Starting phenix.real_space_refine
on Sat May 10 00:25:12 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wtv_37843/05_2025/8wtv_37843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wtv_37843/05_2025/8wtv_37843.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=2.7
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wtv_37843/05_2025/8wtv_37843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wtv_37843/05_2025/8wtv_37843.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wtv_37843/05_2025/8wtv_37843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wtv_37843/05_2025/8wtv_37843.cif"
  }
  resolution = 2.7
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.067
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: 6
    Type Number    sf(0)   Gaussians
     S      20      5.16       5
     Cl      1      4.86       5
     Na      2      4.78       5
     C    2897      2.51       5
     N     667      2.21       5
     O     738      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib"
  Total number of atoms: 4325
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4281
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 536, 4281
          Classifications: {'peptide': 536}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 19, 'TRANS': 516}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 44
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 9, 44
          Unusual residues: {' CL': 1, ' NA': 2, 'E5E': 2, 'NAG': 1}
          Classifications: {'undetermined': 6, 'water': 3}
          Link IDs: {None: 8}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.58, per 1000 atoms: 0.83
  Number of scatterers: 4325
  At special positions: 0
  Unit cell: (77.35, 67.15, 90.95, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 6
    Type Number    sf(0)
     Cl      1     17.00
     S      20     16.00
     Na      2     11.00
     O     738      8.00
     N     667      7.00
     C    2897      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 176 " - pdb=" SG  CYS A 185 " 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 A 706 " - " ASN A 184 "
  Time building additional restraints: 1.11
  Conformation dependent library (CDL) restraints added in 474.2 milliseconds
  

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  986

  Finding SS restraints...
    Secondary structure from input PDB file:
      32 helices and 1 sheets defined
      79.1% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.46
  Creating SS restraints...
    Processing helix  chain 'A' and resid 76 through 89
      removed outlier: 4.670A  pdb=" N   PHE A  82 " --> pdb=" O   ASN A  78 " (cutoff:3.500A)
      Proline residue:  A  83  - end of helix
    Processing helix  chain 'A' and resid 91 through 93
      No H-bonds generated for 'chain 'A' and resid 91 through 93'
    Processing helix  chain 'A' and resid 94 through 105
      removed outlier: 3.504A  pdb=" N   TYR A  98 " --> pdb=" O   PHE A  94 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 105 through 121
      removed outlier: 3.551A  pdb=" N   LEU A 109 " --> pdb=" O   ALA A 105 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 125 through 134
      removed outlier: 3.662A  pdb=" N   TRP A 128 " --> pdb=" O   ALA A 125 " (cutoff:3.500A)
      removed outlier: 3.588A  pdb=" N   LYS A 129 " --> pdb=" O   THR A 126 " (cutoff:3.500A)
      removed outlier: 3.886A  pdb=" N   ILE A 130 " --> pdb=" O   VAL A 127 " (cutoff:3.500A)
      Proline residue:  A 132  - end of helix
    Processing helix  chain 'A' and resid 135 through 166
      removed outlier: 3.788A  pdb=" N   TYR A 139 " --> pdb=" O   LYS A 135 " (cutoff:3.500A)
      removed outlier: 3.974A  pdb=" N   TYR A 151 " --> pdb=" O   TYR A 147 " (cutoff:3.500A)
