Starting phenix.real_space_refine
on Wed Jun  4 14:04:39 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgs_50420/06_2025/9fgs_50420.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgs_50420/06_2025/9fgs_50420.map

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

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

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9fgs_50420/06_2025/9fgs_50420.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgs_50420/06_2025/9fgs_50420.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgs_50420/06_2025/9fgs_50420.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgs_50420/06_2025/9fgs_50420.cif"
  }
  resolution = 4.0
  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=  -0.003 sd=   0.047
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
Construct map_model_manager
Extract box with map and model
Check model and map are aligned
Set scattering table
  Set to: electron
  Number of scattering types: 4
    Type Number    sf(0)   Gaussians
     S      14      5.16       5
     C    2025      2.51       5
     N     532      2.21       5
     O     616      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 3187
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1513
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1513
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 11, 'TRANS': 178}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1660
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1660
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 8, 'TRANS': 213}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 14
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 1, 14
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.67, per 1000 atoms: 1.15
  Number of scatterers: 3187
  At special positions: 0
  Unit cell: (83.566, 63.119, 88.011, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      14     16.00
     O     616      8.00
     N     532      7.00
     C    2025      6.00
    sf(0) = scattering factor at diffraction angle 0.

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

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG C1301 " - " ASN C 343 "
  Time building additional restraints: 0.67
  Conformation dependent library (CDL) restraints added in 370.3 milliseconds
  

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

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 6 sheets defined
      7.3% alpha, 23.8% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.37
  Creating SS restraints...
    Processing helix  chain 'C' and resid 364 through 368
      removed outlier: 4.472A  pdb=" N   VAL C 367 " --> pdb=" O   ASP C 364 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 404 through 411
      removed outlier: 4.192A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
      removed outlier: 3.721A  pdb=" N   ALA C 411 " --> pdb=" O   ARG C 408 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 416 through 422
      removed outlier: 3.640A  pdb=" N   TYR C 421 " --> pdb=" O   LYS C 417 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 86 through 90
      removed outlier: 3.801A  pdb=" N   THR E  90 " --> pdb=" O   VAL E  87 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 213 through 217
      removed outlier: 3.972A  pdb=" N   LEU E 217 " --> pdb=" O   ALA E 214 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 355 through 358
      removed outlier: 4.253A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   ASP C 398 " --> pdb=" O   VAL C 512 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   VAL C 512 " --> pdb=" O   ASP C 398 " (cutoff:3.500A)
      removed outlier: 3.977A  pdb=" N   GLY C 431 " --> pdb=" O   TYR C 380 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454
    Processing sheet with id=AA3, first strand: chain 'E' and resid 3 through 7
      removed outlier: 3.591A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   SER E  21 " --> pdb=" O   SER E   7 " (cutoff:3.500A)
      removed outlier: 4.060A  pdb=" N   LEU E  18 " --> pdb=" O   MET E  82 " (cutoff:3.500A)
    Processing sheet with id=AA4, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.799A  pdb=" N   THR E 115 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 3.789A  pdb=" N   VAL E  12 " --> pdb=" O   THR E 115 " (cutoff:3.500A)
      removed outlier: 3.532A  pdb=" N   VAL E 114 " --> pdb=" O   ALA E  91 " (cutoff:3.500A)
      removed outlier: 3.541A  pdb=" N   ALA E  91 " --> pdb=" O   VAL E 114 " (cutoff:3.500A)
      removed outlier: 7.022A  pdb=" N   MET E  34 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
      removed outlier: 4.637A  pdb=" N   VAL E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.567A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.892A  pdb=" N   VAL E  50 " --> pdb=" O   PHE E  58 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 137 through 139
      removed outlier: 3.539A  pdb=" N   ALA E 152 " --> pdb=" O   ILE E 209 " (cutoff:3.500A)
      removed outlier: 3.941A  pdb=" N   THR E 206 " --> pdb=" O   SER E 199 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 187 through 188
      removed outlier: 7.038A  pdb=" N   TRP E 169 " --> pdb=" O   LEU E 181 " (cutoff:3.500A)
      removed outlier: 5.325A  pdb=" N   TYR E 183 " --> pdb=" O   LEU E 167 " (cutoff:3.500A)
      removed outlier: 7.031A  pdb=" N   LEU E 167 " --> pdb=" O   TYR E 183 " (cutoff:3.500A)
      removed outlier: 3.530A  pdb=" N   GLN E 223 " --> pdb=" O   ALA E 168 " (cutoff:3.500A)
      removed outlier: 3.508A  pdb=" N   THR E 236 " --> pdb=" O   TYR E 220 " (cutoff:3.500A)

