Starting phenix.real_space_refine
on Fri Aug 22 14:02:19 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8j76_36029/08_2025/8j76_36029.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8j76_36029/08_2025/8j76_36029.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/8j76_36029/08_2025/8j76_36029.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8j76_36029/08_2025/8j76_36029.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8j76_36029/08_2025/8j76_36029.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8j76_36029/08_2025/8j76_36029.cif"
  }
  resolution = 3.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.106
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    2508      2.51       5
     N     576      2.21       5
     O     668      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 3771
  Number of models: 1
  Model: ""
    Number of chains: 2
    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, 'GLU:plan': 1, 'ASP:plan': 2}
          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
  Time building chain proxies: 1.04, per 1000 atoms: 0.28
  Number of scatterers: 3771
  At special positions: 0
  Unit cell: (86.1, 70.52, 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     668      8.00
     N     576      7.00
     C    2508      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: 0.35
  Conformation dependent library (CDL) restraints added in 136.9 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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:
      21 helices and 0 sheets defined
      75.9% alpha, 0.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.10
  Creating SS restraints...
    Processing helix  chain 'A' and resid 3 through 28
      removed outlier: 3.805A  pdb=" N   GLY A   7 " --> pdb=" O   PHE A   3 " (cutoff:3.500A)
      removed outlier: 3.863A  pdb=" N   ARG A  28 " --> pdb=" O   TRP A  24 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 49 through 63
      removed outlier: 4.026A  pdb=" N   VAL A  53 " --> pdb=" O   ILE A  49 " (cutoff:3.500A)
      removed outlier: 3.800A  pdb=" N   GLY A  54 " --> pdb=" O   GLY A  50 " (cutoff:3.500A)
      removed outlier: 4.061A  pdb=" N   TRP A  62 " --> pdb=" O   MET A  58 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 65 through 77
      removed outlier: 4.218A  pdb=" N   ASN A  69 " --> pdb=" O   GLY A  65 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 81 through 84
    Processing helix  chain 'A' and resid 85 through 103
      removed outlier: 3.979A  pdb=" N   ILE A  89 " --> pdb=" O   ALA A  85 " (cutoff:3.500A)
      removed outlier: 4.785A  pdb=" N   SER A  92 " --> pdb=" O   PRO A  88 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 103 through 108
      removed outlier: 4.056A  pdb=" N   ARG A 107 " --> pdb=" O   ALA A 103 " (cutoff:3.500A)
      removed outlier: 3.646A  pdb=" N   SER A 108 " --> pdb=" O   LYS A 104 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 103 through 108'
    Processing helix  chain 'A' and resid 114 through 122
      removed outlier: 4.167A  pdb=" N   PHE A 118 " --> pdb=" O   MET A 114 " (cutoff:3.500A)
      removed outlier: 3.587A  pdb=" N   ILE A 121 " --> pdb=" O   PRO A 117 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 157
      removed outlier: 4.032A  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 178
      removed outlier: 3.646A  pdb=" N   VAL A 165 " --> pdb=" O   MET A 161 " (cutoff:3.500A)
      removed outlier: 3.891A  pdb=" N   VAL A 178 " --> pdb=" O   LEU A 174 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 207
      removed outlier: 4.006A  pdb=" N   LEU A 192 " --> pdb=" O   ASP A 188 " (cutoff:3.500A)
      removed outlier: 3.642A  pdb=" N   SER A 202 " --> pdb=" O   GLY A 198 " (cutoff:3.500A)
      Proline residue:  A 204  - end of helix
    Processing helix  chain 'A' and resid 214 through 221
      removed outlier: 3.670A  pdb=" N   THR A 218 " --> pdb=" O   ASP A 214 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   ALA A 219 " --> pdb=" O   ILE A 215 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   VAL A 220 " --> pdb=" O   GLY A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 236 through 251
    Processing helix  chain 'A' and resid 254 through 263
      removed outlier: 3.826A  pdb=" N   PHE A 258 " --> pdb=" O   TRP A 254 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 266 through 298
      removed outlier: 3.658A  pdb=" N   ALA A 270 " --> pdb=" O   SER A 266 " (cutoff:3.500A)
      Proline residue:  A 287  - end of helix
      removed outlier: 3.572A  pdb=" N   LEU A 290 " --> pdb=" O   ILE A 286 " (cutoff:3.500A)
      removed outlier: 3.526A  pdb=" N   GLY A 292 " --> pdb=" O   ALA A 288 " (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: 4.035A  pdb=" N   PHE A 334 " --> pdb=" O   VAL A 330 " (cutoff:3.500A)
      removed outlier: 4.545A  pdb=" N   PHE A 335 " --> pdb=" O   TYR A 331 " (cutoff:3.500A)
      removed outlier: 3.698A  pdb=" N   GLY A 336 " --> pdb=" O   ILE A 332 " (cutoff:3.500A)
      removed outlier: 3.576A  pdb=" N   ASP A 349 " --> pdb=" O   MET A 345 " (cutoff:3.500A)
      removed outlier: 3.627A  pdb=" N   SER A 350 " --> pdb=" O   SER A 346 " (cutoff:3.500A)
      removed outlier: 3.661A  pdb=" N   PHE A 359 " --> pdb=" O   ALA A 355 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 375 through 399
      removed outlier: 3.862A  pdb=" N   LEU A 398 " --> pdb=" O   ALA A 394 " (cutoff:3.500A)
      removed outlier: 3.604A  pdb=" N   THR A 399 " --> pdb=" O   MET A 395 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 402 through 426
      removed outlier: 4.481A  pdb=" N   PHE A 418 " --> pdb=" O   TYR A 414 " (cutoff:3.500A)
      Proline residue:  A 419  - end of helix
    Processing helix  chain 'A' and resid 431 through 448
    Processing helix  chain 'A' and resid 479 through 501

