : angle       6.12727 (  165)
  link_NAG-ASN         : bond        0.00013 (    1)
  link_NAG-ASN         : angle       3.28094 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.146 
Fit side-chains
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8526 (t0) cc_final: 0.8256 (t0)
REVERT: C  452 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8249 (pp)
REVERT: E   75 LYS cc_start: 0.7550 (tmtt) cc_final: 0.6956 (tptm)
  outliers start: 9
  outliers final: 6
  residues processed: 51
  average time/residue: 0.0750
  time to fit residues: 4.6421
Evaluate side-chains
  51 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 44
  time to evaluate  : 0.119 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 13 optimal weight:    0.0980
   chunk 35 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 14 optimal weight:    1.9990
   chunk 21 optimal weight:    0.5980
   chunk 7 optimal weight:    0.0970
   chunk 19 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 33 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 4 optimal weight:    0.1980
   overall best weight:    0.3378

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 519 HIS
E 234 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3491 r_free = 0.3491 target = 0.115523 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.103849 restraints weight = 7317.837|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3351 r_free = 0.3351 target = 0.106012 restraints weight = 4504.701|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.107504 restraints weight = 3104.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3386 r_free = 0.3386 target = 0.108468 restraints weight = 2334.609|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.109241 restraints weight = 1896.048|
|-----------------------------------------------------------------------------|
r_work (final): 0.3397
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7963
moved from start:          0.2918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3270  Z= 0.119
  Angle     :  0.625   7.107   4455  Z= 0.329
  Chirality :  0.044   0.148    489
  Planarity :  0.004   0.044    573
  Dihedral  :  5.967  53.727    476
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 8.49
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.18 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.05 %
    Favored  : 76.02 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.83 (0.40), residues: 404
  helix: -4.84 (0.33), residues: 12
  sheet: -0.31 (0.47), residues: 126
  loop : -1.57 (0.37), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG E 211 
 TYR   0.011   0.001   TYR E  79 
 PHE   0.013   0.001   PHE C 400 
 TRP   0.006   0.001   TRP C 436 
 HIS   0.004   0.003   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3263)
  covalent geometry    : angle       0.61706 ( 4440)
  SS BOND              : bond        0.00414 (    6)
  SS BOND              : angle       1.23698 (   12)
  hydrogen bonds       : bond        0.02461 (   71)
  hydrogen bonds       : angle       6.13137 (  165)
  link_NAG-ASN         : bond        0.00069 (    1)
  link_NAG-ASN         : angle       3.09335 (    3)

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 51
  time to evaluate  : 0.126 
Fit side-chains
   revert: symmetry clash
REVERT: C  452 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8310 (pp)
REVERT: E   75 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6927 (tptm)
  outliers start: 10
  outliers final: 7
  residues processed: 57
  average time/residue: 0.0707
  time to fit residues: 4.8761
Evaluate side-chains
  57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 48
  time to evaluate  : 0.106 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  336 CYS
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    0.0970
   chunk 6 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 19 optimal weight:    0.6980
   chunk 7 optimal weight:    0.4980
   chunk 21 optimal weight:    0.4980
   chunk 0 optimal weight:    1.9990
   chunk 38 optimal weight:    2.9990
   chunk 25 optimal weight:    0.9990
   chunk 2 optimal weight:    1.9990
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
C 409 GLN
C 519 HIS
E 234 GLN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3477 r_free = 0.3477 target = 0.114561 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3300 r_free = 0.3300 target = 0.102509 restraints weight = 7530.906|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.104761 restraints weight = 4582.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3354 r_free = 0.3354 target = 0.106289 restraints weight = 3128.417|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3370 r_free = 0.3370 target = 0.107359 restraints weight = 2344.517|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.108029 restraints weight = 1882.423|
|-----------------------------------------------------------------------------|
r_work (final): 0.3372
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7990
moved from start:          0.2856

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3270  Z= 0.145
  Angle     :  0.669   7.683   4455  Z= 0.353
  Chirality :  0.045   0.176    489
  Planarity :  0.005   0.044    573
  Dihedral  :  6.035  52.790    476
  Min Nonbonded Distance : 2.418

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.92 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.35 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -1.87 (0.40), residues: 404
  helix: -4.83 (0.33), residues: 12
  sheet: -0.35 (0.47), residues: 126
  loop : -1.59 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.001   ARG E 195 
 TYR   0.011   0.001   TYR E  79 
 PHE   0.011   0.001   PHE C 374 
 TRP   0.009   0.001   TRP C 436 
 HIS   0.004   0.003   HIS C 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00342 ( 3263)
  covalent geometry    : angle       0.66154 ( 4440)
  SS BOND              : bond        0.00445 (    6)
  SS BOND              : angle       1.39324 (   12)
  hydrogen bonds       : bond        0.02602 (   71)
  hydrogen bonds       : angle       6.43604 (  165)
  link_NAG-ASN         : bond        0.00004 (    1)
  link_NAG-ASN         : angle       3.04432 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 831.72 seconds
wall clock time: 15 minutes 2.30 seconds (902.30 seconds total)