Starting phenix.real_space_refine
on Fri Aug 22 18:00:10 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8dv2_27731/08_2025/8dv2_27731.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8dv2_27731/08_2025/8dv2_27731.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.5
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8dv2_27731/08_2025/8dv2_27731.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8dv2_27731/08_2025/8dv2_27731.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8dv2_27731/08_2025/8dv2_27731.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8dv2_27731/08_2025/8dv2_27731.map"
  }
  resolution = 3.5
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.001 sd=   0.029
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      37      5.16       5
     C    4186      2.51       5
     N    1075      2.21       5
     O    1247      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 38 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 6545
  Number of models: 1
  Model: ""
    Number of chains: 4
    Chain: "A"
      Number of atoms: 1590
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 201, 1590
          Classifications: {'peptide': 201}
          Link IDs: {'PTRANS': 11, 'TRANS': 189}
    Chain: "D"
      Number of atoms: 4857
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 595, 4857
          Classifications: {'peptide': 595}
          Link IDs: {'PTRANS': 27, 'TRANS': 567}
    Chain: "A"
      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
    Chain: "D"
      Number of atoms: 84
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 6, 84
          Unusual residues: {'NAG': 6}
          Classifications: {'undetermined': 6}
          Link IDs: {None: 5}
          Unresolved non-hydrogen bonds: 6
          Unresolved non-hydrogen angles: 12
          Unresolved non-hydrogen dihedrals: 18
          Unresolved non-hydrogen chiralities: 6
  Time building chain proxies: 1.81, per 1000 atoms: 0.28
  Number of scatterers: 6545
  At special positions: 0
  Unit cell: (76.608, 88.704, 122.976, 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      37     16.00
     O    1247      8.00
     N    1075      7.00
     C    4186      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 336 " - pdb=" SG  CYS A 361 " distance=2.01
    Simple disulfide: pdb=" SG  CYS A 379 " - pdb=" SG  CYS A 432 " distance=2.04
    Simple disulfide: pdb=" SG  CYS A 391 " - pdb=" SG  CYS A 525 " distance=2.05
    Simple disulfide: pdb=" SG  CYS A 480 " - pdb=" SG  CYS A 488 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 133 " - pdb=" SG  CYS D 141 " distance=2.03
    Simple disulfide: pdb=" SG  CYS D 344 " - pdb=" SG  CYS D 361 " distance=2.06
    Simple disulfide: pdb=" SG  CYS D 530 " - pdb=" SG  CYS D 542 " distance=2.02

  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 A1301 " - " ASN A 343 "
      " NAG D1101 " - " ASN D 322 "
      " NAG D1102 " - " ASN D 103 "
      " NAG D1103 " - " ASN D 432 "
      " NAG D1104 " - " ASN D 546 "
      " NAG D1105 " - " ASN D  90 "
      " NAG D1106 " - " ASN D  53 "
  Time building additional restraints: 0.58
  Conformation dependent library (CDL) restraints added in 613.0 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1498

  Finding SS restraints...
    Secondary structure from input PDB file:
      41 helices and 7 sheets defined
      57.2% alpha, 6.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.24
  Creating SS restraints...
    Processing helix  chain 'A' and resid 338 through 343
    Processing helix  chain 'A' and resid 349 through 353
      removed outlier: 3.623A  pdb=" N   TRP A 353 " --> pdb=" O   VAL A 350 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 365 through 370
    Processing helix  chain 'A' and resid 386 through 389
    Processing helix  chain 'A' and resid 405 through 410
      removed outlier: 4.367A  pdb=" N   ARG A 408 " --> pdb=" O   ASP A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 416 through 422
      removed outlier: 3.645A  pdb=" N   TYR A 421 " --> pdb=" O   LYS A 417 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 438 through 443
    Processing helix  chain 'D' and resid 22 through 53
      removed outlier: 4.268A  pdb=" N   ASP D  38 " --> pdb=" O   ILE D  34 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 55 through 80
    Processing helix  chain 'D' and resid 81 through 83
      No H-bonds generated for 'chain 'D' and resid 81 through 83'
    Processing helix  chain 'D' and resid 84 through 88
    Processing helix  chain 'D' and resid 90 through 101
    Processing helix  chain 'D' and resid 109 through 129
    Processing helix  chain 'D' and resid 147 through 155
    Processing helix  chain 'D' and resid 157 through 170
      removed outlier: 3.605A  pdb=" N   TRP D 168 " --> pdb=" O   ALA D 164 " (cutoff:3.500A)
      removed outlier: 3.759A  pdb=" N   ARG D 169 " --> pdb=" O   TRP D 165 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 171 through 194
      Proline residue:  D 178  - end of helix
      removed outlier: 3.790A  pdb=" N   GLU D 182 " --> pdb=" O   PRO D 178 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 198 through 205
    Processing helix  chain 'D' and resid 206 through 208
      No H-bonds generated for 'chain 'D' and resid 206 through 208'
    Processing helix  chain 'D' and resid 219 through 249
      removed outlier: 4.248A  pdb=" N   ILE D 223 " --> pdb=" O   ARG D 219 " (cutoff:3.500A)
      Proline residue:  D 235  - end of helix
    Processing helix  chain 'D' and resid 265 through 267
      No H-bonds generated for 'chain 'D' and resid 265 through 267'
    Processing helix  chain 'D' and resid 275 through 277
      No H-bonds generated for 'chain 'D' and resid 275 through 277'
    Processing helix  chain 'D' and resid 278 through 283
    Processing helix  chain 'D' and resid 293 through 300
    Processing helix  chain 'D' and resid 303 through 318
    Processing helix  chain 'D' and resid 324 through 331
    Processing helix  chain 'D' and resid 365 through 385
    Processing helix  chain 'D' and resid 386 through 388
      No H-bonds generated for 'chain 'D' and resid 386 through 388'
    Processing helix  chain 'D' and resid 389 through 393
    Processing helix  chain 'D' and resid 399 through 414
      removed outlier: 3.685A  pdb=" N   THR D 414 " --> pdb=" O   LEU D 410 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 414 through 421
    Processing helix  chain 'D' and resid 431 through 447
    Processing helix  chain 'D' and resid 449 through 465
    Processing helix  chain 'D' and resid 472 through 484
    Processing helix  chain 'D' and resid 498 through 502
    Processing helix  chain 'D' and resid 503 through 508
    Processing helix  chain 'D' and resid 513 through 533
    Processing helix  chain 'D' and resid 538 through 542
    Processing helix  chain 'D' and resid 547 through 559
      removed outlier: 4.107A  pdb=" N   MET D 557 " --> pdb=" O   LYS D 553 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 565 through 575
    Processing helix  chain 'D' and resid 581 through 599
      Proline residue:  D 590  - end of helix
      removed outlier: 3.617A  pdb=" N   ASP D 597 " --> pdb=" O   THR D 593 " (cutoff:3.500A)
    Processing helix  chain 'D' and resid 600 through 602
      No H-bonds generated for 'chain 'D' and resid 600 through 602'
    Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358
    Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362
      removed outlier: 6.709A  pdb=" N   CYS A 361 " --> pdb=" O   CYS A 525 " (cutoff:3.500A)
    Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454
    Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474
    Processing sheet with id=AA5, first strand: chain 'D' and resid 131 through 133
    Processing sheet with id=AA6, first strand: chain 'D' and resid 262 through 263
      removed outlier: 6.082A  pdb=" N   LEU D 262 " --> pdb=" O   VAL D 488 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA6
    Processing sheet with id=AA7, first strand: chain 'D' and resid 347 through 350

