Starting phenix.real_space_refine
on Sat Apr 26 23:19:52 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j77_36030/04_2025/8j77_36030.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j77_36030/04_2025/8j77_36030.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8j77_36030/04_2025/8j77_36030.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j77_36030/04_2025/8j77_36030.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j77_36030/04_2025/8j77_36030.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j77_36030/04_2025/8j77_36030.cif"
  }
  resolution = 3.7
  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=   0.000 sd=   0.157
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      19      5.16       5
     C    2513      2.51       5
     N     577      2.21       5
     O     669      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3778
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 3732
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 493, 3732
          Classifications: {'peptide': 493}
          Incomplete info: {'truncation_to_alanine': 22}
          Link IDs: {'PTRANS': 22, 'TRANS': 470}
          Chain breaks: 2
          Unresolved chain link angles: 2
          Unresolved non-hydrogen bonds: 78
          Unresolved non-hydrogen angles: 101
          Unresolved non-hydrogen dihedrals: 67
          Unresolved non-hydrogen chiralities: 8
          Planarities with less than four sites: {'TYR:plan': 2, 'PHE:plan': 2, 'ASP:plan': 2, 'GLU:plan': 1}
          Unresolved non-hydrogen planarities: 36
    Chain: "B"
      Number of atoms: 39
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 3, 39
          Unusual residues: {'BMA': 1, 'NAG': 2}
          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: "A"
      Number of atoms: 7
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 7
          Unusual residues: {'CHT': 1}
          Classifications: {'undetermined': 1}
  Time building chain proxies: 3.16, per 1000 atoms: 0.84
  Number of scatterers: 3778
  At special positions: 0
  Unit cell: (86.1, 69.7, 91.02, 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      19     16.00
     O     669      8.00
     N     577      7.00
     C    2513      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=0, symmetry=0

  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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
      " NAG B   2 " - " BMA B   3 "
    NAG-ASN
      " NAG B   1 " - " ASN A 301 "
  Time building additional restraints: 1.09
  Conformation dependent library (CDL) restraints added in 514.5 milliseconds
  

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  898

  Finding SS restraints...
    Secondary structure from input PDB file:
      23 helices and 1 sheets defined
      74.4% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.36
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 28
    Processing helix  chain 'A' and resid 49 through 63
      removed outlier: 3.775A  pdb=" N   TRP A  62 " --> pdb=" O   MET A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 66 through 77
    Processing helix  chain 'A' and resid 81 through 84
    Processing helix  chain 'A' and resid 85 through 103
      removed outlier: 4.763A  pdb=" N   ILE A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 3.670A  pdb=" N   SER A  92 " --> pdb=" O   PRO A  88 " (cutoff:3.500A)
      removed outlier: 3.518A  pdb=" N   LEU A  93 " --> pdb=" O   ILE A  89 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 104 through 107
      removed outlier: 3.514A  pdb=" N   ARG A 107 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 104 through 107'
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 4.538A  pdb=" N   PHE A 118 " --> pdb=" O   MET A 114 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 158
      removed outlier: 3.926A  pdb=" N   LEU A 129 " --> pdb=" O   ARG A 125 " (cutoff:3.500A)
      Proline residue:  A 133  - end of helix
    Processing helix  chain 'A' and resid 161 through 179
    Processing helix  chain 'A' and resid 187 through 201
    Processing helix  chain 'A' and resid 216 through 220
      removed outlier: 3.577A  pdb=" N   ALA A 219 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 235
      No H-bonds generated for 'chain 'A' and resid 233 through 235'
    Processing helix  chain 'A' and resid 236 through 251
      removed outlier: 3.945A  pdb=" N   LEU A 247 " --> pdb=" O   SER A 243 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 254 through 263
      removed outlier: 3.526A  pdb=" N   PHE A 258 " --> pdb=" O   TRP A 254 " (cutoff:3.500A)
      removed outlier: 3.505A  pdb=" N   LEU A 262 " --> pdb=" O   PHE A 258 " (cutoff:3.500A)
      removed outlier: 3.889A  pdb=" N   SER A 263 " --> pdb=" O   GLN A 259 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 298
      removed outlier: 3.912A  pdb=" N   ALA A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      removed outlier: 4.300A  pdb=" N   GLN A 271 " --> pdb=" O   ALA A 267 " (cutoff:3.500A)
      removed outlier: 3.629A  pdb=" N   ILE A 286 " --> pdb=" O   LEU A 282 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
      removed outlier: 3.637A  pdb=" N   ILE A 291 " --> pdb=" O   PRO A 287 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 315 through 317
      No H-bonds generated for 'chain 'A' and resid 315 through 317'
    Processing helix  chain 'A' and resid 318 through 327
    Processing helix  chain 'A' and resid 329 through 367
      removed outlier: 3.699A  pdb=" N   PHE A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 3.930A  pdb=" N   PHE A 335 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 3.733A  pdb=" N   GLY A 336 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
      removed outlier: 3.725A  pdb=" N   ASP A 349 " --> pdb=" O   MET A 345 " (cutoff:3.500A)
      removed outlier: 3.824A  pdb=" N   SER A 350 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   PHE A 359 " --> pdb=" O   ALA A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 397
    Processing helix  chain 'A' and resid 402 through 417
      removed outlier: 4.261A  pdb=" N   TRP A 406 " --> pdb=" O   VAL A 402 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 417 through 426
    Processing helix  chain 'A' and resid 431 through 448
      removed outlier: 3.746A  pdb=" N   ALA A 435 " --> pdb=" O   ASN A 431 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 479 through 502
    Processing sheet with id=AA1, first strand: chain 'A' and resid 466 through 467
      removed outlier: 3.752A  pdb=" N   ASN A 474 " --> pdb=" O   TYR A 466 " (cutoff:3.500A)

