Starting phenix.real_space_refine
on Wed Sep 17 04:25:42 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9jcv_61377/09_2025/9jcv_61377.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9jcv_61377/09_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 {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9jcv_61377/09_2025/9jcv_61377.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9jcv_61377/09_2025/9jcv_61377.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9jcv_61377/09_2025/9jcv_61377.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9jcv_61377/09_2025/9jcv_61377.map"
  }
  resolution = 3.41
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=  -0.001 sd=   0.079
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): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 1.37, per 1000 atoms: 0.33
  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: 0.38
  Conformation dependent library (CDL) restraints added in 175.8 milliseconds
  
  Enol-peptide restraints added in 715.3 nanoseconds
  

  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: 0.14
  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: 0.63

  Time building geometry restraints manager: 0.50 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:             0.800
  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:          0.060
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     6.520
  Find NCS groups from input model:        0.020
  Set up NCS constraints:                  0.000
  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:1.370
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:    8.810
-------------------------------------------------------------------------------
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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.09 (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
 ARG   0.003   0.001   ARG A 263 
 TYR   0.019   0.001   TYR A 489 
 PHE   0.046   0.002   PHE A 404 
 TRP   0.016   0.001   TRP A 236 
 HIS   0.003   0.001   HIS A 212 

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

*********************** 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  : 0.161 
Fit side-chains
  outliers start: 0
  outliers final: 0
  residues processed: 92
  average time/residue: 0.0683
  time to fit residues: 8.0429
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  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 24 optimal weight:    0.8980
   chunk 48 optimal weight:    0.9990
   chunk 26 optimal weight:    4.9990
   chunk 2 optimal weight:    0.8980
   chunk 16 optimal weight:    3.9990
   chunk 32 optimal weight:    0.0470
   chunk 31 optimal weight:    0.6980
   chunk 25 optimal weight:    6.9990
   chunk 50 optimal weight:    0.9980
   chunk 19 optimal weight:    0.0970
   chunk 30 optimal weight:    0.7980
   overall best weight:    0.5076

-------------------------------------------------------------------------------
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 = 0.4343 r_free = 0.4343 target = 0.199194 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.4006 r_free = 0.4006 target = 0.162645 restraints weight = 4986.983|
|-----------------------------------------------------------------------------|
r_work (start): 0.3993 rms_B_bonded: 3.09
r_work: 0.3841 rms_B_bonded: 4.26 restraints_weight: 0.5000
r_work (final): 0.3841
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7209
moved from start:          0.1149

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= 0.117
  Angle     :  0.577   8.627   5797  Z= 0.290
  Chirality :  0.043   0.329    647
  Planarity :  0.004   0.036    700
  Dihedral  :  4.726  52.893    617
  Min Nonbonded Distance : 2.609

Molprobity Statistics.
  All-atom Clashscore : 8.91
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.38 %
    Favored  : 98.62 %
  Rotamer:
    Outliers :  0.23 %
    Allowed  :  7.80 %
    Favored  : 91.97 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.28 (0.38), residues: 508
  helix:  1.49 (0.28), residues: 358
  sheet:  None (None), residues: 0
  loop : -0.63 (0.49), residues: 150

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 201 
 TYR   0.014   0.001   TYR A 137 
 PHE   0.024   0.002   PHE A 391 
 TRP   0.010   0.001   TRP A 470 
 HIS   0.002   0.001   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00259 ( 4243)
  covalent geometry    : angle       0.56413 ( 5786)
  SS BOND              : bond        0.00077 (    1)
  SS BOND              : angle       0.69294 (    2)
  hydrogen bonds       : bond        0.03762 (  257)
  hydrogen bonds       : angle       4.15654 (  756)
  link_NAG-ASN         : bond        0.00941 (    3)
  link_NAG-ASN         : angle       3.11949 (    9)