    71 hydrogen bonds defined for protein.
    165 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 0.81

  Time building geometry restraints manager: 0.84 seconds

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

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

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

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

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

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

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

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=0.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             2.620
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.010
  Extract box with map and model:          0.110
  Check model and map are aligned:         0.020
  Set scattering table:                    0.040
  Process input model:                     13.160
  Find NCS groups from input model:        0.040
  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:3.000
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.010
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7956
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   3270  Z= 0.156
  Angle     :  0.666   6.316   4455  Z= 0.362
  Chirality :  0.043   0.218    489
  Planarity :  0.004   0.041    573
  Dihedral  : 13.377  89.545   1162
  Min Nonbonded Distance : 2.251

Molprobity Statistics.
  All-atom Clashscore : 10.57
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.58 %
    Favored  : 99.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.99 (0.39), residues: 404
  helix: -4.31 (0.76), residues: 12
  sheet: -0.72 (0.47), residues: 124
  loop : -1.53 (0.35), residues: 268

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

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

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.364 
Fit side-chains
REVERT: C  368 LEU cc_start: 0.8618 (mm) cc_final: 0.8229 (mt)
  outliers start: 0
  outliers final: 0
  residues processed: 64
  average time/residue: 0.1547
  time to fit residues: 12.1554
Evaluate side-chains
  45 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 45
  time to evaluate  : 0.325 
-------------------------------------------------------------------------------
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:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 17 optimal weight:    1.9990
   chunk 10 optimal weight:    0.4980
   chunk 20 optimal weight:    0.1980
   chunk 16 optimal weight:    0.3980
   chunk 32 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 37 optimal weight:    0.4980
   overall best weight:    0.4580

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.115004 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3336 r_free = 0.3336 target = 0.104218 restraints weight = 7446.989|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3363 r_free = 0.3363 target = 0.106180 restraints weight = 4569.285|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3385 r_free = 0.3385 target = 0.107639 restraints weight = 3152.570|
|-----------------------------------------------------------------------------|
r_work (final): 0.3384
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.1415

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   3270  Z= 0.132
  Angle     :  0.611   6.402   4455  Z= 0.311
  Chirality :  0.043   0.136    489
  Planarity :  0.004   0.037    573
  Dihedral  :  6.778  57.023    476
  Min Nonbonded Distance : 2.413

Molprobity Statistics.
  All-atom Clashscore : 9.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.66 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  :  9.94 %
    Favored  : 88.01 %
  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: -1.73 (0.40), residues: 404
  helix: -4.58 (0.67), residues: 12
  sheet: -0.43 (0.47), residues: 125
  loop : -1.39 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 353 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.020   0.002   PHE C 429 
 TYR   0.018   0.001   TYR C 380 
 ARG   0.003   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00069 (    1)
  link_NAG-ASN         : angle       2.23824 (    3)
  hydrogen bonds       : bond        0.03666 (   71)
  hydrogen bonds       : angle       7.16151 (  165)
  SS BOND              : bond        0.00665 (    6)
  SS BOND              : angle       1.36511 (   12)
  covalent geometry    : bond        0.00307 ( 3263)
  covalent geometry    : angle       0.60508 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  60 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 53
  time to evaluate  : 0.335 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  368 LEU cc_start: 0.8712 (mm) cc_final: 0.8261 (mt)
REVERT: C  405 ASP cc_start: 0.8747 (t0) cc_final: 0.8541 (t0)
REVERT: C  462 LYS cc_start: 0.9010 (mmmt) cc_final: 0.8771 (mtmt)
REVERT: E   75 LYS cc_start: 0.7548 (mmtt) cc_final: 0.7003 (tptm)
  outliers start: 7
  outliers final: 4
  residues processed: 57
  average time/residue: 0.1468
  time to fit residues: 10.3811
Evaluate side-chains
  50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  393 THR
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 14 optimal weight:    4.9990
   chunk 15 optimal weight:    0.6980
   chunk 26 optimal weight:    0.0770
   chunk 21 optimal weight:    0.9980
   chunk 27 optimal weight:    0.1980
   chunk 17 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 1 optimal weight:    0.0770
   chunk 30 optimal weight:    2.9990
   chunk 23 optimal weight:    2.9990
   chunk 36 optimal weight:    0.0370
   overall best weight:    0.2174

