Starting phenix.real_space_refine
on Fri May  9 20:45:07 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j77_36030/05_2025/8j77_36030.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j77_36030/05_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_36030/05_2025/8j77_36030.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j77_36030/05_2025/8j77_36030.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j77_36030/05_2025/8j77_36030.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j77_36030/05_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-5687/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: 3.21, per 1000 atoms: 0.85
  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: 1.16
  Conformation dependent library (CDL) restraints added in 475.2 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: 0.33
  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: 0.94

  Time building geometry restraints manager: 1.32 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:             1.130
  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:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     13.960
  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:2.800
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   18.200
-------------------------------------------------------------------------------
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  : 0.385 
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: 0.1396
  time to fit residues: 11.7055
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  : 0.379 
-------------------------------------------------------------------------------
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 = 0.3793 r_free = 0.3793 target = 0.173862 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3611 r_free = 0.3611 target = 0.154601 restraints weight = 4453.205|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.156805 restraints weight = 3097.325|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3647 r_free = 0.3647 target = 0.158419 restraints weight = 2376.044|
|-----------------------------------------------------------------------------|
r_work (final): 0.3641
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7506
moved from start:          0.1319

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= 0.167
  Angle     :  0.769  11.111   5311  Z= 0.381
  Chirality :  0.044   0.322    626
  Planarity :  0.005   0.042    642
  Dihedral  :  9.260  65.473    592
  Min Nonbonded Distance : 2.561

Molprobity Statistics.
  All-atom Clashscore : 7.44
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  8.21 %
    Favored  : 91.58 %
  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: -0.47 (0.40), residues: 487
  helix:  1.34 (0.30), residues: 314
  sheet: -1.71 (1.52), residues: 10
  loop : -3.76 (0.43), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 254 
 HIS   0.007   0.002   HIS A 221 
 PHE   0.016   0.002   PHE A 244 
 TYR   0.019   0.002   TYR A  67 
 ARG   0.003   0.001   ARG A 369 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01557 (    1)
  link_NAG-ASN         : angle       7.91611 (    3)
  link_BETA1-4         : bond        0.00631 (    2)
  link_BETA1-4         : angle       3.64831 (    6)
  hydrogen bonds       : bond        0.05098 (  251)
  hydrogen bonds       : angle       5.55527 (  744)
  covalent geometry    : bond        0.00371 ( 3880)
  covalent geometry    : angle       0.73592 ( 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  : 0.379 
Fit side-chains
REVERT: A   76 TYR cc_start: 0.8692 (t80) cc_final: 0.8324 (t80)
REVERT: A  161 MET cc_start: 0.6593 (tmm) cc_final: 0.5664 (tpt)
REVERT: A  242 ASP cc_start: 0.7986 (t70) cc_final: 0.7733 (t0)
  outliers start: 6
  outliers final: 4
  residues processed: 59
  average time/residue: 0.1460
  time to fit residues: 11.1954
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  : 0.362 
-------------------------------------------------------------------------------
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:    0.6980
   chunk 25 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 46 optimal weight:    2.9990
   chunk 19 optimal weight:    0.7980
   chunk 21 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9990
   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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.174291 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3620 r_free = 0.3620 target = 0.156188 restraints weight = 4475.359|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3640 r_free = 0.3640 target = 0.158354 restraints weight = 3168.749|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3654 r_free = 0.3654 target = 0.159832 restraints weight = 2436.040|
|-----------------------------------------------------------------------------|
r_work (final): 0.3649
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7472
moved from start:          0.1712

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= 0.152
  Angle     :  0.718  10.477   5311  Z= 0.356
  Chirality :  0.043   0.321    626
  Planarity :  0.004   0.042    642
  Dihedral  :  7.307  56.437    592
  Min Nonbonded Distance : 2.514

