Starting phenix.real_space_refine
on Tue Aug  4 16:15:15 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8uo8_42430/08_2026/8uo8_42430.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8uo8_42430/08_2026/8uo8_42430.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.2
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8uo8_42430/08_2026/8uo8_42430.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8uo8_42430/08_2026/8uo8_42430.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8uo8_42430/08_2026/8uo8_42430.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8uo8_42430/08_2026/8uo8_42430.cif"
  }
  resolution = 3.2
  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=   0.002 sd=   0.077
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: 7
    Type Number    sf(0)   Gaussians
     P       2      5.49       5
     S      45      5.16       5
     Cl      1      4.86       5
     C    3146      2.51       5
     N     737      2.21       5
     O     851      1.98       5
     F       5      1.80       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 11 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib"
  Total number of atoms: 4787
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4554
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 574, 4554
          Classifications: {'peptide': 574}
          Modifications used: {'COO': 1}
          Link IDs: {'PTRANS': 14, 'TRANS': 559}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 233
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 14, 233
          Unusual residues: {'43Y': 1, '9Z9': 2, 'NAG': 3, 'PS1': 1, 'X3U': 1, 'Y01': 1}
          Classifications: {'undetermined': 9, 'water': 5}
          Link IDs: {None: 13}
          Unresolved non-hydrogen bonds: 19
          Unresolved non-hydrogen angles: 22
          Unresolved non-hydrogen dihedrals: 25
          Unresolved non-hydrogen chiralities: 3
  Residues with excluded nonbonded symmetry interactions: 2
    residue:
      pdb=" N   ARG A 106 " occ=0.50
      ... (9 atoms not shown)
      pdb=" NH2 ARG A 106 " occ=0.50
    residue:
      pdb=" N   GLU A 234 " occ=0.50
      ... (7 atoms not shown)
      pdb=" OE2 GLU A 234 " occ=0.50
  Time building chain proxies: 1.49, per 1000 atoms: 0.31
  Number of scatterers: 4787
  At special positions: 0
  Unit cell: (97.2, 105.12, 66.24, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 7
    Type Number    sf(0)
     Cl      1     17.00
     S      45     16.00
     P       2     15.00
     F       5      9.00
     O     851      8.00
     N     737      7.00
     C    3146      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 492 " - pdb=" SG  CYS A 512 " distance=2.03

  Automatic linking
    Parameters for automatic linking
      Linking & cutoffs
        Metal                : Auto  - 3.00
        Amino acid           : True  - 1.90
        Carbohydrate         : True  - 1.99
        Ligands              : True  - 1.99
        Small molecules      : False - 1.98
        Amino acid - RNA/DNA : False
      
  Number of custom bonds: simple=0, symmetry=0
  Links applied
    NAG-ASN
      " NAG A 701 " - " ASN A 441 "
      " NAG A 702 " - " ASN A 516 "
      " NAG A 703 " - " ASN A 491 "
  Time building additional restraints: 0.52
  Conformation dependent library (CDL) restraints added in 208.3 milliseconds
  

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1052

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 1 sheets defined
      65.2% alpha, 4.9% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.14
  Creating SS restraints...
    Processing helix  chain 'A' and resid 87 through 103
    Processing helix  chain 'A' and resid 105 through 131
      removed outlier: 3.769A  pdb=" N   ILE A 110 " --> pdb=" O   ARG A 106 " (cutoff:3.500A)
      removed outlier: 3.579A  pdb=" N   LEU A 117 " --> pdb=" O   PHE A 113 " (cutoff:3.500A)
      removed outlier: 3.849A  pdb=" N   ALA A 118 " --> pdb=" O   VAL A 114 " (cutoff:3.500A)
      removed outlier: 3.592A  pdb=" N   LEU A 119 " --> pdb=" O   LEU A 115 " (cutoff:3.500A)
      removed outlier: 3.665A  pdb=" N   ASP A 122 " --> pdb=" O   ALA A 118 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 133 through 137
      removed outlier: 3.878A  pdb=" N   ALA A 136 " --> pdb=" O   LEU A 133 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 151 through 168
      removed outlier: 3.801A  pdb=" N   LEU A 156 " --> pdb=" O   MET A 152 " (cutoff:3.500A)
      removed outlier: 3.688A  pdb=" N   PHE A 163 " --> pdb=" O   MET A 159 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 168 through 173
    Processing helix  chain 'A' and resid 175 through 191
    Processing helix  chain 'A' and resid 197 through 224
      removed outlier: 3.558A  pdb=" N   PHE A 201 " --> pdb=" O   GLY A 197 " (cutoff:3.500A)
      removed outlier: 3.732A  pdb=" N   ILE A 207 " --> pdb=" O   PHE A 203 " (cutoff:3.500A)
      Proline residue:  A 217  - end of helix
      removed outlier: 3.641A  pdb=" N   PHE A 220 " --> pdb=" O   LEU A 216 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 228 through 232
      removed outlier: 3.951A  pdb=" N   ARG A 232 " --> pdb=" O   ARG A 229 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 233 through 238
    Processing helix  chain 'A' and resid 239 through 256
      removed outlier: 4.069A  pdb=" N   TRP A 243 " --> pdb=" O   LEU A 239 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 275 through 283
    Processing helix  chain 'A' and resid 284 through 296
      removed outlier: 3.780A  pdb=" N   VAL A 292 " --> pdb=" O   THR A 288 " (cutoff:3.500A)
      removed outlier: 3.647A  pdb=" N   LYS A 295 " --> pdb=" O   MET A 291 " (cutoff:3.500A)
      removed outlier: 4.116A  pdb=" N   PHE A 296 " --> pdb=" O   VAL A 292 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 300 through 307
    Processing helix  chain 'A' and resid 310 through 328
      removed outlier: 3.780A  pdb=" N   MET A 315 " --> pdb=" O   ASP A 311 " (cutoff:3.500A)
      removed outlier: 4.462A  pdb=" N   ILE A 316 " --> pdb=" O   GLU A 312 " (cutoff:3.500A)
      removed outlier: 3.936A  pdb=" N   ALA A 327 " --> pdb=" O   THR A 323 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   LYS A 328 " --> pdb=" O   ASN A 324 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 369 through 383
      removed outlier: 3.548A  pdb=" N   VAL A 382 " --> pdb=" O   ALA A 378 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 387 through 425
      removed outlier: 3.504A  pdb=" N   ILE A 392 " --> pdb=" O   MET A 388 " (cutoff:3.500A)
      removed outlier: 3.890A  pdb=" N   VAL A 395 " --> pdb=" O   LEU A 391 " (cutoff:3.500A)
      Proline residue:  A 412  - end of helix
    Processing helix  chain 'A' and resid 532 through 547
    Processing helix  chain 'A' and resid 548 through 560
      removed outlier: 4.247A  pdb=" N   GLY A 552 " --> pdb=" O   SER A 548 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 565 through 584
      removed outlier: 3.846A  pdb=" N   ILE A 569 " --> pdb=" O   ARG A 565 " (cutoff:3.500A)
      removed outlier: 3.834A  pdb=" N   GLY A 570 " --> pdb=" O   LEU A 566 " (cutoff:3.500A)
      removed outlier: 3.798A  pdb=" N   PHE A 584 " --> pdb=" O   CYS A 580 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 590 through 616
      removed outlier: 4.825A  pdb=" N   ALA A 605 " --> pdb=" O   GLY A 601 " (cutoff:3.500A)
      removed outlier: 4.393A  pdb=" N   ALA A 606 " --> pdb=" O   THR A 602 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 623 through 645
    Processing helix  chain 'A' and resid 646 through 649
      removed outlier: 4.140A  pdb=" N   VAL A 649 " --> pdb=" O   ALA A 646 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 646 through 649'
    Processing helix  chain 'A' and resid 654 through 670
      removed outlier: 3.525A  pdb=" N   ILE A 670 " --> pdb=" O   GLY A 666 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 671 through 674
    Processing sheet with id=AA1, first strand: chain 'A' and resid 428 through 429
  WARNING: can't find start of bonding for strands!
    previous: chain 'A' and resid 428 through 429
    current: chain 'A' and resid 454 through 474
      removed outlier: 6.506A  pdb=" N   CYS A 477 " --> pdb=" O   ASN A 456 " (cutoff:3.500A)
      removed outlier: 6.521A  pdb=" N   LYS A 458 " --> pdb=" O   CYS A 477 " (cutoff:3.500A)
      removed outlier: 6.896A  pdb=" N   PHE A 479 " --> pdb=" O   LYS A 458 " (cutoff:3.500A)
      removed outlier: 6.776A  pdb=" N   THR A 460 " --> pdb=" O   PHE A 479 " (cutoff:3.500A)
      removed outlier: 6.738A  pdb=" N   ASP A 481 " --> pdb=" O   THR A 460 " (cutoff:3.500A)

