Starting phenix.real_space_refine
on Wed Jul 23 13:15:54 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/7v27_31638/07_2025/7v27_31638.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/7v27_31638/07_2025/7v27_31638.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=4.18
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2025/7v27_31638.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2025/7v27_31638.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2025/7v27_31638.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/7v27_31638/07_2025/7v27_31638.cif"
  }
  resolution = 4.18
  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=   0.000
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      16      5.16       5
     C    2065      2.51       5
     N     535      2.21       5
     O     636      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib"
  Total number of atoms: 3252
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "C"
      Number of atoms: 1536
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 194, 1536
          Classifications: {'peptide': 194}
          Link IDs: {'PTRANS': 11, 'TRANS': 182}
    Chain: "B"
      Number of atoms: 920
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 120, 920
          Classifications: {'peptide': 120}
          Link IDs: {'PTRANS': 7, 'TRANS': 112}
    Chain: "A"
      Number of atoms: 782
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 107, 782
          Classifications: {'peptide': 107}
          Link IDs: {'PTRANS': 5, 'TRANS': 101}
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.81, per 1000 atoms: 1.17
  Number of scatterers: 3252
  At special positions: 0
  Unit cell: (80.542, 58.576, 99.37, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      16     16.00
     O     636      8.00
     N     535      7.00
     C    2065      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS C 336 " - pdb=" SG  CYS C 361 " distance=2.03
    Simple disulfide: pdb=" SG  CYS C 379 " - pdb=" SG  CYS C 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 391 " - pdb=" SG  CYS C 525 " distance=2.04
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS B  22 " - pdb=" SG  CYS B  97 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  22 " - pdb=" SG  CYS A  90 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C 601 " - " ASN C 343 "
  Time building additional restraints: 0.85
  Conformation dependent library (CDL) restraints added in 527.1 milliseconds
  

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  774

  Finding SS restraints...
    Secondary structure from input PDB file:
      4 helices and 10 sheets defined
      5.5% alpha, 26.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.50
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 343
      removed outlier: 3.892A  pdb=" N   VAL C 341 " --> pdb=" O   PRO C 337 " (cutoff:3.500A)
      removed outlier: 3.959A  pdb=" N   PHE C 342 " --> pdb=" O   PHE C 338 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 349 through 353
      removed outlier: 3.642A  pdb=" N   TRP C 353 " --> pdb=" O   VAL C 350 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 365 through 370
    Processing helix  chain 'B' and resid 88 through 92
    Processing sheet with id=AA1, first strand: chain 'C' and resid 356 through 357
      removed outlier: 3.604A  pdb=" N   VAL C 512 " --> pdb=" O   ASP C 398 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 379 through 380
      removed outlier: 4.202A  pdb=" N   GLY C 431 " --> pdb=" O   TYR C 380 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454
      removed outlier: 4.024A  pdb=" N   TYR C 453 " --> pdb=" O   GLN C 493 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'B' and resid 3 through 7
      removed outlier: 3.680A  pdb=" N   ARG B   5 " --> pdb=" O   THR B  23 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.717A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR B 114 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
      removed outlier: 6.908A  pdb=" N   VAL B  36 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
      removed outlier: 4.725A  pdb=" N   LEU B  52 " --> pdb=" O   VAL B  36 " (cutoff:3.500A)
      removed outlier: 6.928A  pdb=" N   TRP B  38 " --> pdb=" O   LEU B  50 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   ARG B  60 " --> pdb=" O   LEU B  52 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'B' and resid 11 through 12
      removed outlier: 3.717A  pdb=" N   VAL B  12 " --> pdb=" O   THR B 117 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   THR B 114 " --> pdb=" O   TYR B  95 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'A' and resid 11 through 12
    Processing sheet with id=AA8, first strand: chain 'A' and resid 19 through 22
      removed outlier: 3.639A  pdb=" N   SER A  67 " --> pdb=" O   SER A  74 " (cutoff:3.500A)
    Processing sheet with id=AA9, first strand: chain 'A' and resid 48 through 50
      removed outlier: 6.028A  pdb=" N   LEU A  48 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE A  50 " --> pdb=" O   TRP A  37 " (cutoff:3.500A)
    Processing sheet with id=AB1, first strand: chain 'A' and resid 48 through 50
      removed outlier: 6.028A  pdb=" N   LEU A  48 " --> pdb=" O   GLN A  39 " (cutoff:3.500A)
      removed outlier: 5.908A  pdb=" N   GLN A  39 " --> pdb=" O   LEU A  48 " (cutoff:3.500A)
      removed outlier: 4.171A  pdb=" N   ILE A  50 " --> pdb=" O   TRP A  37 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   TYR A  88 " --> pdb=" O   THR A 104 " (cutoff:3.500A)
      removed outlier: 3.874A  pdb=" N   THR A 104 " --> pdb=" O   TYR A  88 " (cutoff:3.500A)

    72 hydrogen bonds defined for protein.
    171 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.21

