Starting phenix.real_space_refine
on Sun Apr 27 01:37:57 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jcv_61377/04_2025/9jcv_61377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jcv_61377/04_2025/9jcv_61377.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.41
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jcv_61377/04_2025/9jcv_61377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jcv_61377/04_2025/9jcv_61377.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jcv_61377/04_2025/9jcv_61377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jcv_61377/04_2025/9jcv_61377.cif"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.079
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: 5
    Type Number    sf(0)   Gaussians
     S      32      5.16       5
     Cl      1      4.86       5
     C    2756      2.51       5
     N     617      2.21       5
     O     705      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/chem_data/mon_lib"
  Total number of atoms: 4111
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 4068
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 512, 4068
          Classifications: {'peptide': 512}
          Link IDs: {'PTRANS': 24, 'TRANS': 487}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 43
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 43
          Unusual residues: {' CL': 1, 'NAG': 3}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 3
          Unresolved non-hydrogen angles: 6
          Unresolved non-hydrogen dihedrals: 9
          Unresolved non-hydrogen chiralities: 3
  Time building chain proxies: 3.37, per 1000 atoms: 0.82
  Number of scatterers: 4111
  At special positions: 0
  Unit cell: (80.152, 68.036, 84.812, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 5
    Type Number    sf(0)
     Cl      1     17.00
     S      32     16.00
     O     705      8.00
     N     617      7.00
     C    2756      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=1, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 162 " - pdb=" SG  CYS A 171 " 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 163 "
      " NAG A 702 " - " ASN A 179 "
      " NAG A 703 " - " ASN A 190 "
  Time building additional restraints: 1.18
  Conformation dependent library (CDL) restraints added in 492.4 milliseconds
  

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  930

  Finding SS restraints...
    Secondary structure from input PDB file:
      28 helices and 1 sheets defined
      79.7% alpha, 0.4% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.42
  Creating SS restraints...
    Processing helix  chain 'A' and resid 47 through 56
    Processing helix  chain 'A' and resid 60 through 74
      removed outlier: 3.662A  pdb=" N   VAL A  64 " --> pdb=" O   GLY A  60 " (cutoff:3.500A)
      removed outlier: 4.742A  pdb=" N   PHE A  67 " --> pdb=" O   ASN A  63 " (cutoff:3.500A)
      Proline residue:  A  68  - end of helix
      removed outlier: 4.202A  pdb=" N   ASN A  74 " --> pdb=" O   LEU A  70 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 76 through 105
      removed outlier: 3.551A  pdb=" N   LEU A  80 " --> pdb=" O   GLY A  76 " (cutoff:3.500A)
      removed outlier: 4.169A  pdb=" N   ILE A  81 " --> pdb=" O   GLY A  77 " (cutoff:3.500A)
      Proline residue:  A  82  - end of helix
      removed outlier: 6.084A  pdb=" N   LEU A  92 " --> pdb=" O   PHE A  88 " (cutoff:3.500A)
      Proline residue:  A  93  - end of helix
    Processing helix  chain 'A' and resid 109 through 111
      No H-bonds generated for 'chain 'A' and resid 109 through 111'
    Processing helix  chain 'A' and resid 112 through 117
      removed outlier: 3.980A  pdb=" N   ILE A 116 " --> pdb=" O   CYS A 112 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 118 through 120
      No H-bonds generated for 'chain 'A' and resid 118 through 120'
    Processing helix  chain 'A' and resid 121 through 152
      removed outlier: 4.163A  pdb=" N   TYR A 125 " --> pdb=" O   SER A 121 " (cutoff:3.500A)
      removed outlier: 3.810A  pdb=" N   ILE A 139 " --> pdb=" O   ASN A 135 " (cutoff:3.500A)
      removed outlier: 4.758A  pdb=" N   VAL A 140 " --> pdb=" O   VAL A 136 " (cutoff:3.500A)
      removed outlier: 4.517A  pdb=" N   ILE A 141 " --> pdb=" O   TYR A 137 " (cutoff:3.500A)
      removed outlier: 3.752A  pdb=" N   LEU A 142 " --> pdb=" O   TYR A 138 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 193 through 202
    Processing helix  chain 'A' and resid 218 through 238
      removed outlier: 3.952A  pdb=" N   LYS A 237 " --> pdb=" O   PHE A 233 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 244 through 266
      removed outlier: 3.709A  pdb=" N   PHE A 248 " --> pdb=" O   LYS A 244 " (cutoff:3.500A)
      Proline residue:  A 253  - end of helix
    Processing helix  chain 'A' and resid 269 through 279
      removed outlier: 3.913A  pdb=" N   GLY A 273 " --> pdb=" O   GLY A 269 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 281 through 286
    Processing helix  chain 'A' and resid 287 through 302
      removed outlier: 4.473A  pdb=" N   TRP A 291 " --> pdb=" O   ASP A 287 " (cutoff:3.500A)
      removed outlier: 3.746A  pdb=" N   THR A 296 " --> pdb=" O   ILE A 292 " (cutoff:3.500A)
      removed outlier: 3.847A  pdb=" N   ILE A 298 " --> pdb=" O   ALA A 294 " (cutoff:3.500A)
      removed outlier: 4.608A  pdb=" N   PHE A 299 " --> pdb=" O   GLY A 295 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 308 through 313
      removed outlier: 3.821A  pdb=" N   GLY A 313 " --> pdb=" O   MET A 309 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 314 through 316
      No H-bonds generated for 'chain 'A' and resid 314 through 316'
    Processing helix  chain 'A' and resid 321 through 356
      removed outlier: 4.067A  pdb=" N   ASP A 325 " --> pdb=" O   ASN A 321 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 358 through 362
    Processing helix  chain 'A' and resid 368 through 381
      Proline residue:  A 375  - end of helix
      removed outlier: 3.881A  pdb=" N   MET A 380 " --> pdb=" O   LYS A 376 " (cutoff:3.500A)
      removed outlier: 3.582A  pdb=" N   MET A 381 " --> pdb=" O   ALA A 377 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 383 through 418
      removed outlier: 3.620A  pdb=" N   TRP A 387 " --> pdb=" O   LEU A 383 " (cutoff:3.500A)
      removed outlier: 3.533A  pdb=" N   LEU A 417 " --> pdb=" O   SER A 413 " (cutoff:3.500A)
      removed outlier: 3.617A  pdb=" N   TYR A 418 " --> pdb=" O   LEU A 414 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 426 through 444
    Processing helix  chain 'A' and resid 445 through 448
      removed outlier: 4.008A  pdb=" N   THR A 448 " --> pdb=" O   THR A 445 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 445 through 448'
    Processing helix  chain 'A' and resid 451 through 463
      removed outlier: 3.980A  pdb=" N   ALA A 463 " --> pdb=" O   ASP A 459 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 466 through 482
    Processing helix  chain 'A' and resid 484 through 496
    Processing helix  chain 'A' and resid 502 through 510
    Processing helix  chain 'A' and resid 510 through 526
    Processing helix  chain 'A' and resid 539 through 555
      removed outlier: 3.621A  pdb=" N   SER A 553 " --> pdb=" O   LEU A 549 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 555 through 567
      removed outlier: 3.685A  pdb=" N   GLN A 567 " --> pdb=" O   ILE A 563 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 531 through 532
      removed outlier: 3.580A  pdb=" N   TYR A 532 " --> pdb=" O   TYR A 536 " (cutoff:3.500A)
      removed outlier: 3.727A  pdb=" N   TYR A 536 " --> pdb=" O   TYR A 532 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA1