      removed outlier: 4.184A  pdb=" N   ASN A 153 " --> pdb=" O   GLY A 149 " (cutoff:3.500A)
      removed outlier: 5.768A  pdb=" N   VAL A 154 " --> pdb=" O   PHE A 150 " (cutoff:3.500A)
      removed outlier: 4.324A  pdb=" N   ILE A 155 " --> pdb=" O   TYR A 151 " (cutoff:3.500A)
      removed outlier: 3.904A  pdb=" N   ILE A 156 " --> pdb=" O   TYR A 152 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 208 through 217
    Processing helix  chain 'A' and resid 220 through 224
    Processing helix  chain 'A' and resid 234 through 251
    Processing helix  chain 'A' and resid 261 through 267
      removed outlier: 3.639A  pdb=" N   ILE A 265 " --> pdb=" O   LYS A 261 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 268 through 283
      removed outlier: 3.620A  pdb=" N   PHE A 272 " --> pdb=" O   THR A 268 " (cutoff:3.500A)
      removed outlier: 4.219A  pdb=" N   THR A 283 " --> pdb=" O   VAL A 279 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 286 through 295
      removed outlier: 3.761A  pdb=" N   GLY A 290 " --> pdb=" O   GLY A 286 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 304 through 320
      removed outlier: 4.362A  pdb=" N   TRP A 308 " --> pdb=" O   GLU A 304 " (cutoff:3.500A)
      removed outlier: 3.558A  pdb=" N   PHE A 316 " --> pdb=" O   ALA A 312 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 324 through 331
    Processing helix  chain 'A' and resid 338 through 373
      removed outlier: 3.732A  pdb=" N   ASP A 342 " --> pdb=" O   ASN A 338 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 386 through 396
      Proline residue:  A 392  - end of helix
    Processing helix  chain 'A' and resid 400 through 435
      removed outlier: 3.525A  pdb=" N   TRP A 404 " --> pdb=" O   GLY A 400 " (cutoff:3.500A)
      removed outlier: 3.827A  pdb=" N   ASP A 434 " --> pdb=" O   GLY A 430 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 436 through 440
    Processing helix  chain 'A' and resid 441 through 458
    Processing helix  chain 'A' and resid 459 through 462
      removed outlier: 3.868A  pdb=" N   THR A 462 " --> pdb=" O   PHE A 459 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 459 through 462'
    Processing helix  chain 'A' and resid 464 through 476
      removed outlier: 3.876A  pdb=" N   VAL A 468 " --> pdb=" O   GLY A 464 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 478 through 495
    Processing helix  chain 'A' and resid 497 through 510
      removed outlier: 3.557A  pdb=" N   MET A 508 " --> pdb=" O   ASP A 504 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 514 through 523
    Processing helix  chain 'A' and resid 523 through 539
    Processing helix  chain 'A' and resid 551 through 567
      removed outlier: 3.688A  pdb=" N   ASN A 555 " --> pdb=" O   PRO A 551 " (cutoff:3.500A)
      removed outlier: 4.056A  pdb=" N   SER A 565 " --> pdb=" O   ILE A 561 " (cutoff:3.500A)
      removed outlier: 3.667A  pdb=" N   MET A 566 " --> pdb=" O   ALA A 562 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 567 through 579
    Processing helix  chain 'A' and resid 583 through 593
      removed outlier: 3.577A  pdb=" N   ILE A 592 " --> pdb=" O   LEU A 588 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 594 through 598
      removed outlier: 3.944A  pdb=" N   HIS A 598 " --> pdb=" O   GLU A 595 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 599 through 604
      removed outlier: 3.856A  pdb=" N   GLN A 603 " --> pdb=" O   HIS A 599 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 606 through 609
    Processing helix  chain 'A' and resid 610 through 616
      removed outlier: 4.076A  pdb=" N   TRP A 614 " --> pdb=" O   GLN A 610 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 544 through 545