  Time building geometry restraints manager: 1.02 seconds

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

  Histogram of bond lengths:
        1.23 -     1.35: 1026
        1.35 -     1.47: 885
        1.47 -     1.59: 1403
        1.59 -     1.71: 0
        1.71 -     1.83: 19
  Bond restraints: 3333
  Sorted by residual:
  bond pdb=" C   VAL C 382 "
       pdb=" N   SER C 383 "
    ideal  model  delta    sigma   weight residual
    1.330  1.354 -0.024 1.37e-02 5.33e+03 2.96e+00
  bond pdb=" C1  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.406  1.433 -0.027 2.00e-02 2.50e+03 1.78e+00
  bond pdb=" C5  NAG C 601 "
       pdb=" O5  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.413  1.434 -0.021 2.00e-02 2.50e+03 1.14e+00
  bond pdb=" C3  NAG C 601 "
       pdb=" O3  NAG C 601 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 1.04e+00
  bond pdb=" N   CYS C 391 "
       pdb=" CA  CYS C 391 "
    ideal  model  delta    sigma   weight residual
    1.455  1.465 -0.010 1.21e-02 6.83e+03 6.90e-01
  ... (remaining 3328 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     0.83: 4149
        0.83 -     1.67: 303
        1.67 -     2.50: 51
        2.50 -     3.34: 36
        3.34 -     4.17: 5
  Bond angle restraints: 4544
  Sorted by residual:
  angle pdb=" N   MET A  49 "
        pdb=" CA  MET A  49 "
        pdb=" C   MET A  49 "
      ideal   model   delta    sigma   weight residual
     114.04  110.56    3.48 1.24e+00 6.50e-01 7.89e+00
  angle pdb=" N   CYS C 432 "
        pdb=" CA  CYS C 432 "
        pdb=" C   CYS C 432 "
      ideal   model   delta    sigma   weight residual
     107.88  111.39   -3.51 1.41e+00 5.03e-01 6.18e+00
  angle pdb=" N   SER A  97 "
        pdb=" CA  SER A  97 "
        pdb=" C   SER A  97 "
      ideal   model   delta    sigma   weight residual
     108.34  111.47   -3.13 1.31e+00 5.83e-01 5.70e+00
  angle pdb=" CA  GLY C 504 "
        pdb=" C   GLY C 504 "
        pdb=" N   TYR C 505 "
      ideal   model   delta    sigma   weight residual
     118.95  116.79    2.16 1.06e+00 8.90e-01 4.17e+00
  angle pdb=" C   PHE C 486 "
        pdb=" N   ASN C 487 "
        pdb=" CA  ASN C 487 "
      ideal   model   delta    sigma   weight residual
     121.54  125.16   -3.62 1.91e+00 2.74e-01 3.60e+00
  ... (remaining 4539 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.03: 1763
       15.03 -    30.06: 183
       30.06 -    45.10: 30
       45.10 -    60.13: 6
       60.13 -    75.16: 1
  Dihedral angle restraints: 1983
    sinusoidal: 765
      harmonic: 1218
  Sorted by residual:
  dihedral pdb=" CB  CYS C 379 "
           pdb=" SG  CYS C 379 "
           pdb=" SG  CYS C 432 "
           pdb=" CB  CYS C 432 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   53.66   39.34     1      1.00e+01 1.00e-02 2.18e+01
  dihedral pdb=" CB  CYS B  22 "
           pdb=" SG  CYS B  22 "
           pdb=" SG  CYS B  97 "
           pdb=" CB  CYS B  97 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00  123.94  -30.94     1      1.00e+01 1.00e-02 1.37e+01
  dihedral pdb=" CB  CYS C 391 "
           pdb=" SG  CYS C 391 "
           pdb=" SG  CYS C 525 "
           pdb=" CB  CYS C 525 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00  -58.76  -27.24     1      1.00e+01 1.00e-02 1.06e+01
  ... (remaining 1980 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.038: 364
       0.038 -    0.075: 103
       0.075 -    0.113: 38
       0.113 -    0.150: 5
       0.150 -    0.188: 1
  Chirality restraints: 511
  Sorted by residual:
  chirality pdb=" CB  ILE C 410 "
            pdb=" CA  ILE C 410 "
            pdb=" CG1 ILE C 410 "
            pdb=" CG2 ILE C 410 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.64    2.46    0.19 2.00e-01 2.50e+01 8.80e-01
  chirality pdb=" CB  THR C 500 "
            pdb=" CA  THR C 500 "
            pdb=" OG1 THR C 500 "
            pdb=" CG2 THR C 500 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.55    2.43    0.12 2.00e-01 2.50e+01 3.59e-01
  chirality pdb=" CA  ILE B  39 "
            pdb=" N   ILE B  39 "
            pdb=" C   ILE B  39 "
            pdb=" CB  ILE B  39 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.55   -0.12 2.00e-01 2.50e+01 3.41e-01
  ... (remaining 508 not shown)