    257 hydrogen bonds defined for protein.
    756 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.13

  Time building geometry restraints manager: 1.38 seconds

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

  Histogram of bond lengths:
        1.22 -     1.34: 1143
        1.34 -     1.46: 897
        1.46 -     1.58: 2157
        1.58 -     1.70: 0
        1.70 -     1.82: 46
  Bond restraints: 4243
  Sorted by residual:
  bond pdb=" N   THR A 105 "
       pdb=" CA  THR A 105 "
    ideal  model  delta    sigma   weight residual
    1.457  1.423  0.034 1.23e-02 6.61e+03 7.81e+00
  bond pdb=" C1  NAG A 701 "
       pdb=" O5  NAG A 701 "
    ideal  model  delta    sigma   weight residual
    1.406  1.446 -0.040 2.00e-02 2.50e+03 4.00e+00
  bond pdb=" CA  THR A 105 "
       pdb=" CB  THR A 105 "
    ideal  model  delta    sigma   weight residual
    1.529  1.503  0.025 1.34e-02 5.57e+03 3.61e+00
  bond pdb=" C   TYR A 104 "
       pdb=" N   THR A 105 "
    ideal  model  delta    sigma   weight residual
    1.330  1.305  0.025 1.46e-02 4.69e+03 2.85e+00
  bond pdb=" C   THR A 105 "
       pdb=" O   THR A 105 "
    ideal  model  delta    sigma   weight residual
    1.236  1.217  0.019 1.22e-02 6.72e+03 2.53e+00
  ... (remaining 4238 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.61: 5631
        1.61 -     3.22: 119
        3.22 -     4.83: 27
        4.83 -     6.44: 7
        6.44 -     8.05: 2
  Bond angle restraints: 5786
  Sorted by residual:
  angle pdb=" C   TYR A 104 "
        pdb=" N   THR A 105 "
        pdb=" CA  THR A 105 "
      ideal   model   delta    sigma   weight residual
     122.77  117.44    5.33 1.33e+00 5.65e-01 1.60e+01
  angle pdb=" N   PHE A 404 "
        pdb=" CA  PHE A 404 "
        pdb=" CB  PHE A 404 "
      ideal   model   delta    sigma   weight residual
     110.12  114.41   -4.29 1.47e+00 4.63e-01 8.52e+00
  angle pdb=" N   VAL A 405 "
        pdb=" CA  VAL A 405 "
        pdb=" CB  VAL A 405 "
      ideal   model   delta    sigma   weight residual
     110.58  114.85   -4.27 1.50e+00 4.44e-01 8.12e+00
  angle pdb=" C   VAL A 136 "
        pdb=" N   TYR A 137 "
        pdb=" CA  TYR A 137 "
      ideal   model   delta    sigma   weight residual
     122.54  117.88    4.66 1.65e+00 3.67e-01 7.99e+00
  angle pdb=" CB  MET A 176 "
        pdb=" CG  MET A 176 "
        pdb=" SD  MET A 176 "
      ideal   model   delta    sigma   weight residual
     112.70  120.75   -8.05 3.00e+00 1.11e-01 7.21e+00
  ... (remaining 5781 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    17.42: 2194
       17.42 -    34.85: 181
       34.85 -    52.27: 45
       52.27 -    69.69: 2
       69.69 -    87.12: 4
  Dihedral angle restraints: 2426
    sinusoidal: 954
      harmonic: 1472
  Sorted by residual:
  dihedral pdb=" CB  CYS A 162 "
           pdb=" SG  CYS A 162 "
           pdb=" SG  CYS A 171 "
           pdb=" CB  CYS A 171 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -124.02   38.02     1      1.00e+01 1.00e-02 2.04e+01
  dihedral pdb=" CA  VAL A 510 "
           pdb=" C   VAL A 510 "
           pdb=" N   ILE A 511 "
           pdb=" CA  ILE A 511 "
      ideal   model   delta  harmonic     sigma   weight residual
    -180.00 -162.76  -17.24     0      5.00e+00 4.00e-02 1.19e+01
  dihedral pdb=" CA  ASP A 494 "
           pdb=" CB  ASP A 494 "
           pdb=" CG  ASP A 494 "
           pdb=" OD1 ASP A 494 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -30.00  -81.99   51.99     1      2.00e+01 2.50e-03 9.22e+00
  ... (remaining 2423 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.050: 512
       0.050 -    0.100: 111
       0.100 -    0.150: 20
       0.150 -    0.200: 3
       0.200 -    0.250: 1
  Chirality restraints: 647
  Sorted by residual:
  chirality pdb=" C1  NAG A 701 "
            pdb=" ND2 ASN A 163 "
            pdb=" C2  NAG A 701 "
            pdb=" O5  NAG A 701 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.15   -0.25 2.00e-01 2.50e+01 1.56e+00
  chirality pdb=" CB  VAL A 447 "
            pdb=" CA  VAL A 447 "
            pdb=" CG1 VAL A 447 "
            pdb=" CG2 VAL A 447 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.63   -2.44   -0.19 2.00e-01 2.50e+01 8.78e-01
  chirality pdb=" CA  THR A 105 "
            pdb=" N   THR A 105 "
            pdb=" C   THR A 105 "
            pdb=" CB  THR A 105 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.53    2.36    0.16 2.00e-01 2.50e+01 6.54e-01
  ... (remaining 644 not shown)