    251 hydrogen bonds defined for protein.
    744 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: 1.07

  Time building geometry restraints manager: 1.27 seconds

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

  Histogram of bond lengths:
        1.16 -     1.29: 566
        1.29 -     1.42: 1080
        1.42 -     1.55: 2197
        1.55 -     1.68: 3
        1.68 -     1.81: 34
  Bond restraints: 3880
  Sorted by residual:
  bond pdb=" C   TRP A  62 "
       pdb=" O   TRP A  62 "
    ideal  model  delta    sigma   weight residual
    1.237  1.158  0.079 1.16e-02 7.43e+03 4.63e+01
  bond pdb=" CA  TRP A  62 "
       pdb=" CB  TRP A  62 "
    ideal  model  delta    sigma   weight residual
    1.529  1.444  0.085 1.58e-02 4.01e+03 2.87e+01
  bond pdb=" CA  TRP A  62 "
       pdb=" C   TRP A  62 "
    ideal  model  delta    sigma   weight residual
    1.524  1.467  0.057 1.26e-02 6.30e+03 2.02e+01
  bond pdb=" N   TRP A  62 "
       pdb=" CA  TRP A  62 "
    ideal  model  delta    sigma   weight residual
    1.459  1.416  0.043 1.20e-02 6.94e+03 1.31e+01
  bond pdb=" C   THR A  61 "
       pdb=" N   TRP A  62 "
    ideal  model  delta    sigma   weight residual
    1.334  1.290  0.044 1.33e-02 5.65e+03 1.09e+01
  ... (remaining 3875 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     4.16: 5240
        4.16 -     8.32: 57
        8.32 -    12.48: 3
       12.48 -    16.64: 0
       16.64 -    20.81: 2
  Bond angle restraints: 5302
  Sorted by residual:
  angle pdb=" N   ALA A 222 "
        pdb=" CA  ALA A 222 "
        pdb=" C   ALA A 222 "
      ideal   model   delta    sigma   weight residual
     110.91  131.72  -20.81 1.17e+00 7.31e-01 3.16e+02
  angle pdb=" N   GLY A 123 "
        pdb=" CA  GLY A 123 "
        pdb=" C   GLY A 123 "
      ideal   model   delta    sigma   weight residual
     111.73   93.88   17.85 1.73e+00 3.34e-01 1.06e+02
  angle pdb=" N   SER A 367 "
        pdb=" CA  SER A 367 "
        pdb=" C   SER A 367 "
      ideal   model   delta    sigma   weight residual
     110.97  118.10   -7.13 1.09e+00 8.42e-01 4.28e+01
  angle pdb=" C   ALA A 222 "
        pdb=" CA  ALA A 222 "
        pdb=" CB  ALA A 222 "
      ideal   model   delta    sigma   weight residual
     112.27  100.85   11.42 1.75e+00 3.27e-01 4.26e+01
  angle pdb=" CA  THR A  61 "
        pdb=" C   THR A  61 "
        pdb=" N   TRP A  62 "
      ideal   model   delta    sigma   weight residual
     117.30  123.91   -6.61 1.16e+00 7.43e-01 3.25e+01
  ... (remaining 5297 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.80: 2086
       21.80 -    43.59: 126
       43.59 -    65.39: 10
       65.39 -    87.19: 10
       87.19 -   108.98: 4
  Dihedral angle restraints: 2236
    sinusoidal: 820
      harmonic: 1416
  Sorted by residual:
  dihedral pdb=" CA  VAL A 203 "
           pdb=" C   VAL A 203 "
           pdb=" N   PRO A 204 "
           pdb=" CA  PRO A 204 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  152.24   27.76     0      5.00e+00 4.00e-02 3.08e+01
  dihedral pdb=" CA  LYS A 428 "
           pdb=" C   LYS A 428 "
           pdb=" N   GLY A 429 "
           pdb=" CA  GLY A 429 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  156.03   23.97     0      5.00e+00 4.00e-02 2.30e+01
  dihedral pdb=" CA  TYR A 364 "
           pdb=" C   TYR A 364 "
           pdb=" N   GLN A 365 "
           pdb=" CA  GLN A 365 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  157.37   22.63     0      5.00e+00 4.00e-02 2.05e+01
  ... (remaining 2233 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.102: 596
       0.102 -    0.205: 25
       0.205 -    0.307: 3
       0.307 -    0.410: 0
       0.410 -    0.512: 2
  Chirality restraints: 626
  Sorted by residual:
  chirality pdb=" CA  ALA A 222 "
            pdb=" N   ALA A 222 "
            pdb=" C   ALA A 222 "
            pdb=" CB  ALA A 222 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.48    1.97    0.51 2.00e-01 2.50e+01 6.56e+00
  chirality pdb=" C1  NAG B   1 "
            pdb=" ND2 ASN A 301 "
            pdb=" C2  NAG B   1 "
            pdb=" O5  NAG B   1 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -1.95   -0.45 2.00e-01 2.50e+01 5.12e+00
  chirality pdb=" C5  BMA B   3 "
            pdb=" C4  BMA B   3 "
            pdb=" C6  BMA B   3 "
            pdb=" O5  BMA B   3 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.27   -2.56    0.28 2.00e-01 2.50e+01 2.02e+00
  ... (remaining 623 not shown)