Molprobity Statistics.
  All-atom Clashscore : 7.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  1.59 %
    Allowed  : 14.59 %
    Favored  : 83.82 %
  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 (0.41), residues: 487
  helix:  1.57 (0.30), residues: 314
  sheet: -1.63 (1.57), residues: 10
  loop : -3.59 (0.46), 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   0.024   0.001   PHE A 386 
 TYR   0.012   0.001   TYR A 364 
 ARG   0.002   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01555 (    1)
  link_NAG-ASN         : angle       7.44625 (    3)
  link_BETA1-4         : bond        0.00508 (    2)
  link_BETA1-4         : angle       3.39589 (    6)
  hydrogen bonds       : bond        0.04585 (  251)
  hydrogen bonds       : angle       5.29911 (  744)
  covalent geometry    : bond        0.00341 ( 3880)
  covalent geometry    : angle       0.68731 ( 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
  61 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 55
  time to evaluate  : 0.413 
Fit side-chains
REVERT: A   76 TYR cc_start: 0.8698 (t80) cc_final: 0.8435 (t80)
REVERT: A  106 MET cc_start: 0.8377 (tpt) cc_final: 0.7953 (tpt)
REVERT: A  119 GLN cc_start: 0.8012 (mt0) cc_final: 0.7764 (mp10)
REVERT: A  161 MET cc_start: 0.6559 (tmm) cc_final: 0.5669 (tpt)
  outliers start: 6
  outliers final: 6
  residues processed: 59
  average time/residue: 0.1460
  time to fit residues: 11.0736
Evaluate side-chains
  53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
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  346 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    0.4980
   chunk 46 optimal weight:    2.9990
   chunk 5 optimal weight:    0.0050
   chunk 3 optimal weight:    0.7980
   chunk 11 optimal weight:    3.9990
   chunk 2 optimal weight:    1.9990
   chunk 27 optimal weight:    3.9990
   chunk 16 optimal weight:    0.9990
   chunk 42 optimal weight:    0.9980
   chunk 6 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.6194

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3809 r_free = 0.3809 target = 0.175584 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 52)----------------|
| r_work = 0.3631 r_free = 0.3631 target = 0.157375 restraints weight = 4482.291|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3652 r_free = 0.3652 target = 0.159613 restraints weight = 3136.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.161227 restraints weight = 2420.589|
|-----------------------------------------------------------------------------|
r_work (final): 0.3664
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.1988

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= 0.142
  Angle     :  0.700  10.236   5311  Z= 0.345
  Chirality :  0.042   0.324    626
  Planarity :  0.004   0.041    642
  Dihedral  :  6.948  59.372    592
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.83 %
    Favored  : 91.17 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 17.77 %
    Favored  : 79.31 %
  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:  1.65 (0.30), residues: 313
  sheet: -1.59 (1.61), residues: 10
  loop : -3.49 (0.46), residues: 164

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   0.019   0.001   PHE A 386 
 TYR   0.011   0.001   TYR A 364 
 ARG   0.005   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01504 (    1)
  link_NAG-ASN         : angle       7.30500 (    3)
  link_BETA1-4         : bond        0.00475 (    2)
  link_BETA1-4         : angle       3.12684 (    6)
  hydrogen bonds       : bond        0.04304 (  251)
  hydrogen bonds       : angle       5.16941 (  744)
  covalent geometry    : bond        0.00319 ( 3880)
  covalent geometry    : angle       0.67099 ( 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
  60 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 49
  time to evaluate  : 0.359 
Fit side-chains
REVERT: A   76 TYR cc_start: 0.8676 (t80) cc_final: 0.8459 (t80)
REVERT: A  106 MET cc_start: 0.8239 (tpt) cc_final: 0.7906 (tpt)
REVERT: A  119 GLN cc_start: 0.7992 (mt0) cc_final: 0.7681 (mp10)
REVERT: A  161 MET cc_start: 0.6457 (tmm) cc_final: 0.5919 (tpp)
  outliers start: 11
  outliers final: 9
  residues processed: 56
  average time/residue: 0.1440
  time to fit residues: 10.3765
Evaluate side-chains
  54 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
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  352 ILE
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:    2.9990
   chunk 31 optimal weight:    5.9990
   chunk 23 optimal weight:    0.9980
   chunk 8 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    0.3980
   chunk 26 optimal weight:    0.0670
   chunk 29 optimal weight:    0.4980
   chunk 40 optimal weight:    2.9990
   chunk 4 optimal weight:    2.9990
   chunk 44 optimal weight:    3.9990
   overall best weight:    0.5518

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3817 r_free = 0.3817 target = 0.176638 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3637 r_free = 0.3637 target = 0.158193 restraints weight = 4561.161|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.160500 restraints weight = 3164.350|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3672 r_free = 0.3672 target = 0.161862 restraints weight = 2454.424|
|-----------------------------------------------------------------------------|
r_work (final): 0.3677
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7420
moved from start:          0.2210