  Planarity restraints: 581
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA C 520 "    0.016 5.00e-02 4.00e+02   2.43e-02 9.46e-01
        pdb=" N   PRO C 521 "   -0.042 5.00e-02 4.00e+02
        pdb=" CA  PRO C 521 "    0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO C 521 "    0.014 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   ALA A  45 "   -0.015 5.00e-02 4.00e+02   2.26e-02 8.18e-01
        pdb=" N   PRO A  46 "    0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO A  46 "   -0.012 5.00e-02 4.00e+02
        pdb=" CD  PRO A  46 "   -0.013 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   THR B  31 "    0.015 5.00e-02 4.00e+02   2.24e-02 8.03e-01
        pdb=" N   PRO B  32 "   -0.039 5.00e-02 4.00e+02
        pdb=" CA  PRO B  32 "    0.011 5.00e-02 4.00e+02
        pdb=" CD  PRO B  32 "    0.012 5.00e-02 4.00e+02
  ... (remaining 578 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 546
        2.76 -     3.30: 3043
        3.30 -     3.83: 5332
        3.83 -     4.37: 5987
        4.37 -     4.90: 10409
  Nonbonded interactions: 25317
  Sorted by model distance:
  nonbonded pdb=" OG1 THR C 430 "
            pdb=" O   PHE C 515 "
     model   vdw
     2.229 3.040
  nonbonded pdb=" OD2 ASP C 398 "
            pdb=" OH  TYR C 423 "
     model   vdw
     2.252 3.040
  nonbonded pdb=" O   ILE B 106 "
            pdb=" OH  TYR A  38 "
     model   vdw
     2.272 3.040
  nonbonded pdb=" OG  SER A   9 "
            pdb=" O   LYS A 105 "
     model   vdw
     2.309 3.040
  nonbonded pdb=" O   ARG C 408 "
            pdb=" NE2 GLN C 414 "
     model   vdw
     2.313 3.120
  ... (remaining 25312 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:             55.400
  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:          0.150
  Check model and map are aligned:         0.030
  Set scattering table:                    0.030
  Process input model:                     16.660
  Find NCS groups from input model:        0.060
  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:             0.010
  Load rotamer database and sin/cos tables:3.110
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   75.460
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8014
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      :  0.002   0.027   3340  Z= 0.124
  Angle     :  0.537   4.173   4559  Z= 0.306
  Chirality :  0.040   0.188    511
  Planarity :  0.003   0.024    580
  Dihedral  : 11.752  75.160   1191
  Min Nonbonded Distance : 2.229

Molprobity Statistics.
  All-atom Clashscore : 9.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  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: -4.40 (0.34), residues: 415
  helix: -3.86 (0.99), residues: 13
  sheet: -2.42 (0.44), residues: 126
  loop : -3.32 (0.29), residues: 276

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP B  55 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.008   0.001   PHE C 338 
 TYR   0.007   0.001   TYR B  96 
 ARG   0.001   0.000   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00202 (    1)
  link_NAG-ASN         : angle       1.03656 (    3)
  hydrogen bonds       : bond        0.31656 (   58)
  hydrogen bonds       : angle      11.20114 (  171)
  SS BOND              : bond        0.00420 (    6)
  SS BOND              : angle       0.90340 (   12)
  covalent geometry    : bond        0.00217 ( 3333)
  covalent geometry    : angle       0.53502 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  112 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 112
  time to evaluate  : 0.350 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  358 ILE cc_start: 0.9209 (mm) cc_final: 0.8991 (mt)
REVERT: C  365 TYR cc_start: 0.8446 (m-80) cc_final: 0.8231 (m-80)
REVERT: C  405 ASP cc_start: 0.9094 (m-30) cc_final: 0.8536 (m-30)
REVERT: C  408 ARG cc_start: 0.8609 (ptt90) cc_final: 0.8409 (ptt90)
REVERT: C  449 TYR cc_start: 0.8758 (m-80) cc_final: 0.8529 (m-10)
REVERT: C  458 LYS cc_start: 0.8492 (pptt) cc_final: 0.8042 (pttm)
REVERT: B   13 LYS cc_start: 0.7872 (mmtm) cc_final: 0.7520 (tmtt)
REVERT: B   49 TRP cc_start: 0.8957 (t60) cc_final: 0.8684 (t60)
REVERT: B   56 ASP cc_start: 0.8641 (m-30) cc_final: 0.8436 (m-30)
REVERT: B  104 ASP cc_start: 0.8474 (t0) cc_final: 0.8220 (t0)
REVERT: A   64 PHE cc_start: 0.8558 (m-80) cc_final: 0.8332 (m-10)
REVERT: A   68 LYS cc_start: 0.7546 (tmmt) cc_final: 0.7346 (ptmt)
  outliers start: 0
  outliers final: 0
  residues processed: 112
  average time/residue: 0.2601
  time to fit residues: 33.3231
Evaluate side-chains
  67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.361 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    0.1980
   chunk 31 optimal weight:    0.8980
   chunk 17 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 20 optimal weight:    0.0370
   chunk 16 optimal weight:    0.7980
   chunk 32 optimal weight:    1.9990
   chunk 12 optimal weight:    0.9980
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.9980
   overall best weight:    0.5658

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

Flipped N/Q/H residues before XYZ refinement:
C 354 ASN
C 360 ASN
C 448 ASN
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  62 ASN
A  81 GLN

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3460 r_free = 0.3460 target = 0.084738 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3163 r_free = 0.3163 target = 0.069609 restraints weight = 11480.451|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.072301 restraints weight = 6682.354|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3257 r_free = 0.3257 target = 0.074209 restraints weight = 4545.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3251
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8180
moved from start:          0.2970

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.029   3340  Z= 0.189
  Angle     :  0.642   6.032   4559  Z= 0.330
  Chirality :  0.045   0.201    511
  Planarity :  0.004   0.030    580
  Dihedral  :  4.879  40.044    480
  Min Nonbonded Distance : 2.437

