Starting phenix.real_space_refine
on Fri Oct 10 11:52:30 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8wtv_37843/10_2025/8wtv_37843.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8wtv_37843/10_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/8wtv_37843/10_2025/8wtv_37843.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8wtv_37843/10_2025/8wtv_37843.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/8wtv_37843/10_2025/8wtv_37843.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8wtv_37843/10_2025/8wtv_37843.map"
  }
  resolution = 2.7
  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=   0.067
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/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: 1.18, per 1000 atoms: 0.27
  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: 0.25
  Conformation dependent library (CDL) restraints added in 103.4 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.16
  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: 0.64

  Time building geometry restraints manager: 0.35 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:             1.890
  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:         0.020
  Set scattering table:                    0.010
  Process input model:                     5.590
  Find NCS groups from input model:        0.010
  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:6.790
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   14.400
-------------------------------------------------------------------------------
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 : 1.97
  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 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:  1.82 (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
 ARG   0.001   0.000   ARG A 216 
 TYR   0.016   0.001   TYR A  84 
 PHE   0.010   0.001   PHE A 409 
 TRP   0.016   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 599 

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

*********************** 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  : 0.164 
Fit side-chains
  outliers start: 1
  outliers final: 1
  residues processed: 46
  average time/residue: 0.5168
  time to fit residues: 24.8263
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  : 0.145 
-------------------------------------------------------------------------------
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 24 optimal weight:    3.9990
   chunk 48 optimal weight:    3.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    3.9990
   chunk 16 optimal weight:    1.9990
   chunk 32 optimal weight:    0.6980
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    0.5980
   chunk 50 optimal weight:    0.0980
   chunk 19 optimal weight:    0.7980
   chunk 30 optimal weight:    0.5980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
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 = 0.3147 r_free = 0.3147 target = 0.112114 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2953 r_free = 0.2953 target = 0.097686 restraints weight = 4738.711|
|-----------------------------------------------------------------------------|
r_work (start): 0.2947 rms_B_bonded: 1.05
r_work: 0.2862 rms_B_bonded: 1.53 restraints_weight: 0.5000
r_work: 0.2762 rms_B_bonded: 2.62 restraints_weight: 0.2500
r_work (final): 0.2762
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8657
moved from start:          0.0608

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.022   4461  Z= 0.112
  Angle     :  0.458   5.535   6091  Z= 0.246
  Chirality :  0.038   0.124    681
  Planarity :  0.004   0.034    738
  Dihedral  :  5.961  50.774    614
  Min Nonbonded Distance : 2.299

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.88 %
    Favored  : 98.12 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.96 %
    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:  2.12 (0.39), residues: 532
  helix:  2.21 (0.29), residues: 362
  sheet:  None (None), residues: 0
  loop : -0.35 (0.50), residues: 170

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.000   ARG A 604 
 TYR   0.017   0.001   TYR A  84 
 PHE   0.008   0.001   PHE A 362 
 TRP   0.014   0.001   TRP A 553 
 HIS   0.001   0.000   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00212 ( 4459)
  covalent geometry    : angle       0.45626 ( 6086)
  SS BOND              : bond        0.00125 (    1)
  SS BOND              : angle       1.37219 (    2)
  hydrogen bonds       : bond        0.05593 (  265)
  hydrogen bonds       : angle       3.82516 (  771)
  link_NAG-ASN         : bond        0.00054 (    1)
  link_NAG-ASN         : angle       1.29365 (    3)

*********************** 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: 8
    poor density    : 45
  time to evaluate  : 0.168 
Fit side-chains
  outliers start: 8
  outliers final: 4
  residues processed: 51
  average time/residue: 0.4646
  time to fit residues: 24.7544
Evaluate side-chains
  45 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 41
  time to evaluate  : 0.116 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  169 LEU
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 41 optimal weight:    2.9990
   chunk 26 optimal weight:    4.9990
   chunk 0 optimal weight:    7.9990
   chunk 49 optimal weight:    3.9990
   chunk 43 optimal weight:    0.9980
   chunk 17 optimal weight:    2.9990
   chunk 14 optimal weight:    0.8980
   chunk 52 optimal weight:    3.9990
   chunk 45 optimal weight:    1.9990
   chunk 11 optimal weight:    0.4980
   chunk 16 optimal weight:    1.9990
   overall best weight:    1.2784