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= 0.137
  Angle     :  0.676   9.871   5311  Z= 0.335
  Chirality :  0.041   0.318    626
  Planarity :  0.004   0.039    642
  Dihedral  :  6.734  57.005    592
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.42 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 17.51 %
    Favored  : 78.78 %
  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:  0.10 (0.41), residues: 487
  helix:  1.77 (0.30), residues: 310
  sheet: -1.43 (1.68), residues: 10
  loop : -3.38 (0.47), residues: 167

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 364 
 ARG   0.005   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01505 (    1)
  link_NAG-ASN         : angle       7.04105 (    3)
  link_BETA1-4         : bond        0.00539 (    2)
  link_BETA1-4         : angle       2.99576 (    6)
  hydrogen bonds       : bond        0.04141 (  251)
  hydrogen bonds       : angle       5.04368 (  744)
  covalent geometry    : bond        0.00305 ( 3880)
  covalent geometry    : angle       0.64743 ( 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
  60 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 46
  time to evaluate  : 0.416 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.8304 (OUTLIER) cc_final: 0.7057 (m-90)
REVERT: A  111 TYR cc_start: 0.6581 (m-80) cc_final: 0.6314 (m-80)
REVERT: A  119 GLN cc_start: 0.7984 (mt0) cc_final: 0.7603 (mp10)
REVERT: A  161 MET cc_start: 0.6424 (tmm) cc_final: 0.5511 (tpt)
REVERT: A  484 MET cc_start: 0.8083 (tmm) cc_final: 0.7319 (ttp)
  outliers start: 14
  outliers final: 8
  residues processed: 57
  average time/residue: 0.1295
  time to fit residues: 9.8259
Evaluate side-chains
  54 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.387 
-------------------------------------------------------------------------------
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  391 SER
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:    0.8980
   chunk 11 optimal weight:    1.9990
   chunk 45 optimal weight:    4.9990
   chunk 19 optimal weight:    0.6980
   chunk 8 optimal weight:    3.9990
   chunk 10 optimal weight:    0.6980
   chunk 41 optimal weight:    0.9990
   chunk 44 optimal weight:    0.9990
   chunk 30 optimal weight:    2.9990
   chunk 9 optimal weight:    1.9990
   chunk 40 optimal weight:    0.9980
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3799 r_free = 0.3799 target = 0.174765 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3621 r_free = 0.3621 target = 0.156344 restraints weight = 4516.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3643 r_free = 0.3643 target = 0.158700 restraints weight = 3149.920|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 44)----------------|
| r_work = 0.3659 r_free = 0.3659 target = 0.160308 restraints weight = 2411.398|
|-----------------------------------------------------------------------------|
r_work (final): 0.3666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7456
moved from start:          0.2307

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= 0.154
  Angle     :  0.698   9.925   5311  Z= 0.344
  Chirality :  0.042   0.329    626
  Planarity :  0.004   0.039    642
  Dihedral  :  6.649  55.725    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 :  3.98 %
    Allowed  : 18.04 %
    Favored  : 77.98 %
  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:  0.05 (0.41), residues: 487
  helix:  1.71 (0.30), residues: 313
  sheet: -1.57 (1.65), residues: 10
  loop : -3.41 (0.48), residues: 164

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.018   0.001   PHE A 386 
 TYR   0.012   0.001   TYR A 364 
 ARG   0.005   0.001   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01522 (    1)
  link_NAG-ASN         : angle       7.07065 (    3)
  link_BETA1-4         : bond        0.00539 (    2)
  link_BETA1-4         : angle       2.86817 (    6)
  hydrogen bonds       : bond        0.04360 (  251)
  hydrogen bonds       : angle       5.04431 (  744)
  covalent geometry    : bond        0.00353 ( 3880)
  covalent geometry    : angle       0.67103 ( 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
  60 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 45
  time to evaluate  : 0.401 
Fit side-chains
REVERT: A  111 TYR cc_start: 0.6880 (m-80) cc_final: 0.6608 (m-80)
REVERT: A  161 MET cc_start: 0.6349 (tmm) cc_final: 0.5536 (tpt)
REVERT: A  207 LEU cc_start: 0.6589 (OUTLIER) cc_final: 0.6023 (pt)
  outliers start: 15
  outliers final: 10
  residues processed: 56
  average time/residue: 0.1175
  time to fit residues: 8.9674
Evaluate side-chains
  54 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 43
  time to evaluate  : 0.390 
-------------------------------------------------------------------------------
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
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:    0.9990
   chunk 19 optimal weight:    0.7980
   chunk 20 optimal weight:    0.8980
   chunk 17 optimal weight:    0.9990
   chunk 47 optimal weight:    5.9990
   chunk 25 optimal weight:    0.6980
   chunk 35 optimal weight:    1.9990
   chunk 14 optimal weight:    0.9990
   chunk 7 optimal weight:    1.9990
   chunk 34 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.8784