  Planarity restraints: 643
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  HIS A 221 "    0.016 2.00e-02 2.50e+03   3.15e-02 9.92e+00
        pdb=" C   HIS A 221 "   -0.054 2.00e-02 2.50e+03
        pdb=" O   HIS A 221 "    0.020 2.00e-02 2.50e+03
        pdb=" N   ALA A 222 "    0.019 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ILE A 377 "   -0.010 2.00e-02 2.50e+03   1.99e-02 3.95e+00
        pdb=" C   ILE A 377 "    0.034 2.00e-02 2.50e+03
        pdb=" O   ILE A 377 "   -0.013 2.00e-02 2.50e+03
        pdb=" N   VAL A 378 "   -0.012 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLU A 314 "    0.010 2.00e-02 2.50e+03   1.89e-02 3.59e+00
        pdb=" C   GLU A 314 "   -0.033 2.00e-02 2.50e+03
        pdb=" O   GLU A 314 "    0.012 2.00e-02 2.50e+03
        pdb=" N   GLU A 315 "    0.011 2.00e-02 2.50e+03
  ... (remaining 640 not shown)

  Histogram of nonbonded interaction distances:
        2.15 -     2.70: 92
        2.70 -     3.25: 3949
        3.25 -     3.80: 5988
        3.80 -     4.35: 7159
        4.35 -     4.90: 12071
  Nonbonded interactions: 29259
  Sorted by model distance:
  nonbonded pdb=" NH1 ARG A 369 "
            pdb=" O   GLN A 370 "
     model   vdw
     2.149 3.120
  nonbonded pdb=" OH  TYR A  91 "
            pdb=" OG  SER A 410 "
     model   vdw
     2.235 3.040
  nonbonded pdb=" OD1 ASP A 188 "
            pdb=" OE1 GLN A 191 "
     model   vdw
     2.244 3.040
  nonbonded pdb=" O   ALA A 343 "
            pdb=" OG  SER A 346 "
     model   vdw
     2.269 3.040
  nonbonded pdb=" NH1 ARG A 125 "
            pdb=" O   LEU A 366 "
     model   vdw
     2.296 3.120
  ... (remaining 29254 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.390
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     14.990
  Find NCS groups from input model:        0.040
  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:3.240
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.910
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7532
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      :  0.006   0.085   3883  Z= 0.321
  Angle     :  1.054  20.805   5311  Z= 0.620
  Chirality :  0.057   0.512    626
  Planarity :  0.005   0.047    642
  Dihedral  : 15.385 108.985   1338
  Min Nonbonded Distance : 2.149