-------------------------------------------------------------------------------
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 = 0.3074 r_free = 0.3074 target = 0.106909 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2870 r_free = 0.2870 target = 0.092293 restraints weight = 4668.244|
|-----------------------------------------------------------------------------|
r_work (start): 0.2863 rms_B_bonded: 1.04
r_work: 0.2778 rms_B_bonded: 1.48 restraints_weight: 0.5000
r_work: 0.2673 rms_B_bonded: 2.60 restraints_weight: 0.2500
r_work (final): 0.2673
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8748
moved from start:          0.0672

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4461  Z= 0.155
  Angle     :  0.534   5.576   6091  Z= 0.289
  Chirality :  0.042   0.146    681
  Planarity :  0.005   0.035    738
  Dihedral  :  5.729  46.046    610
  Min Nonbonded Distance : 2.257

Molprobity Statistics.
  All-atom Clashscore : 1.16
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 15.08 %
    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 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:  1.81 (0.38), residues: 532
  helix:  1.97 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.49 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.005   0.001   ARG A 604 
 TYR   0.020   0.002   TYR A  84 
 PHE   0.015   0.002   PHE A 409 
 TRP   0.013   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00333 ( 4459)
  covalent geometry    : angle       0.53254 ( 6086)
  SS BOND              : bond        0.00229 (    1)
  SS BOND              : angle       1.50540 (    2)
  hydrogen bonds       : bond        0.07643 (  265)
  hydrogen bonds       : angle       4.07248 (  771)
  link_NAG-ASN         : bond        0.00052 (    1)
  link_NAG-ASN         : angle       1.51791 (    3)

*********************** 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: 9
    poor density    : 41
  time to evaluate  : 0.173 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 47
  average time/residue: 0.4628
  time to fit residues: 22.7285
Evaluate side-chains
  46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 41
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
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  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 35 optimal weight:    0.8980
   chunk 27 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 34 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    3.9990
   chunk 8 optimal weight:    4.9990
   chunk 18 optimal weight:    0.1980
   chunk 5 optimal weight:    2.9990
   chunk 3 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    0.9784

-------------------------------------------------------------------------------
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 = 0.3108 r_free = 0.3108 target = 0.109148 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 53)----------------|
| r_work = 0.2939 r_free = 0.2939 target = 0.096724 restraints weight = 4621.296|
|-----------------------------------------------------------------------------|
r_work (start): 0.2909 rms_B_bonded: 0.94
r_work: 0.2818 rms_B_bonded: 1.36 restraints_weight: 0.5000
r_work: 0.2721 rms_B_bonded: 2.38 restraints_weight: 0.2500
r_work (final): 0.2721
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8754
moved from start:          0.0639

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= 0.136
  Angle     :  0.502   5.691   6091  Z= 0.271
  Chirality :  0.040   0.138    681
  Planarity :  0.004   0.035    738
  Dihedral  :  5.515  42.290    610
  Min Nonbonded Distance : 2.278

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  Rotamer:
    Outliers :  2.00 %
    Allowed  : 14.86 %
    Favored  : 83.15 %
  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:  1.92 (0.38), residues: 532
  helix:  2.07 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.51 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 604 
 TYR   0.019   0.001   TYR A  84 
 PHE   0.012   0.001   PHE A 409 
 TRP   0.014   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00280 ( 4459)
  covalent geometry    : angle       0.50002 ( 6086)
  SS BOND              : bond        0.00246 (    1)
  SS BOND              : angle       1.27502 (    2)
  hydrogen bonds       : bond        0.06859 (  265)
  hydrogen bonds       : angle       3.99136 (  771)
  link_NAG-ASN         : bond        0.00047 (    1)
  link_NAG-ASN         : angle       1.53670 (    3)