    265 hydrogen bonds defined for protein.
    771 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: 1.12

  Time building geometry restraints manager: 1.29 seconds

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

  Histogram of bond lengths:
        1.18 -     1.31: 635
        1.31 -     1.43: 1405
        1.43 -     1.56: 2387
        1.56 -     1.68: 1
        1.68 -     1.81: 31
  Bond restraints: 4459
  Sorted by residual:
  bond pdb=" CA  MET A 107 "
       pdb=" C   MET A 107 "
    ideal  model  delta    sigma   weight residual
    1.520  1.572 -0.052 1.23e-02 6.61e+03 1.80e+01
  bond pdb=" C   LYS A 576 "
       pdb=" O   LYS A 576 "
    ideal  model  delta    sigma   weight residual
    1.236  1.184  0.052 1.26e-02 6.30e+03 1.70e+01
  bond pdb=" C   LYS A 576 "
       pdb=" N   PHE A 577 "
    ideal  model  delta    sigma   weight residual
    1.335  1.288  0.047 1.36e-02 5.41e+03 1.19e+01
  bond pdb=" C   MET A 107 "
       pdb=" N   PRO A 108 "
    ideal  model  delta    sigma   weight residual
    1.335  1.382 -0.047 1.36e-02 5.41e+03 1.17e+01
  bond pdb=" C   SER A 182 "
       pdb=" N   PRO A 183 "
    ideal  model  delta    sigma   weight residual
    1.337  1.370 -0.033 9.80e-03 1.04e+04 1.14e+01
  ... (remaining 4454 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.31: 5906
        1.31 -     2.61: 139
        2.61 -     3.92: 25
        3.92 -     5.23: 11
        5.23 -     6.53: 5
  Bond angle restraints: 6086
  Sorted by residual:
  angle pdb=" N   TRP A 253 "
        pdb=" CA  TRP A 253 "
        pdb=" C   TRP A 253 "
      ideal   model   delta    sigma   weight residual
     113.01  118.40   -5.39 1.20e+00 6.94e-01 2.02e+01
  angle pdb=" CA  SER A 182 "
        pdb=" C   SER A 182 "
        pdb=" N   PRO A 183 "
      ideal   model   delta    sigma   weight residual
     117.48  122.12   -4.64 1.15e+00 7.56e-01 1.63e+01
  angle pdb=" O   SER A 182 "
        pdb=" C   SER A 182 "
        pdb=" N   PRO A 183 "
      ideal   model   delta    sigma   weight residual
     121.53  117.15    4.38 1.12e+00 7.97e-01 1.53e+01
  angle pdb=" N   ASN A 184 "
        pdb=" CA  ASN A 184 "
        pdb=" C   ASN A 184 "
      ideal   model   delta    sigma   weight residual
     113.38  108.98    4.40 1.23e+00 6.61e-01 1.28e+01
  angle pdb=" O   TYR A 575 "
        pdb=" C   TYR A 575 "
        pdb=" N   LYS A 576 "
      ideal   model   delta    sigma   weight residual
     122.12  118.36    3.76 1.06e+00 8.90e-01 1.26e+01
  ... (remaining 6081 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.99: 2187
       17.99 -    35.97: 236
       35.97 -    53.96: 63
       53.96 -    71.95: 12
       71.95 -    89.94: 2
  Dihedral angle restraints: 2500
    sinusoidal: 951
      harmonic: 1549
  Sorted by residual:
  dihedral pdb=" CB  CYS A 176 "
           pdb=" SG  CYS A 176 "
           pdb=" SG  CYS A 185 "
           pdb=" CB  CYS A 185 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -175.94   89.94     1      1.00e+01 1.00e-02 9.59e+01
  dihedral pdb=" CG  ARG A 442 "
           pdb=" CD  ARG A 442 "
           pdb=" NE  ARG A 442 "
           pdb=" CZ  ARG A 442 "
      ideal   model   delta sinusoidal    sigma   weight residual
      90.00  132.55  -42.55     2      1.50e+01 4.44e-03 9.76e+00
  dihedral pdb=" CA  LYS A 576 "
           pdb=" CB  LYS A 576 "
           pdb=" CG  LYS A 576 "
           pdb=" CD  LYS A 576 "
      ideal   model   delta sinusoidal    sigma   weight residual
     180.00  120.06   59.94     3      1.50e+01 4.44e-03 9.48e+00
  ... (remaining 2497 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.045: 504
       0.045 -    0.090: 148
       0.090 -    0.134: 25
       0.134 -    0.179: 0
       0.179 -    0.224: 4
  Chirality restraints: 681
  Sorted by residual:
  chirality pdb=" C1  NAG A 706 "
            pdb=" ND2 ASN A 184 "
            pdb=" C2  NAG A 706 "
            pdb=" O5  NAG A 706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.18   -0.22 2.00e-01 2.50e+01 1.25e+00
  chirality pdb=" CA  TRP A 253 "
            pdb=" N   TRP A 253 "
            pdb=" C   TRP A 253 "
            pdb=" CB  TRP A 253 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.31    0.21 2.00e-01 2.50e+01 1.05e+00
  chirality pdb=" CAL E5E A 704 "
            pdb=" CAH E5E A 704 "
            pdb=" CAK E5E A 704 "
            pdb=" OAD E5E A 704 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.31   -2.51    0.20 2.00e-01 2.50e+01 1.00e+00
  ... (remaining 678 not shown)

  Planarity restraints: 739
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 706 "    0.248 2.00e-02 2.50e+03   2.09e-01 5.45e+02
        pdb=" C7  NAG A 706 "   -0.067 2.00e-02 2.50e+03
        pdb=" C8  NAG A 706 "    0.170 2.00e-02 2.50e+03
        pdb=" N2  NAG A 706 "   -0.351 2.00e-02 2.50e+03
        pdb=" O7  NAG A 706 "   -0.001 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 106 "   -0.009 2.00e-02 2.50e+03   1.69e-02 2.87e+00
        pdb=" C   GLY A 106 "    0.029 2.00e-02 2.50e+03
        pdb=" O   GLY A 106 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   MET A 107 "   -0.010 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   PHE A  82 "   -0.024 5.00e-02 4.00e+02   3.65e-02 2.13e+00
        pdb=" N   PRO A  83 "    0.063 5.00e-02 4.00e+02
        pdb=" CA  PRO A  83 "   -0.018 5.00e-02 4.00e+02
        pdb=" CD  PRO A  83 "   -0.021 5.00e-02 4.00e+02
  ... (remaining 736 not shown)

