Starting phenix.real_space_refine
on Sat Apr 26 19:23:05 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9fgr_50418/04_2025/9fgr_50418.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9fgr_50418/04_2025/9fgr_50418.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/9fgr_50418/04_2025/9fgr_50418.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9fgr_50418/04_2025/9fgr_50418.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9fgr_50418/04_2025/9fgr_50418.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9fgr_50418/04_2025/9fgr_50418.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=   0.051
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    2042      2.51       5
     N     537      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-5669/modules/chem_data/mon_lib"
  Total number of atoms: 3209
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "C"
      Number of atoms: 1511
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 190, 1511
          Classifications: {'peptide': 190}
          Link IDs: {'PTRANS': 10, 'TRANS': 179}
          Chain breaks: 1
    Chain: "E"
      Number of atoms: 1683
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 222, 1683
          Classifications: {'peptide': 222}
          Link IDs: {'PTRANS': 10, 'TRANS': 211}
          Chain breaks: 1
    Chain: "C"
      Number of atoms: 15
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 15
          Unusual residues: {'NAG': 1}
          Classifications: {'undetermined': 1, 'water': 1}
          Link IDs: {None: 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: 3.55, per 1000 atoms: 1.11
  Number of scatterers: 3209
  At special positions: 0
  Unit cell: (82.677, 62.23, 81.788, 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     537      7.00
     C    2042      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=2.03
    Simple disulfide: pdb=" SG  CYS C 480 " - pdb=" SG  CYS C 488 " distance=2.03
    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=2.03

  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 C1301 " - " ASN C 343 "
  Time building additional restraints: 0.78
  Conformation dependent library (CDL) restraints added in 393.6 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:  744

  Finding SS restraints...
    Secondary structure from input PDB file:
      5 helices and 8 sheets defined
      7.3% alpha, 29.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.48
  Creating SS restraints...
    Processing helix  chain 'C' and resid 337 through 342
    Processing helix  chain 'C' and resid 365 through 371
    Processing helix  chain 'C' and resid 384 through 388
      removed outlier: 4.099A  pdb=" N   ASN C 388 " --> pdb=" O   THR C 385 " (cutoff:3.500A)
    Processing helix  chain 'C' and resid 405 through 411
      removed outlier: 4.389A  pdb=" N   ARG C 408 " --> pdb=" O   ASP C 405 " (cutoff:3.500A)
    Processing helix  chain 'E' and resid 213 through 217
      removed outlier: 3.963A  pdb=" N   PHE E 217 " --> pdb=" O   PRO E 214 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358
      removed outlier: 4.015A  pdb=" N   ASN C 354 " --> pdb=" O   SER C 399 " (cutoff:3.500A)
      removed outlier: 3.695A  pdb=" N   SER C 399 " --> pdb=" O   ASN C 354 " (cutoff:3.500A)
      removed outlier: 4.557A  pdb=" N   VAL C 395 " --> pdb=" O   ILE C 358 " (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 'C' and resid 473 through 474
    Processing sheet with id=AA4, first strand: chain 'E' and resid 3 through 6
      removed outlier: 3.959A  pdb=" N   GLN E   3 " --> pdb=" O   SER E  25 " (cutoff:3.500A)
      removed outlier: 3.857A  pdb=" N   SER E  25 " --> pdb=" O   GLN E   3 " (cutoff:3.500A)
      removed outlier: 3.596A  pdb=" N   CYS E  22 " --> pdb=" O   LEU E  78 " (cutoff:3.500A)
      removed outlier: 3.745A  pdb=" N   LEU E  78 " --> pdb=" O   CYS E  22 " (cutoff:3.500A)
    Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 12
      removed outlier: 3.649A  pdb=" N   GLY E  10 " --> pdb=" O   LEU E 113 " (cutoff:3.500A)
      removed outlier: 3.684A  pdb=" N   THR E 115 " --> pdb=" O   GLY E  10 " (cutoff:3.500A)
      removed outlier: 6.595A  pdb=" N   MET E  34 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
      removed outlier: 4.311A  pdb=" N   VAL E  50 " --> pdb=" O   MET E  34 " (cutoff:3.500A)
      removed outlier: 6.514A  pdb=" N   TRP E  36 " --> pdb=" O   VAL E  48 " (cutoff:3.500A)
      removed outlier: 3.550A  pdb=" N   VAL E  50 " --> pdb=" O   PHE E  58 " (cutoff:3.500A)
      removed outlier: 3.706A  pdb=" N   PHE E  58 " --> pdb=" O   VAL E  50 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'E' and resid 137 through 139
      removed outlier: 3.514A  pdb=" N   THR E 138 " --> pdb=" O   ARG E 157 " (cutoff:3.500A)
    Processing sheet with id=AA7, first strand: chain 'E' and resid 187 through 188
      removed outlier: 5.792A  pdb=" N   LEU E 180 " --> pdb=" O   GLN E 171 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   GLN E 171 " --> pdb=" O   LEU E 180 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE E 182 " --> pdb=" O   TRP E 169 " (cutoff:3.500A)
    Processing sheet with id=AA8, first strand: chain 'E' and resid 187 through 188
      removed outlier: 5.792A  pdb=" N   LEU E 180 " --> pdb=" O   GLN E 171 " (cutoff:3.500A)
      removed outlier: 6.320A  pdb=" N   GLN E 171 " --> pdb=" O   LEU E 180 " (cutoff:3.500A)
      removed outlier: 3.560A  pdb=" N   ILE E 182 " --> pdb=" O   TRP E 169 " (cutoff:3.500A)