Molprobity Statistics.
  All-atom Clashscore : 13.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.88 %
    Favored  : 90.12 %
  Rotamer:
    Outliers :  0.28 %
    Allowed  :  6.94 %
    Favored  : 92.78 %
  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: -3.77 (0.36), residues: 415
  helix: -3.35 (1.03), residues: 13
  sheet: -2.13 (0.46), residues: 120
  loop : -2.80 (0.31), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.010   0.001   PHE A  64 
 TYR   0.013   0.002   TYR C 473 
 ARG   0.004   0.001   ARG B  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00266 (    1)
  link_NAG-ASN         : angle       1.64398 (    3)
  hydrogen bonds       : bond        0.04407 (   58)
  hydrogen bonds       : angle       7.34483 (  171)
  SS BOND              : bond        0.00757 (    6)
  SS BOND              : angle       1.68031 (   12)
  covalent geometry    : bond        0.00416 ( 3333)
  covalent geometry    : angle       0.63618 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  87 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 86
  time to evaluate  : 0.359 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8038 (p0) cc_final: 0.7716 (p0)
REVERT: C  390 LEU cc_start: 0.8627 (tp) cc_final: 0.8333 (tp)
REVERT: C  398 ASP cc_start: 0.9188 (m-30) cc_final: 0.8757 (m-30)
REVERT: C  458 LYS cc_start: 0.8734 (pptt) cc_final: 0.8344 (pttm)
REVERT: B   13 LYS cc_start: 0.7930 (mmtm) cc_final: 0.7700 (tmtt)
REVERT: B   40 ARG cc_start: 0.8779 (ptt180) cc_final: 0.7982 (ptt180)
REVERT: B   45 LYS cc_start: 0.9279 (tptp) cc_final: 0.9058 (tptp)
REVERT: B   49 TRP cc_start: 0.8888 (t60) cc_final: 0.8546 (t60)
REVERT: B   57 ASP cc_start: 0.8681 (t0) cc_final: 0.8445 (t0)
REVERT: A   64 PHE cc_start: 0.8306 (m-80) cc_final: 0.7431 (m-10)
  outliers start: 1
  outliers final: 0
  residues processed: 87
  average time/residue: 0.2905
  time to fit residues: 29.1509
Evaluate side-chains
  62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 62
  time to evaluate  : 0.579 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 3 optimal weight:    0.7980
   chunk 30 optimal weight:    0.6980
   chunk 38 optimal weight:    0.8980
   chunk 5 optimal weight:    1.9990
   chunk 23 optimal weight:    0.9990
   chunk 26 optimal weight:    1.9990
   chunk 15 optimal weight:    0.9980
   chunk 20 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 36 optimal weight:    0.0970
   chunk 8 optimal weight:    0.5980
   overall best weight:    0.5578

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

Flipped N/Q/H residues before XYZ refinement:
** A  39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
A  41 HIS
A  71 ASN

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.082641 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.067862 restraints weight = 11544.694|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3183 r_free = 0.3183 target = 0.070445 restraints weight = 6687.534|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.072272 restraints weight = 4552.949|
|-----------------------------------------------------------------------------|
r_work (final): 0.3217
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8205
moved from start:          0.3471

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3340  Z= 0.182
  Angle     :  0.630   7.696   4559  Z= 0.322
  Chirality :  0.045   0.197    511
  Planarity :  0.004   0.028    580
  Dihedral  :  5.072  42.149    480
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 11.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.64 %
    Favored  : 90.36 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  6.39 %
    Favored  : 93.61 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -3.37 (0.37), residues: 415
  helix: -2.84 (1.21), residues: 13
  sheet: -1.88 (0.47), residues: 121
  loop : -2.52 (0.33), residues: 281

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.012   0.002   PHE C 338 
 TYR   0.027   0.002   TYR C 495 
 ARG   0.004   0.001   ARG B  40 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00202 (    1)
  link_NAG-ASN         : angle       1.25321 (    3)
  hydrogen bonds       : bond        0.03769 (   58)
  hydrogen bonds       : angle       6.42311 (  171)
  SS BOND              : bond        0.00688 (    6)
  SS BOND              : angle       1.51769 (   12)
  covalent geometry    : bond        0.00403 ( 3333)
  covalent geometry    : angle       0.62526 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 0.476 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  390 LEU cc_start: 0.8719 (tp) cc_final: 0.8475 (tp)
REVERT: C  394 ASN cc_start: 0.7736 (t0) cc_final: 0.6966 (t0)
REVERT: C  398 ASP cc_start: 0.9136 (m-30) cc_final: 0.8687 (m-30)
REVERT: C  405 ASP cc_start: 0.9157 (m-30) cc_final: 0.8727 (m-30)
REVERT: B   49 TRP cc_start: 0.8917 (t60) cc_final: 0.8326 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.3057
  time to fit residues: 29.1946
Evaluate side-chains
  66 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 66
  time to evaluate  : 0.396 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.0010
   chunk 5 optimal weight:    2.9990
   chunk 15 optimal weight:    0.0870
   chunk 32 optimal weight:    1.9990
   chunk 20 optimal weight:    1.9990
   chunk 8 optimal weight:    0.4980
   chunk 14 optimal weight:    0.8980
   chunk 30 optimal weight:    0.5980
   chunk 17 optimal weight:    1.9990
   chunk 7 optimal weight:    0.4980
   chunk 39 optimal weight:    1.9990
   overall best weight:    0.3364