  Histogram of nonbonded interaction distances:
        2.30 -     2.82: 1259
        2.82 -     3.34: 3885
        3.34 -     3.86: 7037
        3.86 -     4.38: 8265
        4.38 -     4.90: 14400
  Nonbonded interactions: 34846
  Sorted by model distance:
  nonbonded pdb=" OD1 ASN A 350 "
            pdb="NA    NA A 701 "
     model   vdw
     2.297 2.470
  nonbonded pdb=" O   ALA A 394 "
            pdb=" OG1 THR A 397 "
     model   vdw
     2.299 3.040
  nonbonded pdb=" O   SER A 259 "
            pdb=" OG  SER A 259 "
     model   vdw
     2.319 3.040
  nonbonded pdb=" NH2 ARG A 341 "
            pdb=" OD1 ASP A 342 "
     model   vdw
     2.319 3.120
  nonbonded pdb=" O   ARG A 442 "
            pdb=" OG1 THR A 446 "
     model   vdw
     2.346 3.040
  ... (remaining 34841 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
========== 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 individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             1.570
  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:          0.180
  Check model and map are aligned:         0.030
  Set scattering table:                    0.050
  Process input model:                     14.930
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:11.630
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   28.440
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8612
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      :  0.004   0.052   4461  Z= 0.212
  Angle     :  0.548   6.532   6091  Z= 0.311
  Chirality :  0.043   0.224    681
  Planarity :  0.009   0.209    738
  Dihedral  : 15.806  81.789   1511
  Min Nonbonded Distance : 2.297

Molprobity Statistics.
  All-atom Clashscore : 1.86
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  Rotamer:
    Outliers :  0.22 %
    Allowed  : 16.41 %
    Favored  : 83.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.82 (0.38), residues: 532
  helix:  1.99 (0.29), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.41 (0.48), residues: 174

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 599 
 PHE   0.010   0.001   PHE A 409 
 TYR   0.016   0.001   TYR A  84 
 ARG   0.001   0.000   ARG A 216 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00941 (    1)
  link_NAG-ASN         : angle       1.45844 (    3)
  hydrogen bonds       : bond        0.12253 (  265)
  hydrogen bonds       : angle       4.30574 (  771)
  SS BOND              : bond        0.00760 (    1)
  SS BOND              : angle       2.68512 (    2)
  covalent geometry    : bond        0.00360 ( 4459)
  covalent geometry    : angle       0.54472 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 45
  time to evaluate  : 0.496 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 46
  average time/residue: 1.0770
  time to fit residues: 51.9822
Evaluate side-chains
  45 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 44
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  576 LYS
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 44 optimal weight:    3.9990
   chunk 40 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9990
   chunk 13 optimal weight:    5.9990
   chunk 27 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 41 optimal weight:    1.9990
   chunk 16 optimal weight:    1.9990
   chunk 25 optimal weight:    3.9990
   chunk 30 optimal weight:    0.6980
   chunk 48 optimal weight:    3.9990
   overall best weight:    1.5388

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.105606 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2865 r_free = 0.2865 target = 0.091903 restraints weight = 4697.722|
|-----------------------------------------------------------------------------|
r_work (start): 0.2857 rms_B_bonded: 0.95
r_work: 0.2765 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.2663 rms_B_bonded: 2.55 restraints_weight: 0.2500
r_work (final): 0.2663
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8801
moved from start:          0.0730

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.031   4461  Z= 0.174
  Angle     :  0.569   5.571   6091  Z= 0.308
  Chirality :  0.043   0.150    681
  Planarity :  0.005   0.037    738
  Dihedral  :  6.823  53.794    614
  Min Nonbonded Distance : 2.253

Molprobity Statistics.
  All-atom Clashscore : 1.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  2.66 %
    Allowed  : 14.41 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.64 (0.38), residues: 532
  helix:  1.84 (0.28), residues: 361
  sheet:  None (None), residues: 0
  loop : -0.53 (0.48), residues: 171

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.002   TRP A 553 
 HIS   0.003   0.001   HIS A 222 
 PHE   0.017   0.002   PHE A 409 
 TYR   0.021   0.002   TYR A  84 
 ARG   0.005   0.001   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00004 (    1)
  link_NAG-ASN         : angle       1.67676 (    3)
  hydrogen bonds       : bond        0.08287 (  265)
  hydrogen bonds       : angle       4.19585 (  771)
  SS BOND              : bond        0.00272 (    1)
  SS BOND              : angle       1.78403 (    2)
  covalent geometry    : bond        0.00385 ( 4459)
  covalent geometry    : angle       0.56667 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 41
  time to evaluate  : 0.529 
Fit side-chains
  outliers start: 12
  outliers final: 6
  residues processed: 50
  average time/residue: 1.0731
  time to fit residues: 56.3441
Evaluate side-chains
  46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.467 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  376 ILE
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 32 optimal weight:    0.7980
   chunk 13 optimal weight:    0.9990
   chunk 0 optimal weight:    7.9990
   chunk 38 optimal weight:    0.7980
   chunk 23 optimal weight:    0.7980
   chunk 15 optimal weight:    4.9990
   chunk 27 optimal weight:    1.9990
   chunk 20 optimal weight:    5.9990
   chunk 42 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 34 optimal weight:    0.7980
   overall best weight:    0.7580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.108984 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2906 r_free = 0.2906 target = 0.094554 restraints weight = 4650.748|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.04
r_work: 0.2818 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8705
moved from start:          0.0578