    247 hydrogen bonds defined for protein.
    738 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: 0.50

  Time building geometry restraints manager: 0.45 seconds

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

  Histogram of bond lengths:
        1.15 -     1.29: 568
        1.29 -     1.42: 1066
        1.42 -     1.55: 2200
        1.55 -     1.68: 6
        1.68 -     1.81: 34
  Bond restraints: 3874
  Sorted by residual:
  bond pdb=" CA  ILE A 252 "
       pdb=" C   ILE A 252 "
    ideal  model  delta    sigma   weight residual
    1.523  1.444  0.079 9.20e-03 1.18e+04 7.40e+01
  bond pdb=" C   ILE A 252 "
       pdb=" O   ILE A 252 "
    ideal  model  delta    sigma   weight residual
    1.242  1.179  0.063 8.60e-03 1.35e+04 5.30e+01
  bond pdb=" C   TYR A  91 "
       pdb=" O   TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.237  1.154  0.082 1.16e-02 7.43e+03 5.02e+01
  bond pdb=" N   TYR A  91 "
       pdb=" CA  TYR A  91 "
    ideal  model  delta    sigma   weight residual
    1.459  1.380  0.080 1.20e-02 6.94e+03 4.41e+01
  bond pdb=" CA  PRO A 253 "
       pdb=" C   PRO A 253 "
    ideal  model  delta    sigma   weight residual
    1.517  1.422  0.095 1.46e-02 4.69e+03 4.21e+01
  ... (remaining 3869 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     5.38: 5260
        5.38 -    10.77: 27
       10.77 -    16.15: 2
       16.15 -    21.53: 3
       21.53 -    26.92: 2
  Bond angle restraints: 5294
  Sorted by residual:
  angle pdb=" N   ASP A 469 "
        pdb=" CA  ASP A 469 "
        pdb=" C   ASP A 469 "
      ideal   model   delta    sigma   weight residual
     114.16   89.53   24.63 1.48e+00 4.57e-01 2.77e+02
  angle pdb=" N   GLN A 255 "
        pdb=" CA  GLN A 255 "
        pdb=" C   GLN A 255 "
      ideal   model   delta    sigma   weight residual
     111.33  130.05  -18.72 1.21e+00 6.83e-01 2.39e+02
  angle pdb=" N   GLU A 503 "
        pdb=" CA  GLU A 503 "
        pdb=" C   GLU A 503 "
      ideal   model   delta    sigma   weight residual
     110.33  129.19  -18.86 1.29e+00 6.01e-01 2.14e+02
  angle pdb=" N   ASP A 468 "
        pdb=" CA  ASP A 468 "
        pdb=" C   ASP A 468 "
      ideal   model   delta    sigma   weight residual
     110.80  137.72  -26.92 2.13e+00 2.20e-01 1.60e+02
  angle pdb=" N   ASP A 469 "
        pdb=" CA  ASP A 469 "
        pdb=" CB  ASP A 469 "
      ideal   model   delta    sigma   weight residual
     110.88  130.68  -19.80 1.88e+00 2.83e-01 1.11e+02
  ... (remaining 5289 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    21.89: 2086
       21.89 -    43.78: 124
       43.78 -    65.67: 11
       65.67 -    87.56: 9
       87.56 -   109.46: 4
  Dihedral angle restraints: 2234
    sinusoidal: 818
      harmonic: 1416
  Sorted by residual:
  dihedral pdb=" N   ASP A 468 "
           pdb=" C   ASP A 468 "
           pdb=" CA  ASP A 468 "
           pdb=" CB  ASP A 468 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  153.22  -30.42     0      2.50e+00 1.60e-01 1.48e+02
  dihedral pdb=" C   ASP A 468 "
           pdb=" N   ASP A 468 "
           pdb=" CA  ASP A 468 "
           pdb=" CB  ASP A 468 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -150.72   28.12     0      2.50e+00 1.60e-01 1.27e+02
  dihedral pdb=" C   TYR A 364 "
           pdb=" N   TYR A 364 "
           pdb=" CA  TYR A 364 "
           pdb=" CB  TYR A 364 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -136.60   14.00     0      2.50e+00 1.60e-01 3.14e+01
  ... (remaining 2231 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.294: 618
       0.294 -    0.588: 5
       0.588 -    0.882: 2
       0.882 -    1.175: 0
       1.175 -    1.469: 1
  Chirality restraints: 626
  Sorted by residual:
  chirality pdb=" CA  ASP A 468 "
            pdb=" N   ASP A 468 "
            pdb=" C   ASP A 468 "
            pdb=" CB  ASP A 468 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.04    1.47 2.00e-01 2.50e+01 5.40e+01
  chirality pdb=" CA  PRO A 253 "
            pdb=" N   PRO A 253 "
            pdb=" C   PRO A 253 "
            pdb=" CB  PRO A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.72    1.98    0.74 2.00e-01 2.50e+01 1.36e+01
  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   -1.71   -0.69 2.00e-01 2.50e+01 1.19e+01
  ... (remaining 623 not shown)