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.084454 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3149 r_free = 0.3149 target = 0.069137 restraints weight = 12172.687|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.071815 restraints weight = 7092.168|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3239 r_free = 0.3239 target = 0.073741 restraints weight = 4838.856|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8178
moved from start:          0.3768

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   3340  Z= 0.139
  Angle     :  0.618   9.095   4559  Z= 0.312
  Chirality :  0.044   0.196    511
  Planarity :  0.004   0.036    580
  Dihedral  :  4.848  39.832    480
  Min Nonbonded Distance : 2.480

Molprobity Statistics.
  All-atom Clashscore : 11.89
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  3.33 %
    Favored  : 96.67 %
  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: -3.16 (0.38), residues: 415
  helix: -2.91 (1.12), residues: 13
  sheet: -1.60 (0.49), residues: 120
  loop : -2.43 (0.33), residues: 282

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP B  55 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.011   0.001   PHE A  64 
 TYR   0.017   0.002   TYR C 495 
 ARG   0.011   0.001   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       1.03889 (    3)
  hydrogen bonds       : bond        0.03164 (   58)
  hydrogen bonds       : angle       6.00743 (  171)
  SS BOND              : bond        0.01027 (    6)
  SS BOND              : angle       1.53622 (   12)
  covalent geometry    : bond        0.00312 ( 3333)
  covalent geometry    : angle       0.61375 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 82
  time to evaluate  : 1.129 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8024 (p0) cc_final: 0.7679 (p0)
REVERT: C  390 LEU cc_start: 0.8646 (tp) cc_final: 0.8363 (tp)
REVERT: C  394 ASN cc_start: 0.7292 (t0) cc_final: 0.6425 (t0)
REVERT: C  398 ASP cc_start: 0.9064 (m-30) cc_final: 0.8543 (m-30)
REVERT: C  405 ASP cc_start: 0.8965 (m-30) cc_final: 0.8352 (p0)
REVERT: C  408 ARG cc_start: 0.8560 (pmt170) cc_final: 0.7864 (pmt170)
REVERT: B   49 TRP cc_start: 0.8872 (t60) cc_final: 0.8466 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 82
  average time/residue: 0.2702
  time to fit residues: 26.2060
Evaluate side-chains
  63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 63
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 31 optimal weight:    1.9990
   chunk 16 optimal weight:    0.7980
   chunk 18 optimal weight:    1.9990
   chunk 27 optimal weight:    0.9990
   chunk 15 optimal weight:    0.5980
   chunk 29 optimal weight:    0.9980
   chunk 0 optimal weight:    0.9980
   chunk 9 optimal weight:    0.8980
   chunk 26 optimal weight:    0.6980
   chunk 35 optimal weight:    0.6980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 = 0.3395 r_free = 0.3395 target = 0.081224 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3100 r_free = 0.3100 target = 0.066346 restraints weight = 12105.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3154 r_free = 0.3154 target = 0.068864 restraints weight = 7237.918|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.070669 restraints weight = 5005.436|
|-----------------------------------------------------------------------------|
r_work (final): 0.3177
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8254
moved from start:          0.4249

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.043   3340  Z= 0.222
  Angle     :  0.699   7.906   4559  Z= 0.356
  Chirality :  0.046   0.230    511
  Planarity :  0.004   0.038    580
  Dihedral  :  5.415  43.752    480
  Min Nonbonded Distance : 2.484

Molprobity Statistics.
  All-atom Clashscore : 14.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.57 %
    Favored  : 88.43 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.44 %
    Favored  : 95.56 %
  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: -2.92 (0.38), residues: 415
  helix: -2.27 (1.78), residues: 7
  sheet: -1.55 (0.48), residues: 125
  loop : -2.24 (0.33), residues: 283

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.002   TRP B  55 
 HIS   0.002   0.001   HIS A  41 
 PHE   0.016   0.002   PHE A  64 
 TYR   0.015   0.002   TYR A  93 
 ARG   0.011   0.001   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00388 (    1)
  link_NAG-ASN         : angle       1.55768 (    3)
  hydrogen bonds       : bond        0.03661 (   58)
  hydrogen bonds       : angle       6.22227 (  171)
  SS BOND              : bond        0.00286 (    6)
  SS BOND              : angle       1.81324 (   12)
  covalent geometry    : bond        0.00487 ( 3333)
  covalent geometry    : angle       0.69235 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 85
  time to evaluate  : 0.887 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  378 LYS cc_start: 0.8776 (pttt) cc_final: 0.8571 (pttm)
REVERT: C  390 LEU cc_start: 0.8692 (tp) cc_final: 0.8436 (tp)
REVERT: C  394 ASN cc_start: 0.7512 (t0) cc_final: 0.6658 (t0)
REVERT: C  398 ASP cc_start: 0.9088 (m-30) cc_final: 0.8585 (m-30)
REVERT: C  405 ASP cc_start: 0.9060 (m-30) cc_final: 0.8640 (m-30)
REVERT: C  408 ARG cc_start: 0.8675 (pmt170) cc_final: 0.7880 (pmt170)
REVERT: B   20 LEU cc_start: 0.9205 (tp) cc_final: 0.8992 (tp)
  outliers start: 0
  outliers final: 0
  residues processed: 85
  average time/residue: 0.2561
  time to fit residues: 25.6918
Evaluate side-chains
  67 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.495 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   chunk 16 optimal weight:    0.0870
   chunk 28 optimal weight:    0.8980
   chunk 11 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   chunk 33 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 35 optimal weight:    0.0980
   chunk 7 optimal weight:    0.0870
   overall best weight:    0.3136