*********************** 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
  90 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 89
  time to evaluate  : 0.150 
Fit side-chains
   revert: symmetry clash
REVERT: A  538 TYR cc_start: 0.8128 (m-10) cc_final: 0.7728 (m-80)
  outliers start: 1
  outliers final: 0
  residues processed: 89
  average time/residue: 0.0643
  time to fit residues: 7.4725
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  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 14 optimal weight:    2.9990
   chunk 21 optimal weight:    1.9990
   chunk 24 optimal weight:    0.9980
   chunk 1 optimal weight:    2.9990
   chunk 39 optimal weight:    1.9990
   chunk 9 optimal weight:    0.9990
   chunk 11 optimal weight:    0.0270
   chunk 31 optimal weight:    0.6980
   chunk 4 optimal weight:    0.9980
   chunk 49 optimal weight:    0.9990
   chunk 6 optimal weight:    0.1980
   overall best weight:    0.5838

-------------------------------------------------------------------------------
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 = 0.4334 r_free = 0.4334 target = 0.197898 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3979 r_free = 0.3979 target = 0.160963 restraints weight = 5041.685|
|-----------------------------------------------------------------------------|
r_work (start): 0.3969 rms_B_bonded: 3.14
r_work: 0.3821 rms_B_bonded: 4.28 restraints_weight: 0.5000
r_work (final): 0.3821
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7224
moved from start:          0.1484

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= 0.118
  Angle     :  0.577   8.666   5797  Z= 0.287
  Chirality :  0.042   0.314    647
  Planarity :  0.004   0.034    700
  Dihedral  :  4.663  53.077    617
  Min Nonbonded Distance : 2.613

Molprobity Statistics.
  All-atom Clashscore : 8.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.57 %
    Favored  : 98.43 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 11.70 %
    Favored  : 87.39 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.34 (0.38), residues: 508
  helix:  1.57 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.70 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 201 
 TYR   0.012   0.001   TYR A 137 
 PHE   0.031   0.001   PHE A 522 
 TRP   0.009   0.001   TRP A 236 
 HIS   0.002   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00265 ( 4243)
  covalent geometry    : angle       0.56436 ( 5786)
  SS BOND              : bond        0.00043 (    1)
  SS BOND              : angle       0.74238 (    2)
  hydrogen bonds       : bond        0.03663 (  257)
  hydrogen bonds       : angle       4.16791 (  756)
  link_NAG-ASN         : bond        0.00869 (    3)
  link_NAG-ASN         : angle       3.12006 (    9)

*********************** 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
  91 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 87
  time to evaluate  : 0.124 
Fit side-chains
   revert: symmetry clash
REVERT: A  266 THR cc_start: 0.8424 (t) cc_final: 0.8156 (p)
REVERT: A  403 GLN cc_start: 0.7440 (tp-100) cc_final: 0.6897 (mm-40)
REVERT: A  474 PHE cc_start: 0.7759 (m-80) cc_final: 0.7472 (t80)
REVERT: A  494 ASP cc_start: 0.7878 (m-30) cc_final: 0.7449 (m-30)
REVERT: A  522 PHE cc_start: 0.6900 (t80) cc_final: 0.5859 (m-80)
REVERT: A  538 TYR cc_start: 0.8144 (m-10) cc_final: 0.7786 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 90
  average time/residue: 0.0592
  time to fit residues: 6.9268
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  : 0.146 
-------------------------------------------------------------------------------
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 48 optimal weight:    0.5980
   chunk 27 optimal weight:    3.9990
   chunk 24 optimal weight:    0.8980
   chunk 17 optimal weight:    0.5980
   chunk 13 optimal weight:    3.9990
   chunk 22 optimal weight:    0.9980
   chunk 41 optimal weight:    0.9990
   chunk 19 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 43 optimal weight:    0.9980
   chunk 8 optimal weight:    2.9990
   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 = 0.4368 r_free = 0.4368 target = 0.198845 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.4019 r_free = 0.4019 target = 0.162215 restraints weight = 4986.551|
|-----------------------------------------------------------------------------|
r_work (start): 0.4003 rms_B_bonded: 3.00
r_work: 0.3850 rms_B_bonded: 4.16 restraints_weight: 0.5000
r_work (final): 0.3850
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7324
moved from start:          0.1732