    248 hydrogen bonds defined for protein.
    735 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: 0.83

  Time building geometry restraints manager: 0.67 seconds

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

  Histogram of bond lengths:
        1.21 -     1.34: 1413
        1.34 -     1.47: 1336
        1.47 -     1.60: 2088
        1.60 -     1.73: 3
        1.73 -     1.87: 77
  Bond restraints: 4917
  Sorted by residual:
  bond pdb=" C3  PS1 A 705 "
       pdb=" O4  PS1 A 705 "
    ideal  model  delta    sigma   weight residual
    1.247  1.342 -0.095 2.00e-02 2.50e+03 2.25e+01
  bond pdb=" CAX Y01 A 709 "
       pdb=" OAH Y01 A 709 "
    ideal  model  delta    sigma   weight residual
    1.248  1.343 -0.095 2.00e-02 2.50e+03 2.24e+01
  bond pdb=" C22 X3U A 704 "
       pdb=" N06 X3U A 704 "
    ideal  model  delta    sigma   weight residual
    1.440  1.366  0.074 2.00e-02 2.50e+03 1.36e+01
  bond pdb=" C22 X3U A 704 "
       pdb=" S23 X3U A 704 "
    ideal  model  delta    sigma   weight residual
    1.732  1.799 -0.067 2.00e-02 2.50e+03 1.11e+01
  bond pdb=" C4  43Y A 708 "
       pdb=" O4P 43Y A 708 "
    ideal  model  delta    sigma   weight residual
    1.433  1.369  0.064 2.00e-02 2.50e+03 1.03e+01
  ... (remaining 4912 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     3.32: 6576
        3.32 -     6.64: 84
        6.64 -     9.96: 11
        9.96 -    13.27: 2
       13.27 -    16.59: 1
  Bond angle restraints: 6674
  Sorted by residual:
  angle pdb=" O3  PS1 A 705 "
        pdb=" P1  PS1 A 705 "
        pdb=" O6  PS1 A 705 "
      ideal   model   delta    sigma   weight residual
      93.15  109.74  -16.59 3.00e+00 1.11e-01 3.06e+01
  angle pdb=" N   MET A 152 "
        pdb=" CA  MET A 152 "
        pdb=" C   MET A 152 "
      ideal   model   delta    sigma   weight residual
     111.33  105.79    5.54 1.21e+00 6.83e-01 2.09e+01
  angle pdb=" C4  PS1 A 705 "
        pdb=" O6  PS1 A 705 "
        pdb=" P1  PS1 A 705 "
      ideal   model   delta    sigma   weight residual
     118.96  107.29   11.67 3.00e+00 1.11e-01 1.51e+01
  angle pdb=" N   LEU A 156 "
        pdb=" CA  LEU A 156 "
        pdb=" C   LEU A 156 "
      ideal   model   delta    sigma   weight residual
     111.71  107.26    4.45 1.15e+00 7.56e-01 1.50e+01
  angle pdb=" CA  GLY A 157 "
        pdb=" C   GLY A 157 "
        pdb=" O   GLY A 157 "
      ideal   model   delta    sigma   weight residual
     121.00  117.27    3.73 1.08e+00 8.57e-01 1.19e+01
  ... (remaining 6669 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    24.85: 2871
       24.85 -    49.70: 174
       49.70 -    74.54: 27
       74.54 -    99.39: 11
       99.39 -   124.24: 7
  Dihedral angle restraints: 3090
    sinusoidal: 1445
      harmonic: 1645
  Sorted by residual:
  dihedral pdb=" CA  VAL A 615 "
           pdb=" C   VAL A 615 "
           pdb=" N   GLU A 616 "
           pdb=" CA  GLU A 616 "
      ideal   model   delta  harmonic     sigma   weight residual
     180.00  158.63   21.37     0      5.00e+00 4.00e-02 1.83e+01
  dihedral pdb=" O7  PS1 A 705 "
           pdb=" C5  PS1 A 705 "
           pdb=" C6  PS1 A 705 "
           pdb=" O9  PS1 A 705 "
      ideal   model   delta sinusoidal    sigma   weight residual
      57.39  -66.85  124.24     1      3.00e+01 1.11e-03 1.67e+01
  dihedral pdb=" C1  PS1 A 705 "
           pdb=" O3  PS1 A 705 "
           pdb=" P1  PS1 A 705 "
           pdb=" O6  PS1 A 705 "
      ideal   model   delta sinusoidal    sigma   weight residual
    -176.99  -66.57 -110.42     1      3.00e+01 1.11e-03 1.44e+01
  ... (remaining 3087 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.091: 683
       0.091 -    0.182: 38
       0.182 -    0.273: 9
       0.273 -    0.363: 7
       0.363 -    0.454: 2
  Chirality restraints: 739
  Sorted by residual:
  chirality pdb=" CBG Y01 A 709 "
            pdb=" CAQ Y01 A 709 "
            pdb=" CBD Y01 A 709 "
            pdb=" CBI Y01 A 709 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.33   -2.79    0.45 2.00e-01 2.50e+01 5.16e+00
  chirality pdb=" C74 9Z9 A 707 "
            pdb=" C03 9Z9 A 707 "
            pdb=" C73 9Z9 A 707 "
            pdb=" C75 9Z9 A 707 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.95    0.39 2.00e-01 2.50e+01 3.78e+00
  chirality pdb=" C74 9Z9 A 706 "
            pdb=" C03 9Z9 A 706 "
            pdb=" C73 9Z9 A 706 "
            pdb=" C75 9Z9 A 706 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.56   -2.92    0.36 2.00e-01 2.50e+01 3.26e+00
  ... (remaining 736 not shown)