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4461  Z= 0.125
  Angle     :  0.485   5.412   6091  Z= 0.263
  Chirality :  0.039   0.132    681
  Planarity :  0.004   0.036    738
  Dihedral  :  5.538  45.696    610
  Min Nonbonded Distance : 2.287

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.30 %
    Favored  : 82.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.94 (0.38), residues: 532
  helix:  2.09 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.51 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 222 
 PHE   0.010   0.001   PHE A 409 
 TYR   0.019   0.001   TYR A  84 
 ARG   0.005   0.000   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00010 (    1)
  link_NAG-ASN         : angle       1.52537 (    3)
  hydrogen bonds       : bond        0.06375 (  265)
  hydrogen bonds       : angle       3.93762 (  771)
  SS BOND              : bond        0.00207 (    1)
  SS BOND              : angle       1.33375 (    2)
  covalent geometry    : bond        0.00247 ( 4459)
  covalent geometry    : angle       0.48332 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.508 
Fit side-chains
REVERT: A  256 VAL cc_start: 0.7695 (OUTLIER) cc_final: 0.7479 (m)
  outliers start: 8
  outliers final: 5
  residues processed: 47
  average time/residue: 1.0593
  time to fit residues: 52.2148
Evaluate side-chains
  48 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 42
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 15 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 29 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 17 optimal weight:    0.0370
   chunk 5 optimal weight:    3.9990
   chunk 21 optimal weight:    4.9990
   chunk 4 optimal weight:    0.8980
   chunk 28 optimal weight:    0.7980
   chunk 52 optimal weight:    3.9990
   overall best weight:    0.7260

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3105 r_free = 0.3105 target = 0.109137 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2897 r_free = 0.2897 target = 0.094035 restraints weight = 4740.451|
|-----------------------------------------------------------------------------|
r_work (start): 0.2903 rms_B_bonded: 1.14
r_work: 0.2811 rms_B_bonded: 1.67 restraints_weight: 0.5000
r_work: 0.2706 rms_B_bonded: 2.88 restraints_weight: 0.2500
r_work (final): 0.2706
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8702
moved from start:          0.0630

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4461  Z= 0.121
  Angle     :  0.475   5.466   6091  Z= 0.256
  Chirality :  0.039   0.130    681
  Planarity :  0.004   0.035    738
  Dihedral  :  5.259  39.664    610
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.52 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.05 (0.38), residues: 532
  helix:  2.16 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.45 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.014   0.001   TRP A 553 
 HIS   0.001   0.000   HIS A 222 
 PHE   0.010   0.001   PHE A 409 
 TYR   0.018   0.001   TYR A  84 
 ARG   0.006   0.000   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00017 (    1)
  link_NAG-ASN         : angle       1.42857 (    3)
  hydrogen bonds       : bond        0.06154 (  265)
  hydrogen bonds       : angle       3.87729 (  771)
  SS BOND              : bond        0.00212 (    1)
  SS BOND              : angle       1.15860 (    2)
  covalent geometry    : bond        0.00238 ( 4459)
  covalent geometry    : angle       0.47345 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  53 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 44
  time to evaluate  : 0.493 
Fit side-chains
REVERT: A  256 VAL cc_start: 0.7692 (OUTLIER) cc_final: 0.7465 (m)
  outliers start: 9
  outliers final: 5
  residues processed: 51
  average time/residue: 1.0818
  time to fit residues: 57.9605
Evaluate side-chains
  49 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 43
  time to evaluate  : 0.503 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 31 optimal weight:    0.0970
   chunk 24 optimal weight:    1.9990
   chunk 1 optimal weight:    2.9990
   chunk 4 optimal weight:    0.8980
   chunk 42 optimal weight:    2.9990
   chunk 34 optimal weight:    4.9990
   chunk 14 optimal weight:    0.9980
   chunk 38 optimal weight:    0.3980
   chunk 45 optimal weight:    1.9990
   chunk 47 optimal weight:    0.6980
   chunk 48 optimal weight:    1.9990
   overall best weight:    0.6178

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3124 r_free = 0.3124 target = 0.110521 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2921 r_free = 0.2921 target = 0.095622 restraints weight = 4780.398|
|-----------------------------------------------------------------------------|
r_work (start): 0.2929 rms_B_bonded: 1.11
r_work: 0.2839 rms_B_bonded: 1.63 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 2.80 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8686
moved from start:          0.0671