  Planarity restraints: 643
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 251 "    0.019 2.00e-02 2.50e+03   3.56e-02 1.27e+01
        pdb=" C   GLY A 251 "   -0.062 2.00e-02 2.50e+03
        pdb=" O   GLY A 251 "    0.022 2.00e-02 2.50e+03
        pdb=" N   ILE A 252 "    0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PRO A 467 "   -0.017 2.00e-02 2.50e+03   3.44e-02 1.19e+01
        pdb=" C   PRO A 467 "    0.060 2.00e-02 2.50e+03
        pdb=" O   PRO A 467 "   -0.023 2.00e-02 2.50e+03
        pdb=" N   ASP A 468 "   -0.020 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  TRP A 254 "    0.012 2.00e-02 2.50e+03   2.42e-02 5.85e+00
        pdb=" C   TRP A 254 "   -0.042 2.00e-02 2.50e+03
        pdb=" O   TRP A 254 "    0.016 2.00e-02 2.50e+03
        pdb=" N   GLN A 255 "    0.014 2.00e-02 2.50e+03
  ... (remaining 640 not shown)

  Histogram of nonbonded interaction distances:
        1.93 -     2.52: 18
        2.52 -     3.12: 3125
        3.12 -     3.71: 5795
        3.71 -     4.31: 7648
        4.31 -     4.90: 12708
  Nonbonded interactions: 29294
  Sorted by model distance:
  nonbonded pdb=" O   ASP A 468 "
            pdb=" OD1 ASP A 468 "
     model   vdw
     1.926 3.040
  nonbonded pdb=" C   ASP A 468 "
            pdb=" OD1 ASP A 468 "
     model   vdw
     2.079 3.270
  nonbonded pdb=" N   ASP A 469 "
            pdb=" N   ASN A 470 "
     model   vdw
     2.182 2.560
  nonbonded pdb=" OG1 THR A 218 "
            pdb=" OG  SER A 297 "
     model   vdw
     2.211 3.040
  nonbonded pdb=" OE1 GLN A  86 "
            pdb=" NE1 TRP A 240 "
     model   vdw
     2.300 3.120
  ... (remaining 29289 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:             1.080
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.220
  Find NCS groups from input model:        0.010
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    7.760
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7151
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      :  0.007   0.096   3877  Z= 0.448
  Angle     :  1.261  26.915   5303  Z= 0.753
  Chirality :  0.095   1.469    626
  Planarity :  0.005   0.039    642
  Dihedral  : 15.608 109.455   1336
  Min Nonbonded Distance : 1.926

Molprobity Statistics.
  All-atom Clashscore : 14.52
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.98 %
    Favored  : 93.02 %
  Rotamer:
    Outliers :  0.27 %
    Allowed  :  0.80 %
    Favored  : 98.94 %
  Cbeta Deviations :  0.89 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -1.36 (0.37), residues: 487
  helix:  0.14 (0.29), residues: 313
  sheet:  None (None), residues: 0
  loop : -2.87 (0.44), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 382 
 TYR   0.020   0.002   TYR A 111 
 PHE   0.022   0.002   PHE A 334 
 TRP   0.028   0.002   TRP A  62 
 HIS   0.003   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00674 ( 3874)
  covalent geometry    : angle       1.23592 ( 5294)
  hydrogen bonds       : bond        0.14630 (  247)
  hydrogen bonds       : angle       6.72881 (  738)
  link_BETA1-4         : bond        0.00889 (    2)
  link_BETA1-4         : angle       4.82294 (    6)
  link_NAG-ASN         : bond        0.01491 (    1)
  link_NAG-ASN         : angle       8.29707 (    3)

*********************** 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
  122 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 121
  time to evaluate  : 0.130 
Fit side-chains
REVERT: A  249 LEU cc_start: 0.8260 (mp) cc_final: 0.8057 (mp)
REVERT: A  484 MET cc_start: 0.8614 (tmm) cc_final: 0.8362 (tmm)
  outliers start: 1
  outliers final: 1
  residues processed: 122
  average time/residue: 0.0487
  time to fit residues: 7.6636
Evaluate side-chains
  100 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 99
  time to evaluate  : 0.140 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  406 TRP
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 24 optimal weight:    3.9990
   chunk 48 optimal weight:    4.9990
   chunk 26 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 25 optimal weight:    0.8980
   chunk 19 optimal weight:    3.9990
   chunk 30 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.4145 r_free = 0.4145 target = 0.187590 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3992 r_free = 0.3992 target = 0.173103 restraints weight = 6968.476|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.176662 restraints weight = 3754.317|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 29)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.178866 restraints weight = 2363.487|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 38)----------------|
| r_work = 0.4072 r_free = 0.4072 target = 0.180489 restraints weight = 1687.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 19)----------------|
| r_work = 0.4081 r_free = 0.4081 target = 0.181322 restraints weight = 1272.566|
|-----------------------------------------------------------------------------|
r_work (final): 0.4065
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7173
moved from start:          0.1614

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.055   3877  Z= 0.168
  Angle     :  0.783  10.495   5303  Z= 0.387
  Chirality :  0.048   0.398    626
  Planarity :  0.005   0.042    642
  Dihedral  : 10.426  64.185    590
  Min Nonbonded Distance : 2.447