  Planarity restraints: 802
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C   LEU A 133 "   -0.037 5.00e-02 4.00e+02   5.52e-02 4.87e+00
        pdb=" N   PRO A 134 "    0.095 5.00e-02 4.00e+02
        pdb=" CA  PRO A 134 "   -0.028 5.00e-02 4.00e+02
        pdb=" CD  PRO A 134 "   -0.031 5.00e-02 4.00e+02
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  ALA A 160 "   -0.007 2.00e-02 2.50e+03   1.34e-02 1.79e+00
        pdb=" C   ALA A 160 "    0.023 2.00e-02 2.50e+03
        pdb=" O   ALA A 160 "   -0.009 2.00e-02 2.50e+03
        pdb=" N   GLY A 161 "   -0.008 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  GLY A 157 "   -0.006 2.00e-02 2.50e+03   1.27e-02 1.62e+00
        pdb=" C   GLY A 157 "    0.022 2.00e-02 2.50e+03
        pdb=" O   GLY A 157 "   -0.008 2.00e-02 2.50e+03
        pdb=" N   MET A 158 "   -0.008 2.00e-02 2.50e+03
  ... (remaining 799 not shown)

  Histogram of nonbonded interaction distances:
        2.01 -     2.59: 49
        2.59 -     3.17: 4406
        3.17 -     3.74: 7412
        3.74 -     4.32: 10841
        4.32 -     4.90: 18005
  Nonbonded interactions: 40713
  Sorted by model distance:
  nonbonded pdb=" OE1 GLU A 225 "
            pdb=" OG  SER A 300 "
     model   vdw
     2.012 3.040
  nonbonded pdb=" O   LEU A 142 "
            pdb=" OG  SER A 143 "
     model   vdw
     2.087 3.040
  nonbonded pdb=" NH2 ARG A 174 "
            pdb=" O   THR A 620 "
     model   vdw
     2.202 3.120
  nonbonded pdb=" OD1 ASP A 529 "
            pdb=" N   LEU A 530 "
     model   vdw
     2.265 3.120
  nonbonded pdb=" OH  TYR A 222 "
            pdb=" O   PRO A 298 "
     model   vdw
     2.271 3.040
  ... (remaining 40708 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=0.50 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:             2.460
  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:          0.120
  Check model and map are aligned:         0.010
  Set scattering table:                    0.010
  Process input model:                     7.360
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.330
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   11.330
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7461
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      :  0.006   0.095   4921  Z= 0.312
  Angle     :  0.873  16.593   6685  Z= 0.400
  Chirality :  0.063   0.454    739
  Planarity :  0.003   0.055    799
  Dihedral  : 17.513 124.241   2035
  Min Nonbonded Distance : 2.012

Molprobity Statistics.
  All-atom Clashscore : 6.51
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  7.19 %
    Favored  : 92.81 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  3.70 %
    Favored  : 95.47 %
  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 are not related in a simple way.
  whole: -4.02 (0.30), residues: 570
  helix: -1.91 (0.25), residues: 334
  sheet: -2.64 (1.41), residues: 10
  loop : -3.82 (0.34), residues: 226

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 565 
 TYR   0.016   0.001   TYR A 505 
 PHE   0.008   0.001   PHE A 112 
 TRP   0.018   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00636 /  0.31 ( 4917)
  covalent geometry    : angle       0.87239 /  0.40 ( 6674)
  SS BOND              : bond        0.00119 /  0.06 (    1)
  SS BOND              : angle       1.20931 /  0.66 (    2)
  hydrogen bonds       : bond        0.15527 /  9.47 (  248)
  hydrogen bonds       : angle       7.19593 /  4.97 (  735)
  link_NAG-ASN         : bond        0.00284 /  0.14 (    3)
  link_NAG-ASN         : angle       1.12931 /  0.66 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.157 
Fit side-chains
REVERT: A  140 MET cc_start: 0.4982 (mmp) cc_final: 0.3937 (mmp)
REVERT: A  146 LYS cc_start: 0.7970 (ptmt) cc_final: 0.7626 (pttt)
REVERT: A  488 TYR cc_start: 0.7198 (m-80) cc_final: 0.6665 (m-80)
REVERT: A  528 MET cc_start: 0.2693 (ttt) cc_final: 0.2425 (tmm)
  outliers start: 4
  outliers final: 1
  residues processed: 52
  average time/residue: 0.0705
  time to fit residues: 4.9424
Evaluate side-chains
  44 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 43
  time to evaluate  : 0.161 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 MET
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 54 optimal weight:    0.9980
   chunk 24 optimal weight:    0.0770
   chunk 48 optimal weight:    1.9990
   chunk 56 optimal weight:    4.9990
   chunk 26 optimal weight:    0.9990
   chunk 2 optimal weight:    0.7980
   chunk 16 optimal weight:    0.6980
   chunk 32 optimal weight:    5.9990
   chunk 31 optimal weight:    0.8980
   chunk 25 optimal weight:    0.9990
   chunk 50 optimal weight:    0.5980
   overall best weight:    0.6138

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 185 ASN
A 260 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4381 r_free = 0.4381 target = 0.216780 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.181031 restraints weight = 4881.014|
|-----------------------------------------------------------------------------|
r_work (start): 0.4044 rms_B_bonded: 1.65
r_work: 0.3864 rms_B_bonded: 3.24 restraints_weight: 0.5000
r_work (final): 0.3864
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3876
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3876 r_free = 0.3876    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.50   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3871 r_free = 0.3871    target_work(ls_wunit_k1) = 0.163         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 4 (10 function evaluations)
r_final: 0.3871
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7859
moved from start:          0.1776

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.042   4921  Z= 0.156
  Angle     :  0.626   9.235   6685  Z= 0.305
  Chirality :  0.042   0.174    739
  Planarity :  0.004   0.038    799
  Dihedral  : 13.100 110.130   1012
  Min Nonbonded Distance : 2.381

Molprobity Statistics.
  All-atom Clashscore : 6.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  0.82 %
    Allowed  :  7.82 %
    Favored  : 91.36 %
  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 are not related in a simple way.
  whole: -2.23 (0.34), residues: 570
  helix: -0.36 (0.27), residues: 343
  sheet: -1.65 (1.69), residues: 10
  loop : -3.35 (0.38), residues: 217

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.004   0.000   ARG A 565 
 TYR   0.019   0.002   TYR A 505 
 PHE   0.013   0.001   PHE A 112 
 TRP   0.021   0.002   TRP A 255 
 HIS   0.003   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00345 /  0.16 ( 4917)
  covalent geometry    : angle       0.62484 /  0.31 ( 6674)
  SS BOND              : bond        0.00214 /  0.11 (    1)
  SS BOND              : angle       1.69032 /  0.94 (    2)
  hydrogen bonds       : bond        0.04180 /  2.85 (  248)
  hydrogen bonds       : angle       4.59276 /  3.27 (  735)
  link_NAG-ASN         : bond        0.00355 /  0.17 (    3)
  link_NAG-ASN         : angle       1.05862 /  0.59 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  54 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 50
  time to evaluate  : 0.165 
Fit side-chains
REVERT: A  140 MET cc_start: 0.5513 (mmp) cc_final: 0.4291 (mmp)
REVERT: A  146 LYS cc_start: 0.8242 (ptmt) cc_final: 0.7713 (pttt)
REVERT: A  147 LYS cc_start: 0.7251 (ttpp) cc_final: 0.6676 (tttt)
REVERT: A  291 MET cc_start: 0.6696 (ttp) cc_final: 0.6456 (tpt)
REVERT: A  488 TYR cc_start: 0.7163 (m-80) cc_final: 0.6801 (m-80)
REVERT: A  528 MET cc_start: 0.3491 (ttt) cc_final: 0.2400 (tmm)
  outliers start: 4
  outliers final: 4
  residues processed: 51
  average time/residue: 0.0714
  time to fit residues: 4.8316
Evaluate side-chains
  51 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 47
  time to evaluate  : 0.185 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  152 MET
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  548 SER
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 14 optimal weight:    1.9990
   chunk 46 optimal weight:    1.9990
   chunk 11 optimal weight:    1.9990
   chunk 50 optimal weight:    0.5980
   chunk 23 optimal weight:    0.7980
   chunk 24 optimal weight:    0.9980
   chunk 41 optimal weight:    0.1980
   chunk 33 optimal weight:    0.9980
   chunk 39 optimal weight:    0.9980
   overall best weight:    0.6780