Molprobity Statistics.
  All-atom Clashscore : 13.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.00 %
    Favored  : 99.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.89 (0.39), residues: 487
  helix:  0.90 (0.30), residues: 313
  sheet:  None (None), residues: 0
  loop : -3.56 (0.42), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.018   0.002   TRP A  62 
 HIS   0.006   0.002   HIS A 162 
 PHE   0.014   0.002   PHE A  14 
 TYR   0.019   0.002   TYR A  67 
 ARG   0.004   0.001   ARG A 369 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01739 (    1)
  link_NAG-ASN         : angle       8.22372 (    3)
  link_BETA1-4         : bond        0.00389 (    2)
  link_BETA1-4         : angle       3.56125 (    6)
  hydrogen bonds       : bond        0.14458 (  251)
  hydrogen bonds       : angle       6.80963 (  744)
  covalent geometry    : bond        0.00584 ( 3880)
  covalent geometry    : angle       1.02921 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  65 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 64
  time to evaluate  : 0.322 
Fit side-chains
REVERT: A  284 MET cc_start: 0.7773 (tpp) cc_final: 0.7381 (tpt)
REVERT: A  403 TYR cc_start: 0.8519 (t80) cc_final: 0.8116 (t80)
REVERT: A  484 MET cc_start: 0.8101 (tmm) cc_final: 0.7529 (ttt)
  outliers start: 1
  outliers final: 1
  residues processed: 65
  average time/residue: 0.1544
  time to fit residues: 12.6877
Evaluate side-chains
  57 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 56
  time to evaluate  : 0.341 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 41 optimal weight:    2.9990
   chunk 37 optimal weight:    0.9990
   chunk 20 optimal weight:    4.9990
   chunk 12 optimal weight:    0.5980
   chunk 25 optimal weight:    0.6980
   chunk 19 optimal weight:    0.7980
   chunk 38 optimal weight:    0.9990
   chunk 14 optimal weight:    0.9980
   chunk 23 optimal weight:    0.8980
   chunk 28 optimal weight:    1.9990
   chunk 44 optimal weight:    4.9990
   overall best weight:    0.7980

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

Flipped N/Q/H residues before XYZ refinement:
** A 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 431 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3792 r_free = 0.3792 target = 0.173858 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.155077 restraints weight = 4451.678|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.156900 restraints weight = 3153.267|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.158592 restraints weight = 2500.082|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7510
moved from start:          0.1309

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.042   3883  Z= 0.168
  Angle     :  0.770  11.064   5311  Z= 0.382
  Chirality :  0.044   0.321    626
  Planarity :  0.005   0.042    642
  Dihedral  :  9.304  65.596    592
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.01 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  :  9.28 %
    Favored  : 89.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.48 (0.40), residues: 487
  helix:  1.34 (0.30), residues: 314
  sheet: -1.71 (1.52), residues: 10
  loop : -3.77 (0.43), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 254 
 HIS   0.006   0.002   HIS A 221 
 PHE   0.016   0.002   PHE A 244 
 TYR   0.018   0.002   TYR A  67 
 ARG   0.003   0.001   ARG A 369 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01512 (    1)
  link_NAG-ASN         : angle       7.88825 (    3)
  link_BETA1-4         : bond        0.00585 (    2)
  link_BETA1-4         : angle       3.62364 (    6)
  hydrogen bonds       : bond        0.05102 (  251)
  hydrogen bonds       : angle       5.56086 (  744)
  covalent geometry    : bond        0.00373 ( 3880)
  covalent geometry    : angle       0.73741 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.326 
Fit side-chains
REVERT: A   76 TYR cc_start: 0.8692 (t80) cc_final: 0.8320 (t80)
REVERT: A  161 MET cc_start: 0.6604 (tmm) cc_final: 0.5684 (tpt)
REVERT: A  242 ASP cc_start: 0.7959 (t70) cc_final: 0.7705 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 59
  average time/residue: 0.1728
  time to fit residues: 13.0752
Evaluate side-chains
  52 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 48
  time to evaluate  : 0.420 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  345 MET
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 11 optimal weight:    2.9990
   chunk 42 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    0.6980
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    0.7980
   chunk 16 optimal weight:    0.7980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3792 r_free = 0.3792 target = 0.174014 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.156061 restraints weight = 4464.928|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.158164 restraints weight = 3173.953|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3651 r_free = 0.3651 target = 0.159433 restraints weight = 2444.514|
|-----------------------------------------------------------------------------|
r_work (final): 0.3646
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7484
moved from start:          0.1636

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3883  Z= 0.153
  Angle     :  0.725  10.588   5311  Z= 0.358
  Chirality :  0.043   0.322    626
  Planarity :  0.004   0.042    642
  Dihedral  :  7.569  58.283    592
  Min Nonbonded Distance : 2.559