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3795 r_free = 0.3795 target = 0.174190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.3613 r_free = 0.3613 target = 0.155629 restraints weight = 4473.463|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3635 r_free = 0.3635 target = 0.157933 restraints weight = 3146.747|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.3648 r_free = 0.3648 target = 0.159221 restraints weight = 2454.828|
|-----------------------------------------------------------------------------|
r_work (final): 0.3651
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7492
moved from start:          0.2412

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3883  Z= 0.156
  Angle     :  0.695   9.806   5311  Z= 0.344
  Chirality :  0.042   0.327    626
  Planarity :  0.004   0.040    642
  Dihedral  :  6.610  55.725    592
  Min Nonbonded Distance : 2.579

Molprobity Statistics.
  All-atom Clashscore : 8.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.62 %
    Favored  : 91.38 %
  Rotamer:
    Outliers :  3.98 %
    Allowed  : 18.83 %
    Favored  : 77.19 %
  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:  0.06 (0.41), residues: 487
  helix:  1.76 (0.30), residues: 309
  sheet: -1.40 (1.68), residues: 10
  loop : -3.41 (0.47), residues: 168

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   0.018   0.001   PHE A 386 
 TYR   0.011   0.001   TYR A 364 
 ARG   0.004   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01543 (    1)
  link_NAG-ASN         : angle       6.97598 (    3)
  link_BETA1-4         : bond        0.00515 (    2)
  link_BETA1-4         : angle       2.87047 (    6)
  hydrogen bonds       : bond        0.04363 (  251)
  hydrogen bonds       : angle       5.05437 (  744)
  covalent geometry    : bond        0.00359 ( 3880)
  covalent geometry    : angle       0.66849 ( 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
  61 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 46
  time to evaluate  : 0.363 
Fit side-chains
REVERT: A  119 GLN cc_start: 0.7990 (mt0) cc_final: 0.7625 (mp10)
REVERT: A  161 MET cc_start: 0.6391 (tmm) cc_final: 0.5677 (tpt)
REVERT: A  207 LEU cc_start: 0.6601 (OUTLIER) cc_final: 0.6029 (pt)
  outliers start: 15
  outliers final: 12
  residues processed: 56
  average time/residue: 0.1146
  time to fit residues: 8.8778
Evaluate side-chains
  56 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 43
  time to evaluate  : 0.366 
-------------------------------------------------------------------------------
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  283 VAL
Chi-restraints excluded: chain A residue  298 THR
Chi-restraints excluded: chain A residue  352 ILE
Chi-restraints excluded: chain A residue  391 SER
Chi-restraints excluded: chain A residue  411 ASP
Chi-restraints excluded: chain A residue  443 LEU
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 25 optimal weight:    0.5980
   chunk 19 optimal weight:    0.6980
   chunk 21 optimal weight:    2.9990
   chunk 42 optimal weight:    0.0000
   chunk 29 optimal weight:    0.9980
   chunk 12 optimal weight:    0.6980
   chunk 28 optimal weight:    0.5980
   chunk 22 optimal weight:    0.8980
   chunk 9 optimal weight:    1.9990
   chunk 6 optimal weight:    0.8980
   chunk 17 optimal weight:    2.9990
   overall best weight:    0.5184

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3823 r_free = 0.3823 target = 0.177262 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3644 r_free = 0.3644 target = 0.158550 restraints weight = 4430.503|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 54)----------------|
| r_work = 0.3667 r_free = 0.3667 target = 0.160935 restraints weight = 3114.461|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3679 r_free = 0.3679 target = 0.162276 restraints weight = 2414.056|
|-----------------------------------------------------------------------------|
r_work (final): 0.3683
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7417
moved from start:          0.2576

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= 0.134
  Angle     :  0.668   9.540   5311  Z= 0.331
  Chirality :  0.041   0.317    626
  Planarity :  0.004   0.038    642
  Dihedral  :  6.463  56.053    592
  Min Nonbonded Distance : 2.576