    88 hydrogen bonds defined for protein.
    213 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: 0.82

  Time building geometry restraints manager: 0.94 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: 1025
        1.35 -     1.47: 884
        1.47 -     1.59: 1362
        1.59 -     1.70: 0
        1.70 -     1.82: 16
  Bond restraints: 3287
  Sorted by residual:
  bond pdb=" CA  THR C 470 "
       pdb=" CB  THR C 470 "
    ideal  model  delta    sigma   weight residual
    1.528  1.583 -0.055 2.61e-02 1.47e+03 4.40e+00
  bond pdb=" C1  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.406  1.434 -0.028 2.00e-02 2.50e+03 1.96e+00
  bond pdb=" C5  NAG C1301 "
       pdb=" O5  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.413  1.435 -0.022 2.00e-02 2.50e+03 1.19e+00
  bond pdb=" C3  NAG C1301 "
       pdb=" O3  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.403  1.423 -0.020 2.00e-02 2.50e+03 9.80e-01
  bond pdb=" C2  NAG C1301 "
       pdb=" N2  NAG C1301 "
    ideal  model  delta    sigma   weight residual
    1.439  1.457 -0.018 2.00e-02 2.50e+03 7.88e-01
  ... (remaining 3282 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.24: 4282
        1.24 -     2.49: 139
        2.49 -     3.73: 32
        3.73 -     4.98: 8
        4.98 -     6.22: 2
  Bond angle restraints: 4463
  Sorted by residual:
  angle pdb=" N   SER E 140 "
        pdb=" CA  SER E 140 "
        pdb=" C   SER E 140 "
      ideal   model   delta    sigma   weight residual
     109.81  116.03   -6.22 2.21e+00 2.05e-01 7.92e+00
  angle pdb=" N   CYS C 432 "
        pdb=" CA  CYS C 432 "
        pdb=" C   CYS C 432 "
      ideal   model   delta    sigma   weight residual
     108.60  112.37   -3.77 1.46e+00 4.69e-01 6.67e+00
  angle pdb=" CA  LYS C 386 "
        pdb=" CB  LYS C 386 "
        pdb=" CG  LYS C 386 "
      ideal   model   delta    sigma   weight residual
     114.10  118.22   -4.12 2.00e+00 2.50e-01 4.25e+00
  angle pdb=" N   GLY E 198 "
        pdb=" CA  GLY E 198 "
        pdb=" C   GLY E 198 "
      ideal   model   delta    sigma   weight residual
     110.90  114.03   -3.13 1.53e+00 4.27e-01 4.18e+00
  angle pdb=" N   SER E  35 "
        pdb=" CA  SER E  35 "
        pdb=" C   SER E  35 "
      ideal   model   delta    sigma   weight residual
     108.55  111.69   -3.14 1.62e+00 3.81e-01 3.75e+00
  ... (remaining 4458 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    16.77: 1748
       16.77 -    33.55: 154
       33.55 -    50.32: 37
       50.32 -    67.09: 3
       67.09 -    83.87: 1
  Dihedral angle restraints: 1943
    sinusoidal: 764
      harmonic: 1179
  Sorted by residual:
  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  142.95  -49.95     1      1.00e+01 1.00e-02 3.42e+01
  dihedral pdb=" CB  CYS E  22 "
           pdb=" SG  CYS E  22 "
           pdb=" SG  CYS E  95 "
           pdb=" CB  CYS E  95 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -128.20   42.20     1      1.00e+01 1.00e-02 2.49e+01
  dihedral pdb=" CA  SER E 140 "
           pdb=" C   SER E 140 "
           pdb=" N   PRO E 141 "
           pdb=" CA  PRO E 141 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -156.80  -23.20     0      5.00e+00 4.00e-02 2.15e+01
  ... (remaining 1940 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.034: 327
       0.034 -    0.069: 100
       0.069 -    0.103: 37
       0.103 -    0.137: 16
       0.137 -    0.171: 1
  Chirality restraints: 481
  Sorted by residual:
  chirality pdb=" C1  NAG C1301 "
            pdb=" ND2 ASN C 343 "
            pdb=" C2  NAG C1301 "
            pdb=" O5  NAG C1301 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.23   -0.17 2.00e-01 2.50e+01 7.35e-01
  chirality pdb=" CA  SER E 228 "
            pdb=" N   SER E 228 "
            pdb=" C   SER E 228 "
            pdb=" CB  SER E 228 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.38    0.13 2.00e-01 2.50e+01 4.53e-01
  chirality pdb=" CA  ILE E 182 "
            pdb=" N   ILE E 182 "
            pdb=" C   ILE E 182 "
            pdb=" CB  ILE E 182 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.57   -0.13 2.00e-01 2.50e+01 4.38e-01
  ... (remaining 478 not shown)