    322 hydrogen bonds defined for protein.
    909 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.18

  Time building geometry restraints manager: 0.75 seconds

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

  Histogram of bond lengths:
        1.19 -     1.32: 1305
        1.32 -     1.45: 2125
        1.45 -     1.58: 3229
        1.58 -     1.71: 10
        1.71 -     1.84: 58
  Bond restraints: 6727
  Sorted by residual:
  bond pdb=" CB  HIS D 265 "
       pdb=" CG  HIS D 265 "
    ideal  model  delta    sigma   weight residual
    1.497  1.425  0.072 1.40e-02 5.10e+03 2.68e+01
  bond pdb=" CB  HIS D 535 "
       pdb=" CG  HIS D 535 "
    ideal  model  delta    sigma   weight residual
    1.497  1.425  0.072 1.40e-02 5.10e+03 2.64e+01
  bond pdb=" CB  ASN A 422 "
       pdb=" CG  ASN A 422 "
    ideal  model  delta    sigma   weight residual
    1.516  1.391  0.125 2.50e-02 1.60e+03 2.50e+01
  bond pdb=" CZ  ARG D 460 "
       pdb=" NH2 ARG D 460 "
    ideal  model  delta    sigma   weight residual
    1.330  1.274  0.056 1.30e-02 5.92e+03 1.83e+01
  bond pdb=" CZ  ARG D 161 "
       pdb=" NH2 ARG D 161 "
    ideal  model  delta    sigma   weight residual
    1.330  1.278  0.052 1.30e-02 5.92e+03 1.60e+01
  ... (remaining 6722 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.33: 7882
        2.33 -     4.67: 1070
        4.67 -     7.00: 171
        7.00 -     9.33: 15
        9.33 -    11.67: 5
  Bond angle restraints: 9143
  Sorted by residual:
  angle pdb=" N   SER D 170 "
        pdb=" CA  SER D 170 "
        pdb=" C   SER D 170 "
      ideal   model   delta    sigma   weight residual
     110.35   98.98   11.37 1.38e+00 5.25e-01 6.79e+01
  angle pdb=" C   GLU D 489 "
        pdb=" N   PRO D 490 "
        pdb=" CA  PRO D 490 "
      ideal   model   delta    sigma   weight residual
     119.87  128.34   -8.47 1.04e+00 9.25e-01 6.63e+01
  angle pdb=" C   GLY A 526 "
        pdb=" N   PRO A 527 "
        pdb=" CA  PRO A 527 "
      ideal   model   delta    sigma   weight residual
     119.85  127.88   -8.03 1.01e+00 9.80e-01 6.33e+01
  angle pdb=" CB  ASN D  90 "
        pdb=" CG  ASN D  90 "
        pdb=" ND2 ASN D  90 "
      ideal   model   delta    sigma   weight residual
     116.40  128.07  -11.67 1.50e+00 4.44e-01 6.05e+01
  angle pdb=" N   TYR A 380 "
        pdb=" CA  TYR A 380 "
        pdb=" C   TYR A 380 "
      ideal   model   delta    sigma   weight residual
     114.31  104.49    9.82 1.29e+00 6.01e-01 5.80e+01
  ... (remaining 9138 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.29: 3878
       17.29 -    34.58: 140
       34.58 -    51.88: 25
       51.88 -    69.17: 15
       69.17 -    86.46: 5
  Dihedral angle restraints: 4063
    sinusoidal: 1728
      harmonic: 2335
  Sorted by residual:
  dihedral pdb=" C   TYR A 421 "
           pdb=" N   TYR A 421 "
           pdb=" CA  TYR A 421 "
           pdb=" CB  TYR A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -134.06   11.46     0      2.50e+00 1.60e-01 2.10e+01
  dihedral pdb=" N   TYR A 421 "
           pdb=" C   TYR A 421 "
           pdb=" CA  TYR A 421 "
           pdb=" CB  TYR A 421 "
      ideal   model   delta  harmonic     sigma   weight residual
     122.80  133.46  -10.66     0      2.50e+00 1.60e-01 1.82e+01
  dihedral pdb=" CA  PRO D 389 "
           pdb=" C   PRO D 389 "
           pdb=" N   PHE D 390 "
           pdb=" CA  PHE D 390 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -161.18  -18.82     0      5.00e+00 4.00e-02 1.42e+01
  ... (remaining 4060 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.114: 739
       0.114 -    0.229: 209
       0.229 -    0.343: 21
       0.343 -    0.457: 7
       0.457 -    0.572: 1
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  TYR A 421 "
            pdb=" N   TYR A 421 "
            pdb=" C   TYR A 421 "
            pdb=" CB  TYR A 421 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.94    0.57 2.00e-01 2.50e+01 8.17e+00
  chirality pdb=" C1  NAG D1102 "
            pdb=" ND2 ASN D 103 "
            pdb=" C2  NAG D1102 "
            pdb=" O5  NAG D1102 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.84    0.44 2.00e-01 2.50e+01 4.84e+00
  chirality pdb=" C1  NAG D1104 "
            pdb=" ND2 ASN D 546 "
            pdb=" C2  NAG D1104 "
            pdb=" O5  NAG D1104 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.79    0.39 2.00e-01 2.50e+01 3.83e+00
  ... (remaining 974 not shown)

  Planarity restraints: 1184
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D  53 "    0.015 2.00e-02 2.50e+03   7.67e-02 7.35e+01
        pdb=" CG  ASN D  53 "    0.023 2.00e-02 2.50e+03
        pdb=" OD1 ASN D  53 "   -0.076 2.00e-02 2.50e+03
        pdb=" ND2 ASN D  53 "    0.125 2.00e-02 2.50e+03
        pdb=" C1  NAG D1106 "   -0.086 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 103 "   -0.013 2.00e-02 2.50e+03   4.66e-02 2.71e+01
        pdb=" CG  ASN D 103 "   -0.011 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 103 "    0.046 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 103 "   -0.075 2.00e-02 2.50e+03
        pdb=" C1  NAG D1102 "    0.053 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  ASN D 432 "   -0.008 2.00e-02 2.50e+03   4.30e-02 2.31e+01
        pdb=" CG  ASN D 432 "   -0.014 2.00e-02 2.50e+03
        pdb=" OD1 ASN D 432 "    0.043 2.00e-02 2.50e+03
        pdb=" ND2 ASN D 432 "   -0.069 2.00e-02 2.50e+03
        pdb=" C1  NAG D1103 "    0.048 2.00e-02 2.50e+03
  ... (remaining 1181 not shown)