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

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

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3513 r_free = 0.3513 target = 0.116943 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.105340 restraints weight = 7291.158|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3384 r_free = 0.3384 target = 0.107728 restraints weight = 4212.256|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3407 r_free = 0.3407 target = 0.109366 restraints weight = 2775.571|
|-----------------------------------------------------------------------------|
r_work (final): 0.3416
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7938
moved from start:          0.1792

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.030   3270  Z= 0.102
  Angle     :  0.550   4.564   4455  Z= 0.282
  Chirality :  0.042   0.128    489
  Planarity :  0.004   0.037    573
  Dihedral  :  6.190  53.681    476
  Min Nonbonded Distance : 2.449

Molprobity Statistics.
  All-atom Clashscore : 7.69
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  8.17 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  1.46 %
    Allowed  : 12.87 %
    Favored  : 85.67 %
  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: -1.55 (0.41), residues: 404
  helix: -4.62 (0.64), residues: 12
  sheet: -0.15 (0.48), residues: 123
  loop : -1.34 (0.36), residues: 269

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP E  47 
 HIS   0.001   0.001   HIS C 519 
 PHE   0.013   0.001   PHE C 429 
 TYR   0.012   0.001   TYR C 380 
 ARG   0.002   0.000   ARG E 211 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00272 (    1)
  link_NAG-ASN         : angle       1.86113 (    3)
  hydrogen bonds       : bond        0.02875 (   71)
  hydrogen bonds       : angle       6.58665 (  165)
  SS BOND              : bond        0.00519 (    6)
  SS BOND              : angle       1.21909 (   12)
  covalent geometry    : bond        0.00235 ( 3263)
  covalent geometry    : angle       0.54520 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 56
  time to evaluate  : 0.296 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  368 LEU cc_start: 0.8578 (mm) cc_final: 0.8156 (mt)
REVERT: C  405 ASP cc_start: 0.8692 (t0) cc_final: 0.8427 (t0)
REVERT: C  462 LYS cc_start: 0.8987 (mmmt) cc_final: 0.8767 (mtmt)
REVERT: E   75 LYS cc_start: 0.7460 (mmtt) cc_final: 0.6977 (tptm)
  outliers start: 5
  outliers final: 4
  residues processed: 60
  average time/residue: 0.1480
  time to fit residues: 10.9409
Evaluate side-chains
  50 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 46
  time to evaluate  : 0.360 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    0.6980
   chunk 35 optimal weight:    0.5980
   chunk 14 optimal weight:    0.1980
   chunk 25 optimal weight:    0.7980
   chunk 23 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 12 optimal weight:    1.9990
   chunk 15 optimal weight:    0.7980
   chunk 34 optimal weight:    0.8980
   chunk 37 optimal weight:    2.9990
   chunk 32 optimal weight:    0.9990
   overall best weight:    0.6180

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114281 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3299 r_free = 0.3299 target = 0.102469 restraints weight = 7306.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.104678 restraints weight = 4346.363|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 25)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.106162 restraints weight = 2950.618|
|-----------------------------------------------------------------------------|
r_work (final): 0.3351
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8028
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3270  Z= 0.139
  Angle     :  0.585   7.929   4455  Z= 0.298
  Chirality :  0.042   0.135    489
  Planarity :  0.004   0.039    573
  Dihedral  :  6.860  59.544    476
  Min Nonbonded Distance : 2.369