*********************** 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
  51 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 9
    poor density    : 42
  time to evaluate  : 0.164 
Fit side-chains
  outliers start: 9
  outliers final: 5
  residues processed: 48
  average time/residue: 0.4644
  time to fit residues: 23.3149
Evaluate side-chains
  47 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 5
    poor density    : 42
  time to evaluate  : 0.108 
-------------------------------------------------------------------------------
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  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 27 optimal weight:    0.9980
   chunk 31 optimal weight:    0.2980
   chunk 5 optimal weight:    4.9990
   chunk 8 optimal weight:    2.9990
   chunk 18 optimal weight:    0.0370
   chunk 4 optimal weight:    2.9990
   chunk 7 optimal weight:    1.9990
   chunk 28 optimal weight:    0.8980
   chunk 45 optimal weight:    2.9990
   chunk 29 optimal weight:    3.9990
   chunk 51 optimal weight:    2.9990
   overall best weight:    0.8460

-------------------------------------------------------------------------------
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 = 0.3103 r_free = 0.3103 target = 0.108810 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2904 r_free = 0.2904 target = 0.094405 restraints weight = 4671.389|
|-----------------------------------------------------------------------------|
r_work (start): 0.2902 rms_B_bonded: 1.03
r_work: 0.2817 rms_B_bonded: 1.50 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 2.59 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8709
moved from start:          0.0628

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4461  Z= 0.128
  Angle     :  0.486   5.665   6091  Z= 0.263
  Chirality :  0.040   0.134    681
  Planarity :  0.004   0.034    738
  Dihedral  :  5.303  37.419    610
  Min Nonbonded Distance : 2.285

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  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 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:  2.01 (0.38), residues: 532
  helix:  2.13 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.45 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 604 
 TYR   0.018   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 409 
 TRP   0.014   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00257 ( 4459)
  covalent geometry    : angle       0.48435 ( 6086)
  SS BOND              : bond        0.00231 (    1)
  SS BOND              : angle       1.17374 (    2)
  hydrogen bonds       : bond        0.06485 (  265)
  hydrogen bonds       : angle       3.93768 (  771)
  link_NAG-ASN         : bond        0.00055 (    1)
  link_NAG-ASN         : angle       1.46050 (    3)

*********************** 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
  50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 42
  time to evaluate  : 0.171 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 48
  average time/residue: 0.4561
  time to fit residues: 22.9495
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  : 0.165 
-------------------------------------------------------------------------------
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 0 optimal weight:    7.9990
   chunk 36 optimal weight:    0.6980
   chunk 34 optimal weight:    0.9980
   chunk 18 optimal weight:    0.9990
   chunk 23 optimal weight:    3.9990
   chunk 22 optimal weight:    0.5980
   chunk 51 optimal weight:    3.9990
   chunk 35 optimal weight:    1.9990
   chunk 15 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 48 optimal weight:    0.9980
   overall best weight:    0.8580

-------------------------------------------------------------------------------
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 = 0.108908 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.2917 r_free = 0.2917 target = 0.095235 restraints weight = 4784.370|
|-----------------------------------------------------------------------------|
r_work (start): 0.2907 rms_B_bonded: 0.95
r_work: 0.2818 rms_B_bonded: 1.49 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 2.57 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.0648

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.024   4461  Z= 0.128
  Angle     :  0.487   5.705   6091  Z= 0.263
  Chirality :  0.040   0.134    681
  Planarity :  0.004   0.035    738
  Dihedral  :  5.235  34.496    610
  Min Nonbonded Distance : 2.284

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  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 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:  2.02 (0.38), residues: 532
  helix:  2.13 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.42 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.006   0.000   ARG A 604 
 TYR   0.018   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 409 
 TRP   0.014   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4459)
  covalent geometry    : angle       0.48546 ( 6086)
  SS BOND              : bond        0.00225 (    1)
  SS BOND              : angle       1.16000 (    2)
  hydrogen bonds       : bond        0.06531 (  265)
  hydrogen bonds       : angle       3.93822 (  771)
  link_NAG-ASN         : bond        0.00060 (    1)
  link_NAG-ASN         : angle       1.44825 (    3)