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 534 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4340 r_free = 0.4340 target = 0.212035 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 49)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.176288 restraints weight = 4976.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.3999 rms_B_bonded: 1.67
r_work: 0.3818 rms_B_bonded: 3.22 restraints_weight: 0.5000
r_work (final): 0.3818
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3823
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.81   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3823 r_free = 0.3823    target_work(ls_wunit_k1) = 0.158         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3823
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7900
moved from start:          0.2437

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.049   4921  Z= 0.149
  Angle     :  0.586   8.924   6685  Z= 0.288
  Chirality :  0.041   0.160    739
  Planarity :  0.003   0.029    799
  Dihedral  : 11.653 104.215   1012
  Min Nonbonded Distance : 2.558

Molprobity Statistics.
  All-atom Clashscore : 6.83
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  1.44 %
    Allowed  : 11.73 %
    Favored  : 86.83 %
  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 are not related in a simple way.
  whole: -1.52 (0.35), residues: 570
  helix:  0.23 (0.28), residues: 344
  sheet: -1.13 (1.82), residues: 10
  loop : -3.15 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 565 
 TYR   0.019   0.002   TYR A 505 
 PHE   0.012   0.001   PHE A 188 
 TRP   0.021   0.002   TRP A 255 
 HIS   0.003   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00342 /  0.15 ( 4917)
  covalent geometry    : angle       0.58471 /  0.29 ( 6674)
  SS BOND              : bond        0.00249 /  0.13 (    1)
  SS BOND              : angle       1.39163 /  0.77 (    2)
  hydrogen bonds       : bond        0.04057 /  2.75 (  248)
  hydrogen bonds       : angle       4.33564 /  3.11 (  735)
  link_NAG-ASN         : bond        0.00261 /  0.12 (    3)
  link_NAG-ASN         : angle       1.05017 /  0.58 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 7
    poor density    : 62
  time to evaluate  : 0.107 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.5784 (mmp) cc_final: 0.4932 (ptm)
REVERT: A  146 LYS cc_start: 0.8028 (ptmt) cc_final: 0.7613 (pttt)
REVERT: A  156 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7682 (mt)
REVERT: A  307 MET cc_start: 0.7555 (mtt) cc_final: 0.7234 (tpp)
REVERT: A  488 TYR cc_start: 0.7198 (m-80) cc_final: 0.6900 (m-80)
REVERT: A  561 ASP cc_start: 0.8395 (m-30) cc_final: 0.8085 (m-30)
  outliers start: 7
  outliers final: 5
  residues processed: 64
  average time/residue: 0.0425
  time to fit residues: 3.6914
Evaluate side-chains
  62 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 56
  time to evaluate  : 0.095 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  665 VAL
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 47 optimal weight:    3.9990
   chunk 37 optimal weight:    4.9990
   chunk 30 optimal weight:    0.3980
   chunk 56 optimal weight:    5.9990
   chunk 19 optimal weight:    0.6980
   chunk 24 optimal weight:    3.9990
   chunk 15 optimal weight:    1.9990
   chunk 54 optimal weight:    1.9990
   chunk 1 optimal weight:    5.9990
   chunk 50 optimal weight:    0.2980
   chunk 9 optimal weight:    1.9990
   overall best weight:    1.0784

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A 319 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4059 r_free = 0.4059 target = 0.188650 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3710 r_free = 0.3710 target = 0.152487 restraints weight = 5094.939|
|-----------------------------------------------------------------------------|
r_work (start): 0.3707 rms_B_bonded: 1.55
r_work: 0.3582 rms_B_bonded: 2.58 restraints_weight: 0.5000
r_work: 0.3433 rms_B_bonded: 4.36 restraints_weight: 0.2500
r_work (final): 0.3433
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8042
moved from start:          0.3116

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.056   4921  Z= 0.196
  Angle     :  0.660   9.237   6685  Z= 0.324
  Chirality :  0.043   0.179    739
  Planarity :  0.003   0.031    799
  Dihedral  : 11.499 105.290   1009
  Min Nonbonded Distance : 2.553

Molprobity Statistics.
  All-atom Clashscore : 8.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 13.79 %
    Favored  : 83.33 %
  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 are not related in a simple way.
  whole: -1.41 (0.34), residues: 570
  helix:  0.29 (0.28), residues: 344
  sheet: -0.73 (1.84), residues: 10
  loop : -3.06 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 565 
 TYR   0.031   0.002   TYR A 505 
 PHE   0.016   0.002   PHE A 112 
 TRP   0.021   0.002   TRP A 255 
 HIS   0.004   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00463 /  0.20 ( 4917)
  covalent geometry    : angle       0.65864 /  0.32 ( 6674)
  SS BOND              : bond        0.00263 /  0.14 (    1)
  SS BOND              : angle       1.35832 /  0.75 (    2)
  hydrogen bonds       : bond        0.04469 /  3.06 (  248)
  hydrogen bonds       : angle       4.43792 /  3.19 (  735)
  link_NAG-ASN         : bond        0.00317 /  0.15 (    3)
  link_NAG-ASN         : angle       1.16282 /  0.60 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 72
  time to evaluate  : 0.213 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.6338 (mmp) cc_final: 0.5180 (ptm)
REVERT: A  146 LYS cc_start: 0.8302 (ptmt) cc_final: 0.7919 (pttt)
REVERT: A  156 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7821 (mt)
REVERT: A  176 ARG cc_start: 0.8297 (ttt180) cc_final: 0.7937 (ttm110)
REVERT: A  244 MET cc_start: 0.7252 (tmm) cc_final: 0.6959 (tmm)
REVERT: A  307 MET cc_start: 0.7730 (OUTLIER) cc_final: 0.7458 (tpp)
REVERT: A  387 ARG cc_start: 0.8184 (ttp-110) cc_final: 0.7595 (ttp-110)
REVERT: A  416 ARG cc_start: 0.7405 (ttt-90) cc_final: 0.7047 (ttp80)
REVERT: A  480 GLU cc_start: 0.6859 (tt0) cc_final: 0.6654 (tt0)
REVERT: A  528 MET cc_start: 0.3901 (ttt) cc_final: 0.2864 (pmm)
REVERT: A  531 GLU cc_start: 0.7556 (tp30) cc_final: 0.7209 (tp30)
REVERT: A  616 GLU cc_start: 0.7583 (OUTLIER) cc_final: 0.6348 (mp0)
REVERT: A  627 PHE cc_start: 0.8138 (OUTLIER) cc_final: 0.7291 (m-80)
  outliers start: 14
  outliers final: 7
  residues processed: 80
  average time/residue: 0.0686
  time to fit residues: 7.0355
Evaluate side-chains
  79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 68
  time to evaluate  : 0.156 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  616 GLU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  665 VAL
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 1 optimal weight:    4.9990
   chunk 8 optimal weight:    1.9990
   chunk 26 optimal weight:    0.7980
   chunk 11 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 7 optimal weight:    0.7980
   chunk 0 optimal weight:    4.9990
   chunk 15 optimal weight:    1.9990
   chunk 25 optimal weight:    0.3980
   chunk 48 optimal weight:    0.5980
   chunk 40 optimal weight:    0.0980
   overall best weight:    0.5380