  Planarity restraints: 703
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CB  PHE A 404 "    0.013 2.00e-02 2.50e+03   2.05e-02 7.33e+00
        pdb=" CG  PHE A 404 "   -0.046 2.00e-02 2.50e+03
        pdb=" CD1 PHE A 404 "    0.014 2.00e-02 2.50e+03
        pdb=" CD2 PHE A 404 "    0.020 2.00e-02 2.50e+03
        pdb=" CE1 PHE A 404 "    0.002 2.00e-02 2.50e+03
        pdb=" CE2 PHE A 404 "   -0.004 2.00e-02 2.50e+03
        pdb=" CZ  PHE A 404 "    0.000 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A 400 "   -0.009 2.00e-02 2.50e+03   1.81e-02 3.26e+00
        pdb=" C   LEU A 400 "    0.031 2.00e-02 2.50e+03
        pdb=" O   LEU A 400 "   -0.012 2.00e-02 2.50e+03
        pdb=" N   ASP A 401 "   -0.011 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  LEU A  87 "   -0.008 2.00e-02 2.50e+03   1.65e-02 2.72e+00
        pdb=" C   LEU A  87 "    0.029 2.00e-02 2.50e+03
        pdb=" O   LEU A  87 "   -0.011 2.00e-02 2.50e+03
        pdb=" N   PHE A  88 "   -0.010 2.00e-02 2.50e+03
  ... (remaining 700 not shown)

  Histogram of nonbonded interaction distances:
        2.25 -     2.78: 985
        2.78 -     3.31: 4105
        3.31 -     3.84: 6930
        3.84 -     4.37: 7600
        4.37 -     4.90: 13583
  Nonbonded interactions: 33203
  Sorted by model distance:
  nonbonded pdb=" ND2 ASN A  74 "
            pdb=" OD2 ASP A 293 "
     model   vdw
     2.250 3.120
  nonbonded pdb=" OH  TYR A  72 "
            pdb=" O   ILE A 359 "
     model   vdw
     2.251 3.040
  nonbonded pdb=" OG  SER A 207 "
            pdb=" O   GLY A 209 "
     model   vdw
     2.256 3.040
  nonbonded pdb=" OG1 THR A 531 "
            pdb=" O   TYR A 536 "
     model   vdw
     2.280 3.040
  nonbonded pdb=" OE2 GLU A 197 "
            pdb=" NH1 ARG A 201 "
     model   vdw
     2.288 3.120
  ... (remaining 33198 not shown)

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

  No NCS relation were found !!!