*********************** 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
  50 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 43
  time to evaluate  : 0.165 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 48
  average time/residue: 0.4752
  time to fit residues: 23.8557
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  : 0.175 
-------------------------------------------------------------------------------
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 1 optimal weight:    1.9990
   chunk 7 optimal weight:    7.9990
   chunk 45 optimal weight:    2.9990
   chunk 25 optimal weight:    3.9990
   chunk 34 optimal weight:    2.9990
   chunk 49 optimal weight:    0.7980
   chunk 33 optimal weight:    0.7980
   chunk 0 optimal weight:    6.9990
   chunk 37 optimal weight:    3.9990
   chunk 18 optimal weight:    3.9990
   chunk 41 optimal weight:    2.9990
   overall best weight:    1.9186

-------------------------------------------------------------------------------
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 = 0.3066 r_free = 0.3066 target = 0.106087 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.2887 r_free = 0.2887 target = 0.093202 restraints weight = 4686.001|
|-----------------------------------------------------------------------------|
r_work (start): 0.2851 rms_B_bonded: 0.87
r_work: 0.2766 rms_B_bonded: 1.32 restraints_weight: 0.5000
r_work: 0.2666 rms_B_bonded: 2.35 restraints_weight: 0.2500
r_work (final): 0.2666
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8817
moved from start:          0.0927

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.037   4461  Z= 0.198
  Angle     :  0.598   5.969   6091  Z= 0.324
  Chirality :  0.045   0.160    681
  Planarity :  0.005   0.037    738
  Dihedral  :  5.889  39.562    610
  Min Nonbonded Distance : 2.234

Molprobity Statistics.
  All-atom Clashscore : 1.28
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.82 %
    Favored  : 97.18 %
  Rotamer:
    Outliers :  1.77 %
    Allowed  : 15.52 %
    Favored  : 82.71 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z 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:  1.57 (0.37), residues: 532
  helix:  1.78 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.59 (0.48), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 604 
 TYR   0.021   0.002   TYR A  84 
 PHE   0.019   0.002   PHE A 409 
 TRP   0.012   0.002   TRP A 553 
 HIS   0.003   0.001   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00455 ( 4459)
  covalent geometry    : angle       0.59659 ( 6086)
  SS BOND              : bond        0.00342 (    1)
  SS BOND              : angle       1.51753 (    2)
  hydrogen bonds       : bond        0.08909 (  265)
  hydrogen bonds       : angle       4.26077 (  771)
  link_NAG-ASN         : bond        0.00335 (    1)
  link_NAG-ASN         : angle       1.79090 (    3)

*********************** 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
  48 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 40
  time to evaluate  : 0.175 
Fit side-chains
  outliers start: 8
  outliers final: 6
  residues processed: 45
  average time/residue: 0.4050
  time to fit residues: 19.2116
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  : 0.105 
-------------------------------------------------------------------------------
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=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 21 optimal weight:    4.9990
   chunk 10 optimal weight:    0.9990
   chunk 23 optimal weight:    0.8980
   chunk 31 optimal weight:    1.9990
   chunk 40 optimal weight:    2.9990
   chunk 39 optimal weight:    2.9990
   chunk 17 optimal weight:    4.9990
   chunk 37 optimal weight:    1.9990
   chunk 18 optimal weight:    0.8980
   chunk 34 optimal weight:    4.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.1184

-------------------------------------------------------------------------------
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 = 0.3096 r_free = 0.3096 target = 0.108190 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.2925 r_free = 0.2925 target = 0.095682 restraints weight = 4662.414|
|-----------------------------------------------------------------------------|
r_work (start): 0.2896 rms_B_bonded: 0.93
r_work: 0.2804 rms_B_bonded: 1.36 restraints_weight: 0.5000
r_work: 0.2705 rms_B_bonded: 2.39 restraints_weight: 0.2500
r_work (final): 0.2705
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8775
moved from start:          0.0729

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4461  Z= 0.146
  Angle     :  0.521   5.775   6091  Z= 0.282
  Chirality :  0.041   0.143    681
  Planarity :  0.005   0.035    738
  Dihedral  :  5.500  34.638    610
  Min Nonbonded Distance : 2.269