  Histogram of nonbonded interaction distances:
        2.22 -     2.76: 1264
        2.76 -     3.29: 6404
        3.29 -     3.83: 11299
        3.83 -     4.36: 14413
        4.36 -     4.90: 22737
  Nonbonded interactions: 56117
  Sorted by model distance:
  nonbonded pdb=" O4  NAG D1102 "
            pdb=" O6  NAG D1102 "
     model   vdw
     2.222 3.040
  nonbonded pdb=" O4  NAG D1101 "
            pdb=" O6  NAG D1101 "
     model   vdw
     2.241 3.040
  nonbonded pdb=" N   SER D 170 "
            pdb=" O   SER D 170 "
     model   vdw
     2.348 2.496
  nonbonded pdb=" O4  NAG D1104 "
            pdb=" O6  NAG D1104 "
     model   vdw
     2.372 3.040
  nonbonded pdb=" N   TYR A 380 "
            pdb=" N   GLY A 381 "
     model   vdw
     2.385 2.560
  ... (remaining 56112 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as group one per residue
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.010
  Normalize map: mean=0, sd=1:             11.220
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.000
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.080
  Check model and map are aligned:         0.030
  Set scattering table:                    0.020
  Process input model:                     8.180
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.680
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   21.260
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7886
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      :  0.018   0.135   6741  Z= 0.965
  Angle     :  1.707  12.716   9178  Z= 1.149
  Chirality :  0.104   0.572    977
  Planarity :  0.009   0.067   1177
  Dihedral  : 10.740  86.458   2544
  Min Nonbonded Distance : 2.222

Molprobity Statistics.
  All-atom Clashscore : 1.33
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.89 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  0.14 %
    Allowed  :  1.00 %
    Favored  : 98.86 %
  Cbeta Deviations :  0.13 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole: -0.17 (0.28), residues: 792
  helix: -0.42 (0.23), residues: 391
  sheet:  0.78 (0.73), residues: 61
  loop :  0.38 (0.34), residues: 340

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.010   0.001   ARG D 161 
 TYR   0.059   0.008   TYR D 199 
 PHE   0.028   0.006   PHE D 390 
 TRP   0.047   0.009   TRP D 349 
 HIS   0.014   0.003   HIS D 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.01778 ( 6727)
  covalent geometry    : angle       1.67848 ( 9143)
  SS BOND              : bond        0.01568 (    7)
  SS BOND              : angle       2.49216 (   14)
  hydrogen bonds       : bond        0.17310 (  322)
  hydrogen bonds       : angle       7.10652 (  909)
  link_NAG-ASN         : bond        0.10760 (    7)
  link_NAG-ASN         : angle       6.52173 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  207 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 206
  time to evaluate  : 0.223 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  334 ASN cc_start: 0.7073 (t0) cc_final: 0.6510 (m110)
REVERT: A  418 ILE cc_start: 0.9251 (mm) cc_final: 0.8602 (mm)
REVERT: D  119 ILE cc_start: 0.8518 (mt) cc_final: 0.8258 (mt)
REVERT: D  155 SER cc_start: 0.8440 (t) cc_final: 0.8028 (p)
REVERT: D  291 ILE cc_start: 0.8495 (pt) cc_final: 0.7995 (mp)
REVERT: D  362 THR cc_start: 0.7357 (m) cc_final: 0.6891 (m)
REVERT: D  441 LYS cc_start: 0.8693 (tttt) cc_final: 0.8471 (tptp)
REVERT: D  474 MET cc_start: 0.8360 (mmp) cc_final: 0.8030 (mmm)
REVERT: D  480 MET cc_start: 0.8661 (mtp) cc_final: 0.8432 (mtt)
  outliers start: 1
  outliers final: 1
  residues processed: 207
  average time/residue: 0.0946
  time to fit residues: 24.9963
Evaluate side-chains
  117 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 116
  time to evaluate  : 0.217 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 ASN
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 49 optimal weight:    0.8980
   chunk 53 optimal weight:    0.5980
   chunk 5 optimal weight:    0.8980
   chunk 33 optimal weight:    0.7980
   chunk 65 optimal weight:    0.9990
   chunk 62 optimal weight:    0.6980
   chunk 51 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 61 optimal weight:    0.8980
   chunk 45 optimal weight:    0.8980
   chunk 74 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:
A 414 GLN
A 493 GLN
A 498 GLN
A 506 GLN
D 154 ASN
** D 373 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 5

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.094342 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3342 r_free = 0.3342 target = 0.083333 restraints weight = 18527.978|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3389 r_free = 0.3389 target = 0.085922 restraints weight = 8396.839|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.087621 restraints weight = 4833.764|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3439 r_free = 0.3439 target = 0.088706 restraints weight = 3242.471|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 39)----------------|
| r_work = 0.3453 r_free = 0.3453 target = 0.089471 restraints weight = 2423.595|
|-----------------------------------------------------------------------------|
r_work (final): 0.3452
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7837
moved from start:          0.3484

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.039   6741  Z= 0.183
  Angle     :  0.857  20.972   9178  Z= 0.400
  Chirality :  0.057   0.771    977
  Planarity :  0.005   0.054   1177
  Dihedral  :  7.901  79.466   1013
  Min Nonbonded Distance : 2.477

Molprobity Statistics.
  All-atom Clashscore : 7.36
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.77 %
    Favored  : 98.11 %
  Rotamer:
    Outliers :  2.15 %
    Allowed  :  8.87 %
    Favored  : 88.98 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.94 (0.30), residues: 792
  helix:  1.09 (0.26), residues: 390
  sheet:  0.09 (0.72), residues: 61
  loop :  0.36 (0.34), residues: 341

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 219 
 TYR   0.016   0.002   TYR D 385 
 PHE   0.017   0.002   PHE D 369 
 TRP   0.021   0.002   TRP D 478 
 HIS   0.004   0.001   HIS D 535 