  Planarity restraints: 579
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 147 "    0.024 5.00e-02 4.00e+02   3.57e-02 2.04e+00
        pdb=" N   PRO E 148 "   -0.062 5.00e-02 4.00e+02
        pdb=" CA  PRO E 148 "    0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO E 148 "    0.020 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   SER E 140 "   -0.021 5.00e-02 4.00e+02   3.21e-02 1.65e+00
        pdb=" N   PRO E 141 "    0.056 5.00e-02 4.00e+02
        pdb=" CA  PRO E 141 "   -0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO E 141 "   -0.018 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   GLN C 498 "    0.020 5.00e-02 4.00e+02   3.05e-02 1.49e+00
        pdb=" N   PRO C 499 "   -0.053 5.00e-02 4.00e+02
        pdb=" CA  PRO C 499 "    0.016 5.00e-02 4.00e+02
        pdb=" CD  PRO C 499 "    0.017 5.00e-02 4.00e+02
  ... (remaining 576 not shown)

  Histogram of nonbonded interaction distances:
        2.18 -     2.72: 126
        2.72 -     3.27: 3136
        3.27 -     3.81: 4692
        3.81 -     4.36: 5568
        4.36 -     4.90: 9744
  Nonbonded interactions: 23266
  Sorted by model distance:
  nonbonded pdb=" OG  SER E 147 "
            pdb=" OE1 GLU E 150 "
     model   vdw
     2.176 3.040
  nonbonded pdb=" O   ALA C 475 "
            pdb=" OG1 THR E  28 "
     model   vdw
     2.186 3.040
  nonbonded pdb=" OG  SER E 159 "
            pdb=" OE1 GLN E 160 "
     model   vdw
     2.206 3.040
  nonbonded pdb=" O   ALA E 104 "
            pdb=" OH  TYR E 170 "
     model   vdw
     2.212 3.040
  nonbonded pdb=" OG  SER C 349 "
            pdb=" O   LEU C 452 "
     model   vdw
     2.286 3.040
  ... (remaining 23261 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:             2.680
  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:          0.130
  Check model and map are aligned:         0.020
  Set scattering table:                    0.030
  Process input model:                     13.920
  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:3.070
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.900
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8013
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   0.055   3294  Z= 0.120
  Angle     :  0.592   6.986   4478  Z= 0.311
  Chirality :  0.042   0.171    481
  Planarity :  0.004   0.036    578
  Dihedral  : 12.554  83.866   1181
  Min Nonbonded Distance : 2.176

Molprobity Statistics.
  All-atom Clashscore : 8.75
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.44 %
    Favored  : 93.56 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.87 %
    Favored  : 99.13 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.53 (0.40), residues: 404
  helix: -4.11 (0.47), residues: 20
  sheet:  0.12 (0.52), residues: 112
  loop : -1.33 (0.36), residues: 272

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP E 169 
 PHE   0.014   0.001   PHE C 429 
 TYR   0.011   0.001   TYR E 225 
 ARG   0.002   0.000   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00096 (    1)
  link_NAG-ASN         : angle       5.16495 (    3)
  hydrogen bonds       : bond        0.29890 (   79)
  hydrogen bonds       : angle      10.79930 (  213)
  SS BOND              : bond        0.00349 (    6)
  SS BOND              : angle       0.78810 (   12)
  covalent geometry    : bond        0.00251 ( 3287)
  covalent geometry    : angle       0.57633 ( 4463)

*********************** 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
  78 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 78
  time to evaluate  : 0.355 
Fit side-chains
   revert: symmetry clash
REVERT: E   89 ASP cc_start: 0.8686 (m-30) cc_final: 0.8345 (m-30)
REVERT: E  238 ARG cc_start: 0.7467 (pmt170) cc_final: 0.6991 (ptp90)
  outliers start: 0
  outliers final: 0
  residues processed: 78
  average time/residue: 0.1770
  time to fit residues: 16.4253
Evaluate side-chains
  64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 64
  time to evaluate  : 0.331 
-------------------------------------------------------------------------------
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:    1.9990
   chunk 31 optimal weight:    0.7980
   chunk 17 optimal weight:    0.3980
   chunk 10 optimal weight:    0.5980
   chunk 20 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 12 optimal weight:    1.9990
   chunk 19 optimal weight:    0.9990
   chunk 23 optimal weight:    0.3980
   chunk 37 optimal weight:    0.8980
   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 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E   6 GLN
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3550 r_free = 0.3550 target = 0.131982 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3289 r_free = 0.3289 target = 0.113274 restraints weight = 6097.767|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3314 r_free = 0.3314 target = 0.115087 restraints weight = 4537.826|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116342 restraints weight = 3681.497|
|-----------------------------------------------------------------------------|
r_work (final): 0.3338
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8079
moved from start:          0.1717

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   3294  Z= 0.147
  Angle     :  0.603   6.247   4478  Z= 0.316
  Chirality :  0.044   0.154    481
  Planarity :  0.004   0.035    578
  Dihedral  :  5.656  54.045    476
  Min Nonbonded Distance : 2.581

Molprobity Statistics.
  All-atom Clashscore : 7.00
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.43 %
    Favored  : 92.57 %
  Rotamer:
    Outliers :  2.32 %
    Allowed  : 11.59 %
    Favored  : 86.09 %
  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: -1.39 (0.39), residues: 404
  helix: -3.96 (0.54), residues: 23
  sheet:  0.22 (0.46), residues: 123
  loop : -1.26 (0.36), residues: 258