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4461  Z= 0.114
  Angle     :  0.458   5.401   6091  Z= 0.247
  Chirality :  0.039   0.126    681
  Planarity :  0.004   0.034    738
  Dihedral  :  4.973  33.182    610
  Min Nonbonded Distance : 2.302

Molprobity Statistics.
  All-atom Clashscore : 1.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 15.96 %
    Favored  : 82.48 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.38), residues: 532
  helix:  2.24 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.39 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 553 
 HIS   0.001   0.000   HIS A 222 
 PHE   0.008   0.001   PHE A 409 
 TYR   0.017   0.001   TYR A  84 
 ARG   0.006   0.000   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00019 (    1)
  link_NAG-ASN         : angle       1.33668 (    3)
  hydrogen bonds       : bond        0.05733 (  265)
  hydrogen bonds       : angle       3.81612 (  771)
  SS BOND              : bond        0.00191 (    1)
  SS BOND              : angle       1.04271 (    2)
  covalent geometry    : bond        0.00220 ( 4459)
  covalent geometry    : angle       0.45706 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.467 
Fit side-chains
REVERT: A  256 VAL cc_start: 0.7667 (OUTLIER) cc_final: 0.7445 (m)
  outliers start: 7
  outliers final: 5
  residues processed: 50
  average time/residue: 1.0102
  time to fit residues: 53.0089
Evaluate side-chains
  50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 44
  time to evaluate  : 0.477 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 14 optimal weight:    0.0970
   chunk 47 optimal weight:    0.9980
   chunk 34 optimal weight:    0.9990
   chunk 27 optimal weight:    1.9990
   chunk 7 optimal weight:    5.9990
   chunk 30 optimal weight:    0.3980
   chunk 31 optimal weight:    2.9990
   chunk 36 optimal weight:    0.9980
   chunk 8 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 44 optimal weight:    2.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3123 r_free = 0.3123 target = 0.110416 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.095973 restraints weight = 4658.499|
|-----------------------------------------------------------------------------|
r_work (start): 0.2918 rms_B_bonded: 1.05
r_work: 0.2833 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.2733 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.2733
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8683
moved from start:          0.0655

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4461  Z= 0.119
  Angle     :  0.468   5.514   6091  Z= 0.252
  Chirality :  0.039   0.129    681
  Planarity :  0.004   0.033    738
  Dihedral  :  4.948  30.585    610
  Min Nonbonded Distance : 2.298

Molprobity Statistics.
  All-atom Clashscore : 1.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.41 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.16 (0.38), residues: 532
  helix:  2.23 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.35 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 222 
 PHE   0.010   0.001   PHE A 409 
 TYR   0.018   0.001   TYR A  84 
 ARG   0.006   0.000   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00008 (    1)
  link_NAG-ASN         : angle       1.31499 (    3)
  hydrogen bonds       : bond        0.06029 (  265)
  hydrogen bonds       : angle       3.84753 (  771)
  SS BOND              : bond        0.00203 (    1)
  SS BOND              : angle       1.08001 (    2)
  covalent geometry    : bond        0.00233 ( 4459)
  covalent geometry    : angle       0.46651 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.491 
Fit side-chains
REVERT: A  256 VAL cc_start: 0.7679 (OUTLIER) cc_final: 0.7468 (m)
  outliers start: 6
  outliers final: 5
  residues processed: 49
  average time/residue: 1.0579
  time to fit residues: 54.3636
Evaluate side-chains
  51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.498 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 18 optimal weight:    0.0070
   chunk 48 optimal weight:    1.9990
   chunk 10 optimal weight:    0.6980
   chunk 3 optimal weight:    3.9990
   chunk 36 optimal weight:    0.6980
   chunk 23 optimal weight:    0.9980
   chunk 32 optimal weight:    0.9980
   chunk 26 optimal weight:    0.9990
   chunk 39 optimal weight:    4.9990
   chunk 46 optimal weight:    4.9990
   chunk 30 optimal weight:    4.9990
   overall best weight:    0.6798

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3139 r_free = 0.3139 target = 0.111497 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2961 r_free = 0.2961 target = 0.098236 restraints weight = 4662.355|
|-----------------------------------------------------------------------------|
r_work (start): 0.2943 rms_B_bonded: 0.90
r_work: 0.2859 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 2.45 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8712
moved from start:          0.0659