Details of bonding type rmsd
  covalent geometry    : bond        0.00380 ( 6727)
  covalent geometry    : angle       0.72022 ( 9143)
  SS BOND              : bond        0.00694 (    7)
  SS BOND              : angle       1.06329 (   14)
  hydrogen bonds       : bond        0.05748 (  322)
  hydrogen bonds       : angle       5.35702 (  909)
  link_NAG-ASN         : bond        0.01357 (    7)
  link_NAG-ASN         : angle       9.70110 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  160 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 145
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  414 GLN cc_start: 0.8782 (mm110) cc_final: 0.8581 (mt0)
REVERT: A  462 LYS cc_start: 0.7848 (mppt) cc_final: 0.7479 (mppt)
REVERT: A  500 THR cc_start: 0.8321 (p) cc_final: 0.8119 (t)
REVERT: D   74 LYS cc_start: 0.9236 (mtmm) cc_final: 0.8910 (mtmm)
REVERT: D  206 ASP cc_start: 0.8680 (t0) cc_final: 0.8306 (t0)
REVERT: D  441 LYS cc_start: 0.8817 (tttt) cc_final: 0.8375 (tptp)
REVERT: D  479 GLU cc_start: 0.8509 (tm-30) cc_final: 0.8272 (tm-30)
REVERT: D  483 GLU cc_start: 0.8443 (tp30) cc_final: 0.8029 (tp30)
  outliers start: 15
  outliers final: 9
  residues processed: 154
  average time/residue: 0.0785
  time to fit residues: 15.9303
Evaluate side-chains
  118 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 109
  time to evaluate  : 0.209 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  379 ILE
Chi-restraints excluded: chain D residue  401 HIS
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  503 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 38 optimal weight:    0.9980
   chunk 77 optimal weight:    1.9990
   chunk 68 optimal weight:    0.9980
   chunk 74 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 29 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 73 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0970
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.7578

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 373 HIS
D 401 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3503 r_free = 0.3503 target = 0.092537 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 22)----------------|
| r_work = 0.3310 r_free = 0.3310 target = 0.081886 restraints weight = 18379.004|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 40)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.084255 restraints weight = 8685.155|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 41)----------------|
| r_work = 0.3381 r_free = 0.3381 target = 0.085804 restraints weight = 5112.493|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 35)----------------|
| r_work = 0.3399 r_free = 0.3399 target = 0.086789 restraints weight = 3487.040|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 25)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.087445 restraints weight = 2647.296|
|-----------------------------------------------------------------------------|
r_work (final): 0.3408
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7927
moved from start:          0.4263

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.047   6741  Z= 0.177
  Angle     :  0.781  21.097   9178  Z= 0.369
  Chirality :  0.053   0.590    977
  Planarity :  0.004   0.050   1177
  Dihedral  :  7.552  77.153   1013
  Min Nonbonded Distance : 2.524

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.25 %
    Allowed  :  2.02 %
    Favored  : 97.73 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 11.02 %
    Favored  : 86.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.04 (0.30), residues: 792
  helix:  1.30 (0.26), residues: 393
  sheet: -0.11 (0.70), residues: 60
  loop :  0.27 (0.35), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.001   ARG D 482 
 TYR   0.019   0.002   TYR A 380 
 PHE   0.021   0.002   PHE D  31 
 TRP   0.026   0.002   TRP D 478 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00373 ( 6727)
  covalent geometry    : angle       0.66794 ( 9143)
  SS BOND              : bond        0.00586 (    7)
  SS BOND              : angle       1.70169 (   14)
  hydrogen bonds       : bond        0.05289 (  322)
  hydrogen bonds       : angle       5.04959 (  909)
  link_NAG-ASN         : bond        0.01140 (    7)
  link_NAG-ASN         : angle       8.38841 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 117
  time to evaluate  : 0.183 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7341 (t0) cc_final: 0.7126 (t0)
REVERT: A  417 LYS cc_start: 0.9178 (tppt) cc_final: 0.8902 (tppt)
REVERT: A  421 TYR cc_start: 0.7471 (OUTLIER) cc_final: 0.6190 (p90)
REVERT: A  462 LYS cc_start: 0.7820 (mppt) cc_final: 0.7519 (mppt)
REVERT: D  206 ASP cc_start: 0.8619 (t0) cc_final: 0.7930 (t0)
REVERT: D  360 MET cc_start: 0.7999 (tmm) cc_final: 0.7609 (ttt)
REVERT: D  406 GLU cc_start: 0.8385 (tp30) cc_final: 0.7743 (tp30)
REVERT: D  435 GLU cc_start: 0.7613 (mt-10) cc_final: 0.7400 (mt-10)
REVERT: D  441 LYS cc_start: 0.8879 (tttt) cc_final: 0.8420 (tptp)
REVERT: D  470 LYS cc_start: 0.7764 (mmmm) cc_final: 0.7156 (mmmm)
REVERT: D  479 GLU cc_start: 0.8521 (tm-30) cc_final: 0.8216 (tm-30)
REVERT: D  483 GLU cc_start: 0.8432 (tp30) cc_final: 0.8136 (tp30)
REVERT: D  601 ASN cc_start: 0.8106 (t0) cc_final: 0.7871 (t0)
  outliers start: 20
  outliers final: 14
  residues processed: 129
  average time/residue: 0.0638
  time to fit residues: 11.2245
Evaluate side-chains
  112 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 97
  time to evaluate  : 0.281 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  132 VAL
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  154 ASN
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 6 optimal weight:    3.9990
   chunk 31 optimal weight:    0.0870
   chunk 52 optimal weight:    0.0170
   chunk 4 optimal weight:    0.0060
   chunk 25 optimal weight:    0.7980
   chunk 48 optimal weight:    0.7980
   chunk 9 optimal weight:    3.9990
   chunk 64 optimal weight:    0.0070
   chunk 27 optimal weight:    0.9990
   chunk 36 optimal weight:    1.9990
   overall best weight:    0.1830

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 154 ASN
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3567 r_free = 0.3567 target = 0.096310 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.085426 restraints weight = 18448.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3416 r_free = 0.3416 target = 0.087866 restraints weight = 8695.900|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 32)----------------|
| r_work = 0.3444 r_free = 0.3444 target = 0.089449 restraints weight = 5116.438|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3462 r_free = 0.3462 target = 0.090479 restraints weight = 3494.784|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3475 r_free = 0.3475 target = 0.091206 restraints weight = 2649.735|
|-----------------------------------------------------------------------------|
r_work (final): 0.3473
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7849
moved from start:          0.4801

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.039   6741  Z= 0.119
  Angle     :  0.697  20.919   9178  Z= 0.321
  Chirality :  0.048   0.451    977
  Planarity :  0.004   0.050   1177
  Dihedral  :  6.210  51.505   1013
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 6.81
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  1.89 %
    Favored  : 97.98 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 12.59 %
    Favored  : 84.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.30), residues: 792
  helix:  1.47 (0.26), residues: 401
  sheet:  0.32 (0.77), residues: 52
  loop :  0.18 (0.34), residues: 339