Molprobity Statistics.
  All-atom Clashscore : 8.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 19.63 %
    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:  0.13 (0.41), residues: 487
  helix:  1.82 (0.30), residues: 310
  sheet: -1.38 (1.71), residues: 10
  loop : -3.43 (0.47), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 406 
 HIS   0.003   0.001   HIS A 162 
 PHE   0.015   0.001   PHE A 386 
 TYR   0.015   0.001   TYR A 111 
 ARG   0.004   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01474 (    1)
  link_NAG-ASN         : angle       6.80117 (    3)
  link_BETA1-4         : bond        0.00531 (    2)
  link_BETA1-4         : angle       2.84650 (    6)
  hydrogen bonds       : bond        0.04078 (  251)
  hydrogen bonds       : angle       4.99029 (  744)
  covalent geometry    : bond        0.00297 ( 3880)
  covalent geometry    : angle       0.64190 ( 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
  59 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 45
  time to evaluate  : 0.379 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.8311 (OUTLIER) cc_final: 0.7234 (m-90)
REVERT: A  161 MET cc_start: 0.6312 (tmm) cc_final: 0.5759 (tpp)
REVERT: A  207 LEU cc_start: 0.6308 (OUTLIER) cc_final: 0.5685 (pt)
  outliers start: 14
  outliers final: 9
  residues processed: 55
  average time/residue: 0.1268
  time to fit residues: 9.2411
Evaluate side-chains
  51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 40
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
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  410 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:    0.9990
   chunk 44 optimal weight:    0.8980
   chunk 37 optimal weight:    0.7980
   chunk 28 optimal weight:    0.0030
   chunk 45 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 29 optimal weight:    0.5980
   chunk 10 optimal weight:    0.0980
   chunk 21 optimal weight:    0.7980
   chunk 39 optimal weight:    0.7980
   overall best weight:    0.4190

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3842 r_free = 0.3842 target = 0.179218 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3664 r_free = 0.3664 target = 0.160740 restraints weight = 4406.710|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.162833 restraints weight = 3091.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3700 r_free = 0.3700 target = 0.164660 restraints weight = 2407.700|
|-----------------------------------------------------------------------------|
r_work (final): 0.3707
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7379
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   0.042   3883  Z= 0.129
  Angle     :  0.672   9.538   5311  Z= 0.329
  Chirality :  0.041   0.314    626
  Planarity :  0.004   0.037    642
  Dihedral  :  6.337  56.275    592
  Min Nonbonded Distance : 2.577

Molprobity Statistics.
  All-atom Clashscore : 8.11
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.21 %
    Favored  : 91.79 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 20.95 %
    Favored  : 76.13 %
  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:  1.90 (0.30), residues: 310
  sheet: -1.32 (1.74), residues: 10
  loop : -3.42 (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   0.012   0.001   TYR A 111 
 ARG   0.003   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01466 (    1)
  link_NAG-ASN         : angle       6.65203 (    3)
  link_BETA1-4         : bond        0.00567 (    2)
  link_BETA1-4         : angle       2.78793 (    6)
  hydrogen bonds       : bond        0.03910 (  251)
  hydrogen bonds       : angle       4.94935 (  744)
  covalent geometry    : bond        0.00285 ( 3880)
  covalent geometry    : angle       0.64721 ( 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
  56 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 45
  time to evaluate  : 0.389 
Fit side-chains
REVERT: A   62 TRP cc_start: 0.8239 (OUTLIER) cc_final: 0.7402 (m-90)
REVERT: A  119 GLN cc_start: 0.7996 (mt0) cc_final: 0.7779 (mp10)
REVERT: A  161 MET cc_start: 0.6335 (tmm) cc_final: 0.5729 (tpp)
REVERT: A  207 LEU cc_start: 0.6168 (OUTLIER) cc_final: 0.5518 (pt)
  outliers start: 11
  outliers final: 9
  residues processed: 53
  average time/residue: 0.1289
  time to fit residues: 9.0479
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  : 0.386 
-------------------------------------------------------------------------------
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  391 SER
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:    0.6980
   chunk 45 optimal weight:    0.6980
   chunk 28 optimal weight:    0.6980
   chunk 15 optimal weight:    1.9990
   chunk 16 optimal weight:    0.0010
   chunk 9 optimal weight:    0.8980
   chunk 7 optimal weight:    1.9990
   chunk 0 optimal weight:    9.9990
   chunk 14 optimal weight:    0.9980
   chunk 17 optimal weight:    0.9990
   overall best weight:    0.5786