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3423 r_free = 0.3423 target = 0.083219 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.067918 restraints weight = 12347.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3180 r_free = 0.3180 target = 0.070546 restraints weight = 7183.227|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3218 r_free = 0.3218 target = 0.072420 restraints weight = 4912.218|
|-----------------------------------------------------------------------------|
r_work (final): 0.3211
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4264

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   3340  Z= 0.133
  Angle     :  0.636   6.229   4559  Z= 0.327
  Chirality :  0.046   0.234    511
  Planarity :  0.004   0.046    580
  Dihedral  :  5.051  40.578    480
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 12.20
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  2.50 %
    Favored  : 97.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.80 (0.38), residues: 415
  helix: -2.39 (1.54), residues: 7
  sheet: -1.47 (0.48), residues: 124
  loop : -2.14 (0.33), residues: 284

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.000   0.000   HIS C 519 
 PHE   0.013   0.001   PHE A  64 
 TYR   0.016   0.002   TYR C 495 
 ARG   0.008   0.001   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00104 (    1)
  link_NAG-ASN         : angle       0.88369 (    3)
  hydrogen bonds       : bond        0.02995 (   58)
  hydrogen bonds       : angle       5.87720 (  171)
  SS BOND              : bond        0.00885 (    6)
  SS BOND              : angle       1.87107 (   12)
  covalent geometry    : bond        0.00300 ( 3333)
  covalent geometry    : angle       0.62981 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  84 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 84
  time to evaluate  : 0.548 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  364 ASP cc_start: 0.8356 (p0) cc_final: 0.8019 (p0)
REVERT: C  394 ASN cc_start: 0.7383 (t0) cc_final: 0.6417 (t0)
REVERT: C  398 ASP cc_start: 0.8954 (m-30) cc_final: 0.8458 (m-30)
REVERT: B   49 TRP cc_start: 0.8920 (t60) cc_final: 0.8449 (t60)
REVERT: B   59 LYS cc_start: 0.9017 (mptt) cc_final: 0.8406 (mptt)
REVERT: B   71 ILE cc_start: 0.9408 (tp) cc_final: 0.8940 (tp)
REVERT: A   49 MET cc_start: 0.8235 (ttm) cc_final: 0.7862 (ttm)
  outliers start: 0
  outliers final: 0
  residues processed: 84
  average time/residue: 0.3768
  time to fit residues: 38.6478
Evaluate side-chains
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 1.502 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 23 optimal weight:    0.0370
   chunk 27 optimal weight:    1.9990
   chunk 21 optimal weight:    1.9990
   chunk 5 optimal weight:    0.9980
   chunk 24 optimal weight:    0.6980
   chunk 22 optimal weight:    0.6980
   chunk 40 optimal weight:    0.9990
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    0.9990
   overall best weight:    0.6258

-------------------------------------------------------------------------------
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 = 0.3398 r_free = 0.3398 target = 0.081628 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.066683 restraints weight = 11983.411|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3156 r_free = 0.3156 target = 0.069203 restraints weight = 7170.627|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3191 r_free = 0.3191 target = 0.070975 restraints weight = 4973.467|
|-----------------------------------------------------------------------------|
r_work (final): 0.3187
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8239
moved from start:          0.4598

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.040   3340  Z= 0.204
  Angle     :  0.704   6.366   4559  Z= 0.361
  Chirality :  0.046   0.256    511
  Planarity :  0.005   0.050    580
  Dihedral  :  5.394  42.724    480
  Min Nonbonded Distance : 2.489

Molprobity Statistics.
  All-atom Clashscore : 15.49
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.81 %
    Favored  : 88.19 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  4.17 %
    Favored  : 95.83 %
  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: -2.73 (0.38), residues: 415
  helix: -2.00 (1.62), residues: 7
  sheet: -1.54 (0.45), residues: 131
  loop : -2.04 (0.34), residues: 277

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.002   TRP B  55 
 HIS   0.001   0.000   HIS C 519 
 PHE   0.021   0.002   PHE A  64 
 TYR   0.015   0.002   TYR C 495 
 ARG   0.009   0.001   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00333 (    1)
  link_NAG-ASN         : angle       1.43195 (    3)
  hydrogen bonds       : bond        0.03366 (   58)
  hydrogen bonds       : angle       6.04005 (  171)
  SS BOND              : bond        0.00696 (    6)
  SS BOND              : angle       1.99072 (   12)
  covalent geometry    : bond        0.00451 ( 3333)
  covalent geometry    : angle       0.69671 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.399 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  378 LYS cc_start: 0.8800 (pttt) cc_final: 0.8573 (pttm)
REVERT: C  394 ASN cc_start: 0.7670 (t0) cc_final: 0.6742 (t0)
REVERT: C  398 ASP cc_start: 0.8967 (m-30) cc_final: 0.8447 (m-30)
REVERT: C  465 GLU cc_start: 0.7012 (tm-30) cc_final: 0.6712 (tm-30)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2291
  time to fit residues: 22.3502
Evaluate side-chains
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.419 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 16 optimal weight:    0.7980
   chunk 18 optimal weight:    0.9990
   chunk 36 optimal weight:    0.1980
   chunk 7 optimal weight:    0.0770
   chunk 40 optimal weight:    0.0980
   chunk 17 optimal weight:    0.5980
   chunk 19 optimal weight:    0.9980
   chunk 11 optimal weight:    0.6980
   chunk 1 optimal weight:    0.9980
   chunk 25 optimal weight:    0.9990
   chunk 31 optimal weight:    0.6980
   overall best weight:    0.3338