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP C 436 
 PHE   0.014   0.001   PHE E 205 
 TYR   0.016   0.001   TYR C 473 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00031 (    1)
  link_NAG-ASN         : angle       2.67018 (    3)
  hydrogen bonds       : bond        0.04200 (   79)
  hydrogen bonds       : angle       7.39279 (  213)
  SS BOND              : bond        0.00586 (    6)
  SS BOND              : angle       1.15169 (   12)
  covalent geometry    : bond        0.00341 ( 3287)
  covalent geometry    : angle       0.59657 ( 4463)

*********************** 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
  71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 63
  time to evaluate  : 0.303 
Fit side-chains
REVERT: C  357 ARG cc_start: 0.7427 (mtp85) cc_final: 0.6313 (mtm180)
REVERT: C  406 GLU cc_start: 0.7878 (mt-10) cc_final: 0.7522 (mt-10)
  outliers start: 8
  outliers final: 4
  residues processed: 66
  average time/residue: 0.1637
  time to fit residues: 13.0502
Evaluate side-chains
  60 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 56
  time to evaluate  : 0.376 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain E residue  135 ILE
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 36 optimal weight:    3.9990
   chunk 14 optimal weight:    3.9990
   chunk 16 optimal weight:    0.4980
   chunk 13 optimal weight:    1.9990
   chunk 10 optimal weight:    2.9990
   chunk 35 optimal weight:    0.8980
   chunk 18 optimal weight:    1.9990
   chunk 21 optimal weight:    0.0370
   chunk 11 optimal weight:    0.8980
   chunk 28 optimal weight:    0.8980
   chunk 8 optimal weight:    0.9980
   overall best weight:    0.6458

-------------------------------------------------------------------------------
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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3535 r_free = 0.3535 target = 0.130105 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3270 r_free = 0.3270 target = 0.111327 restraints weight = 6301.025|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3295 r_free = 0.3295 target = 0.113061 restraints weight = 4732.290|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3312 r_free = 0.3312 target = 0.114311 restraints weight = 3890.629|
|-----------------------------------------------------------------------------|
r_work (final): 0.3307
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8112
moved from start:          0.2050

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   3294  Z= 0.146
  Angle     :  0.584   6.124   4478  Z= 0.306
  Chirality :  0.043   0.147    481
  Planarity :  0.004   0.036    578
  Dihedral  :  5.670  54.508    476
  Min Nonbonded Distance : 2.589

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 13.04 %
    Favored  : 83.48 %
  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: -1.35 (0.39), residues: 404
  helix: -3.86 (0.57), residues: 23
  sheet:  0.28 (0.46), residues: 127
  loop : -1.28 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP C 436 
 PHE   0.014   0.001   PHE E 205 
 TYR   0.011   0.001   TYR C 453 
 ARG   0.002   0.000   ARG C 509 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00154 (    1)
  link_NAG-ASN         : angle       1.80950 (    3)
  hydrogen bonds       : bond        0.03686 (   79)
  hydrogen bonds       : angle       6.66504 (  213)
  SS BOND              : bond        0.00534 (    6)
  SS BOND              : angle       1.05727 (   12)
  covalent geometry    : bond        0.00339 ( 3287)
  covalent geometry    : angle       0.58005 ( 4463)

*********************** 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
  75 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 63
  time to evaluate  : 0.327 
Fit side-chains
   revert: symmetry clash
REVERT: C  357 ARG cc_start: 0.7515 (mtp85) cc_final: 0.6369 (mtm180)
REVERT: E  155 PHE cc_start: 0.7307 (OUTLIER) cc_final: 0.7081 (m-80)
  outliers start: 12
  outliers final: 6
  residues processed: 71
  average time/residue: 0.1695
  time to fit residues: 14.3742
Evaluate side-chains
  65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 58
  time to evaluate  : 0.326 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  155 PHE
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 28 optimal weight:    0.9990
   chunk 39 optimal weight:    0.9980
   chunk 34 optimal weight:    0.7980
   chunk 14 optimal weight:    0.1980
   chunk 18 optimal weight:    1.9990
   chunk 35 optimal weight:    0.9980
   chunk 36 optimal weight:    0.9980
   chunk 22 optimal weight:    0.9980
   chunk 3 optimal weight:    0.0670
   chunk 8 optimal weight:    0.7980
   chunk 4 optimal weight:    3.9990
   overall best weight:    0.5718

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

Flipped N/Q/H residues before XYZ refinement:
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E  73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.131211 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3279 r_free = 0.3279 target = 0.112075 restraints weight = 6215.297|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 22)----------------|
| r_work = 0.3302 r_free = 0.3302 target = 0.113796 restraints weight = 4571.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 37)----------------|
| r_work = 0.3325 r_free = 0.3325 target = 0.115329 restraints weight = 3701.716|
|-----------------------------------------------------------------------------|
r_work (final): 0.3322
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8102
moved from start:          0.2367

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3294  Z= 0.135
  Angle     :  0.578   6.407   4478  Z= 0.302
  Chirality :  0.043   0.157    481
  Planarity :  0.004   0.035    578
  Dihedral  :  5.620  54.265    476
  Min Nonbonded Distance : 2.608