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.21 %
    Allowed  :  6.16 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  2.65 %
    Allowed  : 13.26 %
    Favored  : 84.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.80 (0.38), residues: 487
  helix:  0.53 (0.29), residues: 328
  sheet:  None (None), residues: 0
  loop : -2.82 (0.46), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 446 
 TYR   0.016   0.001   TYR A 364 
 PHE   0.015   0.001   PHE A 477 
 TRP   0.015   0.001   TRP A 254 
 HIS   0.003   0.001   HIS A 162 

Details of bonding type rmsd
  covalent geometry    : bond        0.00364 ( 3874)
  covalent geometry    : angle       0.75034 ( 5294)
  hydrogen bonds       : bond        0.05541 (  247)
  hydrogen bonds       : angle       5.31909 (  738)
  link_BETA1-4         : bond        0.00615 (    2)
  link_BETA1-4         : angle       4.05689 (    6)
  link_NAG-ASN         : bond        0.01573 (    1)
  link_NAG-ASN         : angle       7.58724 (    3)

*********************** 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
  107 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 97
  time to evaluate  : 0.132 
Fit side-chains
  outliers start: 10
  outliers final: 5
  residues processed: 101
  average time/residue: 0.0472
  time to fit residues: 6.3894
Evaluate side-chains
  92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 87
  time to evaluate  : 0.085 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 48 optimal weight:    0.7980
   chunk 16 optimal weight:    2.9990
   chunk 26 optimal weight:    0.9980
   chunk 37 optimal weight:    0.7980
   chunk 33 optimal weight:    6.9990
   chunk 35 optimal weight:    4.9990
   chunk 8 optimal weight:    6.9990
   chunk 45 optimal weight:    2.9990
   chunk 21 optimal weight:    3.9990
   chunk 36 optimal weight:    1.9990
   chunk 41 optimal weight:    0.8980
   overall best weight:    1.0982

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

Flipped N/Q/H residues before XYZ refinement:
A 162 HIS

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4116 r_free = 0.4116 target = 0.184892 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.3969 r_free = 0.3969 target = 0.171202 restraints weight = 6741.324|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.174616 restraints weight = 3661.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4031 r_free = 0.4031 target = 0.176930 restraints weight = 2297.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.178350 restraints weight = 1585.614|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 28)----------------|
| r_work = 0.4056 r_free = 0.4056 target = 0.179286 restraints weight = 1197.967|
|-----------------------------------------------------------------------------|
r_work (final): 0.4060
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7198
moved from start:          0.2019

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3877  Z= 0.162
  Angle     :  0.746   9.962   5303  Z= 0.366
  Chirality :  0.046   0.366    626
  Planarity :  0.005   0.037    642
  Dihedral  :  8.290  59.987    590
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 10.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.54 %
    Favored  : 94.46 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 19.36 %
    Favored  : 77.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.53 (0.38), residues: 487
  helix:  0.75 (0.29), residues: 328
  sheet:  None (None), residues: 0
  loop : -2.77 (0.45), residues: 159

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 446 
 TYR   0.015   0.001   TYR A 331 
 PHE   0.014   0.001   PHE A 334 
 TRP   0.017   0.001   TRP A  62 
 HIS   0.003   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00356 ( 3874)
  covalent geometry    : angle       0.71464 ( 5294)
  hydrogen bonds       : bond        0.05053 (  247)
  hydrogen bonds       : angle       5.08005 (  738)
  link_BETA1-4         : bond        0.00574 (    2)
  link_BETA1-4         : angle       3.99286 (    6)
  link_NAG-ASN         : bond        0.01238 (    1)
  link_NAG-ASN         : angle       7.18114 (    3)

*********************** 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
  103 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 91
  time to evaluate  : 0.084 
Fit side-chains
  outliers start: 12
  outliers final: 7
  residues processed: 95
  average time/residue: 0.0370
  time to fit residues: 4.7372
Evaluate side-chains
  93 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 86
  time to evaluate  : 0.088 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    0.0670
   chunk 15 optimal weight:    5.9990
   chunk 6 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 26 optimal weight:    2.9990
   chunk 34 optimal weight:    7.9990
   chunk 19 optimal weight:    5.9990
   chunk 41 optimal weight:    0.9990
   overall best weight:    1.1724

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.187385 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4027 r_free = 0.4027 target = 0.174139 restraints weight = 6931.733|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4064 r_free = 0.4064 target = 0.177496 restraints weight = 3758.961|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.4086 r_free = 0.4086 target = 0.179683 restraints weight = 2339.088|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 41)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.181062 restraints weight = 1613.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.4111 r_free = 0.4111 target = 0.182114 restraints weight = 1217.954|
|-----------------------------------------------------------------------------|
r_work (final): 0.4111
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7210
moved from start:          0.2295