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4247  Z= 0.135
  Angle     :  0.614   8.821   5797  Z= 0.299
  Chirality :  0.042   0.307    647
  Planarity :  0.004   0.032    700
  Dihedral  :  4.634  53.013    617
  Min Nonbonded Distance : 2.614

Molprobity Statistics.
  All-atom Clashscore : 9.27
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 12.61 %
    Favored  : 86.47 %
  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 aren not related in a simple way.
  whole:  1.25 (0.37), residues: 508
  helix:  1.49 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.71 (0.48), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.012   0.001   TYR A 137 
 PHE   0.030   0.002   PHE A 522 
 TRP   0.012   0.001   TRP A 236 
 HIS   0.002   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00315 ( 4243)
  covalent geometry    : angle       0.60189 ( 5786)
  SS BOND              : bond        0.00029 (    1)
  SS BOND              : angle       0.71229 (    2)
  hydrogen bonds       : bond        0.03826 (  257)
  hydrogen bonds       : angle       4.31875 (  756)
  link_NAG-ASN         : bond        0.00864 (    3)
  link_NAG-ASN         : angle       3.10347 (    9)

*********************** 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
  84 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 80
  time to evaluate  : 0.112 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.6801 (m-80) cc_final: 0.6422 (t80)
REVERT: A  309 MET cc_start: 0.8180 (mmt) cc_final: 0.7881 (mmt)
REVERT: A  429 GLU cc_start: 0.8164 (mt-10) cc_final: 0.7919 (mt-10)
REVERT: A  446 MET cc_start: 0.8691 (ptp) cc_final: 0.8355 (ptp)
REVERT: A  494 ASP cc_start: 0.7933 (m-30) cc_final: 0.7506 (m-30)
REVERT: A  522 PHE cc_start: 0.6885 (t80) cc_final: 0.6074 (m-80)
REVERT: A  538 TYR cc_start: 0.8185 (m-10) cc_final: 0.7796 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 83
  average time/residue: 0.0530
  time to fit residues: 6.0298
Evaluate side-chains
  77 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 75
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  334 SER
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 25 optimal weight:    0.6980
   chunk 30 optimal weight:    0.7980
   chunk 15 optimal weight:    5.9990
   chunk 2 optimal weight:    0.0980
   chunk 7 optimal weight:    0.8980
   chunk 18 optimal weight:    0.0030
   chunk 20 optimal weight:    0.5980
   chunk 33 optimal weight:    1.9990
   chunk 3 optimal weight:    0.7980
   chunk 19 optimal weight:    0.9980
   chunk 31 optimal weight:    0.7980
   overall best weight:    0.4390

-------------------------------------------------------------------------------
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 = 0.4426 r_free = 0.4426 target = 0.203179 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 41)----------------|
| r_work = 0.4088 r_free = 0.4088 target = 0.167850 restraints weight = 4975.565|
|-----------------------------------------------------------------------------|
r_work (start): 0.4079 rms_B_bonded: 3.04
r_work: 0.3931 rms_B_bonded: 4.15 restraints_weight: 0.5000
r_work (final): 0.3931
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7275
moved from start:          0.1917