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 115 
 TYR   0.018   0.001   TYR A 380 
 PHE   0.023   0.001   PHE D  31 
 TRP   0.036   0.001   TRP D 478 
 HIS   0.003   0.001   HIS D 401 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6727)
  covalent geometry    : angle       0.58435 ( 9143)
  SS BOND              : bond        0.00476 (    7)
  SS BOND              : angle       1.39466 (   14)
  hydrogen bonds       : bond        0.04227 (  322)
  hydrogen bonds       : angle       4.69983 (  909)
  link_NAG-ASN         : bond        0.01264 (    7)
  link_NAG-ASN         : angle       7.88285 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  142 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 124
  time to evaluate  : 0.219 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7084 (t0) cc_final: 0.6879 (t0)
REVERT: D  270 MET cc_start: 0.7660 (tpp) cc_final: 0.7324 (tpp)
REVERT: D  360 MET cc_start: 0.7695 (OUTLIER) cc_final: 0.7281 (ttt)
REVERT: D  441 LYS cc_start: 0.8780 (tttt) cc_final: 0.8370 (tptp)
REVERT: D  470 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7750 (mmmm)
REVERT: D  479 GLU cc_start: 0.8524 (tm-30) cc_final: 0.8136 (tm-30)
REVERT: D  483 GLU cc_start: 0.8384 (tp30) cc_final: 0.8098 (tp30)
REVERT: D  488 VAL cc_start: 0.7943 (OUTLIER) cc_final: 0.7536 (m)
  outliers start: 18
  outliers final: 13
  residues processed: 137
  average time/residue: 0.0668
  time to fit residues: 12.2872
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 104
  time to evaluate  : 0.244 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  415 THR
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  125 THR
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  291 ILE
Chi-restraints excluded: chain D residue  360 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 39 optimal weight:    2.9990
   chunk 31 optimal weight:    2.9990
   chunk 8 optimal weight:    0.6980
   chunk 60 optimal weight:    2.9990
   chunk 63 optimal weight:    0.6980
   chunk 1 optimal weight:    0.7980
   chunk 37 optimal weight:    1.9990
   chunk 20 optimal weight:    0.7980
   chunk 2 optimal weight:    0.6980
   chunk 68 optimal weight:    0.6980
   chunk 13 optimal weight:    2.9990
   overall best weight:    0.7180

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
D 210 ASN
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
D 417 HIS

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3505 r_free = 0.3505 target = 0.092747 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3305 r_free = 0.3305 target = 0.081800 restraints weight = 18828.043|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.084210 restraints weight = 8854.288|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3377 r_free = 0.3377 target = 0.085769 restraints weight = 5208.414|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3394 r_free = 0.3394 target = 0.086715 restraints weight = 3568.067|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3408 r_free = 0.3408 target = 0.087450 restraints weight = 2755.671|
|-----------------------------------------------------------------------------|
r_work (final): 0.3405
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.5102

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.056   6741  Z= 0.161
  Angle     :  0.724  21.047   9178  Z= 0.340
  Chirality :  0.051   0.441    977
  Planarity :  0.004   0.048   1177
  Dihedral  :  5.816  52.392   1013
  Min Nonbonded Distance : 2.529

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.78 %
    Favored  : 97.10 %
  Rotamer:
    Outliers :  2.86 %
    Allowed  : 14.02 %
    Favored  : 83.12 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.30), residues: 792
  helix:  1.62 (0.26), residues: 396
  sheet: -0.25 (0.69), residues: 60
  loop :  0.25 (0.35), residues: 336

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 454 
 TYR   0.023   0.001   TYR D 497 
 PHE   0.032   0.002   PHE D 327 
 TRP   0.037   0.002   TRP D 478 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00359 ( 6727)
  covalent geometry    : angle       0.61245 ( 9143)
  SS BOND              : bond        0.00502 (    7)
  SS BOND              : angle       1.30888 (   14)
  hydrogen bonds       : bond        0.04659 (  322)
  hydrogen bonds       : angle       4.68864 (  909)
  link_NAG-ASN         : bond        0.01138 (    7)
  link_NAG-ASN         : angle       8.02164 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  126 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 106
  time to evaluate  : 0.284 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  394 ASN cc_start: 0.7151 (t0) cc_final: 0.6944 (t0)
REVERT: A  462 LYS cc_start: 0.7946 (mppt) cc_final: 0.7615 (mppt)
REVERT: D  115 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.8143 (tpm170)
REVERT: D  190 MET cc_start: 0.8489 (tmm) cc_final: 0.8275 (tmm)
REVERT: D  323 MET cc_start: 0.9196 (mmm) cc_final: 0.8674 (mmm)
REVERT: D  360 MET cc_start: 0.7737 (OUTLIER) cc_final: 0.7029 (tmm)
REVERT: D  375 GLU cc_start: 0.8647 (mm-30) cc_final: 0.8087 (mm-30)
REVERT: D  406 GLU cc_start: 0.8328 (tp30) cc_final: 0.7695 (tp30)
REVERT: D  441 LYS cc_start: 0.8812 (tttt) cc_final: 0.8434 (tptp)
REVERT: D  479 GLU cc_start: 0.8582 (tm-30) cc_final: 0.8339 (tm-30)
REVERT: D  483 GLU cc_start: 0.8481 (tp30) cc_final: 0.8261 (tp30)
REVERT: D  488 VAL cc_start: 0.8232 (OUTLIER) cc_final: 0.7976 (m)
  outliers start: 20
  outliers final: 13
  residues processed: 117
  average time/residue: 0.0917
  time to fit residues: 14.4672
Evaluate side-chains
  114 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 98
  time to evaluate  : 0.261 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  115 ARG
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  360 MET
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  478 TRP
Chi-restraints excluded: chain D residue  488 VAL
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 26 optimal weight:    1.9990
   chunk 62 optimal weight:    2.9990
   chunk 47 optimal weight:    0.6980
   chunk 17 optimal weight:    0.0470
   chunk 71 optimal weight:    0.9980
   chunk 61 optimal weight:    0.9990
   chunk 55 optimal weight:    4.9990
   chunk 33 optimal weight:    1.9990
   chunk 23 optimal weight:    0.5980
   chunk 6 optimal weight:    3.9990
   chunk 70 optimal weight:    0.7980
   overall best weight:    0.6278

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** 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 = 0.3504 r_free = 0.3504 target = 0.092665 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 34)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.081957 restraints weight = 18792.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3352 r_free = 0.3352 target = 0.084321 restraints weight = 8843.403|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 36)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.085856 restraints weight = 5204.842|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 23)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.086832 restraints weight = 3563.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3410 r_free = 0.3410 target = 0.087523 restraints weight = 2727.275|
|-----------------------------------------------------------------------------|
r_work (final): 0.3409
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7964
moved from start:          0.5389

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.057   6741  Z= 0.145
  Angle     :  0.691  21.081   9178  Z= 0.325
  Chirality :  0.050   0.416    977
  Planarity :  0.004   0.045   1177
  Dihedral  :  5.690  53.027   1013
  Min Nonbonded Distance : 2.556

Molprobity Statistics.
  All-atom Clashscore : 7.83
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.65 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 14.45 %
    Favored  : 82.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.32 (0.31), residues: 792
  helix:  1.67 (0.26), residues: 397
  sheet: -0.35 (0.69), residues: 60
  loop :  0.27 (0.36), residues: 335