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  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 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:  1.79 (0.38), residues: 532
  helix:  1.97 (0.28), residues: 364
  sheet:  None (None), residues: 0
  loop : -0.55 (0.49), residues: 168

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 604 
 TYR   0.020   0.001   TYR A  84 
 PHE   0.014   0.001   PHE A 409 
 TRP   0.014   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00307 ( 4459)
  covalent geometry    : angle       0.51905 ( 6086)
  SS BOND              : bond        0.00273 (    1)
  SS BOND              : angle       1.27816 (    2)
  hydrogen bonds       : bond        0.07247 (  265)
  hydrogen bonds       : angle       4.08044 (  771)
  link_NAG-ASN         : bond        0.00181 (    1)
  link_NAG-ASN         : angle       1.59356 (    3)

*********************** 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
  46 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 39
  time to evaluate  : 0.132 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 44
  average time/residue: 0.4253
  time to fit residues: 19.5607
Evaluate side-chains
  45 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 39
  time to evaluate  : 0.111 
-------------------------------------------------------------------------------
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=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 42 optimal weight:    2.9990
   chunk 1 optimal weight:    0.9990
   chunk 13 optimal weight:    0.8980
   chunk 14 optimal weight:    0.5980
   chunk 48 optimal weight:    0.9990
   chunk 5 optimal weight:    2.9990
   chunk 40 optimal weight:    0.6980
   chunk 2 optimal weight:    0.8980
   chunk 39 optimal weight:    0.8980
   chunk 0 optimal weight:    6.9990
   chunk 12 optimal weight:    2.9990
   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 = 0.3103 r_free = 0.3103 target = 0.108887 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.2905 r_free = 0.2905 target = 0.094472 restraints weight = 4726.984|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 1.04
r_work: 0.2820 rms_B_bonded: 1.52 restraints_weight: 0.5000
r_work: 0.2719 rms_B_bonded: 2.61 restraints_weight: 0.2500
r_work (final): 0.2719
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8704
moved from start:          0.0661

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   5.585   6091  Z= 0.262
  Chirality :  0.039   0.132    681
  Planarity :  0.004   0.035    738
  Dihedral  :  5.124  31.780    610
  Min Nonbonded Distance : 2.290

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.07 %
    Favored  : 97.93 %
  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 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:  1.98 (0.38), residues: 532
  helix:  2.11 (0.28), residues: 365
  sheet:  None (None), residues: 0
  loop : -0.47 (0.49), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 604 
 TYR   0.018   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 409 
 TRP   0.015   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 599 

Details of bonding type rmsd
  covalent geometry    : bond        0.00250 ( 4459)
  covalent geometry    : angle       0.48061 ( 6086)
  SS BOND              : bond        0.00226 (    1)
  SS BOND              : angle       1.12186 (    2)
  hydrogen bonds       : bond        0.06342 (  265)
  hydrogen bonds       : angle       3.95169 (  771)
  link_NAG-ASN         : bond        0.00086 (    1)
  link_NAG-ASN         : angle       1.45739 (    3)

*********************** 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
  48 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 41
  time to evaluate  : 0.166 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 46
  average time/residue: 0.4475
  time to fit residues: 21.5730
Evaluate side-chains
  47 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.142 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 20 optimal weight:    5.9990
   chunk 17 optimal weight:    0.9990
   chunk 51 optimal weight:    1.9990
   chunk 45 optimal weight:    2.9990
   chunk 27 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 46 optimal weight:    0.9980
   chunk 24 optimal weight:    6.9990
   chunk 21 optimal weight:    0.4980
   chunk 9 optimal weight:    4.9990
   chunk 42 optimal weight:    0.7980
   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 = 0.3110 r_free = 0.3110 target = 0.109252 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.2934 r_free = 0.2934 target = 0.096364 restraints weight = 4705.699|
|-----------------------------------------------------------------------------|
r_work (start): 0.2919 rms_B_bonded: 0.94
r_work: 0.2828 rms_B_bonded: 1.40 restraints_weight: 0.5000
r_work: 0.2729 rms_B_bonded: 2.44 restraints_weight: 0.2500
r_work (final): 0.2729
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8747
moved from start:          0.0674