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  2.63 %
    Allowed  : 15.50 %
    Favored  : 81.87 %
  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: -1.76 (0.41), residues: 404
  helix: -4.51 (0.69), residues: 12
  sheet: -0.34 (0.46), residues: 134
  loop : -1.52 (0.37), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 353 
 HIS   0.003   0.002   HIS C 519 
 PHE   0.010   0.001   PHE C 429 
 TYR   0.013   0.001   TYR C 380 
 ARG   0.002   0.001   ARG E 188 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00831 (    1)
  link_NAG-ASN         : angle       4.63603 (    3)
  hydrogen bonds       : bond        0.02894 (   71)
  hydrogen bonds       : angle       6.32413 (  165)
  SS BOND              : bond        0.00418 (    6)
  SS BOND              : angle       1.19219 (   12)
  covalent geometry    : bond        0.00331 ( 3263)
  covalent geometry    : angle       0.57026 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 49
  time to evaluate  : 0.367 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  342 PHE cc_start: 0.8496 (OUTLIER) cc_final: 0.8207 (m-10)
REVERT: C  368 LEU cc_start: 0.8685 (mm) cc_final: 0.8241 (mt)
REVERT: C  405 ASP cc_start: 0.8671 (t0) cc_final: 0.8414 (t0)
REVERT: E   75 LYS cc_start: 0.7661 (mmtt) cc_final: 0.7054 (tptm)
  outliers start: 9
  outliers final: 5
  residues processed: 54
  average time/residue: 0.1604
  time to fit residues: 10.7662
Evaluate side-chains
  53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 47
  time to evaluate  : 0.370 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 25 optimal weight:    0.2980
   chunk 23 optimal weight:    0.7980
   chunk 7 optimal weight:    0.8980
   chunk 17 optimal weight:    1.9990
   chunk 19 optimal weight:    1.9990
   chunk 26 optimal weight:    0.9980
   chunk 20 optimal weight:    2.9990
   chunk 3 optimal weight:    0.8980
   chunk 1 optimal weight:    0.5980
   chunk 30 optimal weight:    0.7980
   chunk 6 optimal weight:    0.9990
   overall best weight:    0.6780

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3456 r_free = 0.3456 target = 0.113836 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.102117 restraints weight = 7331.984|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.104232 restraints weight = 4503.816|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3344 r_free = 0.3344 target = 0.105634 restraints weight = 3101.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3340
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8054
moved from start:          0.2075

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   3270  Z= 0.147
  Angle     :  0.592   4.744   4455  Z= 0.305
  Chirality :  0.043   0.162    489
  Planarity :  0.004   0.036    573
  Dihedral  :  6.757  55.548    476
  Min Nonbonded Distance : 2.391

Molprobity Statistics.
  All-atom Clashscore : 9.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  9.16 %
    Favored  : 90.84 %
  Rotamer:
    Outliers :  2.05 %
    Allowed  : 17.25 %
    Favored  : 80.70 %
  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: -1.66 (0.41), residues: 404
  helix: -4.56 (0.67), residues: 12
  sheet: -0.21 (0.49), residues: 123
  loop : -1.44 (0.37), residues: 269

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

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00035 (    1)
  link_NAG-ASN         : angle       3.11728 (    3)
  hydrogen bonds       : bond        0.02839 (   71)
  hydrogen bonds       : angle       6.18603 (  165)
  SS BOND              : bond        0.00437 (    6)
  SS BOND              : angle       1.49706 (   12)
  covalent geometry    : bond        0.00353 ( 3263)
  covalent geometry    : angle       0.58226 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 51
  time to evaluate  : 0.365 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8725 (t0) cc_final: 0.8513 (t0)
REVERT: E   75 LYS cc_start: 0.7711 (mmtt) cc_final: 0.7090 (tptm)
  outliers start: 7
  outliers final: 7
  residues processed: 54
  average time/residue: 0.1663
  time to fit residues: 10.9701
Evaluate side-chains
  53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 46
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 30 optimal weight:    2.9990
   chunk 31 optimal weight:    0.6980
   chunk 37 optimal weight:    2.9990
   chunk 21 optimal weight:    0.1980
   chunk 0 optimal weight:    1.9990
   chunk 26 optimal weight:    0.0980
   chunk 25 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   chunk 16 optimal weight:    1.9990
   chunk 22 optimal weight:    0.7980
   chunk 6 optimal weight:    0.6980
   overall best weight:    0.4980