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.023   4461  Z= 0.117
  Angle     :  0.465   5.506   6091  Z= 0.251
  Chirality :  0.039   0.128    681
  Planarity :  0.004   0.034    738
  Dihedral  :  4.868  30.421    610
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 1.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.74 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.17 (0.38), residues: 532
  helix:  2.24 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.35 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.013   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 222 
 PHE   0.009   0.001   PHE A 409 
 TYR   0.017   0.001   TYR A  84 
 ARG   0.007   0.000   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00006 (    1)
  link_NAG-ASN         : angle       1.27333 (    3)
  hydrogen bonds       : bond        0.05931 (  265)
  hydrogen bonds       : angle       3.84042 (  771)
  SS BOND              : bond        0.00197 (    1)
  SS BOND              : angle       1.01687 (    2)
  covalent geometry    : bond        0.00230 ( 4459)
  covalent geometry    : angle       0.46417 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 45
  time to evaluate  : 0.494 
Fit side-chains
REVERT: A  256 VAL cc_start: 0.7769 (OUTLIER) cc_final: 0.7557 (m)
  outliers start: 9
  outliers final: 6
  residues processed: 51
  average time/residue: 1.0065
  time to fit residues: 53.8265
Evaluate side-chains
  52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.449 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  256 VAL
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  375 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 40 optimal weight:    1.9990
   chunk 4 optimal weight:    3.9990
   chunk 33 optimal weight:    0.8980
   chunk 21 optimal weight:    5.9990
   chunk 13 optimal weight:    3.9990
   chunk 25 optimal weight:    1.9990
   chunk 16 optimal weight:    0.9980
   chunk 31 optimal weight:    1.9990
   chunk 26 optimal weight:    0.4980
   chunk 2 optimal weight:    3.9990
   chunk 6 optimal weight:    0.0870
   overall best weight:    0.8960

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.110049 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2950 r_free = 0.2950 target = 0.097480 restraints weight = 4602.541|
|-----------------------------------------------------------------------------|
r_work (start): 0.2924 rms_B_bonded: 0.96
r_work: 0.2835 rms_B_bonded: 1.37 restraints_weight: 0.5000
r_work: 0.2737 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.2737
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8743
moved from start:          0.0657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4461  Z= 0.130
  Angle     :  0.489   5.703   6091  Z= 0.264
  Chirality :  0.040   0.136    681
  Planarity :  0.004   0.034    738
  Dihedral  :  5.028  31.836    610
  Min Nonbonded Distance : 2.281

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.41 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.38), residues: 532
  helix:  2.14 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.37 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 222 
 PHE   0.012   0.001   PHE A 409 
 TYR   0.018   0.001   TYR A  84 
 ARG   0.007   0.000   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00080 (    1)
  link_NAG-ASN         : angle       1.31033 (    3)
  hydrogen bonds       : bond        0.06597 (  265)
  hydrogen bonds       : angle       3.92648 (  771)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       1.15831 (    2)
  covalent geometry    : bond        0.00265 ( 4459)
  covalent geometry    : angle       0.48796 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  52 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 45
  time to evaluate  : 0.459 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 49
  average time/residue: 1.0284
  time to fit residues: 52.8292
Evaluate side-chains
  51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 45
  time to evaluate  : 0.483 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  375 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 45 optimal weight:    0.8980
   chunk 4 optimal weight:    2.9990
   chunk 13 optimal weight:    3.9990
   chunk 38 optimal weight:    3.9990
   chunk 19 optimal weight:    2.9990
   chunk 7 optimal weight:    3.9990
   chunk 23 optimal weight:    3.9990
   chunk 49 optimal weight:    0.1980
   chunk 37 optimal weight:    1.9990
   chunk 9 optimal weight:    3.9990
   chunk 20 optimal weight:    8.9990
   overall best weight:    1.8186

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3072 r_free = 0.3072 target = 0.106459 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.2903 r_free = 0.2903 target = 0.094153 restraints weight = 4702.403|
|-----------------------------------------------------------------------------|
r_work (start): 0.2866 rms_B_bonded: 0.90
r_work: 0.2772 rms_B_bonded: 1.34 restraints_weight: 0.5000
r_work: 0.2672 rms_B_bonded: 2.33 restraints_weight: 0.2500
r_work (final): 0.2672
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8810
moved from start:          0.0881

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.036   4461  Z= 0.190
  Angle     :  0.588   6.045   6091  Z= 0.318
  Chirality :  0.044   0.159    681
  Planarity :  0.005   0.036    738
  Dihedral  :  5.651  35.190    610
  Min Nonbonded Distance : 2.241

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.55 %
    Allowed  : 16.19 %
    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 (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.67 (0.37), residues: 532
  helix:  1.85 (0.28), residues: 363
  sheet:  None (None), residues: 0
  loop : -0.50 (0.48), residues: 169