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

Found NCS groups:
  found none.
Set up NCS constraints
  No NCS constraints will be used in refinement.
Set refine NCS operators
Adjust number of macro_cycles
  Number of macro_cycles: 10
Reset NCS operators
Extract rigid body selections
Check and reset occupancies
  Occupancies: min=1.00 max=1.00 mean=1.00
Load rotamer database and sin/cos tables
Set ADP refinement strategy
  ADPs will be refined as individual isotropic
Make a string to write initial .geo file
Internal consistency checks
Time:
  Set random seed:                         0.000
  Set model cs if undefined:               0.000
  Decide on map wrapping:                  0.000
  Normalize map: mean=0, sd=1:             0.750
  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:             0.010
  Extract box with map and model:          0.170
  Check model and map are aligned:         0.030
  Set scattering table:                    0.040
  Process input model:                     16.260
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:3.130
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   20.450
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7126
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.040   4247  Z= 0.160
  Angle     :  0.630   8.477   5797  Z= 0.329
  Chirality :  0.044   0.250    647
  Planarity :  0.004   0.036    700
  Dihedral  : 13.635  87.115   1493
  Min Nonbonded Distance : 2.250

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.00 %
    Allowed  :  0.46 %
    Favored  : 99.54 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.38), residues: 508
  helix:  1.24 (0.28), residues: 352
  sheet:  None (None), residues: 0
  loop : -0.33 (0.51), residues: 156

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.016   0.001   TRP A 236 
 HIS   0.003   0.001   HIS A 212 
 PHE   0.046   0.002   PHE A 404 
 TYR   0.019   0.001   TYR A 489 
 ARG   0.003   0.001   ARG A 263 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00802 (    3)
  link_NAG-ASN         : angle       3.03075 (    9)
  hydrogen bonds       : bond        0.11066 (  257)
  hydrogen bonds       : angle       4.85607 (  756)
  SS BOND              : bond        0.00070 (    1)
  SS BOND              : angle       0.75052 (    2)
  covalent geometry    : bond        0.00315 ( 4243)
  covalent geometry    : angle       0.61901 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 92
  time to evaluate  : 0.399 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.1442
  time to fit residues: 16.9469
Evaluate side-chains
  67 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 67
  time to evaluate  : 0.400 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 43 optimal weight:    0.0020
   chunk 38 optimal weight:    2.9990
   chunk 21 optimal weight:    4.9990
   chunk 13 optimal weight:    4.9990
   chunk 26 optimal weight:    4.9990
   chunk 20 optimal weight:    0.9990
   chunk 39 optimal weight:    2.9990
   chunk 15 optimal weight:    2.9990
   chunk 24 optimal weight:    0.8980
   chunk 29 optimal weight:    0.5980
   chunk 46 optimal weight:    0.8980
   overall best weight:    0.6790

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

Flipped N/Q/H residues before XYZ refinement:
** A 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4328 r_free = 0.4328 target = 0.197380 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3988 r_free = 0.3988 target = 0.160861 restraints weight = 4969.761|
|-----------------------------------------------------------------------------|
r_work (start): 0.3972 rms_B_bonded: 3.07
r_work: 0.3820 rms_B_bonded: 4.21 restraints_weight: 0.5000
r_work (final): 0.3820
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7234
moved from start:          0.1156

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4247  Z= 0.126
  Angle     :  0.586   8.680   5797  Z= 0.295
  Chirality :  0.043   0.318    647
  Planarity :  0.004   0.036    700
  Dihedral  :  4.752  52.926    617
  Min Nonbonded Distance : 2.610

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  8.03 %
    Favored  : 91.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.38), residues: 508
  helix:  1.44 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.63 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A 212 
 PHE   0.023   0.002   PHE A 391 
 TYR   0.013   0.001   TYR A 137 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00893 (    3)
  link_NAG-ASN         : angle       3.13015 (    9)
  hydrogen bonds       : bond        0.03864 (  257)
  hydrogen bonds       : angle       4.20293 (  756)
  SS BOND              : bond        0.00073 (    1)
  SS BOND              : angle       0.71885 (    2)
  covalent geometry    : bond        0.00285 ( 4243)
  covalent geometry    : angle       0.57326 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 85
  time to evaluate  : 0.464 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 THR cc_start: 0.8539 (t) cc_final: 0.8245 (p)
REVERT: A  538 TYR cc_start: 0.8110 (m-10) cc_final: 0.7666 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 85
  average time/residue: 0.1551
  time to fit residues: 17.0164
Evaluate side-chains
  74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 0
    poor density    : 74
  time to evaluate  : 0.492 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 4 optimal weight:    2.9990
   chunk 47 optimal weight:    0.7980
   chunk 38 optimal weight:    1.9990
   chunk 7 optimal weight:    0.8980
   chunk 12 optimal weight:    7.9990
   chunk 33 optimal weight:    1.9990
   chunk 49 optimal weight:    2.9990
   chunk 10 optimal weight:    1.9990
   chunk 43 optimal weight:    0.9990
   chunk 22 optimal weight:    2.9990
   chunk 0 optimal weight:    9.9990
   overall best weight:    1.3386

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4325 r_free = 0.4325 target = 0.194369 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.157820 restraints weight = 5013.804|
|-----------------------------------------------------------------------------|
r_work (start): 0.3955 rms_B_bonded: 2.98
r_work: 0.3803 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3803
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7388
moved from start:          0.1675

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.035   4247  Z= 0.175
  Angle     :  0.629   9.075   5797  Z= 0.315
  Chirality :  0.044   0.307    647
  Planarity :  0.004   0.036    700
  Dihedral  :  4.818  53.130    617
  Min Nonbonded Distance : 2.611

Molprobity Statistics.
  All-atom Clashscore : 11.47
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 12.39 %
    Favored  : 86.93 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.96 (0.37), residues: 508
  helix:  1.27 (0.28), residues: 356
  sheet:  None (None), residues: 0
  loop : -0.81 (0.48), residues: 152