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

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

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3467 r_free = 0.3467 target = 0.114305 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3290 r_free = 0.3290 target = 0.102021 restraints weight = 7484.100|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.104379 restraints weight = 4383.076|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 28)----------------|
| r_work = 0.3347 r_free = 0.3347 target = 0.105898 restraints weight = 2927.870|
|-----------------------------------------------------------------------------|
r_work (final): 0.3342
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8043
moved from start:          0.2268

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   3270  Z= 0.129
  Angle     :  0.587   4.854   4455  Z= 0.304
  Chirality :  0.042   0.134    489
  Planarity :  0.004   0.037    573
  Dihedral  :  6.468  52.963    476
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.42 %
    Favored  : 91.34 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 19.01 %
    Favored  : 77.78 %
  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: -1.71 (0.41), residues: 404
  helix: -4.55 (0.68), residues: 12
  sheet: -0.34 (0.48), residues: 125
  loop : -1.42 (0.37), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 HIS   0.003   0.002   HIS C 519 
 PHE   0.011   0.001   PHE C 374 
 TYR   0.011   0.001   TYR C 380 
 ARG   0.003   0.001   ARG C 408 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00084 (    1)
  link_NAG-ASN         : angle       2.78691 (    3)
  hydrogen bonds       : bond        0.02689 (   71)
  hydrogen bonds       : angle       6.01207 (  165)
  SS BOND              : bond        0.00396 (    6)
  SS BOND              : angle       1.22500 (   12)
  covalent geometry    : bond        0.00309 ( 3263)
  covalent geometry    : angle       0.58026 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.379 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8707 (t0) cc_final: 0.8418 (t0)
REVERT: C  452 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.8156 (pp)
REVERT: C  462 LYS cc_start: 0.9055 (mmmt) cc_final: 0.8800 (mtmt)
REVERT: E   75 LYS cc_start: 0.7568 (mmtt) cc_final: 0.6980 (tptm)
  outliers start: 11
  outliers final: 7
  residues processed: 54
  average time/residue: 0.1528
  time to fit residues: 10.2432
Evaluate side-chains
  54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 46
  time to evaluate  : 0.320 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 37 optimal weight:    5.9990
   chunk 20 optimal weight:    0.0270
   chunk 19 optimal weight:    0.3980
   chunk 13 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0670
   chunk 38 optimal weight:    4.9990
   chunk 33 optimal weight:    0.5980
   chunk 4 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   overall best weight:    0.3576

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3488 r_free = 0.3488 target = 0.115382 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3319 r_free = 0.3319 target = 0.103768 restraints weight = 7420.226|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.105959 restraints weight = 4509.740|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3372 r_free = 0.3372 target = 0.107360 restraints weight = 3097.412|
|-----------------------------------------------------------------------------|
r_work (final): 0.3374
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8008
moved from start:          0.2342

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.026   3270  Z= 0.114
  Angle     :  0.580   4.464   4455  Z= 0.299
  Chirality :  0.042   0.135    489
  Planarity :  0.004   0.037    573
  Dihedral  :  5.952  53.602    476
  Min Nonbonded Distance : 2.487

Molprobity Statistics.
  All-atom Clashscore : 8.97
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.92 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.34 %
    Allowed  : 20.18 %
    Favored  : 77.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.68 (0.41), residues: 404
  helix: -4.55 (0.67), residues: 12
  sheet: -0.29 (0.48), residues: 128
  loop : -1.42 (0.37), residues: 264