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3836 r_free = 0.3836 target = 0.178467 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3657 r_free = 0.3657 target = 0.159986 restraints weight = 4440.746|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.3677 r_free = 0.3677 target = 0.162211 restraints weight = 3140.742|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3693 r_free = 0.3693 target = 0.163838 restraints weight = 2428.727|
|-----------------------------------------------------------------------------|
r_work (final): 0.3690
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7431
moved from start:          0.2792

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= 0.135
  Angle     :  0.663   9.525   5311  Z= 0.327
  Chirality :  0.041   0.321    626
  Planarity :  0.004   0.037    642
  Dihedral  :  6.293  56.218    592
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.71
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.60 %
    Favored  : 92.40 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.22 %
    Favored  : 75.86 %
  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:  0.19 (0.41), residues: 487
  helix:  1.89 (0.30), residues: 310
  sheet: -1.46 (1.72), residues: 10
  loop : -3.46 (0.46), 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   0.015   0.001   PHE A 386 
 TYR   0.012   0.001   TYR A 111 
 ARG   0.004   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01479 (    1)
  link_NAG-ASN         : angle       6.64255 (    3)
  link_BETA1-4         : bond        0.00545 (    2)
  link_BETA1-4         : angle       2.72968 (    6)
  hydrogen bonds       : bond        0.04013 (  251)
  hydrogen bonds       : angle       4.94045 (  744)
  covalent geometry    : bond        0.00304 ( 3880)
  covalent geometry    : angle       0.63803 ( 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
  53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 42
  time to evaluate  : 0.418 
Fit side-chains
REVERT: A  161 MET cc_start: 0.6417 (tmm) cc_final: 0.5805 (tpp)
REVERT: A  207 LEU cc_start: 0.6230 (OUTLIER) cc_final: 0.5538 (pt)
  outliers start: 11
  outliers final: 9
  residues processed: 50
  average time/residue: 0.1297
  time to fit residues: 8.9204
Evaluate side-chains
  52 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 42
  time to evaluate  : 0.416 
-------------------------------------------------------------------------------
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  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 2 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 12 optimal weight:    0.9980
   chunk 23 optimal weight:    0.5980
   chunk 37 optimal weight:    0.5980
   chunk 29 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0980
   chunk 24 optimal weight:    0.8980
   chunk 28 optimal weight:    0.5980
   overall best weight:    0.5380

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3853 r_free = 0.3853 target = 0.180012 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.3669 r_free = 0.3669 target = 0.160758 restraints weight = 4410.774|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 44)----------------|
| r_work = 0.3692 r_free = 0.3692 target = 0.163233 restraints weight = 3046.079|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3709 r_free = 0.3709 target = 0.165041 restraints weight = 2337.836|
|-----------------------------------------------------------------------------|
r_work (final): 0.3716
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7371
moved from start:          0.2850

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= 0.132
  Angle     :  0.670   9.513   5311  Z= 0.328
  Chirality :  0.041   0.316    626
  Planarity :  0.004   0.037    642
  Dihedral  :  5.776  56.322    590
  Min Nonbonded Distance : 2.580

Molprobity Statistics.
  All-atom Clashscore : 7.84
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 20.95 %
    Favored  : 75.86 %
  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:  0.23 (0.41), residues: 487
  helix:  1.90 (0.30), residues: 311
  sheet: -1.51 (1.72), residues: 10
  loop : -3.41 (0.47), residues: 166

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 406 
 HIS   0.002   0.001   HIS A 162 
 PHE   0.014   0.001   PHE A 386 
 TYR   0.013   0.001   TYR A 111 
 ARG   0.003   0.000   ARG A 446 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.01492 (    1)
  link_NAG-ASN         : angle       6.56278 (    3)
  link_BETA1-4         : bond        0.00570 (    2)
  link_BETA1-4         : angle       2.73241 (    6)
  hydrogen bonds       : bond        0.03935 (  251)
  hydrogen bonds       : angle       4.92670 (  744)
  covalent geometry    : bond        0.00295 ( 3880)
  covalent geometry    : angle       0.64559 ( 5302)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1491.09 seconds
wall clock time: 26 minutes 50.04 seconds (1610.04 seconds total)