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.034   3877  Z= 0.160
  Angle     :  0.723  10.023   5303  Z= 0.354
  Chirality :  0.046   0.358    626
  Planarity :  0.005   0.038    642
  Dihedral  :  7.539  58.043    590
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.53
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  4.77 %
    Allowed  : 21.49 %
    Favored  : 73.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.38 (0.38), residues: 487
  helix:  0.78 (0.28), residues: 331
  sheet:  None (None), residues: 0
  loop : -2.55 (0.48), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 382 
 TYR   0.012   0.001   TYR A 122 
 PHE   0.012   0.001   PHE A 479 
 TRP   0.018   0.001   TRP A  62 
 HIS   0.003   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00352 ( 3874)
  covalent geometry    : angle       0.69294 ( 5294)
  hydrogen bonds       : bond        0.04946 (  247)
  hydrogen bonds       : angle       5.03716 (  738)
  link_BETA1-4         : bond        0.00624 (    2)
  link_BETA1-4         : angle       3.76469 (    6)
  link_NAG-ASN         : bond        0.01157 (    1)
  link_NAG-ASN         : angle       6.92726 (    3)

*********************** 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
  103 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 85
  time to evaluate  : 0.089 
Fit side-chains
REVERT: A  480 LYS cc_start: 0.7605 (OUTLIER) cc_final: 0.7189 (mttt)
REVERT: A  484 MET cc_start: 0.8741 (tmm) cc_final: 0.8509 (tmm)
  outliers start: 18
  outliers final: 8
  residues processed: 97
  average time/residue: 0.0476
  time to fit residues: 6.2660
Evaluate side-chains
  92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 83
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  480 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 45 optimal weight:    3.9990
   chunk 17 optimal weight:    2.9990
   chunk 15 optimal weight:    0.6980
   chunk 44 optimal weight:    0.9980
   chunk 34 optimal weight:    0.0000
   chunk 48 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 18 optimal weight:    2.9990
   chunk 13 optimal weight:    2.9990
   chunk 22 optimal weight:    2.9990
   chunk 12 optimal weight:    0.9980
   overall best weight:    0.7386

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.190016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4054 r_free = 0.4054 target = 0.176669 restraints weight = 7073.265|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.4091 r_free = 0.4091 target = 0.180073 restraints weight = 3841.681|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4114 r_free = 0.4114 target = 0.182268 restraints weight = 2397.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4128 r_free = 0.4128 target = 0.183751 restraints weight = 1661.893|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4139 r_free = 0.4139 target = 0.184800 restraints weight = 1243.776|
|-----------------------------------------------------------------------------|
r_work (final): 0.4148
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7170
moved from start:          0.2552

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3877  Z= 0.139
  Angle     :  0.698   9.893   5303  Z= 0.342
  Chirality :  0.044   0.356    626
  Planarity :  0.005   0.038    642
  Dihedral  :  7.365  57.375    590
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 9.46
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.95 %
    Favored  : 94.05 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 23.87 %
    Favored  : 71.88 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.18 (0.38), residues: 487
  helix:  0.94 (0.28), residues: 329
  sheet:  None (None), residues: 0
  loop : -2.46 (0.48), residues: 158

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 446 
 TYR   0.017   0.001   TYR A 186 
 PHE   0.012   0.001   PHE A 479 
 TRP   0.019   0.001   TRP A  62 
 HIS   0.003   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 3874)
  covalent geometry    : angle       0.66916 ( 5294)
  hydrogen bonds       : bond        0.04614 (  247)
  hydrogen bonds       : angle       4.94009 (  738)
  link_BETA1-4         : bond        0.00621 (    2)
  link_BETA1-4         : angle       3.56793 (    6)
  link_NAG-ASN         : bond        0.01239 (    1)
  link_NAG-ASN         : angle       6.69617 (    3)

*********************** 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
  106 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 90
  time to evaluate  : 0.123 
Fit side-chains
REVERT: A  406 TRP cc_start: 0.8730 (OUTLIER) cc_final: 0.8402 (t60)
REVERT: A  484 MET cc_start: 0.8691 (tmm) cc_final: 0.8473 (tmm)
  outliers start: 16
  outliers final: 10
  residues processed: 97
  average time/residue: 0.0431
  time to fit residues: 5.6924
Evaluate side-chains
  94 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 83
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  275 PHE
Chi-restraints excluded: chain A residue  282 LEU
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 29 optimal weight:    0.1980
   chunk 1 optimal weight:    0.8980
   chunk 8 optimal weight:    4.9990
   chunk 0 optimal weight:    0.8980
   chunk 11 optimal weight:    0.0070
   chunk 34 optimal weight:    5.9990
   chunk 7 optimal weight:    0.8980
   chunk 42 optimal weight:    0.8980
   chunk 32 optimal weight:    5.9990
   chunk 41 optimal weight:    3.9990
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.5798

-------------------------------------------------------------------------------
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 = 0.4204 r_free = 0.4204 target = 0.191281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4063 r_free = 0.4063 target = 0.177507 restraints weight = 7126.539|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 43)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.180969 restraints weight = 3915.853|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4123 r_free = 0.4123 target = 0.183239 restraints weight = 2451.824|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.4136 r_free = 0.4136 target = 0.184603 restraints weight = 1704.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 29)----------------|
| r_work = 0.4147 r_free = 0.4147 target = 0.185744 restraints weight = 1308.359|
|-----------------------------------------------------------------------------|
r_work (final): 0.4156
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7146
moved from start:          0.2765