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= 0.129
  Angle     :  0.490   5.691   6091  Z= 0.265
  Chirality :  0.040   0.134    681
  Planarity :  0.004   0.035    738
  Dihedral  :  5.113  31.935    610
  Min Nonbonded Distance : 2.283

Molprobity Statistics.
  All-atom Clashscore : 0.93
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  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 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:  1.99 (0.38), residues: 532
  helix:  2.10 (0.28), residues: 365
  sheet:  None (None), residues: 0
  loop : -0.43 (0.49), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.000   ARG A 604 
 TYR   0.018   0.001   TYR A  84 
 PHE   0.011   0.001   PHE A 409 
 TRP   0.016   0.001   TRP A 553 
 HIS   0.002   0.000   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00261 ( 4459)
  covalent geometry    : angle       0.48831 ( 6086)
  SS BOND              : bond        0.00219 (    1)
  SS BOND              : angle       1.15965 (    2)
  hydrogen bonds       : bond        0.06568 (  265)
  hydrogen bonds       : angle       3.97057 (  771)
  link_NAG-ASN         : bond        0.00090 (    1)
  link_NAG-ASN         : angle       1.41245 (    3)

********************** 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
  47 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 40
  time to evaluate  : 0.170 
Fit side-chains
  outliers start: 7
  outliers final: 6
  residues processed: 45
  average time/residue: 0.4368
  time to fit residues: 20.5385
Evaluate side-chains
  47 residues out of total 451 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 41
  time to evaluate  : 0.155 
-------------------------------------------------------------------------------
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=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 53
   random chunks:
   chunk 2 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 7 optimal weight:    3.9990
   chunk 1 optimal weight:    1.9990
   chunk 19 optimal weight:    0.5980
   chunk 45 optimal weight:    1.9990
   chunk 31 optimal weight:    0.6980
   chunk 44 optimal weight:    1.9990
   chunk 17 optimal weight:    3.9990
   chunk 39 optimal weight:    0.8980
   chunk 36 optimal weight:    0.6980
   overall best weight:    0.9782

-------------------------------------------------------------------------------
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 = 0.108798 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2927 r_free = 0.2927 target = 0.095850 restraints weight = 4712.004|
|-----------------------------------------------------------------------------|
r_work (start): 0.2906 rms_B_bonded: 0.94
r_work: 0.2813 rms_B_bonded: 1.41 restraints_weight: 0.5000
r_work: 0.2715 rms_B_bonded: 2.43 restraints_weight: 0.2500
r_work (final): 0.2715
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8759
moved from start:          0.0686

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.027   4461  Z= 0.136
  Angle     :  0.501   5.803   6091  Z= 0.272
  Chirality :  0.040   0.138    681
  Planarity :  0.005   0.035    738
  Dihedral  :  5.172  32.569    610
  Min Nonbonded Distance : 2.276

Molprobity Statistics.
  All-atom Clashscore : 1.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.26 %
    Favored  : 97.74 %
  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 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:  1.92 (0.38), residues: 532
  helix:  2.05 (0.28), residues: 365
  sheet:  None (None), residues: 0
  loop : -0.45 (0.49), residues: 167

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.007   0.001   ARG A 604 
 TYR   0.019   0.001   TYR A  84 
 PHE   0.012   0.001   PHE A 409 
 TRP   0.015   0.001   TRP A 553 
 HIS   0.002   0.001   HIS A 222 

Details of bonding type rmsd
  covalent geometry    : bond        0.00281 ( 4459)
  covalent geometry    : angle       0.50022 ( 6086)
  SS BOND              : bond        0.00240 (    1)
  SS BOND              : angle       1.22808 (    2)
  hydrogen bonds       : bond        0.06882 (  265)
  hydrogen bonds       : angle       4.01106 (  771)
  link_NAG-ASN         : bond        0.00114 (    1)
  link_NAG-ASN         : angle       1.39646 (    3)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1372.01 seconds
wall clock time: 24 minutes 6.66 seconds (1446.66 seconds total)