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.009   0.001   TRP A 236 
 HIS   0.002   0.000   HIS A 212 
 PHE   0.040   0.002   PHE A 522 
 TYR   0.018   0.001   TYR A 532 
 ARG   0.002   0.000   ARG A 284 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00907 (    3)
  link_NAG-ASN         : angle       3.06297 (    9)
  hydrogen bonds       : bond        0.04198 (  257)
  hydrogen bonds       : angle       4.51506 (  756)
  SS BOND              : bond        0.00005 (    1)
  SS BOND              : angle       0.79087 (    2)
  covalent geometry    : bond        0.00416 ( 4243)
  covalent geometry    : angle       0.61810 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 82
  time to evaluate  : 0.571 
Fit side-chains
   revert: symmetry clash
REVERT: A  117 CYS cc_start: 0.8436 (t) cc_final: 0.8215 (t)
REVERT: A  288 PRO cc_start: 0.8109 (Cg_exo) cc_final: 0.7659 (Cg_exo)
REVERT: A  429 GLU cc_start: 0.8261 (mt-10) cc_final: 0.7759 (mt-10)
REVERT: A  522 PHE cc_start: 0.6995 (t80) cc_final: 0.6096 (m-80)
REVERT: A  538 TYR cc_start: 0.8262 (m-10) cc_final: 0.7807 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 85
  average time/residue: 0.1376
  time to fit residues: 15.4480
Evaluate side-chains
  78 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 76
  time to evaluate  : 0.446 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  334 SER
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 47 optimal weight:    0.4980
   chunk 42 optimal weight:    2.9990
   chunk 41 optimal weight:    0.9980
   chunk 37 optimal weight:    0.8980
   chunk 46 optimal weight:    0.7980
   chunk 16 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 38 optimal weight:    0.9990
   chunk 17 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9980
   chunk 12 optimal weight:    5.9990
   overall best weight:    0.8180

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4377 r_free = 0.4377 target = 0.197729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.162001 restraints weight = 4997.289|
|-----------------------------------------------------------------------------|
r_work (start): 0.4016 rms_B_bonded: 3.00
r_work: 0.3865 rms_B_bonded: 4.11 restraints_weight: 0.5000
r_work (final): 0.3865
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7351
moved from start:          0.1918

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.030   4247  Z= 0.135
  Angle     :  0.617   9.014   5797  Z= 0.300
  Chirality :  0.042   0.304    647
  Planarity :  0.004   0.033    700
  Dihedral  :  4.718  53.174    617
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 13.53 %
    Favored  : 85.55 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.38), residues: 508
  helix:  1.39 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.68 (0.49), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.011   0.001   TRP A 236 
 HIS   0.002   0.000   HIS A 212 
 PHE   0.028   0.002   PHE A 522 
 TYR   0.014   0.001   TYR A 137 
 ARG   0.001   0.000   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00861 (    3)
  link_NAG-ASN         : angle       3.08495 (    9)
  hydrogen bonds       : bond        0.03892 (  257)
  hydrogen bonds       : angle       4.41819 (  756)
  SS BOND              : bond        0.00006 (    1)
  SS BOND              : angle       0.76336 (    2)
  covalent geometry    : bond        0.00316 ( 4243)
  covalent geometry    : angle       0.60542 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  85 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 81
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 THR cc_start: 0.8478 (t) cc_final: 0.8245 (p)
REVERT: A  446 MET cc_start: 0.8743 (ptp) cc_final: 0.8314 (ptp)
REVERT: A  474 PHE cc_start: 0.7730 (m-80) cc_final: 0.7400 (t80)
REVERT: A  522 PHE cc_start: 0.6919 (t80) cc_final: 0.6197 (m-80)
REVERT: A  538 TYR cc_start: 0.8224 (m-10) cc_final: 0.7712 (m-80)
  outliers start: 4
  outliers final: 3
  residues processed: 84
  average time/residue: 0.1380
  time to fit residues: 15.1235
Evaluate side-chains
  80 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.411 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  531 THR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 0 optimal weight:   10.0000
   chunk 8 optimal weight:    0.7980
   chunk 22 optimal weight:    0.9980
   chunk 30 optimal weight:    0.9990
   chunk 36 optimal weight:    0.9990
   chunk 37 optimal weight:    2.9990
   chunk 46 optimal weight:    1.9990
   chunk 48 optimal weight:    1.9990
   chunk 31 optimal weight:    0.3980
   chunk 20 optimal weight:    0.7980
   chunk 28 optimal weight:    1.9990
   overall best weight:    0.7982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4378 r_free = 0.4378 target = 0.197866 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4030 r_free = 0.4030 target = 0.162035 restraints weight = 5115.372|
|-----------------------------------------------------------------------------|
r_work (start): 0.4019 rms_B_bonded: 3.06
r_work: 0.3871 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3871
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7367
moved from start:          0.2080

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.029   4247  Z= 0.134
  Angle     :  0.620   9.738   5797  Z= 0.299
  Chirality :  0.042   0.302    647
  Planarity :  0.004   0.033    700
  Dihedral  :  4.674  53.152    617
  Min Nonbonded Distance : 2.612