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
A  93 HIS
A 260 HIS

Total number of N/Q/H flips: 2

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.193997 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3770 r_free = 0.3770 target = 0.158267 restraints weight = 5085.513|
|-----------------------------------------------------------------------------|
r_work (start): 0.3699 rms_B_bonded: 1.54
r_work: 0.3587 rms_B_bonded: 2.47 restraints_weight: 0.5000
r_work: 0.3440 rms_B_bonded: 4.18 restraints_weight: 0.2500
r_work (final): 0.3440
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3458
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.90   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3458 r_free = 0.3458    target_work(ls_wunit_k1) = 0.130         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3458
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7913
moved from start:          0.3307

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4921  Z= 0.135
  Angle     :  0.587   9.511   6685  Z= 0.288
  Chirality :  0.041   0.149    739
  Planarity :  0.003   0.027    799
  Dihedral  : 10.945  99.311   1009
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.63 %
    Favored  : 97.37 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 15.64 %
    Favored  : 81.89 %
  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 are not related in a simple way.
  whole: -1.07 (0.35), residues: 570
  helix:  0.60 (0.28), residues: 344
  sheet: -0.53 (1.83), residues: 10
  loop : -3.00 (0.37), residues: 216

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 565 
 TYR   0.018   0.002   TYR A 505 
 PHE   0.012   0.001   PHE A 188 
 TRP   0.021   0.002   TRP A 255 
 HIS   0.004   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00307 /  0.13 ( 4917)
  covalent geometry    : angle       0.58611 /  0.29 ( 6674)
  SS BOND              : bond        0.00207 /  0.11 (    1)
  SS BOND              : angle       1.35380 /  0.75 (    2)
  hydrogen bonds       : bond        0.03802 /  2.60 (  248)
  hydrogen bonds       : angle       4.17290 /  3.02 (  735)
  link_NAG-ASN         : bond        0.00212 /  0.10 (    3)
  link_NAG-ASN         : angle       0.94637 /  0.50 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 69
  time to evaluate  : 0.212 
Fit side-chains
REVERT: A  140 MET cc_start: 0.6165 (mmp) cc_final: 0.4863 (ppp)
REVERT: A  146 LYS cc_start: 0.8105 (ptmt) cc_final: 0.7846 (pttt)
REVERT: A  147 LYS cc_start: 0.7228 (ttpp) cc_final: 0.6664 (tttt)
REVERT: A  156 LEU cc_start: 0.7978 (OUTLIER) cc_final: 0.7653 (mt)
REVERT: A  176 ARG cc_start: 0.8127 (ttt180) cc_final: 0.7704 (ttm110)
REVERT: A  307 MET cc_start: 0.7635 (mtt) cc_final: 0.7371 (tpp)
REVERT: A  387 ARG cc_start: 0.8053 (ttp-110) cc_final: 0.7413 (ttp-110)
REVERT: A  416 ARG cc_start: 0.7213 (ttt-90) cc_final: 0.6867 (ttp80)
REVERT: A  480 GLU cc_start: 0.6802 (tt0) cc_final: 0.6572 (tt0)
REVERT: A  528 MET cc_start: 0.3716 (ttt) cc_final: 0.2563 (tmm)
REVERT: A  531 GLU cc_start: 0.7539 (tp30) cc_final: 0.7071 (tp30)
REVERT: A  610 LEU cc_start: 0.8371 (tp) cc_final: 0.8166 (mp)
REVERT: A  616 GLU cc_start: 0.7358 (OUTLIER) cc_final: 0.6039 (mp0)
REVERT: A  627 PHE cc_start: 0.7957 (OUTLIER) cc_final: 0.7104 (m-80)
  outliers start: 12
  outliers final: 8
  residues processed: 77
  average time/residue: 0.0844
  time to fit residues: 8.1653
Evaluate side-chains
  77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 66
  time to evaluate  : 0.195 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  129 VAL
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  616 GLU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  665 VAL
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 3 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 51 optimal weight:    0.6980
   chunk 16 optimal weight:    0.6980
   chunk 5 optimal weight:    2.9990
   chunk 53 optimal weight:    2.9990
   chunk 56 optimal weight:    0.0370
   chunk 18 optimal weight:    2.9990
   chunk 33 optimal weight:    4.9990
   chunk 26 optimal weight:    0.8980
   chunk 25 optimal weight:    0.0370
   overall best weight:    0.4536

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4110 r_free = 0.4110 target = 0.193749 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 51)----------------|
| r_work = 0.3768 r_free = 0.3768 target = 0.158002 restraints weight = 5124.705|
|-----------------------------------------------------------------------------|
r_work (start): 0.3709 rms_B_bonded: 1.55
r_work: 0.3597 rms_B_bonded: 2.49 restraints_weight: 0.5000
r_work: 0.3450 rms_B_bonded: 4.22 restraints_weight: 0.2500
r_work (final): 0.3450
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3519
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3519 r_free = 0.3519    target_work(ls_wunit_k1) = 0.134         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3519
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7892
moved from start:          0.3470

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.047   4921  Z= 0.127
  Angle     :  0.577   9.422   6685  Z= 0.284
  Chirality :  0.040   0.151    739
  Planarity :  0.003   0.026    799
  Dihedral  : 10.634  94.794   1009
  Min Nonbonded Distance : 2.538