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  1.86 %
    Allowed  : 15.38 %
    Favored  : 82.76 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.22 (0.40), residues: 487
  helix:  1.52 (0.30), residues: 314
  sheet: -1.66 (1.56), residues: 10
  loop : -3.62 (0.45), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.023   0.001   PHE A 386 
 TYR   0.012   0.001   TYR A 364 
 ARG   0.003   0.000   ARG A  28 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01538 (    1)
  link_NAG-ASN         : angle       7.51712 (    3)
  link_BETA1-4         : bond        0.00484 (    2)
  link_BETA1-4         : angle       3.46541 (    6)
  hydrogen bonds       : bond        0.04633 (  251)
  hydrogen bonds       : angle       5.32789 (  744)
  covalent geometry    : bond        0.00344 ( 3880)
  covalent geometry    : angle       0.69392 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  63 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 56
  time to evaluate  : 0.355 
Fit side-chains
REVERT: A   76 TYR cc_start: 0.8685 (t80) cc_final: 0.8425 (t80)
REVERT: A  106 MET cc_start: 0.8378 (tpt) cc_final: 0.7957 (tpt)
REVERT: A  119 GLN cc_start: 0.7989 (mt0) cc_final: 0.7741 (mp10)
REVERT: A  161 MET cc_start: 0.6607 (tmm) cc_final: 0.5732 (tpt)
REVERT: A  242 ASP cc_start: 0.7947 (t70) cc_final: 0.7742 (t0)
  outliers start: 7
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1427
  time to fit residues: 10.9645
Evaluate side-chains
  56 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 49
  time to evaluate  : 0.347 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  346 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    0.9980
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    0.9990
   chunk 3 optimal weight:    0.9980
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 6 optimal weight:    2.9990
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.8982

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3782 r_free = 0.3782 target = 0.173257 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3605 r_free = 0.3605 target = 0.154955 restraints weight = 4502.143|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3625 r_free = 0.3625 target = 0.157120 restraints weight = 3184.084|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3639 r_free = 0.3639 target = 0.158547 restraints weight = 2463.113|
|-----------------------------------------------------------------------------|
r_work (final): 0.3645
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7478
moved from start:          0.1881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3883  Z= 0.162
  Angle     :  0.724  10.408   5311  Z= 0.357
  Chirality :  0.043   0.328    626
  Planarity :  0.004   0.043    642
  Dihedral  :  7.055  58.283    592
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 17.77 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.15 (0.40), residues: 487
  helix:  1.58 (0.30), residues: 313
  sheet: -1.77 (1.58), residues: 10
  loop : -3.56 (0.46), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.022   0.001   PHE A 386 
 TYR   0.014   0.001   TYR A 111 
 ARG   0.004   0.001   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01548 (    1)
  link_NAG-ASN         : angle       7.41524 (    3)
  link_BETA1-4         : bond        0.00501 (    2)
  link_BETA1-4         : angle       3.18700 (    6)
  hydrogen bonds       : bond        0.04609 (  251)
  hydrogen bonds       : angle       5.24442 (  744)
  covalent geometry    : bond        0.00373 ( 3880)
  covalent geometry    : angle       0.69442 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.393 
Fit side-chains
REVERT: A   76 TYR cc_start: 0.8686 (t80) cc_final: 0.8438 (t80)
REVERT: A  106 MET cc_start: 0.8277 (tpt) cc_final: 0.7920 (tpt)
REVERT: A  119 GLN cc_start: 0.8030 (mt0) cc_final: 0.7641 (mp10)
REVERT: A  161 MET cc_start: 0.6471 (tmm) cc_final: 0.5699 (tpt)
  outliers start: 9
  outliers final: 7
  residues processed: 55
  average time/residue: 0.1400
  time to fit residues: 9.9317
Evaluate side-chains
  53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.355 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  411 ASP
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 37 optimal weight:    0.1980
   chunk 31 optimal weight:    0.8980
   chunk 23 optimal weight:    0.5980
   chunk 8 optimal weight:    4.9990
   chunk 19 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 26 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 40 optimal weight:    0.0570
   chunk 4 optimal weight:    0.7980
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.4498

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3825 r_free = 0.3825 target = 0.177427 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3649 r_free = 0.3649 target = 0.159192 restraints weight = 4553.215|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3671 r_free = 0.3671 target = 0.161537 restraints weight = 3143.366|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3684 r_free = 0.3684 target = 0.162963 restraints weight = 2419.958|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7405
moved from start:          0.2189

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3883  Z= 0.130
  Angle     :  0.669   9.853   5311  Z= 0.330
  Chirality :  0.041   0.310    626
  Planarity :  0.004   0.039    642
  Dihedral  :  6.756  57.523    592
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.39 %
    Favored  : 92.61 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 18.57 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.07 (0.41), residues: 487
  helix:  1.71 (0.30), residues: 315
  sheet: -1.42 (1.67), residues: 10
  loop : -3.48 (0.47), residues: 162