Molprobity Statistics.
  All-atom Clashscore : 7.32
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.19 %
    Allowed  : 15.07 %
    Favored  : 81.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (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: -1.34 (0.40), residues: 404
  helix: -3.71 (0.67), residues: 23
  sheet:  0.34 (0.47), residues: 127
  loop : -1.32 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 PHE   0.010   0.001   PHE E 205 
 TYR   0.021   0.001   TYR C 473 
 ARG   0.002   0.000   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00149 (    1)
  link_NAG-ASN         : angle       1.44033 (    3)
  hydrogen bonds       : bond        0.03461 (   79)
  hydrogen bonds       : angle       6.35512 (  213)
  SS BOND              : bond        0.00515 (    6)
  SS BOND              : angle       1.02321 (   12)
  covalent geometry    : bond        0.00313 ( 3287)
  covalent geometry    : angle       0.57507 ( 4463)

*********************** 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
  72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 61
  time to evaluate  : 0.345 
Fit side-chains
   revert: symmetry clash
REVERT: E  238 ARG cc_start: 0.7468 (pmt170) cc_final: 0.7049 (mtm-85)
  outliers start: 11
  outliers final: 8
  residues processed: 68
  average time/residue: 0.1923
  time to fit residues: 15.5548
Evaluate side-chains
  65 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 57
  time to evaluate  : 0.377 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  209 ILE
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 21 optimal weight:    0.2980
   chunk 12 optimal weight:    2.9990
   chunk 20 optimal weight:    1.9990
   chunk 1 optimal weight:    0.1980
   chunk 16 optimal weight:    0.6980
   chunk 17 optimal weight:    0.5980
   chunk 37 optimal weight:    5.9990
   chunk 32 optimal weight:    0.8980
   chunk 9 optimal weight:    0.7980
   chunk 14 optimal weight:    0.9980
   chunk 13 optimal weight:    1.9990
   overall best weight:    0.5180

-------------------------------------------------------------------------------
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  73 ASN
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3537 r_free = 0.3537 target = 0.130672 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3268 r_free = 0.3268 target = 0.111463 restraints weight = 6245.851|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3294 r_free = 0.3294 target = 0.113315 restraints weight = 4637.802|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3315 r_free = 0.3315 target = 0.114795 restraints weight = 3770.565|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8095
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   3294  Z= 0.126
  Angle     :  0.557   6.352   4478  Z= 0.291
  Chirality :  0.043   0.152    481
  Planarity :  0.004   0.033    578
  Dihedral  :  5.559  54.242    476
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 7.48
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.94 %
    Favored  : 94.06 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 15.36 %
    Favored  : 80.87 %
  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: -1.31 (0.40), residues: 404
  helix: -3.67 (0.68), residues: 23
  sheet:  0.44 (0.47), residues: 127
  loop : -1.34 (0.36), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 PHE   0.010   0.001   PHE E 155 
 TYR   0.009   0.001   TYR C 453 
 ARG   0.002   0.000   ARG E 238 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00139 (    1)
  link_NAG-ASN         : angle       1.27845 (    3)
  hydrogen bonds       : bond        0.03225 (   79)
  hydrogen bonds       : angle       6.14420 (  213)
  SS BOND              : bond        0.00501 (    6)
  SS BOND              : angle       0.99290 (   12)
  covalent geometry    : bond        0.00295 ( 3287)
  covalent geometry    : angle       0.55489 ( 4463)

*********************** 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
  76 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 63
  time to evaluate  : 0.333 
Fit side-chains
   revert: symmetry clash
REVERT: E  238 ARG cc_start: 0.7464 (pmt170) cc_final: 0.7084 (mtm-85)
  outliers start: 13
  outliers final: 8
  residues processed: 73
  average time/residue: 0.1663
  time to fit residues: 14.6513
Evaluate side-chains
  64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 56
  time to evaluate  : 0.363 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  228 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 1 optimal weight:    0.9990
   chunk 27 optimal weight:    0.0170
   chunk 17 optimal weight:    1.9990
   chunk 32 optimal weight:    0.9990
   chunk 9 optimal weight:    0.7980
   chunk 7 optimal weight:    0.5980
   chunk 14 optimal weight:    0.0980
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    2.9990
   chunk 23 optimal weight:    0.5980
   chunk 25 optimal weight:    0.7980
   overall best weight:    0.4218

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  73 ASN
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132268 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3330 r_free = 0.3330 target = 0.115941 restraints weight = 6157.715|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 25)----------------|
| r_work = 0.3331 r_free = 0.3331 target = 0.116225 restraints weight = 4551.114|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3333 r_free = 0.3333 target = 0.116431 restraints weight = 4587.096|
|-----------------------------------------------------------------------------|
r_work (final): 0.3328
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8070
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3294  Z= 0.116
  Angle     :  0.578   6.258   4478  Z= 0.298
  Chirality :  0.043   0.144    481
  Planarity :  0.004   0.033    578
  Dihedral  :  5.472  54.095    476
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 7.64
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.69 %
    Favored  : 94.31 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 16.52 %
    Favored  : 79.71 %
  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: -1.22 (0.40), residues: 404
  helix: -3.60 (0.71), residues: 23
  sheet:  0.49 (0.48), residues: 128
  loop : -1.29 (0.36), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 PHE   0.015   0.001   PHE E 205 
 TYR   0.010   0.001   TYR E 170 
 ARG   0.001   0.000   ARG C 457 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00144 (    1)
  link_NAG-ASN         : angle       1.24048 (    3)
  hydrogen bonds       : bond        0.03021 (   79)
  hydrogen bonds       : angle       6.01755 (  213)
  SS BOND              : bond        0.00490 (    6)
  SS BOND              : angle       0.96369 (   12)
  covalent geometry    : bond        0.00268 ( 3287)
  covalent geometry    : angle       0.57542 ( 4463)