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.028   4247  Z= 0.110
  Angle     :  0.593   9.813   5797  Z= 0.285
  Chirality :  0.041   0.307    647
  Planarity :  0.004   0.031    700
  Dihedral  :  4.560  53.204    617
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 8.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 15.83 %
    Favored  : 83.49 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.44 (0.38), residues: 508
  helix:  1.62 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.60 (0.49), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 240 
 TYR   0.014   0.001   TYR A 137 
 PHE   0.023   0.001   PHE A 522 
 TRP   0.014   0.001   TRP A 236 
 HIS   0.002   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00242 ( 4243)
  covalent geometry    : angle       0.58056 ( 5786)
  SS BOND              : bond        0.00024 (    1)
  SS BOND              : angle       0.69799 (    2)
  hydrogen bonds       : bond        0.03549 (  257)
  hydrogen bonds       : angle       4.18469 (  756)
  link_NAG-ASN         : bond        0.00839 (    3)
  link_NAG-ASN         : angle       3.11594 (    9)

*********************** 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
  90 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 87
  time to evaluate  : 0.156 
Fit side-chains
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7417 (mmtt) cc_final: 0.7158 (mmtp)
REVERT: A  309 MET cc_start: 0.8236 (mmt) cc_final: 0.7973 (mmt)
REVERT: A  446 MET cc_start: 0.8731 (ptp) cc_final: 0.8433 (ptp)
REVERT: A  494 ASP cc_start: 0.7881 (m-30) cc_final: 0.7411 (m-30)
REVERT: A  522 PHE cc_start: 0.6642 (t80) cc_final: 0.5964 (m-80)
REVERT: A  538 TYR cc_start: 0.8114 (m-10) cc_final: 0.7804 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 90
  average time/residue: 0.0561
  time to fit residues: 6.9176
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  : 0.151 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  334 SER
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 35 optimal weight:    0.9990
   chunk 15 optimal weight:    4.9990
   chunk 14 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 24 optimal weight:    1.9990
   chunk 47 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 10 optimal weight:    0.9980
   chunk 22 optimal weight:    7.9990
   chunk 9 optimal weight:    0.7980
   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 = 0.4389 r_free = 0.4389 target = 0.199374 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4044 r_free = 0.4044 target = 0.163613 restraints weight = 5076.176|
|-----------------------------------------------------------------------------|
r_work (start): 0.4034 rms_B_bonded: 3.04
r_work: 0.3884 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3884
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7346
moved from start:          0.2154

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4247  Z= 0.140
  Angle     :  0.635  10.220   5797  Z= 0.308
  Chirality :  0.044   0.302    647
  Planarity :  0.004   0.032    700
  Dihedral  :  4.647  53.103    617
  Min Nonbonded Distance : 2.617

Molprobity Statistics.
  All-atom Clashscore : 10.74
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.46 %
    Allowed  : 16.97 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.38), residues: 508
  helix:  1.48 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.69 (0.49), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 177 
 TYR   0.016   0.001   TYR A 137 
 PHE   0.049   0.002   PHE A 404 
 TRP   0.017   0.001   TRP A 236 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00328 ( 4243)
  covalent geometry    : angle       0.62326 ( 5786)
  SS BOND              : bond        0.00060 (    1)
  SS BOND              : angle       0.68265 (    2)
  hydrogen bonds       : bond        0.03817 (  257)
  hydrogen bonds       : angle       4.36325 (  756)
  link_NAG-ASN         : bond        0.00867 (    3)
  link_NAG-ASN         : angle       3.09712 (    9)

*********************** 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
  76 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 74
  time to evaluate  : 0.148 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  178 LYS cc_start: 0.7465 (mmtt) cc_final: 0.7168 (mmtp)
REVERT: A  309 MET cc_start: 0.8255 (mmt) cc_final: 0.7930 (mmt)
REVERT: A  494 ASP cc_start: 0.7888 (m-30) cc_final: 0.7424 (m-30)
REVERT: A  504 MET cc_start: 0.5771 (ttm) cc_final: 0.5540 (ttm)
REVERT: A  538 TYR cc_start: 0.8186 (m-10) cc_final: 0.7750 (m-80)
  outliers start: 2
  outliers final: 2
  residues processed: 76
  average time/residue: 0.0618
  time to fit residues: 6.1901
Evaluate side-chains
  74 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 72
  time to evaluate  : 0.180 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  334 SER
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 27 optimal weight:    0.8980
   chunk 46 optimal weight:    4.9990
   chunk 10 optimal weight:    0.8980
   chunk 0 optimal weight:   10.0000
   chunk 44 optimal weight:    0.2980
   chunk 43 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9980
   chunk 29 optimal weight:    1.9990
   chunk 30 optimal weight:    5.9990
   chunk 35 optimal weight:    2.9990
   chunk 42 optimal weight:    0.9990
   overall best weight:    0.8182