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 245 
 TYR   0.017   0.001   TYR A 380 
 PHE   0.031   0.002   PHE D 327 
 TRP   0.036   0.001   TRP D 478 
 HIS   0.003   0.001   HIS A 519 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6727)
  covalent geometry    : angle       0.57947 ( 9143)
  SS BOND              : bond        0.00514 (    7)
  SS BOND              : angle       1.17149 (   14)
  hydrogen bonds       : bond        0.04421 (  322)
  hydrogen bonds       : angle       4.63730 (  909)
  link_NAG-ASN         : bond        0.01150 (    7)
  link_NAG-ASN         : angle       7.86379 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  130 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 107
  time to evaluate  : 0.261 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 TYR cc_start: 0.7600 (OUTLIER) cc_final: 0.6336 (p90)
REVERT: A  462 LYS cc_start: 0.7926 (mppt) cc_final: 0.7574 (mppt)
REVERT: D  152 MET cc_start: 0.6312 (mmm) cc_final: 0.6001 (mmm)
REVERT: D  190 MET cc_start: 0.8422 (tmm) cc_final: 0.8172 (tmm)
REVERT: D  323 MET cc_start: 0.9320 (mmm) cc_final: 0.8796 (mmm)
REVERT: D  375 GLU cc_start: 0.8644 (mm-30) cc_final: 0.7942 (mm-30)
REVERT: D  441 LYS cc_start: 0.8796 (tttt) cc_final: 0.8407 (tptp)
REVERT: D  479 GLU cc_start: 0.8616 (tm-30) cc_final: 0.8109 (tm-30)
REVERT: D  589 GLU cc_start: 0.7744 (tp30) cc_final: 0.7527 (tp30)
  outliers start: 23
  outliers final: 16
  residues processed: 120
  average time/residue: 0.0658
  time to fit residues: 10.8518
Evaluate side-chains
  119 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 102
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  405 ASP
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 29 optimal weight:    2.9990
   chunk 75 optimal weight:    1.9990
   chunk 68 optimal weight:    0.5980
   chunk 45 optimal weight:    2.9990
   chunk 49 optimal weight:    0.0020
   chunk 4 optimal weight:    3.9990
   chunk 24 optimal weight:    0.9980
   chunk 64 optimal weight:    0.3980
   chunk 26 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 66 optimal weight:    1.9990
   overall best weight:    0.5990

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** 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 = 0.3507 r_free = 0.3507 target = 0.092739 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 26)----------------|
| r_work = 0.3309 r_free = 0.3309 target = 0.082024 restraints weight = 18559.118|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3353 r_free = 0.3353 target = 0.084361 restraints weight = 8827.185|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3380 r_free = 0.3380 target = 0.085882 restraints weight = 5238.882|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 34)----------------|
| r_work = 0.3398 r_free = 0.3398 target = 0.086892 restraints weight = 3594.951|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.087568 restraints weight = 2737.171|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7966
moved from start:          0.5609

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.051   6741  Z= 0.146
  Angle     :  0.703  21.102   9178  Z= 0.334
  Chirality :  0.049   0.409    977
  Planarity :  0.004   0.045   1177
  Dihedral  :  5.632  52.631   1013
  Min Nonbonded Distance : 2.548

Molprobity Statistics.
  All-atom Clashscore : 8.45
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  3.28 %
    Favored  : 96.59 %
  Rotamer:
    Outliers :  3.00 %
    Allowed  : 15.59 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.30), residues: 792
  helix:  1.73 (0.26), residues: 397
  sheet:  0.33 (0.78), residues: 50
  loop :  0.13 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG D 482 
 TYR   0.023   0.001   TYR D 497 
 PHE   0.030   0.002   PHE D 327 
 TRP   0.022   0.001   TRP D 478 
 HIS   0.005   0.001   HIS D 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00321 ( 6727)
  covalent geometry    : angle       0.59506 ( 9143)
  SS BOND              : bond        0.00480 (    7)
  SS BOND              : angle       1.14435 (   14)
  hydrogen bonds       : bond        0.04390 (  322)
  hydrogen bonds       : angle       4.61375 (  909)
  link_NAG-ASN         : bond        0.01148 (    7)
  link_NAG-ASN         : angle       7.80875 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 107
  time to evaluate  : 0.160 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 TYR cc_start: 0.7585 (OUTLIER) cc_final: 0.6373 (p90)
REVERT: A  462 LYS cc_start: 0.7973 (mppt) cc_final: 0.7621 (mppt)
REVERT: D  152 MET cc_start: 0.6401 (mmm) cc_final: 0.6029 (mmm)
REVERT: D  190 MET cc_start: 0.8464 (tmm) cc_final: 0.8203 (tmm)
REVERT: D  249 MET cc_start: 0.6711 (mmm) cc_final: 0.6454 (mmm)
REVERT: D  323 MET cc_start: 0.9326 (mmm) cc_final: 0.8731 (mmm)
REVERT: D  375 GLU cc_start: 0.8661 (mm-30) cc_final: 0.7937 (mm-30)
REVERT: D  441 LYS cc_start: 0.8806 (tttt) cc_final: 0.8302 (tptp)
REVERT: D  479 GLU cc_start: 0.8528 (tm-30) cc_final: 0.8229 (tm-30)
REVERT: D  480 MET cc_start: 0.8684 (mtm) cc_final: 0.8413 (mtm)
REVERT: D  589 GLU cc_start: 0.7780 (tp30) cc_final: 0.7558 (tp30)
  outliers start: 21
  outliers final: 18
  residues processed: 117
  average time/residue: 0.0590
  time to fit residues: 9.6522
Evaluate side-chains
  120 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 101
  time to evaluate  : 0.168 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  356 LYS
Chi-restraints excluded: chain A residue  379 CYS
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain A residue  516 GLU
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 67 optimal weight:    0.9980
   chunk 54 optimal weight:    3.9990
   chunk 4 optimal weight:    1.9990
   chunk 43 optimal weight:    2.9990
   chunk 65 optimal weight:    0.9980
   chunk 66 optimal weight:    0.7980
   chunk 60 optimal weight:    0.2980
   chunk 39 optimal weight:    3.9990
   chunk 17 optimal weight:    1.9990
   chunk 47 optimal weight:    0.0980
   chunk 24 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:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 535 HIS ** 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 = 0.3506 r_free = 0.3506 target = 0.092753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3306 r_free = 0.3306 target = 0.081981 restraints weight = 18737.604|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3350 r_free = 0.3350 target = 0.084352 restraints weight = 8861.940|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3379 r_free = 0.3379 target = 0.085904 restraints weight = 5227.875|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3397 r_free = 0.3397 target = 0.086904 restraints weight = 3580.189|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 36)----------------|
| r_work = 0.3411 r_free = 0.3411 target = 0.087595 restraints weight = 2733.084|
|-----------------------------------------------------------------------------|
r_work (final): 0.3407
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7980
moved from start:          0.5774

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   6741  Z= 0.151
  Angle     :  0.750  21.100   9178  Z= 0.353
  Chirality :  0.049   0.409    977
  Planarity :  0.004   0.044   1177
  Dihedral  :  5.772  48.214   1013
  Min Nonbonded Distance : 2.310