*********************** 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
  73 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 60
  time to evaluate  : 0.373 
Fit side-chains
   revert: symmetry clash
REVERT: C  378 LYS cc_start: 0.8385 (mttp) cc_final: 0.7845 (mmtm)
REVERT: E  224 GLU cc_start: 0.8267 (tm-30) cc_final: 0.8056 (tm-30)
REVERT: E  238 ARG cc_start: 0.7430 (pmt170) cc_final: 0.7095 (mtm-85)
  outliers start: 13
  outliers final: 9
  residues processed: 71
  average time/residue: 0.1649
  time to fit residues: 14.1957
Evaluate side-chains
  64 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 55
  time to evaluate  : 0.353 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  228 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9980
   chunk 26 optimal weight:    1.9990
   chunk 37 optimal weight:    4.9990
   chunk 33 optimal weight:    3.9990
   chunk 6 optimal weight:    0.7980
   chunk 13 optimal weight:    0.5980
   chunk 23 optimal weight:    0.6980
   chunk 12 optimal weight:    1.9990
   chunk 9 optimal weight:    0.1980
   chunk 1 optimal weight:    0.0050
   overall best weight:    0.4594

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

Flipped N/Q/H residues before XYZ refinement:
** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
E  73 ASN
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3548 r_free = 0.3548 target = 0.132463 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3332 r_free = 0.3332 target = 0.116295 restraints weight = 6038.133|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3335 r_free = 0.3335 target = 0.116668 restraints weight = 4433.846|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3337 r_free = 0.3337 target = 0.116895 restraints weight = 4487.957|
|-----------------------------------------------------------------------------|
r_work (final): 0.3332
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8066
moved from start:          0.2600

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   3294  Z= 0.122
  Angle     :  0.581   6.353   4478  Z= 0.300
  Chirality :  0.042   0.135    481
  Planarity :  0.004   0.033    578
  Dihedral  :  5.511  54.407    476
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 7.80
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.19 %
    Favored  : 93.81 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 17.97 %
    Favored  : 78.55 %
  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: -1.21 (0.41), residues: 404
  helix: -3.55 (0.73), residues: 23
  sheet:  0.69 (0.48), residues: 129
  loop : -1.41 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 PHE   0.011   0.001   PHE E 205 
 TYR   0.013   0.001   TYR E 170 
 ARG   0.003   0.000   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00073 (    1)
  link_NAG-ASN         : angle       1.28163 (    3)
  hydrogen bonds       : bond        0.02956 (   79)
  hydrogen bonds       : angle       5.93868 (  213)
  SS BOND              : bond        0.00467 (    6)
  SS BOND              : angle       0.92556 (   12)
  covalent geometry    : bond        0.00285 ( 3287)
  covalent geometry    : angle       0.57953 ( 4463)

*********************** 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
  71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 59
  time to evaluate  : 0.324 
Fit side-chains
   revert: symmetry clash
REVERT: C  378 LYS cc_start: 0.8373 (mttp) cc_final: 0.7841 (mmtm)
REVERT: E  224 GLU cc_start: 0.8269 (tm-30) cc_final: 0.8060 (tm-30)
REVERT: E  238 ARG cc_start: 0.7353 (pmt170) cc_final: 0.6999 (mtm-85)
  outliers start: 12
  outliers final: 9
  residues processed: 69
  average time/residue: 0.1649
  time to fit residues: 13.9785
Evaluate side-chains
  66 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 57
  time to evaluate  : 0.374 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  228 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 12 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 22 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 4 optimal weight:    1.9990
   chunk 14 optimal weight:    0.0670
   chunk 34 optimal weight:    0.5980
   chunk 30 optimal weight:    0.6980
   chunk 15 optimal weight:    0.7980
   chunk 26 optimal weight:    0.5980
   chunk 36 optimal weight:    3.9990
   overall best weight:    0.5118

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

Flipped N/Q/H residues before XYZ refinement:
** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** E 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3544 r_free = 0.3544 target = 0.131974 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115643 restraints weight = 6053.943|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 27)----------------|
| r_work = 0.3323 r_free = 0.3323 target = 0.115783 restraints weight = 4466.834|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3324 r_free = 0.3324 target = 0.115976 restraints weight = 4580.749|
|-----------------------------------------------------------------------------|
r_work (final): 0.3318
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8087
moved from start:          0.2776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.033   3294  Z= 0.129
  Angle     :  0.590   6.001   4478  Z= 0.306
  Chirality :  0.043   0.139    481
  Planarity :  0.004   0.034    578
  Dihedral  :  5.515  54.100    476
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.77 %
    Allowed  : 18.55 %
    Favored  : 77.68 %
  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: -1.22 (0.41), residues: 404
  helix: -3.55 (0.73), residues: 23
  sheet:  0.69 (0.48), residues: 129
  loop : -1.43 (0.36), residues: 252