-------------------------------------------------------------------------------
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 = 0.4388 r_free = 0.4388 target = 0.199240 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.4047 r_free = 0.4047 target = 0.163954 restraints weight = 5050.467|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 3.02
r_work: 0.3886 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7338
moved from start:          0.2205

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.031   4247  Z= 0.134
  Angle     :  0.622  10.845   5797  Z= 0.300
  Chirality :  0.043   0.301    647
  Planarity :  0.004   0.032    700
  Dihedral  :  4.671  53.270    617
  Min Nonbonded Distance : 2.616

Molprobity Statistics.
  All-atom Clashscore : 9.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.77 %
    Favored  : 98.23 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 16.51 %
    Favored  : 82.57 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.25 (0.38), residues: 508
  helix:  1.47 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.66 (0.49), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 284 
 TYR   0.016   0.001   TYR A 137 
 PHE   0.039   0.002   PHE A 404 
 TRP   0.014   0.001   TRP A 236 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00309 ( 4243)
  covalent geometry    : angle       0.61064 ( 5786)
  SS BOND              : bond        0.00094 (    1)
  SS BOND              : angle       0.68798 (    2)
  hydrogen bonds       : bond        0.03795 (  257)
  hydrogen bonds       : angle       4.35956 (  756)
  link_NAG-ASN         : bond        0.00864 (    3)
  link_NAG-ASN         : angle       3.08386 (    9)

*********************** 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
  80 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.158 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  309 MET cc_start: 0.8308 (mmt) cc_final: 0.7983 (mmt)
REVERT: A  446 MET cc_start: 0.8657 (ptp) cc_final: 0.8317 (ptp)
REVERT: A  494 ASP cc_start: 0.7892 (m-30) cc_final: 0.7403 (m-30)
REVERT: A  504 MET cc_start: 0.5842 (ttm) cc_final: 0.5577 (ttm)
REVERT: A  522 PHE cc_start: 0.7590 (t80) cc_final: 0.6256 (m-80)
REVERT: A  538 TYR cc_start: 0.8211 (m-10) cc_final: 0.7710 (m-80)
  outliers start: 4
  outliers final: 2
  residues processed: 79
  average time/residue: 0.0487
  time to fit residues: 5.3383
Evaluate side-chains
  75 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 2
    poor density    : 73
  time to evaluate  : 0.149 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  334 SER
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 5 optimal weight:    3.9990
   chunk 36 optimal weight:    7.9990
   chunk 27 optimal weight:    1.9990
   chunk 22 optimal weight:    0.8980
   chunk 1 optimal weight:    0.0980
   chunk 0 optimal weight:    9.9990
   chunk 19 optimal weight:    6.9990
   chunk 37 optimal weight:    0.9980
   chunk 4 optimal weight:    0.7980
   chunk 7 optimal weight:    4.9990
   chunk 48 optimal weight:    0.8980
   overall best weight:    0.7380

-------------------------------------------------------------------------------
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 = 0.199371 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.4053 r_free = 0.4053 target = 0.164444 restraints weight = 5002.663|
|-----------------------------------------------------------------------------|
r_work (start): 0.4042 rms_B_bonded: 2.98
r_work: 0.3889 rms_B_bonded: 4.08 restraints_weight: 0.5000
r_work (final): 0.3889
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7342
moved from start:          0.2381