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3440 r_free = 0.3440 target = 0.083946 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3153 r_free = 0.3153 target = 0.068773 restraints weight = 11799.361|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3206 r_free = 0.3206 target = 0.071412 restraints weight = 6817.209|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 40)----------------|
| r_work = 0.3241 r_free = 0.3241 target = 0.073235 restraints weight = 4639.933|
|-----------------------------------------------------------------------------|
r_work (final): 0.3241
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8189
moved from start:          0.4631

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.041   3340  Z= 0.140
  Angle     :  0.678   6.506   4559  Z= 0.344
  Chirality :  0.046   0.254    511
  Planarity :  0.005   0.051    580
  Dihedral  :  5.149  40.334    480
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 12.99
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.84 %
    Favored  : 89.16 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  1.67 %
    Favored  : 98.33 %
  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: -2.66 (0.39), residues: 415
  helix: -2.05 (1.53), residues: 7
  sheet: -1.54 (0.45), residues: 128
  loop : -1.95 (0.35), residues: 280

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.000   0.000   HIS A  41 
 PHE   0.016   0.002   PHE C 497 
 TYR   0.011   0.001   TYR C 421 
 ARG   0.009   0.001   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00063 (    1)
  link_NAG-ASN         : angle       0.98961 (    3)
  hydrogen bonds       : bond        0.02908 (   58)
  hydrogen bonds       : angle       5.81415 (  171)
  SS BOND              : bond        0.00723 (    6)
  SS BOND              : angle       1.85441 (   12)
  covalent geometry    : bond        0.00323 ( 3333)
  covalent geometry    : angle       0.67161 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.421 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  378 LYS cc_start: 0.8803 (pttt) cc_final: 0.8558 (pttm)
REVERT: C  394 ASN cc_start: 0.7222 (t0) cc_final: 0.6271 (t0)
REVERT: C  398 ASP cc_start: 0.8939 (m-30) cc_final: 0.8506 (m-30)
REVERT: B   45 LYS cc_start: 0.9068 (tptp) cc_final: 0.8749 (tptp)
REVERT: B   49 TRP cc_start: 0.8869 (t60) cc_final: 0.8416 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.2282
  time to fit residues: 21.2411
Evaluate side-chains
  68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.352 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 32 optimal weight:    0.5980
   chunk 10 optimal weight:    0.9980
   chunk 33 optimal weight:    0.9980
   chunk 7 optimal weight:    0.0470
   chunk 6 optimal weight:    0.7980
   chunk 19 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9980
   chunk 3 optimal weight:    0.8980
   chunk 27 optimal weight:    0.6980
   chunk 15 optimal weight:    0.0020
   chunk 38 optimal weight:    0.6980
   overall best weight:    0.4086

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.083286 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3150 r_free = 0.3150 target = 0.068470 restraints weight = 11561.732|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3204 r_free = 0.3204 target = 0.071069 restraints weight = 6625.891|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3238 r_free = 0.3238 target = 0.072837 restraints weight = 4466.728|
|-----------------------------------------------------------------------------|
r_work (final): 0.3236
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8199
moved from start:          0.4668

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3340  Z= 0.155
  Angle     :  0.669   6.604   4559  Z= 0.343
  Chirality :  0.046   0.265    511
  Planarity :  0.005   0.044    580
  Dihedral  :  5.226  40.562    480
  Min Nonbonded Distance : 2.470

Molprobity Statistics.
  All-atom Clashscore : 14.24
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 11.08 %
    Favored  : 88.92 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.83 %
    Favored  : 99.17 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.50 (0.39), residues: 415
  helix: -1.51 (1.23), residues: 13
  sheet: -1.51 (0.44), residues: 128
  loop : -1.81 (0.36), residues: 274

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  55 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.021   0.002   PHE C 497 
 TYR   0.012   0.002   TYR C 421 
 ARG   0.008   0.001   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00086 (    1)
  link_NAG-ASN         : angle       1.14133 (    3)
  hydrogen bonds       : bond        0.03077 (   58)
  hydrogen bonds       : angle       5.77888 (  171)
  SS BOND              : bond        0.00753 (    6)
  SS BOND              : angle       1.79779 (   12)
  covalent geometry    : bond        0.00353 ( 3333)
  covalent geometry    : angle       0.66288 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 81
  time to evaluate  : 0.395 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  378 LYS cc_start: 0.8841 (pttt) cc_final: 0.8603 (pttm)
REVERT: C  390 LEU cc_start: 0.8659 (tp) cc_final: 0.8449 (tp)
REVERT: C  394 ASN cc_start: 0.7373 (t0) cc_final: 0.6582 (t0)
REVERT: C  398 ASP cc_start: 0.8933 (m-30) cc_final: 0.8460 (m-30)
REVERT: B    1 GLN cc_start: 0.9096 (pp30) cc_final: 0.8893 (pp30)
REVERT: B   49 TRP cc_start: 0.8983 (t60) cc_final: 0.8441 (t60)
  outliers start: 0
  outliers final: 0
  residues processed: 81
  average time/residue: 0.1905
  time to fit residues: 18.0785
Evaluate side-chains
  65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 65
  time to evaluate  : 0.313 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 18 optimal weight:    0.3980
   chunk 21 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 33 optimal weight:    1.9990
   chunk 15 optimal weight:    0.0040
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    0.6980
   chunk 16 optimal weight:    0.0870
   overall best weight:    0.3770