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 353 
 HIS   0.002   0.001   HIS C 519 
 PHE   0.010   0.001   PHE E 196 
 TYR   0.011   0.001   TYR E  79 
 ARG   0.007   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00117 (    1)
  link_NAG-ASN         : angle       2.65491 (    3)
  hydrogen bonds       : bond        0.02546 (   71)
  hydrogen bonds       : angle       5.83751 (  165)
  SS BOND              : bond        0.00301 (    6)
  SS BOND              : angle       1.03431 (   12)
  covalent geometry    : bond        0.00272 ( 3263)
  covalent geometry    : angle       0.57405 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  59 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 51
  time to evaluate  : 0.371 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8589 (t0) cc_final: 0.8292 (t0)
REVERT: C  452 LEU cc_start: 0.8429 (OUTLIER) cc_final: 0.8200 (pp)
REVERT: C  462 LYS cc_start: 0.9044 (mmmt) cc_final: 0.8810 (mtmt)
REVERT: E   75 LYS cc_start: 0.7553 (mmtt) cc_final: 0.6979 (tptm)
  outliers start: 8
  outliers final: 7
  residues processed: 55
  average time/residue: 0.1510
  time to fit residues: 10.3927
Evaluate side-chains
  53 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 45
  time to evaluate  : 0.365 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 34 optimal weight:    1.9990
   chunk 10 optimal weight:    0.9990
   chunk 28 optimal weight:    1.9990
   chunk 18 optimal weight:    0.0970
   chunk 29 optimal weight:    2.9990
   chunk 36 optimal weight:    0.3980
   chunk 2 optimal weight:    1.9990
   chunk 0 optimal weight:    0.9990
   chunk 19 optimal weight:    0.9990
   chunk 3 optimal weight:    0.8980
   chunk 15 optimal weight:    2.9990
   overall best weight:    0.6782

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3459 r_free = 0.3459 target = 0.113469 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3280 r_free = 0.3280 target = 0.101308 restraints weight = 7296.334|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3313 r_free = 0.3313 target = 0.103497 restraints weight = 4411.060|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 42)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.105076 restraints weight = 3030.590|
|-----------------------------------------------------------------------------|
r_work (final): 0.3337
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8052
moved from start:          0.2502

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.037   3270  Z= 0.154
  Angle     :  0.619   5.782   4455  Z= 0.322
  Chirality :  0.043   0.140    489
  Planarity :  0.004   0.032    573
  Dihedral  :  6.112  51.944    476
  Min Nonbonded Distance : 2.499

Molprobity Statistics.
  All-atom Clashscore : 10.09
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.43 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  3.22 %
    Allowed  : 21.05 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.76 (0.40), residues: 404
  helix: -4.69 (0.55), residues: 12
  sheet: -0.24 (0.48), residues: 126
  loop : -1.54 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 353 
 HIS   0.003   0.002   HIS C 519 
 PHE   0.011   0.001   PHE C 374 
 TYR   0.011   0.001   TYR C 380 
 ARG   0.004   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00013 (    1)
  link_NAG-ASN         : angle       2.68511 (    3)
  hydrogen bonds       : bond        0.02674 (   71)
  hydrogen bonds       : angle       5.93108 (  165)
  SS BOND              : bond        0.00447 (    6)
  SS BOND              : angle       2.00352 (   12)
  covalent geometry    : bond        0.00368 ( 3263)
  covalent geometry    : angle       0.60714 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  58 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 47
  time to evaluate  : 0.320 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8562 (t0) cc_final: 0.8255 (t0)
REVERT: C  452 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8231 (pp)
REVERT: C  462 LYS cc_start: 0.9045 (mmmt) cc_final: 0.8811 (mtmt)
REVERT: E   75 LYS cc_start: 0.7732 (mmtt) cc_final: 0.7066 (tptm)
  outliers start: 11
  outliers final: 8
  residues processed: 54
  average time/residue: 0.1551
  time to fit residues: 10.4189
Evaluate side-chains
  54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 6 optimal weight:    0.4980
   chunk 2 optimal weight:    1.9990
   chunk 7 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 29 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 13 optimal weight:    0.7980
   chunk 35 optimal weight:    0.8980
   chunk 10 optimal weight:    0.7980
   chunk 26 optimal weight:    2.9990
   overall best weight:    0.7982