Molprobity Statistics.
  All-atom Clashscore : 8.09
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.68 %
    Favored  : 96.32 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 16.46 %
    Favored  : 80.86 %
  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 are not related in a simple way.
  whole: -0.91 (0.35), residues: 570
  helix:  0.79 (0.28), residues: 345
  sheet: -3.21 (0.99), residues: 25
  loop : -2.81 (0.38), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 232 
 TYR   0.018   0.002   TYR A 505 
 PHE   0.009   0.001   PHE A 112 
 TRP   0.019   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00286 /  0.13 ( 4917)
  covalent geometry    : angle       0.57614 /  0.28 ( 6674)
  SS BOND              : bond        0.00206 /  0.11 (    1)
  SS BOND              : angle       1.30030 /  0.72 (    2)
  hydrogen bonds       : bond        0.03711 /  2.52 (  248)
  hydrogen bonds       : angle       4.06795 /  2.95 (  735)
  link_NAG-ASN         : bond        0.00217 /  0.10 (    3)
  link_NAG-ASN         : angle       0.92894 /  0.52 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  81 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 68
  time to evaluate  : 0.171 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.6165 (mmp) cc_final: 0.4913 (ptm)
REVERT: A  146 LYS cc_start: 0.7872 (ptmt) cc_final: 0.7664 (pttt)
REVERT: A  147 LYS cc_start: 0.7005 (ttpp) cc_final: 0.6482 (tttt)
REVERT: A  156 LEU cc_start: 0.7797 (OUTLIER) cc_final: 0.7488 (mt)
REVERT: A  176 ARG cc_start: 0.8103 (ttt180) cc_final: 0.7681 (ttm110)
REVERT: A  307 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.7304 (tpp)
REVERT: A  387 ARG cc_start: 0.8008 (ttp-110) cc_final: 0.7375 (ttp-110)
REVERT: A  416 ARG cc_start: 0.7193 (ttt-90) cc_final: 0.6824 (ttp80)
REVERT: A  480 GLU cc_start: 0.6667 (tt0) cc_final: 0.6372 (tt0)
REVERT: A  528 MET cc_start: 0.3542 (ttt) cc_final: 0.2312 (tmm)
REVERT: A  531 GLU cc_start: 0.7547 (tp30) cc_final: 0.7132 (tp30)
REVERT: A  616 GLU cc_start: 0.7401 (OUTLIER) cc_final: 0.6114 (mp0)
REVERT: A  627 PHE cc_start: 0.7945 (OUTLIER) cc_final: 0.7013 (m-80)
  outliers start: 13
  outliers final: 6
  residues processed: 77
  average time/residue: 0.0672
  time to fit residues: 6.7425
Evaluate side-chains
  74 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 10
    poor density    : 64
  time to evaluate  : 0.166 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  616 GLU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  665 VAL
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 43 optimal weight:    0.7980
   chunk 39 optimal weight:    4.9990
   chunk 51 optimal weight:    0.9990
   chunk 36 optimal weight:    5.9990
   chunk 55 optimal weight:    6.9990
   chunk 56 optimal weight:    1.9990
   chunk 21 optimal weight:    4.9990
   chunk 42 optimal weight:    0.6980
   chunk 14 optimal weight:    0.7980
   chunk 35 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   overall best weight:    0.8382

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4033 r_free = 0.4033 target = 0.187413 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 56)----------------|
| r_work = 0.3676 r_free = 0.3676 target = 0.150501 restraints weight = 5120.046|
|-----------------------------------------------------------------------------|
r_work (start): 0.3669 rms_B_bonded: 1.63
r_work: 0.3548 rms_B_bonded: 2.68 restraints_weight: 0.5000
r_work: 0.3396 rms_B_bonded: 4.52 restraints_weight: 0.2500
r_work (final): 0.3396
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3477
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3477 r_free = 0.3477    target_work(ls_wunit_k1) = 0.131         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3477
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7985
moved from start:          0.3593

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4921  Z= 0.167
  Angle     :  0.644  12.681   6685  Z= 0.309
  Chirality :  0.043   0.324    739
  Planarity :  0.003   0.025    799
  Dihedral  : 10.752  96.765   1009
  Min Nonbonded Distance : 2.535

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 17.49 %
    Favored  : 79.84 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.03 (0.35), residues: 570
  helix:  0.63 (0.28), residues: 349
  sheet: -3.22 (0.96), residues: 25
  loop : -2.78 (0.39), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 174 
 TYR   0.023   0.002   TYR A 505 
 PHE   0.014   0.001   PHE A 499 
 TRP   0.018   0.002   TRP A 255 
 HIS   0.004   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00394 /  0.17 ( 4917)
  covalent geometry    : angle       0.64260 /  0.31 ( 6674)
  SS BOND              : bond        0.00270 /  0.14 (    1)
  SS BOND              : angle       1.24098 /  0.69 (    2)
  hydrogen bonds       : bond        0.04091 /  2.77 (  248)
  hydrogen bonds       : angle       4.17391 /  3.01 (  735)
  link_NAG-ASN         : bond        0.00168 /  0.08 (    3)
  link_NAG-ASN         : angle       1.01806 /  0.55 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 66
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LEU cc_start: 0.6126 (OUTLIER) cc_final: 0.5881 (pt)
REVERT: A  140 MET cc_start: 0.6357 (mmp) cc_final: 0.5171 (ptm)
REVERT: A  146 LYS cc_start: 0.8066 (ptmt) cc_final: 0.7780 (pttt)
REVERT: A  156 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7641 (mt)
REVERT: A  176 ARG cc_start: 0.8349 (ttt180) cc_final: 0.7899 (ttm110)
REVERT: A  307 MET cc_start: 0.7646 (OUTLIER) cc_final: 0.7361 (tpp)
REVERT: A  416 ARG cc_start: 0.7282 (ttt-90) cc_final: 0.6907 (ttp80)
REVERT: A  480 GLU cc_start: 0.6812 (tt0) cc_final: 0.6588 (tt0)
REVERT: A  528 MET cc_start: 0.3821 (ttt) cc_final: 0.2697 (tmm)
REVERT: A  531 GLU cc_start: 0.7555 (tp30) cc_final: 0.7085 (tp30)
REVERT: A  616 GLU cc_start: 0.7503 (OUTLIER) cc_final: 0.6308 (mp0)
REVERT: A  627 PHE cc_start: 0.8056 (OUTLIER) cc_final: 0.7207 (m-80)
  outliers start: 13
  outliers final: 8
  residues processed: 74
  average time/residue: 0.0850
  time to fit residues: 7.8706
Evaluate side-chains
  77 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 64
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  307 MET
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  616 GLU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  665 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 37 optimal weight:    2.9990
   chunk 0 optimal weight:    7.9990
   chunk 42 optimal weight:    2.9990
   chunk 38 optimal weight:    0.5980
   chunk 3 optimal weight:    0.9980
   chunk 52 optimal weight:    2.9990
   chunk 40 optimal weight:    5.9990
   chunk 29 optimal weight:    0.6980
   chunk 18 optimal weight:    2.9990
   chunk 24 optimal weight:    6.9990
   chunk 45 optimal weight:    0.7980
   overall best weight:    1.2182

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4001 r_free = 0.4001 target = 0.183423 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3630 r_free = 0.3630 target = 0.146152 restraints weight = 5167.898|
|-----------------------------------------------------------------------------|
r_work (start): 0.3612 rms_B_bonded: 1.63
r_work: 0.3485 rms_B_bonded: 2.69 restraints_weight: 0.5000
r_work: 0.3331 rms_B_bonded: 4.51 restraints_weight: 0.2500
r_work (final): 0.3331
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3344
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.89   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3344 r_free = 0.3344    target_work(ls_wunit_k1) = 0.121         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (12 function evaluations)
r_final: 0.3344
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8034
moved from start:          0.3737

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.061   4921  Z= 0.213
  Angle     :  0.684  12.111   6685  Z= 0.332
  Chirality :  0.044   0.273    739
  Planarity :  0.003   0.030    799
  Dihedral  : 11.065 105.851   1009
  Min Nonbonded Distance : 2.492

Molprobity Statistics.
  All-atom Clashscore : 9.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.56 %
    Favored  : 95.44 %
  Rotamer:
    Outliers :  3.29 %
    Allowed  : 16.67 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -1.12 (0.35), residues: 570
  helix:  0.54 (0.28), residues: 343
  sheet: -3.50 (0.88), residues: 25
  loop : -2.65 (0.41), residues: 202