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= 0.131
  Angle     :  0.629  10.557   5797  Z= 0.303
  Chirality :  0.043   0.301    647
  Planarity :  0.004   0.032    700
  Dihedral  :  4.677  53.284    617
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 16.97 %
    Favored  : 82.34 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.24 (0.38), residues: 508
  helix:  1.47 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.68 (0.49), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 240 
 TYR   0.016   0.001   TYR A 137 
 PHE   0.038   0.002   PHE A 404 
 TRP   0.013   0.001   TRP A 236 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00303 ( 4243)
  covalent geometry    : angle       0.61733 ( 5786)
  SS BOND              : bond        0.00052 (    1)
  SS BOND              : angle       0.70468 (    2)
  hydrogen bonds       : bond        0.03802 (  257)
  hydrogen bonds       : angle       4.35140 (  756)
  link_NAG-ASN         : bond        0.00861 (    3)
  link_NAG-ASN         : angle       3.07958 (    9)

*********************** 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
  87 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 84
  time to evaluate  : 0.170 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.5854 (OUTLIER) cc_final: 0.5616 (t80)
REVERT: A  285 LEU cc_start: 0.8998 (mp) cc_final: 0.8704 (mp)
REVERT: A  309 MET cc_start: 0.8327 (mmt) cc_final: 0.7943 (mmt)
REVERT: A  414 LEU cc_start: 0.6685 (pp) cc_final: 0.6319 (pp)
REVERT: A  446 MET cc_start: 0.8647 (ptp) cc_final: 0.8310 (ptp)
REVERT: A  494 ASP cc_start: 0.7855 (m-30) cc_final: 0.7369 (m-30)
REVERT: A  504 MET cc_start: 0.5843 (ttm) cc_final: 0.5589 (ttm)
REVERT: A  522 PHE cc_start: 0.7462 (t80) cc_final: 0.6228 (m-80)
REVERT: A  538 TYR cc_start: 0.8211 (m-10) cc_final: 0.7775 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 86
  average time/residue: 0.0467
  time to fit residues: 5.6652
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  : 0.147 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  334 SER
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 45 optimal weight:    1.9990
   chunk 12 optimal weight:    0.5980
   chunk 46 optimal weight:    0.9990
   chunk 40 optimal weight:    3.9990
   chunk 48 optimal weight:    0.2980
   chunk 4 optimal weight:    0.9990
   chunk 21 optimal weight:    4.9990
   chunk 27 optimal weight:    0.7980
   chunk 18 optimal weight:    0.8980
   chunk 20 optimal weight:    0.8980
   chunk 16 optimal weight:    2.9990
   overall best weight:    0.6980

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.4391 r_free = 0.4391 target = 0.199654 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.4065 r_free = 0.4065 target = 0.165036 restraints weight = 5116.725|
|-----------------------------------------------------------------------------|
r_work (start): 0.4049 rms_B_bonded: 2.97
r_work: 0.3900 rms_B_bonded: 4.03 restraints_weight: 0.5000
r_work (final): 0.3900
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7340
moved from start:          0.2416

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.032   4247  Z= 0.130
  Angle     :  0.646  10.914   5797  Z= 0.310
  Chirality :  0.044   0.300    647
  Planarity :  0.004   0.032    700
  Dihedral  :  4.688  53.277    617
  Min Nonbonded Distance : 2.618

Molprobity Statistics.
  All-atom Clashscore : 10.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  1.97 %
    Favored  : 98.03 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 18.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.20 (0.38), residues: 508
  helix:  1.43 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.67 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 240 
 TYR   0.017   0.001   TYR A 536 
 PHE   0.043   0.002   PHE A 404 
 TRP   0.012   0.001   TRP A 236 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00298 ( 4243)
  covalent geometry    : angle       0.63459 ( 5786)
  SS BOND              : bond        0.00061 (    1)
  SS BOND              : angle       0.68778 (    2)
  hydrogen bonds       : bond        0.03788 (  257)
  hydrogen bonds       : angle       4.36897 (  756)
  link_NAG-ASN         : bond        0.00864 (    3)
  link_NAG-ASN         : angle       3.09130 (    9)