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3435 r_free = 0.3435 target = 0.111922 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3254 r_free = 0.3254 target = 0.099550 restraints weight = 7498.436|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3287 r_free = 0.3287 target = 0.101795 restraints weight = 4589.692|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 26)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.103047 restraints weight = 3156.683|
|-----------------------------------------------------------------------------|
r_work (final): 0.3309
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8097
moved from start:          0.2519

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.040   3270  Z= 0.170
  Angle     :  0.639   5.854   4455  Z= 0.334
  Chirality :  0.044   0.147    489
  Planarity :  0.004   0.031    573
  Dihedral  :  6.220  51.385    476
  Min Nonbonded Distance : 2.443

Molprobity Statistics.
  All-atom Clashscore : 11.37
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.92 %
    Favored  : 91.83 %
  Rotamer:
    Outliers :  2.92 %
    Allowed  : 21.35 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.81 (0.40), residues: 404
  helix: -4.89 (0.40), residues: 12
  sheet: -0.20 (0.48), residues: 125
  loop : -1.61 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP C 436 
 HIS   0.004   0.002   HIS C 519 
 PHE   0.012   0.001   PHE C 374 
 TYR   0.013   0.001   TYR C 495 
 ARG   0.004   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00041 (    1)
  link_NAG-ASN         : angle       2.71332 (    3)
  hydrogen bonds       : bond        0.02788 (   71)
  hydrogen bonds       : angle       6.02024 (  165)
  SS BOND              : bond        0.00580 (    6)
  SS BOND              : angle       1.99687 (   12)
  covalent geometry    : bond        0.00407 ( 3263)
  covalent geometry    : angle       0.62806 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 45
  time to evaluate  : 0.361 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8585 (t0) cc_final: 0.8275 (t0)
REVERT: C  452 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8246 (pp)
REVERT: C  462 LYS cc_start: 0.9008 (mmmt) cc_final: 0.8759 (mtmt)
REVERT: E   75 LYS cc_start: 0.7645 (tmtt) cc_final: 0.7036 (tptm)
  outliers start: 10
  outliers final: 9
  residues processed: 51
  average time/residue: 0.1589
  time to fit residues: 10.0320
Evaluate side-chains
  54 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 44
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue    5 LEU
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 27 optimal weight:    0.1980
   chunk 14 optimal weight:    0.0770
   chunk 9 optimal weight:    0.9990
   chunk 37 optimal weight:    0.5980
   chunk 39 optimal weight:    0.9980
   chunk 5 optimal weight:    0.8980
   chunk 13 optimal weight:    0.8980
   chunk 10 optimal weight:    0.9990
   chunk 11 optimal weight:    0.7980
   chunk 25 optimal weight:    0.9990
   chunk 8 optimal weight:    0.4980
   overall best weight:    0.4338

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3469 r_free = 0.3469 target = 0.114135 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3292 r_free = 0.3292 target = 0.101954 restraints weight = 7383.440|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 29)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.104171 restraints weight = 4507.429|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3349 r_free = 0.3349 target = 0.105776 restraints weight = 3098.305|
|-----------------------------------------------------------------------------|
r_work (final): 0.3346
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8036
moved from start:          0.2656

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   3270  Z= 0.126
  Angle     :  0.609   4.863   4455  Z= 0.318
  Chirality :  0.044   0.177    489
  Planarity :  0.004   0.031    573
  Dihedral  :  6.030  52.795    476
  Min Nonbonded Distance : 2.445

Molprobity Statistics.
  All-atom Clashscore : 10.25
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  7.43 %
    Favored  : 92.33 %
  Rotamer:
    Outliers :  3.51 %
    Allowed  : 20.76 %
    Favored  : 75.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.74 (0.41), residues: 404
  helix: -4.96 (0.33), residues: 12
  sheet: -0.15 (0.48), residues: 126
  loop : -1.56 (0.36), residues: 266