Molprobity Statistics.
  All-atom Clashscore : 9.40
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 16.06 %
    Favored  : 83.03 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.10 (0.38), residues: 508
  helix:  1.39 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.79 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 236 
 HIS   0.002   0.000   HIS A 212 
 PHE   0.024   0.001   PHE A 522 
 TYR   0.015   0.001   TYR A 137 
 ARG   0.001   0.000   ARG A 284 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00863 (    3)
  link_NAG-ASN         : angle       3.08675 (    9)
  hydrogen bonds       : bond        0.03881 (  257)
  hydrogen bonds       : angle       4.43284 (  756)
  SS BOND              : bond        0.00039 (    1)
  SS BOND              : angle       0.76728 (    2)
  covalent geometry    : bond        0.00311 ( 4243)
  covalent geometry    : angle       0.60832 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  86 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 82
  time to evaluate  : 0.456 
Fit side-chains
   revert: symmetry clash
REVERT: A  446 MET cc_start: 0.8756 (ptp) cc_final: 0.8357 (ptp)
REVERT: A  494 ASP cc_start: 0.7883 (m-30) cc_final: 0.7396 (m-30)
REVERT: A  522 PHE cc_start: 0.6797 (t80) cc_final: 0.6266 (m-80)
REVERT: A  538 TYR cc_start: 0.8224 (m-10) cc_final: 0.7751 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 85
  average time/residue: 0.1401
  time to fit residues: 15.5173
Evaluate side-chains
  76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.455 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  531 THR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 22 optimal weight:    0.8980
   chunk 46 optimal weight:    3.9990
   chunk 16 optimal weight:    3.9990
   chunk 45 optimal weight:    0.8980
   chunk 47 optimal weight:    4.9990
   chunk 6 optimal weight:    0.0980
   chunk 30 optimal weight:    0.7980
   chunk 25 optimal weight:    4.9990
   chunk 29 optimal weight:    0.7980
   chunk 17 optimal weight:    0.7980
   chunk 1 optimal weight:    0.7980
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4387 r_free = 0.4387 target = 0.198891 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.4043 r_free = 0.4043 target = 0.163512 restraints weight = 4972.199|
|-----------------------------------------------------------------------------|
r_work (start): 0.4034 rms_B_bonded: 2.98
r_work: 0.3885 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3885
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7355
moved from start:          0.2244

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.028   4247  Z= 0.128
  Angle     :  0.631   9.765   5797  Z= 0.305
  Chirality :  0.043   0.301    647
  Planarity :  0.004   0.031    700
  Dihedral  :  4.657  53.199    617
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 10.01
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 16.97 %
    Favored  : 82.11 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.37), residues: 508
  helix:  1.41 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.79 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.020   0.001   TRP A 236 
 HIS   0.001   0.000   HIS A 212 
 PHE   0.022   0.001   PHE A 522 
 TYR   0.013   0.001   TYR A 137 
 ARG   0.002   0.000   ARG A 240 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00851 (    3)
  link_NAG-ASN         : angle       3.08076 (    9)
  hydrogen bonds       : bond        0.03813 (  257)
  hydrogen bonds       : angle       4.35166 (  756)
  SS BOND              : bond        0.00055 (    1)
  SS BOND              : angle       0.74831 (    2)
  covalent geometry    : bond        0.00294 ( 4243)
  covalent geometry    : angle       0.61998 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 85
  time to evaluate  : 0.845 
Fit side-chains
   revert: symmetry clash
REVERT: A  414 LEU cc_start: 0.6707 (pp) cc_final: 0.6325 (pp)
REVERT: A  446 MET cc_start: 0.8645 (ptp) cc_final: 0.8357 (ptp)
REVERT: A  494 ASP cc_start: 0.7868 (m-30) cc_final: 0.7395 (m-30)
REVERT: A  538 TYR cc_start: 0.8203 (m-10) cc_final: 0.7773 (m-80)
  outliers start: 4
  outliers final: 1
  residues processed: 88
  average time/residue: 0.1811
  time to fit residues: 21.2113
Evaluate side-chains
  79 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 78
  time to evaluate  : 0.628 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 38 optimal weight:    0.0980
   chunk 1 optimal weight:    0.0870
   chunk 10 optimal weight:    0.9990
   chunk 13 optimal weight:    3.9990
   chunk 31 optimal weight:    0.9980
   chunk 46 optimal weight:    4.9990
   chunk 29 optimal weight:    0.6980
   chunk 41 optimal weight:    0.7980
   chunk 21 optimal weight:    0.9990
   chunk 2 optimal weight:    0.6980
   chunk 48 optimal weight:    0.9990
   overall best weight:    0.4758

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4414 r_free = 0.4414 target = 0.202365 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4076 r_free = 0.4076 target = 0.166747 restraints weight = 5034.514|
|-----------------------------------------------------------------------------|
r_work (start): 0.4065 rms_B_bonded: 3.04
r_work: 0.3915 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3915
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7320
moved from start:          0.2308