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3877  Z= 0.136
  Angle     :  0.716  11.252   5303  Z= 0.345
  Chirality :  0.044   0.354    626
  Planarity :  0.005   0.041    642
  Dihedral  :  7.294  59.682    590
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 9.06
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  5.04 %
    Allowed  : 23.61 %
    Favored  : 71.35 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.06 (0.38), residues: 487
  helix:  1.01 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -2.36 (0.48), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 369 
 TYR   0.020   0.001   TYR A 122 
 PHE   0.011   0.001   PHE A 479 
 TRP   0.016   0.001   TRP A  62 
 HIS   0.002   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00291 ( 3874)
  covalent geometry    : angle       0.68994 ( 5294)
  hydrogen bonds       : bond        0.04389 (  247)
  hydrogen bonds       : angle       4.91743 (  738)
  link_BETA1-4         : bond        0.00598 (    2)
  link_BETA1-4         : angle       3.49164 (    6)
  link_NAG-ASN         : bond        0.01217 (    1)
  link_NAG-ASN         : angle       6.51761 (    3)

*********************** 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
  103 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 84
  time to evaluate  : 0.138 
Fit side-chains
REVERT: A  335 PHE cc_start: 0.7840 (OUTLIER) cc_final: 0.7635 (t80)
REVERT: A  480 LYS cc_start: 0.7661 (OUTLIER) cc_final: 0.7302 (mttt)
  outliers start: 19
  outliers final: 12
  residues processed: 94
  average time/residue: 0.0477
  time to fit residues: 6.1553
Evaluate side-chains
  92 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 78
  time to evaluate  : 0.084 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  136 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  480 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 39 optimal weight:    0.5980
   chunk 3 optimal weight:    0.6980
   chunk 36 optimal weight:    0.9990
   chunk 30 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 34 optimal weight:   10.0000
   chunk 6 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 29 optimal weight:    0.4980
   chunk 28 optimal weight:    0.0870
   chunk 5 optimal weight:    0.9990
   overall best weight:    0.5558

-------------------------------------------------------------------------------
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**
A 225 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4153 r_free = 0.4153 target = 0.187782 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.4005 r_free = 0.4005 target = 0.173572 restraints weight = 7073.679|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.177175 restraints weight = 3785.500|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.179524 restraints weight = 2346.394|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.181053 restraints weight = 1616.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.4095 r_free = 0.4095 target = 0.182195 restraints weight = 1215.789|
|-----------------------------------------------------------------------------|
r_work (final): 0.4095
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7134
moved from start:          0.2908

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   3877  Z= 0.132
  Angle     :  0.701   9.823   5303  Z= 0.337
  Chirality :  0.044   0.354    626
  Planarity :  0.005   0.037    642
  Dihedral  :  7.205  58.254    590
  Min Nonbonded Distance : 2.573

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.16 %
    Favored  : 93.84 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 24.67 %
    Favored  : 70.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.10 (0.38), residues: 487
  helix:  1.08 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -2.19 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 369 
 TYR   0.024   0.001   TYR A 122 
 PHE   0.009   0.001   PHE A 334 
 TRP   0.025   0.001   TRP A  62 
 HIS   0.003   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00282 ( 3874)
  covalent geometry    : angle       0.67417 ( 5294)
  hydrogen bonds       : bond        0.04292 (  247)
  hydrogen bonds       : angle       4.90757 (  738)
  link_BETA1-4         : bond        0.00580 (    2)
  link_BETA1-4         : angle       3.44333 (    6)
  link_NAG-ASN         : bond        0.01206 (    1)
  link_NAG-ASN         : angle       6.45263 (    3)

*********************** 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
  100 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 83
  time to evaluate  : 0.140 
Fit side-chains
REVERT: A  330 VAL cc_start: 0.8010 (m) cc_final: 0.7757 (p)
REVERT: A  335 PHE cc_start: 0.7803 (OUTLIER) cc_final: 0.7577 (t80)
REVERT: A  440 VAL cc_start: 0.6720 (m) cc_final: 0.6396 (m)
REVERT: A  480 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7222 (mttt)
  outliers start: 17
  outliers final: 12
  residues processed: 94
  average time/residue: 0.0398
  time to fit residues: 5.1565
Evaluate side-chains
  94 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 80
  time to evaluate  : 0.138 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   48 ASP
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  136 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  480 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 27 optimal weight:    0.9990
   chunk 45 optimal weight:    3.9990
   chunk 8 optimal weight:    3.9990
   chunk 3 optimal weight:    0.7980
   chunk 43 optimal weight:    1.9990
   chunk 48 optimal weight:    0.9990
   chunk 29 optimal weight:    0.6980
   chunk 33 optimal weight:    5.9990
   chunk 14 optimal weight:    1.9990
   chunk 38 optimal weight:    1.9990
   chunk 11 optimal weight:    2.9990
   overall best weight:    1.0986

-------------------------------------------------------------------------------
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 = 0.4165 r_free = 0.4165 target = 0.188058 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 31)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.174642 restraints weight = 6905.916|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.4066 r_free = 0.4066 target = 0.178060 restraints weight = 3763.240|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.4089 r_free = 0.4089 target = 0.180278 restraints weight = 2349.657|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.4104 r_free = 0.4104 target = 0.181839 restraints weight = 1621.402|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.4115 r_free = 0.4115 target = 0.182887 restraints weight = 1198.192|
|-----------------------------------------------------------------------------|
r_work (final): 0.4128
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7183
moved from start:          0.3002

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3877  Z= 0.157
  Angle     :  0.731   9.948   5303  Z= 0.354
  Chirality :  0.046   0.355    626
  Planarity :  0.005   0.037    642
  Dihedral  :  7.222  58.046    590
  Min Nonbonded Distance : 2.568