*********************** 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
  83 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 79
  time to evaluate  : 0.159 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.5882 (OUTLIER) cc_final: 0.5623 (t80)
REVERT: A  178 LYS cc_start: 0.7343 (mmtt) cc_final: 0.7085 (mmtp)
REVERT: A  281 ASP cc_start: 0.8398 (t0) cc_final: 0.8029 (t0)
REVERT: A  285 LEU cc_start: 0.8986 (mp) cc_final: 0.8702 (mp)
REVERT: A  309 MET cc_start: 0.8365 (mmt) cc_final: 0.7986 (mmt)
REVERT: A  446 MET cc_start: 0.8641 (ptp) cc_final: 0.8323 (ptp)
REVERT: A  494 ASP cc_start: 0.7824 (m-30) cc_final: 0.7355 (m-30)
REVERT: A  504 MET cc_start: 0.5845 (ttm) cc_final: 0.5578 (ttm)
REVERT: A  522 PHE cc_start: 0.7404 (t80) cc_final: 0.6225 (m-80)
REVERT: A  538 TYR cc_start: 0.8198 (m-10) cc_final: 0.7765 (m-80)
  outliers start: 4
  outliers final: 3
  residues processed: 81
  average time/residue: 0.0547
  time to fit residues: 6.0666
Evaluate side-chains
  80 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 76
  time to evaluate  : 0.164 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  334 SER
Chi-restraints excluded: chain A residue  426 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 38 optimal weight:    0.3980
   chunk 31 optimal weight:    0.6980
   chunk 27 optimal weight:    2.9990
   chunk 46 optimal weight:    0.9990
   chunk 6 optimal weight:    3.9990
   chunk 3 optimal weight:    0.9990
   chunk 32 optimal weight:    0.9980
   chunk 28 optimal weight:    0.7980
   chunk 17 optimal weight:    0.9990
   chunk 42 optimal weight:    1.9990
   chunk 2 optimal weight:    0.9980
   overall best weight:    0.7780

-------------------------------------------------------------------------------
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 = 0.4384 r_free = 0.4384 target = 0.198753 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.4045 r_free = 0.4045 target = 0.163670 restraints weight = 4983.591|
|-----------------------------------------------------------------------------|
r_work (start): 0.4035 rms_B_bonded: 2.98
r_work: 0.3886 rms_B_bonded: 4.06 restraints_weight: 0.5000
r_work (final): 0.3886
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7350
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   0.036   4247  Z= 0.134
  Angle     :  0.646  11.070   5797  Z= 0.311
  Chirality :  0.044   0.297    647
  Planarity :  0.004   0.032    700
  Dihedral  :  4.706  53.305    617
  Min Nonbonded Distance : 2.619

Molprobity Statistics.
  All-atom Clashscore : 9.88
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.17 %
    Favored  : 97.83 %
  Rotamer:
    Outliers :  0.69 %
    Allowed  : 18.12 %
    Favored  : 81.19 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  1.19 (0.38), residues: 508
  helix:  1.42 (0.28), residues: 357
  sheet:  None (None), residues: 0
  loop : -0.66 (0.50), residues: 151

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 240 
 TYR   0.016   0.001   TYR A 536 
 PHE   0.041   0.002   PHE A 404 
 TRP   0.011   0.001   TRP A 166 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00310 ( 4243)
  covalent geometry    : angle       0.63521 ( 5786)
  SS BOND              : bond        0.00087 (    1)
  SS BOND              : angle       0.64120 (    2)
  hydrogen bonds       : bond        0.03863 (  257)
  hydrogen bonds       : angle       4.42191 (  756)
  link_NAG-ASN         : bond        0.00861 (    3)
  link_NAG-ASN         : angle       3.05426 (    9)