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.017   0.001   PHE A 386 
 TYR   0.010   0.001   TYR A 175 
 ARG   0.003   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01508 (    1)
  link_NAG-ASN         : angle       7.02468 (    3)
  link_BETA1-4         : bond        0.00529 (    2)
  link_BETA1-4         : angle       3.04813 (    6)
  hydrogen bonds       : bond        0.03996 (  251)
  hydrogen bonds       : angle       5.03824 (  744)
  covalent geometry    : bond        0.00286 ( 3880)
  covalent geometry    : angle       0.64020 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  62 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 48
  time to evaluate  : 0.388 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.8274 (OUTLIER) cc_final: 0.7010 (m-90)
REVERT: A  119 GLN cc_start: 0.7991 (mt0) cc_final: 0.7625 (mp10)
REVERT: A  161 MET cc_start: 0.6421 (tmm) cc_final: 0.5530 (tpt)
  outliers start: 14
  outliers final: 7
  residues processed: 60
  average time/residue: 0.1259
  time to fit residues: 10.0797
Evaluate side-chains
  52 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 44
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  411 ASP
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 36 optimal weight:    0.9980
   chunk 11 optimal weight:    2.9990
   chunk 45 optimal weight:    3.9990
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    4.9990
   chunk 10 optimal weight:    0.7980
   chunk 41 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   chunk 30 optimal weight:    4.9990
   chunk 9 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.8980

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3792 r_free = 0.3792 target = 0.174078 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3614 r_free = 0.3614 target = 0.155669 restraints weight = 4522.364|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 48)----------------|
| r_work = 0.3636 r_free = 0.3636 target = 0.158011 restraints weight = 3172.944|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.159348 restraints weight = 2454.014|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7469
moved from start:          0.2275

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3883  Z= 0.160
  Angle     :  0.707  10.043   5311  Z= 0.350
  Chirality :  0.043   0.331    626
  Planarity :  0.004   0.039    642
  Dihedral  :  6.676  55.690    592
  Min Nonbonded Distance : 2.578

Molprobity Statistics.
  All-atom Clashscore : 7.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 18.57 %
    Favored  : 77.72 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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: -0.03 (0.41), residues: 487
  helix:  1.68 (0.30), residues: 312
  sheet: -1.44 (1.65), residues: 10
  loop : -3.53 (0.46), residues: 165

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A  27 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.019   0.001   PHE A 386 
 TYR   0.017   0.002   TYR A 111 
 ARG   0.003   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01520 (    1)
  link_NAG-ASN         : angle       7.16161 (    3)
  link_BETA1-4         : bond        0.00491 (    2)
  link_BETA1-4         : angle       2.88069 (    6)
  hydrogen bonds       : bond        0.04419 (  251)
  hydrogen bonds       : angle       5.07565 (  744)
  covalent geometry    : bond        0.00370 ( 3880)
  covalent geometry    : angle       0.68033 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 47
  time to evaluate  : 0.390 
Fit side-chains
REVERT: A  119 GLN cc_start: 0.8002 (mt0) cc_final: 0.7555 (mp10)
REVERT: A  161 MET cc_start: 0.6361 (tmm) cc_final: 0.5610 (tpt)
REVERT: A  207 LEU cc_start: 0.6595 (OUTLIER) cc_final: 0.6048 (pt)
  outliers start: 14
  outliers final: 9
  residues processed: 58
  average time/residue: 0.1279
  time to fit residues: 9.9076
Evaluate side-chains
  55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.386 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  443 LEU
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 26 optimal weight:    2.9990
   chunk 19 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 17 optimal weight:    2.9990
   chunk 47 optimal weight:    5.9990
   chunk 25 optimal weight:    0.5980
   chunk 35 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    0.9980
   chunk 34 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3816 r_free = 0.3816 target = 0.176062 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3634 r_free = 0.3634 target = 0.157153 restraints weight = 4453.024|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3656 r_free = 0.3656 target = 0.159451 restraints weight = 3102.330|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.161130 restraints weight = 2397.818|
|-----------------------------------------------------------------------------|
r_work (final): 0.3661
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7465
moved from start:          0.2396

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3883  Z= 0.146
  Angle     :  0.691   9.803   5311  Z= 0.342
  Chirality :  0.042   0.323    626
  Planarity :  0.004   0.038    642
  Dihedral  :  6.595  55.819    592
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.42 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.04 (0.41), residues: 487
  helix:  1.76 (0.30), residues: 310
  sheet: -1.45 (1.69), residues: 10
  loop : -3.48 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.017   0.001   PHE A 386 
 TYR   0.013   0.001   TYR A 111 
 ARG   0.004   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01549 (    1)
  link_NAG-ASN         : angle       6.96454 (    3)
  link_BETA1-4         : bond        0.00529 (    2)
  link_BETA1-4         : angle       2.89635 (    6)
  hydrogen bonds       : bond        0.04320 (  251)
  hydrogen bonds       : angle       5.05208 (  744)
  covalent geometry    : bond        0.00331 ( 3880)
  covalent geometry    : angle       0.66458 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.299 
Fit side-chains
REVERT: A  119 GLN cc_start: 0.7987 (mt0) cc_final: 0.7563 (mp10)
REVERT: A  161 MET cc_start: 0.6410 (tmm) cc_final: 0.5931 (tpp)
REVERT: A  207 LEU cc_start: 0.6512 (OUTLIER) cc_final: 0.5949 (pt)
  outliers start: 11
  outliers final: 8
  residues processed: 52
  average time/residue: 0.1132
  time to fit residues: 8.1730
Evaluate side-chains
  50 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 41
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  411 ASP
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9980
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    0.9990
   chunk 28 optimal weight:    0.5980
   chunk 22 optimal weight:    0.7980
   chunk 9 optimal weight:    0.0060
   chunk 6 optimal weight:    0.6980
   chunk 17 optimal weight:    0.8980
   overall best weight:    0.5996