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.37 %
    Favored  : 93.63 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 25.99 %
    Favored  : 70.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.08 (0.39), residues: 487
  helix:  1.06 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -2.19 (0.50), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 382 
 TYR   0.027   0.002   TYR A 122 
 PHE   0.011   0.001   PHE A 426 
 TRP   0.028   0.002   TRP A  62 
 HIS   0.003   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00348 ( 3874)
  covalent geometry    : angle       0.70568 ( 5294)
  hydrogen bonds       : bond        0.04567 (  247)
  hydrogen bonds       : angle       4.97638 (  738)
  link_BETA1-4         : bond        0.00709 (    2)
  link_BETA1-4         : angle       3.53119 (    6)
  link_NAG-ASN         : bond        0.00983 (    1)
  link_NAG-ASN         : angle       6.39692 (    3)

*********************** 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
  99 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 85
  time to evaluate  : 0.116 
Fit side-chains
REVERT: A  121 ILE cc_start: 0.8042 (mt) cc_final: 0.7752 (tt)
REVERT: A  330 VAL cc_start: 0.8046 (m) cc_final: 0.7828 (p)
REVERT: A  335 PHE cc_start: 0.7897 (OUTLIER) cc_final: 0.7673 (t80)
REVERT: A  480 LYS cc_start: 0.7770 (OUTLIER) cc_final: 0.7343 (mttt)
  outliers start: 14
  outliers final: 10
  residues processed: 93
  average time/residue: 0.0436
  time to fit residues: 5.5682
Evaluate side-chains
  95 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 83
  time to evaluate  : 0.105 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  136 MET
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  248 MET
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  358 MET
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  480 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 3 optimal weight:    0.3980
   chunk 32 optimal weight:    3.9990
   chunk 13 optimal weight:    0.9990
   chunk 11 optimal weight:    0.6980
   chunk 2 optimal weight:    2.9990
   chunk 44 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 22 optimal weight:    0.0470
   chunk 24 optimal weight:    2.9990
   chunk 9 optimal weight:    4.9990
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6078

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

Flipped N/Q/H residues before XYZ refinement:
** A 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 = 0.4155 r_free = 0.4155 target = 0.187933 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4012 r_free = 0.4012 target = 0.174116 restraints weight = 6887.050|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.177607 restraints weight = 3675.575|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.4071 r_free = 0.4071 target = 0.179889 restraints weight = 2269.922|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.181328 restraints weight = 1553.415|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 40)----------------|
| r_work = 0.4097 r_free = 0.4097 target = 0.182427 restraints weight = 1174.985|
|-----------------------------------------------------------------------------|
r_work (final): 0.4099
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7131
moved from start:          0.3234

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3877  Z= 0.137
  Angle     :  0.713   9.800   5303  Z= 0.343
  Chirality :  0.045   0.350    626
  Planarity :  0.005   0.037    642
  Dihedral  :  7.226  56.146    590
  Min Nonbonded Distance : 2.560

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  4.51 %
    Allowed  : 27.32 %
    Favored  : 68.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.11 (0.38), residues: 487
  helix:  1.09 (0.28), residues: 330
  sheet:  None (None), residues: 0
  loop : -2.20 (0.49), residues: 157

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.027   0.001   TYR A 122 
 PHE   0.012   0.001   PHE A 479 
 TRP   0.019   0.001   TRP A  62 
 HIS   0.002   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00295 ( 3874)
  covalent geometry    : angle       0.68885 ( 5294)
  hydrogen bonds       : bond        0.04339 (  247)
  hydrogen bonds       : angle       4.99518 (  738)
  link_BETA1-4         : bond        0.00677 (    2)
  link_BETA1-4         : angle       3.35658 (    6)
  link_NAG-ASN         : bond        0.01179 (    1)
  link_NAG-ASN         : angle       6.28560 (    3)

*********************** 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
  99 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 82
  time to evaluate  : 0.098 
Fit side-chains
REVERT: A  121 ILE cc_start: 0.7840 (mt) cc_final: 0.7557 (tt)
REVERT: A  330 VAL cc_start: 0.8053 (m) cc_final: 0.7841 (p)
REVERT: A  335 PHE cc_start: 0.7838 (OUTLIER) cc_final: 0.7633 (t80)
REVERT: A  440 VAL cc_start: 0.6856 (m) cc_final: 0.6563 (m)
REVERT: A  480 LYS cc_start: 0.7659 (OUTLIER) cc_final: 0.7244 (mttt)
  outliers start: 17
  outliers final: 10
  residues processed: 91
  average time/residue: 0.0446
  time to fit residues: 5.4889
Evaluate side-chains
  93 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 81
  time to evaluate  : 0.087 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  101 PHE
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  249 LEU
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  480 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 28 optimal weight:    1.9990
   chunk 33 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    5.9990
   chunk 30 optimal weight:    0.0270
   chunk 18 optimal weight:    0.3980
   chunk 47 optimal weight:   10.0000
   chunk 27 optimal weight:    0.0870
   chunk 29 optimal weight:    0.3980
   chunk 34 optimal weight:    1.9990
   chunk 46 optimal weight:    0.6980
   overall best weight:    0.3216