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 565 
 TYR   0.028   0.002   TYR A 505 
 PHE   0.016   0.002   PHE A 112 
 TRP   0.018   0.002   TRP A 255 
 HIS   0.004   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00505 /  0.21 ( 4917)
  covalent geometry    : angle       0.68347 /  0.33 ( 6674)
  SS BOND              : bond        0.00335 /  0.18 (    1)
  SS BOND              : angle       1.22357 /  0.69 (    2)
  hydrogen bonds       : bond        0.04438 /  3.04 (  248)
  hydrogen bonds       : angle       4.39464 /  3.16 (  735)
  link_NAG-ASN         : bond        0.00151 /  0.07 (    3)
  link_NAG-ASN         : angle       1.10839 /  0.59 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 73
  time to evaluate  : 0.178 
Fit side-chains
   revert: symmetry clash
REVERT: A  133 LEU cc_start: 0.6177 (OUTLIER) cc_final: 0.5935 (pt)
REVERT: A  140 MET cc_start: 0.6656 (mmp) cc_final: 0.5356 (ptm)
REVERT: A  156 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7767 (mt)
REVERT: A  176 ARG cc_start: 0.8409 (ttt180) cc_final: 0.7965 (ttm110)
REVERT: A  380 TYR cc_start: 0.8248 (t80) cc_final: 0.7831 (t80)
REVERT: A  387 ARG cc_start: 0.8147 (ttp-110) cc_final: 0.7478 (ttp-110)
REVERT: A  400 MET cc_start: 0.7750 (mtt) cc_final: 0.7497 (mtp)
REVERT: A  416 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.6948 (ttp80)
REVERT: A  480 GLU cc_start: 0.6988 (tt0) cc_final: 0.6709 (tt0)
REVERT: A  500 TYR cc_start: 0.7794 (t80) cc_final: 0.7498 (t80)
REVERT: A  528 MET cc_start: 0.4365 (ttt) cc_final: 0.3059 (pmm)
REVERT: A  531 GLU cc_start: 0.7537 (tp30) cc_final: 0.7222 (tp30)
REVERT: A  616 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.6411 (mp0)
REVERT: A  618 TYR cc_start: 0.8485 (m-80) cc_final: 0.8163 (m-80)
REVERT: A  627 PHE cc_start: 0.8110 (OUTLIER) cc_final: 0.7228 (m-80)
  outliers start: 16
  outliers final: 10
  residues processed: 82
  average time/residue: 0.0940
  time to fit residues: 9.6867
Evaluate side-chains
  82 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 68
  time to evaluate  : 0.176 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  133 LEU
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  616 GLU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  640 LEU
Chi-restraints excluded: chain A residue  665 VAL
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 25 optimal weight:    1.9990
   chunk 29 optimal weight:    0.7980
   chunk 55 optimal weight:    0.9990
   chunk 50 optimal weight:    1.9990
   chunk 2 optimal weight:    0.8980
   chunk 18 optimal weight:    0.9990
   chunk 38 optimal weight:    3.9990
   chunk 53 optimal weight:    0.5980
   chunk 56 optimal weight:    8.9990
   chunk 42 optimal weight:    1.9990
   chunk 13 optimal weight:    0.4980
   overall best weight:    0.7582

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4067 r_free = 0.4067 target = 0.189554 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3720 r_free = 0.3720 target = 0.154082 restraints weight = 5078.938|
|-----------------------------------------------------------------------------|
r_work (start): 0.3682 rms_B_bonded: 1.50
r_work: 0.3562 rms_B_bonded: 2.52 restraints_weight: 0.5000
r_work: 0.3415 rms_B_bonded: 4.27 restraints_weight: 0.2500
r_work (final): 0.3415
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3392
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.86   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3392 r_free = 0.3392    target_work(ls_wunit_k1) = 0.125         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3392
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8007
moved from start:          0.3836

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.053   4921  Z= 0.159
  Angle     :  0.659  16.358   6685  Z= 0.312
  Chirality :  0.043   0.365    739
  Planarity :  0.003   0.032    799
  Dihedral  : 10.735 101.278   1009
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 9.35
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.21 %
    Favored  : 95.79 %
  Rotamer:
    Outliers :  2.88 %
    Allowed  : 17.08 %
    Favored  : 80.04 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.96 (0.35), residues: 570
  helix:  0.66 (0.28), residues: 347
  sheet: -3.49 (0.87), residues: 25
  loop : -2.63 (0.41), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 174 
 TYR   0.020   0.002   TYR A 505 
 PHE   0.012   0.001   PHE A 112 
 TRP   0.019   0.002   TRP A 255 
 HIS   0.004   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00372 /  0.16 ( 4917)
  covalent geometry    : angle       0.65834 /  0.31 ( 6674)
  SS BOND              : bond        0.00276 /  0.15 (    1)
  SS BOND              : angle       1.25190 /  0.70 (    2)
  hydrogen bonds       : bond        0.04054 /  2.75 (  248)
  hydrogen bonds       : angle       4.23373 /  3.06 (  735)
  link_NAG-ASN         : bond        0.00154 /  0.07 (    3)
  link_NAG-ASN         : angle       0.98911 /  0.53 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  78 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 64
  time to evaluate  : 0.176 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.6586 (mmp) cc_final: 0.5322 (ptm)
REVERT: A  147 LYS cc_start: 0.7352 (ttpp) cc_final: 0.6743 (tttt)
REVERT: A  156 LEU cc_start: 0.7994 (OUTLIER) cc_final: 0.7708 (mt)
REVERT: A  176 ARG cc_start: 0.8393 (ttt180) cc_final: 0.8050 (ttm110)
REVERT: A  380 TYR cc_start: 0.8227 (t80) cc_final: 0.8007 (t80)
REVERT: A  387 ARG cc_start: 0.8164 (ttp-110) cc_final: 0.7567 (ttp-110)
REVERT: A  400 MET cc_start: 0.7581 (mtt) cc_final: 0.7339 (mtp)
REVERT: A  416 ARG cc_start: 0.7291 (ttt-90) cc_final: 0.6964 (ttp80)
REVERT: A  531 GLU cc_start: 0.7609 (tp30) cc_final: 0.7122 (tp30)
REVERT: A  616 GLU cc_start: 0.7447 (OUTLIER) cc_final: 0.6161 (mp0)
REVERT: A  627 PHE cc_start: 0.8073 (OUTLIER) cc_final: 0.7200 (m-80)
  outliers start: 14
  outliers final: 9
  residues processed: 73
  average time/residue: 0.0725
  time to fit residues: 6.7756
Evaluate side-chains
  72 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 60
  time to evaluate  : 0.110 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  616 GLU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  665 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 29 optimal weight:    0.5980
   chunk 50 optimal weight:    0.9990
   chunk 1 optimal weight:    3.9990
   chunk 41 optimal weight:    0.5980
   chunk 6 optimal weight:    0.9980
   chunk 56 optimal weight:    3.9990
   chunk 52 optimal weight:    1.9990
   chunk 3 optimal weight:    1.9990
   chunk 13 optimal weight:    0.5980
   chunk 42 optimal weight:    0.6980
   chunk 39 optimal weight:    0.8980
   overall best weight:    0.6780

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

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4040 r_free = 0.4040 target = 0.187801 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 54)----------------|
| r_work = 0.3683 r_free = 0.3683 target = 0.150994 restraints weight = 5092.882|
|-----------------------------------------------------------------------------|
r_work (start): 0.3665 rms_B_bonded: 1.61
r_work: 0.3545 rms_B_bonded: 2.64 restraints_weight: 0.5000
r_work: 0.3393 rms_B_bonded: 4.46 restraints_weight: 0.2500
r_work (final): 0.3393
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3419
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3419 r_free = 0.3419    target_work(ls_wunit_k1) = 0.127         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3419
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7972
moved from start:          0.3871