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3817 r_free = 0.3817 target = 0.176397 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 47)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.157748 restraints weight = 4443.046|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 41)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.160037 restraints weight = 3124.966|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.161387 restraints weight = 2433.840|
|-----------------------------------------------------------------------------|
r_work (final): 0.3675
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7426
moved from start:          0.2530

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3883  Z= 0.138
  Angle     :  0.672   9.626   5311  Z= 0.332
  Chirality :  0.042   0.324    626
  Planarity :  0.004   0.038    642
  Dihedral  :  6.459  55.918    592
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.16 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.11 (0.41), residues: 487
  helix:  1.80 (0.30), residues: 310
  sheet: -1.46 (1.70), residues: 10
  loop : -3.44 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 406 
 HIS   0.002   0.001   HIS A 162 
 PHE   0.016   0.001   PHE A 386 
 TYR   0.013   0.001   TYR A 111 
 ARG   0.004   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01506 (    1)
  link_NAG-ASN         : angle       6.88737 (    3)
  link_BETA1-4         : bond        0.00531 (    2)
  link_BETA1-4         : angle       2.82023 (    6)
  hydrogen bonds       : bond        0.04143 (  251)
  hydrogen bonds       : angle       5.00023 (  744)
  covalent geometry    : bond        0.00309 ( 3880)
  covalent geometry    : angle       0.64501 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.352 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.8310 (OUTLIER) cc_final: 0.7211 (m-90)
REVERT: A  119 GLN cc_start: 0.8142 (mt0) cc_final: 0.7634 (mp10)
REVERT: A  161 MET cc_start: 0.6355 (tmm) cc_final: 0.5750 (tpp)
REVERT: A  207 LEU cc_start: 0.6341 (OUTLIER) cc_final: 0.5733 (pt)
  outliers start: 11
  outliers final: 8
  residues processed: 51
  average time/residue: 0.1288
  time to fit residues: 8.7456
Evaluate side-chains
  51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 41
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  411 ASP
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 15 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9990
   chunk 37 optimal weight:    0.6980
   chunk 28 optimal weight:    0.0670
   chunk 45 optimal weight:    0.5980
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.7980
   chunk 29 optimal weight:    0.0470
   chunk 10 optimal weight:    3.9990
   chunk 21 optimal weight:    0.9990
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4216

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3841 r_free = 0.3841 target = 0.178962 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3662 r_free = 0.3662 target = 0.160582 restraints weight = 4410.827|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3682 r_free = 0.3682 target = 0.162692 restraints weight = 3102.661|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3698 r_free = 0.3698 target = 0.164443 restraints weight = 2414.513|
|-----------------------------------------------------------------------------|
r_work (final): 0.3703
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2714

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3883  Z= 0.128
  Angle     :  0.673  10.426   5311  Z= 0.327
  Chirality :  0.041   0.313    626
  Planarity :  0.004   0.037    642
  Dihedral  :  6.359  56.220    592
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.39 %
    Allowed  : 21.22 %
    Favored  : 76.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.21 (0.41), residues: 487
  helix:  1.88 (0.30), residues: 310
  sheet: -1.47 (1.74), residues: 10
  loop : -3.40 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 406 
 HIS   0.002   0.001   HIS A 162 
 PHE   0.014   0.001   PHE A 386 
 TYR   0.010   0.001   TYR A 111 
 ARG   0.004   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01496 (    1)
  link_NAG-ASN         : angle       6.67599 (    3)
  link_BETA1-4         : bond        0.00524 (    2)
  link_BETA1-4         : angle       2.83280 (    6)
  hydrogen bonds       : bond        0.03963 (  251)
  hydrogen bonds       : angle       4.97163 (  744)
  covalent geometry    : bond        0.00282 ( 3880)
  covalent geometry    : angle       0.64766 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 46
  time to evaluate  : 0.342 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.8224 (OUTLIER) cc_final: 0.7349 (m-90)
REVERT: A  161 MET cc_start: 0.6341 (tmm) cc_final: 0.5772 (tpp)
  outliers start: 9
  outliers final: 8
  residues processed: 53
  average time/residue: 0.1250
  time to fit residues: 8.7753
Evaluate side-chains
  53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.391 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   62 TRP
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  410 SER
Chi-restraints excluded: chain A residue  411 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 11 optimal weight:    0.7980
   chunk 5 optimal weight:    0.3980
   chunk 45 optimal weight:    0.7980
   chunk 28 optimal weight:    0.3980
   chunk 15 optimal weight:    0.2980
   chunk 16 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9980
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9990
   chunk 17 optimal weight:    0.6980
   overall best weight:    0.5180