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   4247  Z= 0.118
  Angle     :  0.614  10.384   5797  Z= 0.297
  Chirality :  0.043   0.302    647
  Planarity :  0.004   0.031    700
  Dihedral  :  4.678  53.166    617
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 9.15
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 17.89 %
    Favored  : 81.42 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.23 (0.38), residues: 508
  helix:  1.46 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.66 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.019   0.001   TRP A 236 
 HIS   0.001   0.000   HIS A 212 
 PHE   0.030   0.001   PHE A 522 
 TYR   0.016   0.001   TYR A 137 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00849 (    3)
  link_NAG-ASN         : angle       3.09587 (    9)
  hydrogen bonds       : bond        0.03705 (  257)
  hydrogen bonds       : angle       4.35804 (  756)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.78458 (    2)
  covalent geometry    : bond        0.00265 ( 4243)
  covalent geometry    : angle       0.60252 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  82 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.453 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7396 (mmtt) cc_final: 0.7131 (mmtp)
REVERT: A  494 ASP cc_start: 0.7825 (m-30) cc_final: 0.7360 (m-30)
REVERT: A  522 PHE cc_start: 0.7456 (t80) cc_final: 0.6267 (m-80)
REVERT: A  538 TYR cc_start: 0.8120 (m-10) cc_final: 0.7858 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 80
  average time/residue: 0.1201
  time to fit residues: 12.9729
Evaluate side-chains
  76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.418 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  426 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 49 optimal weight:    3.9990
   chunk 41 optimal weight:    3.9990
   chunk 34 optimal weight:    0.9980
   chunk 37 optimal weight:    2.9990
   chunk 40 optimal weight:    0.7980
   chunk 12 optimal weight:    4.9990
   chunk 1 optimal weight:    0.0570
   chunk 23 optimal weight:    0.0470
   chunk 48 optimal weight:    0.9990
   chunk 2 optimal weight:    0.9980
   chunk 35 optimal weight:    1.9990
   overall best weight:    0.5796

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4410 r_free = 0.4410 target = 0.201822 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4069 r_free = 0.4069 target = 0.166081 restraints weight = 4988.113|
|-----------------------------------------------------------------------------|
r_work (start): 0.4057 rms_B_bonded: 3.02
r_work: 0.3912 rms_B_bonded: 4.09 restraints_weight: 0.5000
r_work (final): 0.3912
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7327
moved from start:          0.2462

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   4247  Z= 0.124
  Angle     :  0.641  11.038   5797  Z= 0.306
  Chirality :  0.043   0.302    647
  Planarity :  0.004   0.036    700
  Dihedral  :  4.677  53.228    617
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 18.58 %
    Favored  : 80.96 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.38), residues: 508
  helix:  1.43 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.75 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.015   0.001   TRP A 236 
 HIS   0.001   0.000   HIS A 212 
 PHE   0.024   0.001   PHE A 522 
 TYR   0.016   0.001   TYR A 536 
 ARG   0.003   0.000   ARG A 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00850 (    3)
  link_NAG-ASN         : angle       3.09309 (    9)
  hydrogen bonds       : bond        0.03757 (  257)
  hydrogen bonds       : angle       4.33827 (  756)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.72329 (    2)
  covalent geometry    : bond        0.00283 ( 4243)
  covalent geometry    : angle       0.63016 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 77
  time to evaluate  : 0.411 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7378 (mmtt) cc_final: 0.7130 (mmtp)
REVERT: A  302 TYR cc_start: 0.8022 (m-10) cc_final: 0.6618 (m-10)
REVERT: A  494 ASP cc_start: 0.7769 (m-30) cc_final: 0.7319 (m-30)
REVERT: A  522 PHE cc_start: 0.7389 (t80) cc_final: 0.6213 (m-80)
REVERT: A  538 TYR cc_start: 0.8167 (m-10) cc_final: 0.7815 (m-80)
  outliers start: 2
  outliers final: 1
  residues processed: 79
  average time/residue: 0.1235
  time to fit residues: 13.1383
Evaluate side-chains
  74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 73
  time to evaluate  : 0.469 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 6 optimal weight:    5.9990
   chunk 17 optimal weight:    0.6980
   chunk 21 optimal weight:   20.0000
   chunk 5 optimal weight:    2.9990
   chunk 14 optimal weight:    0.5980
   chunk 3 optimal weight:    0.5980
   chunk 45 optimal weight:    3.9990
   chunk 12 optimal weight:    7.9990
   chunk 19 optimal weight:    2.9990
   chunk 4 optimal weight:    0.5980
   chunk 20 optimal weight:    1.9990
   overall best weight:    0.8982

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4372 r_free = 0.4372 target = 0.197639 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 42)----------------|
| r_work = 0.4029 r_free = 0.4029 target = 0.162192 restraints weight = 5044.315|
|-----------------------------------------------------------------------------|
r_work (start): 0.4018 rms_B_bonded: 3.02
r_work: 0.3869 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3869
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7360
moved from start:          0.2499

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.039   4247  Z= 0.143
  Angle     :  0.658  11.248   5797  Z= 0.315
  Chirality :  0.044   0.299    647
  Planarity :  0.004   0.033    700
  Dihedral  :  4.762  53.283    617
  Min Nonbonded Distance : 2.595