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 PHE   0.010   0.001   PHE E 205 
 TYR   0.028   0.001   TYR C 473 
 ARG   0.003   0.000   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00131 (    1)
  link_NAG-ASN         : angle       1.33442 (    3)
  hydrogen bonds       : bond        0.02948 (   79)
  hydrogen bonds       : angle       5.87710 (  213)
  SS BOND              : bond        0.00477 (    6)
  SS BOND              : angle       0.94665 (   12)
  covalent geometry    : bond        0.00302 ( 3287)
  covalent geometry    : angle       0.58815 ( 4463)

*********************** 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
  71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 58
  time to evaluate  : 0.326 
Fit side-chains
   revert: symmetry clash
REVERT: C  378 LYS cc_start: 0.8390 (mttp) cc_final: 0.7863 (mmtm)
REVERT: E  238 ARG cc_start: 0.7290 (pmt170) cc_final: 0.7005 (mtm-85)
  outliers start: 13
  outliers final: 10
  residues processed: 68
  average time/residue: 0.1590
  time to fit residues: 13.0998
Evaluate side-chains
  69 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 59
  time to evaluate  : 0.375 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  228 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 38 optimal weight:    0.7980
   chunk 5 optimal weight:    0.7980
   chunk 7 optimal weight:    1.9990
   chunk 6 optimal weight:    1.9990
   chunk 0 optimal weight:    2.9990
   chunk 30 optimal weight:    0.9990
   chunk 2 optimal weight:    0.3980
   chunk 29 optimal weight:    0.5980
   chunk 26 optimal weight:    0.8980
   chunk 31 optimal weight:    3.9990
   chunk 34 optimal weight:    0.6980
   overall best weight:    0.6580

-------------------------------------------------------------------------------
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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3524 r_free = 0.3524 target = 0.130495 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3276 r_free = 0.3276 target = 0.112627 restraints weight = 6085.513|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3301 r_free = 0.3301 target = 0.114439 restraints weight = 4499.933|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3321 r_free = 0.3321 target = 0.115798 restraints weight = 3640.781|
|-----------------------------------------------------------------------------|
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8092
moved from start:          0.2833

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.030   3294  Z= 0.152
  Angle     :  0.619   7.793   4478  Z= 0.319
  Chirality :  0.044   0.142    481
  Planarity :  0.004   0.035    578
  Dihedral  :  5.669  54.480    476
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 7.95
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.68 %
    Favored  : 93.32 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.55 %
    Favored  : 77.97 %
  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: -1.22 (0.41), residues: 404
  helix: -3.59 (0.71), residues: 23
  sheet:  0.75 (0.49), residues: 122
  loop : -1.41 (0.36), residues: 259

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 PHE   0.018   0.001   PHE E 205 
 TYR   0.027   0.001   TYR C 473 
 ARG   0.004   0.000   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00096 (    1)
  link_NAG-ASN         : angle       1.61080 (    3)
  hydrogen bonds       : bond        0.03166 (   79)
  hydrogen bonds       : angle       5.96812 (  213)
  SS BOND              : bond        0.00498 (    6)
  SS BOND              : angle       1.00592 (   12)
  covalent geometry    : bond        0.00357 ( 3287)
  covalent geometry    : angle       0.61684 ( 4463)

*********************** 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
  74 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.381 
Fit side-chains
   revert: symmetry clash
REVERT: C  338 PHE cc_start: 0.7004 (p90) cc_final: 0.6710 (p90)
REVERT: C  378 LYS cc_start: 0.8478 (mttp) cc_final: 0.7908 (mmtm)
REVERT: E  167 LEU cc_start: 0.9042 (tt) cc_final: 0.8789 (tt)
REVERT: E  169 TRP cc_start: 0.8902 (m100) cc_final: 0.8679 (m100)
REVERT: E  205 PHE cc_start: 0.8181 (m-10) cc_final: 0.7918 (m-10)
REVERT: E  238 ARG cc_start: 0.7449 (pmt170) cc_final: 0.7093 (mtm-85)
  outliers start: 12
  outliers final: 10
  residues processed: 73
  average time/residue: 0.1697
  time to fit residues: 14.9131
Evaluate side-chains
  71 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 61
  time to evaluate  : 0.348 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  228 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 10 optimal weight:    2.9990
   chunk 14 optimal weight:    3.9990
   chunk 37 optimal weight:    2.9990
   chunk 4 optimal weight:    0.9980
   chunk 3 optimal weight:    1.9990
   chunk 17 optimal weight:    0.9990
   chunk 8 optimal weight:    0.3980
   chunk 38 optimal weight:    0.8980
   chunk 22 optimal weight:    0.5980
   chunk 16 optimal weight:    0.9990
   chunk 12 optimal weight:    0.5980
   overall best weight:    0.6980