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3851 r_free = 0.3851 target = 0.179667 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.159742 restraints weight = 4437.080|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.162334 restraints weight = 3026.335|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3701 r_free = 0.3701 target = 0.164297 restraints weight = 2274.521|
|-----------------------------------------------------------------------------|
r_work (final): 0.3700
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7406
moved from start:          0.2802

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3883  Z= 0.131
  Angle     :  0.681   9.526   5311  Z= 0.328
  Chirality :  0.041   0.322    626
  Planarity :  0.004   0.037    642
  Dihedral  :  6.274  56.167    592
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.42 %
    Favored  : 76.66 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.22 (0.41), residues: 487
  helix:  1.88 (0.30), residues: 311
  sheet: -1.46 (1.74), residues: 10
  loop : -3.39 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 406 
 HIS   0.002   0.001   HIS A 162 
 PHE   0.014   0.001   PHE A 386 
 TYR   0.011   0.001   TYR A 364 
 ARG   0.003   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01467 (    1)
  link_NAG-ASN         : angle       6.63580 (    3)
  link_BETA1-4         : bond        0.00548 (    2)
  link_BETA1-4         : angle       2.70338 (    6)
  hydrogen bonds       : bond        0.03973 (  251)
  hydrogen bonds       : angle       4.94213 (  744)
  covalent geometry    : bond        0.00293 ( 3880)
  covalent geometry    : angle       0.65717 ( 5302)

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

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

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  974 Ramachandran restraints generated.
    487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.357 
Fit side-chains
REVERT: A  119 GLN cc_start: 0.8022 (mt0) cc_final: 0.7635 (mp10)
REVERT: A  161 MET cc_start: 0.6413 (tmm) cc_final: 0.5845 (tpp)
REVERT: A  207 LEU cc_start: 0.6113 (OUTLIER) cc_final: 0.5415 (pt)
  outliers start: 11
  outliers final: 8
  residues processed: 52
  average time/residue: 0.1139
  time to fit residues: 8.2156
Evaluate side-chains
  51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.364 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   16 LEU
Chi-restraints excluded: chain A residue   49 ILE
Chi-restraints excluded: chain A residue   68 ILE
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  190 VAL
Chi-restraints excluded: chain A residue  207 LEU
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  411 ASP
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 2 optimal weight:    0.0170
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.7980
   chunk 29 optimal weight:    0.9980
   chunk 20 optimal weight:    0.2980
   chunk 24 optimal weight:    1.9990
   chunk 28 optimal weight:    0.6980
   overall best weight:    0.4418

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

Flipped N/Q/H residues before XYZ refinement:
** A 191 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 = 0.3855 r_free = 0.3855 target = 0.180268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.161247 restraints weight = 4407.659|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 39)----------------|
| r_work = 0.3694 r_free = 0.3694 target = 0.163688 restraints weight = 3053.312|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3711 r_free = 0.3711 target = 0.165430 restraints weight = 2352.025|
|-----------------------------------------------------------------------------|
r_work (final): 0.3715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7386
moved from start:          0.2893

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   3883  Z= 0.127
  Angle     :  0.668  10.224   5311  Z= 0.323
  Chirality :  0.041   0.313    626
  Planarity :  0.004   0.037    642
  Dihedral  :  5.756  56.378    590
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 20.42 %
    Favored  : 76.92 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    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:  0.28 (0.41), residues: 487
  helix:  1.92 (0.30), residues: 311
  sheet: -1.52 (1.73), residues: 10
  loop : -3.34 (0.48), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 406 
 HIS   0.002   0.001   HIS A 162 
 PHE   0.014   0.001   PHE A 386 
 TYR   0.011   0.001   TYR A 364 
 ARG   0.003   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01469 (    1)
  link_NAG-ASN         : angle       6.49509 (    3)
  link_BETA1-4         : bond        0.00591 (    2)
  link_BETA1-4         : angle       2.73696 (    6)
  hydrogen bonds       : bond        0.03858 (  251)
  hydrogen bonds       : angle       4.90872 (  744)
  covalent geometry    : bond        0.00280 ( 3880)
  covalent geometry    : angle       0.64361 ( 5302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1508.99 seconds
wall clock time: 27 minutes 3.15 seconds (1623.15 seconds total)