-------------------------------------------------------------------------------
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 = 0.4193 r_free = 0.4193 target = 0.191542 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.4046 r_free = 0.4046 target = 0.177261 restraints weight = 7001.845|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4083 r_free = 0.4083 target = 0.180830 restraints weight = 3802.735|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.4107 r_free = 0.4107 target = 0.183181 restraints weight = 2366.971|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.4122 r_free = 0.4122 target = 0.184658 restraints weight = 1638.425|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.4134 r_free = 0.4134 target = 0.185827 restraints weight = 1240.292|
|-----------------------------------------------------------------------------|
r_work (final): 0.4132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7066
moved from start:          0.3478

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3877  Z= 0.130
  Angle     :  0.701   9.750   5303  Z= 0.336
  Chirality :  0.043   0.346    626
  Planarity :  0.004   0.037    642
  Dihedral  :  7.060  55.941    590
  Min Nonbonded Distance : 2.537

Molprobity Statistics.
  All-atom Clashscore : 9.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 29.18 %
    Favored  : 67.64 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.35 (0.38), residues: 487
  helix:  1.30 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -2.03 (0.49), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 361 
 TYR   0.023   0.001   TYR A 122 
 PHE   0.011   0.001   PHE A 479 
 TRP   0.014   0.001   TRP A  62 
 HIS   0.001   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00275 ( 3874)
  covalent geometry    : angle       0.67677 ( 5294)
  hydrogen bonds       : bond        0.04081 (  247)
  hydrogen bonds       : angle       4.94980 (  738)
  link_BETA1-4         : bond        0.00633 (    2)
  link_BETA1-4         : angle       3.30259 (    6)
  link_NAG-ASN         : bond        0.01215 (    1)
  link_NAG-ASN         : angle       6.11119 (    3)

********************** 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
  99 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 87
  time to evaluate  : 0.148 
Fit side-chains
REVERT: A  335 PHE cc_start: 0.7755 (OUTLIER) cc_final: 0.7513 (t80)
REVERT: A  480 LYS cc_start: 0.7621 (OUTLIER) cc_final: 0.7252 (mttt)
  outliers start: 12
  outliers final: 8
  residues processed: 94
  average time/residue: 0.0486
  time to fit residues: 6.1184
Evaluate side-chains
  90 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 80
  time to evaluate  : 0.136 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  159 VAL
Chi-restraints excluded: chain A residue  168 SER
Chi-restraints excluded: chain A residue  214 ASP
Chi-restraints excluded: chain A residue  241 LEU
Chi-restraints excluded: chain A residue  335 PHE
Chi-restraints excluded: chain A residue  353 LEU
Chi-restraints excluded: chain A residue  377 ILE
Chi-restraints excluded: chain A residue  406 TRP
Chi-restraints excluded: chain A residue  427 VAL
Chi-restraints excluded: chain A residue  480 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 49
   random chunks:
   chunk 34 optimal weight:    0.9990
   chunk 29 optimal weight:    0.9990
   chunk 16 optimal weight:    2.9990
   chunk 7 optimal weight:    2.9990
   chunk 33 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9980
   chunk 3 optimal weight:    0.9980
   chunk 35 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 24 optimal weight:    0.0070
   chunk 14 optimal weight:    0.8980
   overall best weight:    0.7800

-------------------------------------------------------------------------------
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 = 0.4167 r_free = 0.4167 target = 0.189019 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.4025 r_free = 0.4025 target = 0.175290 restraints weight = 6787.423|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.4061 r_free = 0.4061 target = 0.178762 restraints weight = 3658.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.4085 r_free = 0.4085 target = 0.181044 restraints weight = 2263.927|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.4100 r_free = 0.4100 target = 0.182566 restraints weight = 1551.616|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.4112 r_free = 0.4112 target = 0.183665 restraints weight = 1157.454|
|-----------------------------------------------------------------------------|
r_work (final): 0.4117
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7115
moved from start:          0.3490

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3877  Z= 0.139
  Angle     :  0.707   9.864   5303  Z= 0.339
  Chirality :  0.044   0.348    626
  Planarity :  0.004   0.037    642
  Dihedral  :  7.019  54.981    590
  Min Nonbonded Distance : 2.530

Molprobity Statistics.
  All-atom Clashscore : 9.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.75 %
    Favored  : 94.25 %
  Rotamer:
    Outliers :  3.71 %
    Allowed  : 28.38 %
    Favored  : 67.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.41 (0.38), residues: 487
  helix:  1.36 (0.28), residues: 324
  sheet:  None (None), residues: 0
  loop : -2.04 (0.48), residues: 163

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 260 
 TYR   0.024   0.001   TYR A 122 
 PHE   0.016   0.001   PHE A 477 
 TRP   0.015   0.001   TRP A  62 
 HIS   0.002   0.001   HIS A   4 

Details of bonding type rmsd
  covalent geometry    : bond        0.00305 ( 3874)
  covalent geometry    : angle       0.68316 ( 5294)
  hydrogen bonds       : bond        0.04208 (  247)
  hydrogen bonds       : angle       4.94093 (  738)
  link_BETA1-4         : bond        0.00639 (    2)
  link_BETA1-4         : angle       3.38096 (    6)
  link_NAG-ASN         : bond        0.01015 (    1)
  link_NAG-ASN         : angle       6.11477 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 761.81 seconds
wall clock time: 13 minutes 54.40 seconds (834.40 seconds total)