********************** 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
  82 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 79
  time to evaluate  : 0.142 
Fit side-chains
   revert: symmetry clash
REVERT: A  120 PHE cc_start: 0.6251 (OUTLIER) cc_final: 0.5840 (t80)
REVERT: A  252 PHE cc_start: 0.8413 (t80) cc_final: 0.7994 (t80)
REVERT: A  281 ASP cc_start: 0.8387 (t0) cc_final: 0.8042 (t0)
REVERT: A  285 LEU cc_start: 0.9017 (mp) cc_final: 0.8732 (mp)
REVERT: A  309 MET cc_start: 0.8397 (mmt) cc_final: 0.8081 (mmt)
REVERT: A  446 MET cc_start: 0.8664 (ptp) cc_final: 0.8337 (ptp)
REVERT: A  494 ASP cc_start: 0.7791 (m-30) cc_final: 0.7329 (m-30)
REVERT: A  504 MET cc_start: 0.5895 (ttm) cc_final: 0.5633 (ttm)
REVERT: A  522 PHE cc_start: 0.7387 (t80) cc_final: 0.6249 (m-80)
REVERT: A  538 TYR cc_start: 0.8216 (m-10) cc_final: 0.7717 (m-80)
  outliers start: 3
  outliers final: 2
  residues processed: 80
  average time/residue: 0.0526
  time to fit residues: 5.7079
Evaluate side-chains
  81 residues out of total 436 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 78
  time to evaluate  : 0.159 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   69 TYR
Chi-restraints excluded: chain A residue  120 PHE
Chi-restraints excluded: chain A residue  426 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 51
   random chunks:
   chunk 16 optimal weight:    1.9990
   chunk 40 optimal weight:    1.9990
   chunk 29 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 30 optimal weight:    2.9990
   chunk 3 optimal weight:    0.9990
   chunk 22 optimal weight:    0.9990
   chunk 44 optimal weight:    5.9990
   chunk 0 optimal weight:    9.9990
   chunk 8 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   overall best weight:    1.1788

-------------------------------------------------------------------------------
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 = 0.4311 r_free = 0.4311 target = 0.193705 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3971 r_free = 0.3971 target = 0.158416 restraints weight = 5112.672|
|-----------------------------------------------------------------------------|
r_work (start): 0.3954 rms_B_bonded: 3.05
r_work: 0.3802 rms_B_bonded: 4.14 restraints_weight: 0.5000
r_work (final): 0.3802
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.7381
moved from start:          0.2657

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.038   4247  Z= 0.165
  Angle     :  0.688  11.194   5797  Z= 0.335
  Chirality :  0.045   0.290    647
  Planarity :  0.004   0.033    700
  Dihedral  :  4.912  53.513    617
  Min Nonbonded Distance : 2.545

Molprobity Statistics.
  All-atom Clashscore : 10.98
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  0.92 %
    Allowed  : 18.35 %
    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 values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they aren not related in a simple way.
  whole:  0.95 (0.38), residues: 508
  helix:  1.24 (0.28), residues: 359
  sheet:  None (None), residues: 0
  loop : -0.78 (0.51), residues: 149

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.003   0.000   ARG A 201 
 TYR   0.017   0.001   TYR A 536 
 PHE   0.042   0.002   PHE A 404 
 TRP   0.008   0.001   TRP A 228 
 HIS   0.001   0.000   HIS A 212 

Details of bonding type rmsd
  covalent geometry    : bond        0.00390 ( 4243)
  covalent geometry    : angle       0.67691 ( 5786)
  SS BOND              : bond        0.00098 (    1)
  SS BOND              : angle       0.68328 (    2)
  hydrogen bonds       : bond        0.04190 (  257)
  hydrogen bonds       : angle       4.59614 (  756)
  link_NAG-ASN         : bond        0.00878 (    3)
  link_NAG-ASN         : angle       3.18433 (    9)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1148.79 seconds
wall clock time: 20 minutes 26.44 seconds (1226.44 seconds total)