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

Flipped N/Q/H residues before XYZ refinement:
A  40 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3421 r_free = 0.3421 target = 0.082855 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3130 r_free = 0.3130 target = 0.067893 restraints weight = 11365.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3184 r_free = 0.3184 target = 0.070458 restraints weight = 6525.379|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3219 r_free = 0.3219 target = 0.072207 restraints weight = 4424.504|
|-----------------------------------------------------------------------------|
r_work (final): 0.3227
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8210
moved from start:          0.4857

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   3340  Z= 0.153
  Angle     :  0.695   7.649   4559  Z= 0.356
  Chirality :  0.046   0.259    511
  Planarity :  0.005   0.045    580
  Dihedral  :  5.219  40.045    480
  Min Nonbonded Distance : 2.442

Molprobity Statistics.
  All-atom Clashscore : 14.55
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 10.60 %
    Favored  : 89.40 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.39 (0.39), residues: 415
  helix: -1.05 (1.40), residues: 13
  sheet: -1.24 (0.48), residues: 116
  loop : -1.86 (0.35), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP B  55 
 HIS   0.000   0.000   HIS A  41 
 PHE   0.018   0.002   PHE C 497 
 TYR   0.010   0.001   TYR C 421 
 ARG   0.011   0.001   ARG A  63 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00050 (    1)
  link_NAG-ASN         : angle       1.03772 (    3)
  hydrogen bonds       : bond        0.03369 (   58)
  hydrogen bonds       : angle       5.73414 (  171)
  SS BOND              : bond        0.00709 (    6)
  SS BOND              : angle       1.78502 (   12)
  covalent geometry    : bond        0.00349 ( 3333)
  covalent geometry    : angle       0.69006 ( 4544)

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

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

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  830 Ramachandran restraints generated.
    415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 79
  time to evaluate  : 0.396 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  394 ASN cc_start: 0.7228 (t0) cc_final: 0.6295 (t0)
REVERT: C  398 ASP cc_start: 0.8851 (m-30) cc_final: 0.8421 (m-30)
REVERT: C  408 ARG cc_start: 0.8840 (pmt-80) cc_final: 0.8497 (pmt-80)
REVERT: B    1 GLN cc_start: 0.9108 (pp30) cc_final: 0.8878 (pp30)
REVERT: B   49 TRP cc_start: 0.8969 (t60) cc_final: 0.8454 (t60)
REVERT: B   59 LYS cc_start: 0.8997 (mppt) cc_final: 0.8554 (tppt)
REVERT: B   87 MET cc_start: 0.7601 (ttm) cc_final: 0.7215 (ttp)
  outliers start: 0
  outliers final: 0
  residues processed: 79
  average time/residue: 0.1865
  time to fit residues: 17.4232
Evaluate side-chains
  68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 68
  time to evaluate  : 0.399 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9980
   chunk 17 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 38 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 29 optimal weight:    0.3980
   chunk 32 optimal weight:    2.9990
   chunk 20 optimal weight:    0.0970
   chunk 1 optimal weight:    0.4980
   chunk 3 optimal weight:    0.9980
   overall best weight:    0.4778

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.082498 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.067428 restraints weight = 11942.042|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3176 r_free = 0.3176 target = 0.069989 restraints weight = 6980.703|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3210 r_free = 0.3210 target = 0.071735 restraints weight = 4786.766|
|-----------------------------------------------------------------------------|
r_work (final): 0.3201
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8227
moved from start:          0.4919

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.041   3340  Z= 0.171
  Angle     :  0.697   6.655   4559  Z= 0.358
  Chirality :  0.047   0.267    511
  Planarity :  0.005   0.044    580
  Dihedral  :  5.370  41.047    480
  Min Nonbonded Distance : 2.465

Molprobity Statistics.
  All-atom Clashscore : 15.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  : 12.05 %
    Favored  : 87.95 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.56 %
    Favored  : 99.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -2.31 (0.39), residues: 415
  helix: -0.77 (1.42), residues: 13
  sheet: -1.20 (0.48), residues: 116
  loop : -1.82 (0.34), residues: 286

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.010   0.001   TRP B  55 
 HIS   0.001   0.000   HIS A  41 
 PHE   0.021   0.002   PHE C 497 
 TYR   0.011   0.002   TYR C 421 
 ARG   0.003   0.001   ARG C 346 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00166 (    1)
  link_NAG-ASN         : angle       1.16111 (    3)
  hydrogen bonds       : bond        0.03406 (   58)
  hydrogen bonds       : angle       5.72067 (  171)
  SS BOND              : bond        0.00747 (    6)
  SS BOND              : angle       1.80673 (   12)
  covalent geometry    : bond        0.00390 ( 3333)
  covalent geometry    : angle       0.69105 ( 4544)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 3659.39 seconds
wall clock time: 67 minutes 7.73 seconds (4027.73 seconds total)