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 18.58 %
    Favored  : 80.73 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.14 (0.38), residues: 508
  helix:  1.37 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.66 (0.51), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.007   0.001   TRP A 166 
 HIS   0.001   0.000   HIS A 212 
 PHE   0.026   0.002   PHE A 522 
 TYR   0.016   0.001   TYR A 536 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00879 (    3)
  link_NAG-ASN         : angle       3.06988 (    9)
  hydrogen bonds       : bond        0.04006 (  257)
  hydrogen bonds       : angle       4.46125 (  756)
  SS BOND              : bond        0.00076 (    1)
  SS BOND              : angle       0.71960 (    2)
  covalent geometry    : bond        0.00336 ( 4243)
  covalent geometry    : angle       0.64731 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  80 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 77
  time to evaluate  : 0.454 
Fit side-chains
   revert: symmetry clash
REVERT: A  494 ASP cc_start: 0.7786 (m-30) cc_final: 0.7319 (m-30)
REVERT: A  522 PHE cc_start: 0.7406 (t80) cc_final: 0.6262 (m-80)
REVERT: A  538 TYR cc_start: 0.8253 (m-10) cc_final: 0.7712 (m-80)
  outliers start: 3
  outliers final: 3
  residues processed: 80
  average time/residue: 0.1098
  time to fit residues: 12.3049
Evaluate side-chains
  75 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 72
  time to evaluate  : 0.442 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  537 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 20 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 46 optimal weight:    2.9990
   chunk 32 optimal weight:    0.8980
   chunk 36 optimal weight:    0.2980
   chunk 12 optimal weight:    9.9990
   chunk 42 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 39 optimal weight:    1.9990
   chunk 1 optimal weight:    0.7980
   chunk 30 optimal weight:    2.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4349 r_free = 0.4349 target = 0.197147 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.4004 r_free = 0.4004 target = 0.162081 restraints weight = 5081.023|
|-----------------------------------------------------------------------------|
r_work (start): 0.3987 rms_B_bonded: 3.06
r_work: 0.3837 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3837
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7322
moved from start:          0.2579

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   4247  Z= 0.130
  Angle     :  0.662  11.286   5797  Z= 0.317
  Chirality :  0.044   0.299    647
  Planarity :  0.004   0.034    700
  Dihedral  :  4.772  53.335    617
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.37
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 18.81 %
    Favored  : 80.50 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.12 (0.38), residues: 508
  helix:  1.35 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.62 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 166 
 HIS   0.001   0.000   HIS A 212 
 PHE   0.025   0.002   PHE A 391 
 TYR   0.016   0.001   TYR A 536 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00852 (    3)
  link_NAG-ASN         : angle       3.18900 (    9)
  hydrogen bonds       : bond        0.03848 (  257)
  hydrogen bonds       : angle       4.45749 (  756)
  SS BOND              : bond        0.00075 (    1)
  SS BOND              : angle       0.72665 (    2)
  covalent geometry    : bond        0.00298 ( 4243)
  covalent geometry    : angle       0.65023 ( 5786)

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

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

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1016 Ramachandran restraints generated.
    508 Oldfield, 0 Emsley, 508 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  79 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 76
  time to evaluate  : 0.424 
Fit side-chains
   revert: symmetry clash
REVERT: A  281 ASP cc_start: 0.8363 (t0) cc_final: 0.7969 (t0)
REVERT: A  282 ILE cc_start: 0.8350 (tp) cc_final: 0.8086 (tp)
REVERT: A  285 LEU cc_start: 0.8984 (mp) cc_final: 0.8650 (mp)
REVERT: A  494 ASP cc_start: 0.7751 (m-30) cc_final: 0.7285 (m-30)
REVERT: A  522 PHE cc_start: 0.7378 (t80) cc_final: 0.6245 (m-80)
REVERT: A  538 TYR cc_start: 0.8207 (m-10) cc_final: 0.7691 (m-80)
  outliers start: 3
  outliers final: 3
  residues processed: 79
  average time/residue: 0.1473
  time to fit residues: 16.1480
Evaluate side-chains
  77 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 74
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  430 ILE
Chi-restraints excluded: chain A residue  537 VAL
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 39 optimal weight:    0.8980
   chunk 2 optimal weight:    0.6980
   chunk 20 optimal weight:    0.5980
   chunk 6 optimal weight:    0.7980
   chunk 10 optimal weight:    0.5980
   chunk 44 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   chunk 37 optimal weight:    0.8980
   chunk 38 optimal weight:    0.9980
   chunk 19 optimal weight:    0.6980
   chunk 36 optimal weight:    5.9990
   overall best weight:    0.6780

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4351 r_free = 0.4351 target = 0.197522 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4010 r_free = 0.4010 target = 0.162588 restraints weight = 5009.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3991 rms_B_bonded: 3.04
r_work: 0.3842 rms_B_bonded: 4.12 restraints_weight: 0.5000
r_work (final): 0.3842
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7319
moved from start:          0.2645

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   4247  Z= 0.128
  Angle     :  0.649  11.679   5797  Z= 0.310
  Chirality :  0.043   0.298    647
  Planarity :  0.004   0.034    700
  Dihedral  :  4.718  53.316    617
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 19.04 %
    Favored  : 80.28 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.15 (0.38), residues: 508
  helix:  1.37 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.62 (0.51), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 166 
 HIS   0.001   0.000   HIS A 212 
 PHE   0.024   0.002   PHE A 342 
 TYR   0.015   0.001   TYR A 536 
 ARG   0.002   0.000   ARG A 201 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00896 (    3)
  link_NAG-ASN         : angle       3.04854 (    9)
  hydrogen bonds       : bond        0.03839 (  257)
  hydrogen bonds       : angle       4.41372 (  756)
  SS BOND              : bond        0.00074 (    1)
  SS BOND              : angle       0.69746 (    2)
  covalent geometry    : bond        0.00294 ( 4243)
  covalent geometry    : angle       0.63839 ( 5786)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2746.08 seconds
wall clock time: 49 minutes 23.17 seconds (2963.17 seconds total)