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.53 %
    Favored  : 97.35 %
  Rotamer:
    Outliers :  3.15 %
    Allowed  : 15.59 %
    Favored  : 81.26 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.36 (0.30), residues: 792
  helix:  1.77 (0.26), residues: 397
  sheet:  0.30 (0.79), residues: 50
  loop :  0.06 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG D 482 
 TYR   0.024   0.001   TYR D 497 
 PHE   0.029   0.002   PHE D 327 
 TRP   0.025   0.001   TRP D 473 
 HIS   0.004   0.001   HIS D 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00332 ( 6727)
  covalent geometry    : angle       0.63002 ( 9143)
  SS BOND              : bond        0.00523 (    7)
  SS BOND              : angle       1.13221 (   14)
  hydrogen bonds       : bond        0.04387 (  322)
  hydrogen bonds       : angle       4.73822 (  909)
  link_NAG-ASN         : bond        0.01139 (    7)
  link_NAG-ASN         : angle       8.51452 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  128 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 106
  time to evaluate  : 0.273 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  462 LYS cc_start: 0.7972 (mppt) cc_final: 0.7583 (mppt)
REVERT: D  152 MET cc_start: 0.6319 (mmm) cc_final: 0.5931 (mmm)
REVERT: D  190 MET cc_start: 0.8510 (tmm) cc_final: 0.8221 (tmm)
REVERT: D  249 MET cc_start: 0.6788 (mmm) cc_final: 0.6527 (mmm)
REVERT: D  323 MET cc_start: 0.9329 (mmm) cc_final: 0.8748 (mmm)
REVERT: D  441 LYS cc_start: 0.8798 (tttt) cc_final: 0.8303 (tptp)
REVERT: D  479 GLU cc_start: 0.8474 (tm-30) cc_final: 0.8264 (tm-30)
REVERT: D  480 MET cc_start: 0.8609 (mtm) cc_final: 0.8405 (mtt)
REVERT: D  589 GLU cc_start: 0.7775 (tp30) cc_final: 0.7564 (tp30)
  outliers start: 22
  outliers final: 18
  residues processed: 118
  average time/residue: 0.0617
  time to fit residues: 10.0713
Evaluate side-chains
  122 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 104
  time to evaluate  : 0.192 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   73 LEU
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  120 LEU
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 20 optimal weight:    1.9990
   chunk 39 optimal weight:    2.9990
   chunk 26 optimal weight:    2.9990
   chunk 32 optimal weight:    0.0070
   chunk 71 optimal weight:    0.9980
   chunk 25 optimal weight:    0.6980
   chunk 73 optimal weight:    1.9990
   chunk 65 optimal weight:    0.6980
   chunk 44 optimal weight:    0.7980
   chunk 56 optimal weight:    0.3980
   chunk 3 optimal weight:    0.4980
   overall best weight:    0.4598

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** 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 = 0.3528 r_free = 0.3528 target = 0.093918 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3327 r_free = 0.3327 target = 0.082992 restraints weight = 18976.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3371 r_free = 0.3371 target = 0.085406 restraints weight = 8965.664|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3400 r_free = 0.3400 target = 0.086979 restraints weight = 5294.183|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3419 r_free = 0.3419 target = 0.087995 restraints weight = 3617.571|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 34)----------------|
| r_work = 0.3432 r_free = 0.3432 target = 0.088680 restraints weight = 2752.706|
|-----------------------------------------------------------------------------|
r_work (final): 0.3432
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7958
moved from start:          0.5961

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.050   6741  Z= 0.133
  Angle     :  0.682  21.033   9178  Z= 0.324
  Chirality :  0.046   0.391    977
  Planarity :  0.004   0.044   1177
  Dihedral  :  5.334  40.605   1013
  Min Nonbonded Distance : 2.507

Molprobity Statistics.
  All-atom Clashscore : 8.30
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.40 %
    Favored  : 97.47 %
  Rotamer:
    Outliers :  2.72 %
    Allowed  : 15.88 %
    Favored  : 81.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.31), residues: 792
  helix:  1.81 (0.26), residues: 397
  sheet:  0.29 (0.80), residues: 50
  loop :  0.02 (0.34), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 482 
 TYR   0.017   0.001   TYR D 385 
 PHE   0.027   0.002   PHE D 327 
 TRP   0.022   0.001   TRP D 473 
 HIS   0.006   0.001   HIS D 493 

Details of bonding type rmsd
  covalent geometry    : bond        0.00289 ( 6727)
  covalent geometry    : angle       0.58176 ( 9143)
  SS BOND              : bond        0.00592 (    7)
  SS BOND              : angle       1.10180 (   14)
  hydrogen bonds       : bond        0.04149 (  322)
  hydrogen bonds       : angle       4.66507 (  909)
  link_NAG-ASN         : bond        0.01110 (    7)
  link_NAG-ASN         : angle       7.41738 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 118
  time to evaluate  : 0.205 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: D  152 MET cc_start: 0.6323 (mmm) cc_final: 0.5915 (mmm)
REVERT: D  190 MET cc_start: 0.8539 (tmm) cc_final: 0.8284 (tmm)
REVERT: D  249 MET cc_start: 0.6901 (mmm) cc_final: 0.6648 (mmm)
REVERT: D  285 PHE cc_start: 0.6406 (m-80) cc_final: 0.6136 (m-80)
REVERT: D  375 GLU cc_start: 0.8648 (mm-30) cc_final: 0.7982 (mm-30)
REVERT: D  441 LYS cc_start: 0.8762 (tttt) cc_final: 0.8280 (tptp)
REVERT: D  493 HIS cc_start: 0.5734 (m-70) cc_final: 0.4853 (m-70)
  outliers start: 19
  outliers final: 17
  residues processed: 128
  average time/residue: 0.0593
  time to fit residues: 10.5161
Evaluate side-chains
  121 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 104
  time to evaluate  : 0.189 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  261 CYS
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  366 MET
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  447 VAL
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 40 optimal weight:    0.9980
   chunk 63 optimal weight:    0.5980
   chunk 28 optimal weight:    0.0570
   chunk 72 optimal weight:    0.6980
   chunk 5 optimal weight:    0.0980
   chunk 52 optimal weight:    2.9990
   chunk 23 optimal weight:    0.7980
   chunk 46 optimal weight:    0.1980
   chunk 8 optimal weight:    0.9990
   chunk 22 optimal weight:    0.6980
   chunk 61 optimal weight:    0.9980
   overall best weight:    0.3298

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

Flipped N/Q/H residues before XYZ refinement:
A 493 GLN
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** 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 = 0.3545 r_free = 0.3545 target = 0.094492 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3345 r_free = 0.3345 target = 0.083619 restraints weight = 18544.597|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3390 r_free = 0.3390 target = 0.086044 restraints weight = 8870.820|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 34)----------------|
| r_work = 0.3418 r_free = 0.3418 target = 0.087602 restraints weight = 5266.991|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 37)----------------|
| r_work = 0.3437 r_free = 0.3437 target = 0.088634 restraints weight = 3613.094|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 27)----------------|
| r_work = 0.3449 r_free = 0.3449 target = 0.089334 restraints weight = 2743.854|
|-----------------------------------------------------------------------------|
r_work (final): 0.3454
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7940
moved from start:          0.6115