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP C 353 
 HIS   0.002   0.001   HIS C 519 
 PHE   0.009   0.001   PHE C 374 
 TYR   0.011   0.001   TYR E  79 
 ARG   0.004   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00080 (    1)
  link_NAG-ASN         : angle       2.52577 (    3)
  hydrogen bonds       : bond        0.02563 (   71)
  hydrogen bonds       : angle       5.96102 (  165)
  SS BOND              : bond        0.00469 (    6)
  SS BOND              : angle       1.63785 (   12)
  covalent geometry    : bond        0.00300 ( 3263)
  covalent geometry    : angle       0.60093 ( 4440)

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

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

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

  808 Ramachandran restraints generated.
    404 Oldfield, 0 Emsley, 404 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  57 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 45
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: C  405 ASP cc_start: 0.8520 (t0) cc_final: 0.8234 (t0)
REVERT: C  452 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8275 (pp)
REVERT: E   75 LYS cc_start: 0.7534 (OUTLIER) cc_final: 0.6954 (tptm)
  outliers start: 12
  outliers final: 9
  residues processed: 52
  average time/residue: 0.1473
  time to fit residues: 9.5376
Evaluate side-chains
  55 residues out of total 342 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 44
  time to evaluate  : 0.332 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  335 LEU
Chi-restraints excluded: chain C residue  342 PHE
Chi-restraints excluded: chain C residue  368 LEU
Chi-restraints excluded: chain C residue  392 PHE
Chi-restraints excluded: chain C residue  409 GLN
Chi-restraints excluded: chain C residue  418 ILE
Chi-restraints excluded: chain C residue  452 LEU
Chi-restraints excluded: chain C residue  519 HIS
Chi-restraints excluded: chain E residue   11 LEU
Chi-restraints excluded: chain E residue   75 LYS
Chi-restraints excluded: chain E residue  234 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 17 optimal weight:    0.9990
   chunk 37 optimal weight:    0.9980
   chunk 0 optimal weight:    1.9990
   chunk 13 optimal weight:    0.8980
   chunk 16 optimal weight:    0.7980
   chunk 20 optimal weight:    0.0970
   chunk 27 optimal weight:    0.7980
   chunk 2 optimal weight:    1.9990
   chunk 30 optimal weight:    1.9990
   chunk 33 optimal weight:    3.9990
   chunk 29 optimal weight:    1.9990
   overall best weight:    0.7178

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

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

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3445 r_free = 0.3445 target = 0.112497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.100211 restraints weight = 7507.547|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 30)----------------|
| r_work = 0.3298 r_free = 0.3298 target = 0.102441 restraints weight = 4564.583|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3322 r_free = 0.3322 target = 0.104026 restraints weight = 3127.283|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8077
moved from start:          0.2674

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   3270  Z= 0.160
  Angle     :  0.638   5.688   4455  Z= 0.332
  Chirality :  0.044   0.177    489
  Planarity :  0.004   0.031    573
  Dihedral  :  6.128  51.577    476
  Min Nonbonded Distance : 2.414

Molprobity Statistics.
  All-atom Clashscore : 10.73
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  8.17 %
    Favored  : 91.58 %
  Rotamer:
    Outliers :  3.80 %
    Allowed  : 20.76 %
    Favored  : 75.44 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.81 (0.41), residues: 404
  helix: -4.94 (0.31), residues: 12
  sheet: -0.11 (0.48), residues: 125
  loop : -1.66 (0.36), residues: 267

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 HIS   0.003   0.002   HIS C 519 
 PHE   0.011   0.001   PHE C 400 
 TYR   0.012   0.001   TYR C 495 
 ARG   0.004   0.001   ARG E 195 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00009 (    1)
  link_NAG-ASN         : angle       2.61367 (    3)
  hydrogen bonds       : bond        0.02689 (   71)
  hydrogen bonds       : angle       6.00754 (  165)
  SS BOND              : bond        0.00538 (    6)
  SS BOND              : angle       1.84991 (   12)
  covalent geometry    : bond        0.00383 ( 3263)
  covalent geometry    : angle       0.62856 ( 4440)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1566.92 seconds
wall clock time: 27 minutes 53.64 seconds (1673.64 seconds total)