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.054   4921  Z= 0.152
  Angle     :  0.654  15.941   6685  Z= 0.310
  Chirality :  0.043   0.353    739
  Planarity :  0.003   0.032    799
  Dihedral  : 10.489  99.193   1009
  Min Nonbonded Distance : 2.453

Molprobity Statistics.
  All-atom Clashscore : 8.82
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.04 %
    Favored  : 95.96 %
  Rotamer:
    Outliers :  2.47 %
    Allowed  : 18.52 %
    Favored  : 79.01 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole: -0.88 (0.35), residues: 570
  helix:  0.73 (0.28), residues: 348
  sheet: -3.45 (0.86), residues: 25
  loop : -2.64 (0.41), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 174 
 TYR   0.019   0.002   TYR A 505 
 PHE   0.011   0.001   PHE A 112 
 TRP   0.019   0.001   TRP A 255 
 HIS   0.004   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00352 /  0.15 ( 4917)
  covalent geometry    : angle       0.65356 /  0.31 ( 6674)
  SS BOND              : bond        0.00265 /  0.14 (    1)
  SS BOND              : angle       1.22734 /  0.69 (    2)
  hydrogen bonds       : bond        0.03983 /  2.70 (  248)
  hydrogen bonds       : angle       4.19292 /  3.04 (  735)
  link_NAG-ASN         : bond        0.00167 /  0.08 (    3)
  link_NAG-ASN         : angle       0.96234 /  0.53 (    9)

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

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

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1140 Ramachandran restraints generated.
    570 Oldfield, 0 Emsley, 570 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  76 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 64
  time to evaluate  : 0.103 
Fit side-chains
   revert: symmetry clash
REVERT: A  140 MET cc_start: 0.6469 (mmp) cc_final: 0.5178 (ptm)
REVERT: A  147 LYS cc_start: 0.7330 (ttpp) cc_final: 0.6751 (tttt)
REVERT: A  156 LEU cc_start: 0.7935 (OUTLIER) cc_final: 0.7651 (mt)
REVERT: A  176 ARG cc_start: 0.8376 (ttt180) cc_final: 0.7967 (ttm110)
REVERT: A  380 TYR cc_start: 0.8210 (t80) cc_final: 0.8006 (t80)
REVERT: A  387 ARG cc_start: 0.8097 (ttp-110) cc_final: 0.7469 (ttp-110)
REVERT: A  400 MET cc_start: 0.7616 (mtt) cc_final: 0.7343 (mtp)
REVERT: A  416 ARG cc_start: 0.7277 (ttt-90) cc_final: 0.6914 (ttp80)
REVERT: A  528 MET cc_start: 0.3997 (ttt) cc_final: 0.2874 (pmm)
REVERT: A  531 GLU cc_start: 0.7564 (tp30) cc_final: 0.7058 (tp30)
REVERT: A  616 GLU cc_start: 0.7452 (OUTLIER) cc_final: 0.6099 (mp0)
REVERT: A  627 PHE cc_start: 0.8016 (OUTLIER) cc_final: 0.7116 (m-80)
  outliers start: 12
  outliers final: 9
  residues processed: 71
  average time/residue: 0.0670
  time to fit residues: 5.9803
Evaluate side-chains
  74 residues out of total 486 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 62
  time to evaluate  : 0.160 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  104 HIS
Chi-restraints excluded: chain A residue  156 LEU
Chi-restraints excluded: chain A residue  267 MET
Chi-restraints excluded: chain A residue  281 ILE
Chi-restraints excluded: chain A residue  369 THR
Chi-restraints excluded: chain A residue  472 THR
Chi-restraints excluded: chain A residue  483 THR
Chi-restraints excluded: chain A residue  548 SER
Chi-restraints excluded: chain A residue  616 GLU
Chi-restraints excluded: chain A residue  627 PHE
Chi-restraints excluded: chain A residue  639 ILE
Chi-restraints excluded: chain A residue  665 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 57
   random chunks:
   chunk 47 optimal weight:    0.8980
   chunk 14 optimal weight:    0.6980
   chunk 27 optimal weight:    0.0020
   chunk 49 optimal weight:    0.9990
   chunk 5 optimal weight:    4.9990
   chunk 55 optimal weight:    0.7980
   chunk 6 optimal weight:    0.0000
   chunk 32 optimal weight:    7.9990
   chunk 54 optimal weight:    1.9990
   chunk 15 optimal weight:    0.5980
   chunk 0 optimal weight:    7.9990
   overall best weight:    0.4192

-------------------------------------------------------------------------------
NQH flips
*********
Analyzing N/Q/H residues for possible flip corrections...
** A 527 HIS ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.191102 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 48)----------------|
| r_work = 0.3722 r_free = 0.3722 target = 0.154477 restraints weight = 5071.679|
|-----------------------------------------------------------------------------|
r_work (start): 0.3704 rms_B_bonded: 1.62
r_work: 0.3584 rms_B_bonded: 2.70 restraints_weight: 0.5000
r_work: 0.3431 rms_B_bonded: 4.56 restraints_weight: 0.2500
r_work (final): 0.3431
-------------------------------------------------------------------------------
Occupancy refinement
********************
r_start: 0.3546
|-occupancy refinement: start-------------------------------------------------|
| r_work = 0.3546 r_free = 0.3546    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.83   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|
|-occupancy refinement: end---------------------------------------------------|
| r_work = 0.3546 r_free = 0.3546    target_work(ls_wunit_k1) = 0.136         |
| occupancies: max = 1.00  min = 0.88   number of occupancies < 0.1:        0 |
|-----------------------------------------------------------------------------|

Number of minimizer iterations: 3 (9 function evaluations)
r_final: 0.3546
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7920
moved from start:          0.3965

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.048   4921  Z= 0.126
  Angle     :  0.623  14.842   6685  Z= 0.294
  Chirality :  0.041   0.319    739
  Planarity :  0.003   0.030    799
  Dihedral  : 10.049  92.523   1009
  Min Nonbonded Distance : 2.420

Molprobity Statistics.
  All-atom Clashscore : 8.19
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.51 %
    Favored  : 96.49 %
  Rotamer:
    Outliers :  2.67 %
    Allowed  : 18.11 %
    Favored  : 79.22 %
  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 are not related in a simple way.
  whole: -0.74 (0.35), residues: 570
  helix:  0.90 (0.28), residues: 349
  sheet: -3.26 (0.89), residues: 25
  loop : -2.75 (0.40), residues: 196

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 174 
 TYR   0.014   0.001   TYR A 380 
 PHE   0.009   0.001   PHE A 112 
 TRP   0.020   0.001   TRP A 255 
 HIS   0.003   0.001   HIS A 272 



Details of bonding type rmsd/Z
  covalent geometry    : bond        0.00284 /  0.13 ( 4917)
  covalent geometry    : angle       0.62237 /  0.29 ( 6674)
  SS BOND              : bond        0.00231 /  0.12 (    1)
  SS BOND              : angle       1.25471 /  0.70 (    2)
  hydrogen bonds       : bond        0.03680 /  2.48 (  248)
  hydrogen bonds       : angle       4.03113 /  2.93 (  735)
  link_NAG-ASN         : bond        0.00182 /  0.09 (    3)
  link_NAG-ASN         : angle       0.88432 /  0.48 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1415.32 seconds
wall clock time: 24 minutes 59.49 seconds (1499.49 seconds total)