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   6741  Z= 0.132
  Angle     :  0.719  20.996   9178  Z= 0.341
  Chirality :  0.046   0.380    977
  Planarity :  0.005   0.051   1177
  Dihedral  :  5.161  40.793   1013
  Min Nonbonded Distance : 2.534

Molprobity Statistics.
  All-atom Clashscore : 8.06
  Ramachandran Plot:
    Outliers :  0.13 %
    Allowed  :  2.65 %
    Favored  : 97.22 %
  Rotamer:
    Outliers :  2.58 %
    Allowed  : 17.02 %
    Favored  : 80.40 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.37 (0.31), residues: 792
  helix:  1.74 (0.26), residues: 397
  sheet:  0.34 (0.79), residues: 50
  loop :  0.10 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 482 
 TYR   0.016   0.001   TYR D 385 
 PHE   0.028   0.001   PHE D 327 
 TRP   0.027   0.001   TRP D 473 
 HIS   0.003   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00299 ( 6727)
  covalent geometry    : angle       0.62816 ( 9143)
  SS BOND              : bond        0.00496 (    7)
  SS BOND              : angle       1.22633 (   14)
  hydrogen bonds       : bond        0.04107 (  322)
  hydrogen bonds       : angle       4.70061 (  909)
  link_NAG-ASN         : bond        0.01109 (    7)
  link_NAG-ASN         : angle       7.28453 (   21)

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

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

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1584 Ramachandran restraints generated.
    792 Oldfield, 0 Emsley, 792 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  137 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 119
  time to evaluate  : 0.263 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  421 TYR cc_start: 0.7552 (OUTLIER) cc_final: 0.6269 (p90)
REVERT: D  152 MET cc_start: 0.6325 (mmm) cc_final: 0.5945 (mmm)
REVERT: D  249 MET cc_start: 0.6897 (mmm) cc_final: 0.6643 (mmm)
REVERT: D  285 PHE cc_start: 0.6431 (m-80) cc_final: 0.6098 (m-80)
REVERT: D  375 GLU cc_start: 0.8664 (mm-30) cc_final: 0.7972 (mm-30)
REVERT: D  406 GLU cc_start: 0.8180 (tp30) cc_final: 0.7619 (tp30)
REVERT: D  441 LYS cc_start: 0.8775 (tttt) cc_final: 0.8316 (tptp)
REVERT: D  474 MET cc_start: 0.8378 (mmp) cc_final: 0.8104 (mmm)
REVERT: D  497 TYR cc_start: 0.6281 (m-10) cc_final: 0.6046 (m-10)
  outliers start: 18
  outliers final: 15
  residues processed: 130
  average time/residue: 0.0639
  time to fit residues: 11.6101
Evaluate side-chains
  129 residues out of total 699 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 113
  time to evaluate  : 0.152 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  385 THR
Chi-restraints excluded: chain A residue  421 TYR
Chi-restraints excluded: chain A residue  430 THR
Chi-restraints excluded: chain A residue  468 ILE
Chi-restraints excluded: chain A residue  488 CYS
Chi-restraints excluded: chain D residue   79 LEU
Chi-restraints excluded: chain D residue   90 ASN
Chi-restraints excluded: chain D residue  111 ASP
Chi-restraints excluded: chain D residue  123 MET
Chi-restraints excluded: chain D residue  142 LEU
Chi-restraints excluded: chain D residue  172 VAL
Chi-restraints excluded: chain D residue  184 VAL
Chi-restraints excluded: chain D residue  364 VAL
Chi-restraints excluded: chain D residue  376 MET
Chi-restraints excluded: chain D residue  498 CYS
Chi-restraints excluded: chain D residue  522 GLN
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 79
   random chunks:
   chunk 61 optimal weight:    2.9990
   chunk 60 optimal weight:    0.9990
   chunk 38 optimal weight:    0.9990
   chunk 68 optimal weight:    0.8980
   chunk 41 optimal weight:    0.6980
   chunk 1 optimal weight:    0.4980
   chunk 77 optimal weight:    0.7980
   chunk 19 optimal weight:    0.3980
   chunk 45 optimal weight:    0.5980
   chunk 0 optimal weight:    0.4980
   chunk 3 optimal weight:    1.9990
   overall best weight:    0.5380

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

Flipped N/Q/H residues before XYZ refinement:
** D  58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  60 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D  61 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
** D 265 HIS ** 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 = 0.3530 r_free = 0.3530 target = 0.093899 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.3328 r_free = 0.3328 target = 0.083079 restraints weight = 18697.261|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 32)----------------|
| r_work = 0.3373 r_free = 0.3373 target = 0.085456 restraints weight = 8983.707|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3402 r_free = 0.3402 target = 0.087033 restraints weight = 5345.673|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 33)----------------|
| r_work = 0.3420 r_free = 0.3420 target = 0.088027 restraints weight = 3664.228|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 32)----------------|
| r_work = 0.3434 r_free = 0.3434 target = 0.088747 restraints weight = 2806.500|
|-----------------------------------------------------------------------------|
r_work (final): 0.3434
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7965
moved from start:          0.6206

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.043   6741  Z= 0.144
  Angle     :  0.719  20.989   9178  Z= 0.343
  Chirality :  0.047   0.385    977
  Planarity :  0.005   0.047   1177
  Dihedral  :  5.139  40.800   1013
  Min Nonbonded Distance : 2.511

Molprobity Statistics.
  All-atom Clashscore : 9.08
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.54 %
    Favored  : 96.46 %
  Rotamer:
    Outliers :  2.29 %
    Allowed  : 18.03 %
    Favored  : 79.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.13 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.41 (0.31), residues: 792
  helix:  1.80 (0.26), residues: 397
  sheet:  0.25 (0.78), residues: 50
  loop :  0.10 (0.35), residues: 345

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG D 482 
 TYR   0.016   0.002   TYR D 385 
 PHE   0.031   0.002   PHE D 327 
 TRP   0.027   0.001   TRP D 473 
 HIS   0.002   0.001   HIS D 374 

Details of bonding type rmsd
  covalent geometry    : bond        0.00326 ( 6727)
  covalent geometry    : angle       0.62938 ( 9143)
  SS BOND              : bond        0.00509 (    7)
  SS BOND              : angle       1.16991 (   14)
  hydrogen bonds       : bond        0.04184 (  322)
  hydrogen bonds       : angle       4.74558 (  909)
  link_NAG-ASN         : bond        0.01070 (    7)
  link_NAG-ASN         : angle       7.23458 (   21)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1271.17 seconds
wall clock time: 22 minutes 34.83 seconds (1354.83 seconds total)