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.012   0.002   TRP A 585 
 HIS   0.003   0.001   HIS A 222 
 PHE   0.020   0.002   PHE A 409 
 TYR   0.022   0.002   TYR A  84 
 ARG   0.007   0.001   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00344 (    1)
  link_NAG-ASN         : angle       1.70784 (    3)
  hydrogen bonds       : bond        0.08665 (  265)
  hydrogen bonds       : angle       4.20711 (  771)
  SS BOND              : bond        0.00362 (    1)
  SS BOND              : angle       1.50370 (    2)
  covalent geometry    : bond        0.00435 ( 4459)
  covalent geometry    : angle       0.58621 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  47 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.452 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 43
  average time/residue: 1.0039
  time to fit residues: 45.3897
Evaluate side-chains
  46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.456 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  375 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 40 optimal weight:    2.9990
   chunk 16 optimal weight:    0.9980
   chunk 0 optimal weight:    7.9990
   chunk 52 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 43 optimal weight:    0.8980
   chunk 44 optimal weight:    0.8980
   chunk 22 optimal weight:    3.9990
   chunk 51 optimal weight:    0.9990
   chunk 11 optimal weight:    0.4980
   chunk 9 optimal weight:    4.9990
   overall best weight:    0.8582

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.108246 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2895 r_free = 0.2895 target = 0.093825 restraints weight = 4631.776|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 1.04
r_work: 0.2809 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.2708 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.2708
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8710
moved from start:          0.0677

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4461  Z= 0.130
  Angle     :  0.492   5.744   6091  Z= 0.267
  Chirality :  0.040   0.136    681
  Planarity :  0.004   0.033    738
  Dihedral  :  5.156  32.567    610
  Min Nonbonded Distance : 2.279

Molprobity Statistics.
  All-atom Clashscore : 1.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.63 %
    Favored  : 82.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.97 (0.38), residues: 532
  helix:  2.09 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.42 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 585 
 HIS   0.002   0.000   HIS A 222 
 PHE   0.012   0.001   PHE A 409 
 TYR   0.019   0.001   TYR A  84 
 ARG   0.007   0.000   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00116 (    1)
  link_NAG-ASN         : angle       1.46372 (    3)
  hydrogen bonds       : bond        0.06587 (  265)
  hydrogen bonds       : angle       3.97621 (  771)
  SS BOND              : bond        0.00253 (    1)
  SS BOND              : angle       1.10608 (    2)
  covalent geometry    : bond        0.00262 ( 4459)
  covalent geometry    : angle       0.49100 ( 6086)

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

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

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1064 Ramachandran restraints generated.
    532 Oldfield, 0 Emsley, 532 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.504 
Fit side-chains
  outliers start: 6
  outliers final: 6
  residues processed: 43
  average time/residue: 1.1966
  time to fit residues: 53.8245
Evaluate side-chains
  46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 40
  time to evaluate  : 0.493 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
Chi-restraints excluded: chain A residue  263 VAL
Chi-restraints excluded: chain A residue  375 ASN
Chi-restraints excluded: chain A residue  535 VAL
Chi-restraints excluded: chain A residue  538 ILE
Chi-restraints excluded: chain A residue  541 LYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 30 optimal weight:    3.9990
   chunk 42 optimal weight:    2.9990
   chunk 38 optimal weight:    0.7980
   chunk 26 optimal weight:    0.9990
   chunk 4 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9990
   chunk 7 optimal weight:    5.9990
   chunk 40 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 51 optimal weight:    1.9990
   chunk 1 optimal weight:    0.6980
   overall best weight:    0.7980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3104 r_free = 0.3104 target = 0.108952 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.094457 restraints weight = 4703.208|
|-----------------------------------------------------------------------------|
r_work (start): 0.2910 rms_B_bonded: 1.05
r_work: 0.2825 rms_B_bonded: 1.51 restraints_weight: 0.5000
r_work: 0.2723 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.2723
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8700
moved from start:          0.0670

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.025   4461  Z= 0.125
  Angle     :  0.482   5.550   6091  Z= 0.261
  Chirality :  0.039   0.133    681
  Planarity :  0.004   0.034    738
  Dihedral  :  4.965  31.512    610
  Min Nonbonded Distance : 2.292

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.44 %
    Favored  : 97.56 %
  Rotamer:
    Outliers :  1.33 %
    Allowed  : 16.85 %
    Favored  : 81.82 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  2.06 (0.38), residues: 532
  helix:  2.15 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.38 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 585 
 HIS   0.002   0.000   HIS A 222 
 PHE   0.011   0.001   PHE A 409 
 TYR   0.018   0.001   TYR A  84 
 ARG   0.007   0.000   ARG A 604 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00092 (    1)
  link_NAG-ASN         : angle       1.36717 (    3)
  hydrogen bonds       : bond        0.06364 (  265)
  hydrogen bonds       : angle       3.93104 (  771)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       1.09400 (    2)
  covalent geometry    : bond        0.00251 ( 4459)
  covalent geometry    : angle       0.48106 ( 6086)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2882.57 seconds
wall clock time: 50 minutes 49.41 seconds (3049.41 seconds total)