-------------------------------------------------------------------------------
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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3521 r_free = 0.3521 target = 0.130016 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3265 r_free = 0.3265 target = 0.111847 restraints weight = 6096.373|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 24)----------------|
| r_work = 0.3293 r_free = 0.3293 target = 0.113784 restraints weight = 4501.018|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.114972 restraints weight = 3622.991|
|-----------------------------------------------------------------------------|
r_work (final): 0.3299
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8109
moved from start:          0.2907

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.028   3294  Z= 0.158
  Angle     :  0.626   7.437   4478  Z= 0.322
  Chirality :  0.044   0.138    481
  Planarity :  0.004   0.034    578
  Dihedral  :  5.711  54.304    476
  Min Nonbonded Distance : 2.586

Molprobity Statistics.
  All-atom Clashscore : 8.43
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 19.13 %
    Favored  : 77.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -1.25 (0.41), residues: 404
  helix: -3.62 (0.70), residues: 23
  sheet:  0.59 (0.48), residues: 127
  loop : -1.38 (0.37), residues: 254

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP C 436 
 PHE   0.017   0.001   PHE E 205 
 TYR   0.027   0.001   TYR C 473 
 ARG   0.004   0.000   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00125 (    1)
  link_NAG-ASN         : angle       1.98618 (    3)
  hydrogen bonds       : bond        0.03167 (   79)
  hydrogen bonds       : angle       5.99140 (  213)
  SS BOND              : bond        0.00501 (    6)
  SS BOND              : angle       1.02916 (   12)
  covalent geometry    : bond        0.00371 ( 3287)
  covalent geometry    : angle       0.62244 ( 4463)

********************** 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
  72 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.381 
Fit side-chains
REVERT: C  378 LYS cc_start: 0.8514 (mttp) cc_final: 0.7953 (mmtm)
REVERT: E  167 LEU cc_start: 0.9030 (tt) cc_final: 0.8798 (tt)
REVERT: E  169 TRP cc_start: 0.8906 (m100) cc_final: 0.8571 (m100)
REVERT: E  205 PHE cc_start: 0.8230 (m-10) cc_final: 0.7911 (m-10)
REVERT: E  238 ARG cc_start: 0.7417 (pmt170) cc_final: 0.7058 (mtm-85)
  outliers start: 12
  outliers final: 11
  residues processed: 70
  average time/residue: 0.1562
  time to fit residues: 13.3813
Evaluate side-chains
  68 residues out of total 345 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 57
  time to evaluate  : 0.357 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain C residue  349 SER
Chi-restraints excluded: chain C residue  382 VAL
Chi-restraints excluded: chain C residue  433 VAL
Chi-restraints excluded: chain C residue  470 THR
Chi-restraints excluded: chain C residue  503 VAL
Chi-restraints excluded: chain E residue   57 THR
Chi-restraints excluded: chain E residue  112 THR
Chi-restraints excluded: chain E residue  135 ILE
Chi-restraints excluded: chain E residue  155 PHE
Chi-restraints excluded: chain E residue  209 ILE
Chi-restraints excluded: chain E residue  228 SER
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 41
   random chunks:
   chunk 8 optimal weight:    0.9990
   chunk 13 optimal weight:    0.0670
   chunk 10 optimal weight:    2.9990
   chunk 0 optimal weight:    2.9990
   chunk 1 optimal weight:    0.4980
   chunk 20 optimal weight:    0.9980
   chunk 40 optimal weight:    0.9980
   chunk 25 optimal weight:    0.4980
   chunk 2 optimal weight:    0.7980
   chunk 24 optimal weight:    0.4980
   chunk 18 optimal weight:    0.8980
   overall best weight:    0.4718

-------------------------------------------------------------------------------
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 139 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3549 r_free = 0.3549 target = 0.132716 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.3317 r_free = 0.3317 target = 0.115534 restraints weight = 5918.766|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3341 r_free = 0.3341 target = 0.117326 restraints weight = 4282.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 33)----------------|
| r_work = 0.3361 r_free = 0.3361 target = 0.118703 restraints weight = 3415.930|
|-----------------------------------------------------------------------------|
r_work (final): 0.3354
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8049
moved from start:          0.2937

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   3294  Z= 0.126
  Angle     :  0.597   7.984   4478  Z= 0.306
  Chirality :  0.043   0.135    481
  Planarity :  0.004   0.034    578
  Dihedral  :  5.559  53.529    476
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 8.59
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  6.93 %
    Favored  : 93.07 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 18.84 %
    Favored  : 77.68 %
  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: -1.25 (0.41), residues: 404
  helix: -3.53 (0.73), residues: 23
  sheet:  0.63 (0.48), residues: 128
  loop : -1.42 (0.37), residues: 253

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP C 436 
 PHE   0.016   0.001   PHE E 205 
 TYR   0.025   0.001   TYR C 473 
 ARG   0.004   0.000   ARG E  19 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00109 (    1)
  link_NAG-ASN         : angle       1.93082 (    3)
  hydrogen bonds       : bond        0.02944 (   79)
  hydrogen bonds       : angle       5.86021 (  213)
  SS BOND              : bond        0.00469 (    6)
  SS BOND              : angle       0.92642 (   12)
  covalent geometry    : bond        0.00295 ( 3287)
  covalent geometry    : angle       0.59412 ( 4463)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1527.14 seconds
wall clock time: 27 minutes 8.35 seconds (1628.35 seconds total)