Starting phenix.real_space_refine
on Wed Feb  4 05:22:08 2026 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/9kb6_62218/02_2026/9kb6_62218.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/9kb6_62218/02_2026/9kb6_62218.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.53
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    model {
      file = "/net/cci-nas-00/data/ceres_data/9kb6_62218/02_2026/9kb6_62218.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/9kb6_62218/02_2026/9kb6_62218.cif"
    real_map_files = "/net/cci-nas-00/data/ceres_data/9kb6_62218/02_2026/9kb6_62218.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/9kb6_62218/02_2026/9kb6_62218.map"
  }
  resolution = 3.53
  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=   0.000 sd=   0.003
Set stop_for_unknowns flag
  Set to: True
Assert model is a single copy model
Assert all atoms have isotropic ADPs
  Anisotropic ADP refinement not supported. Converting 3473 atoms to isotropic.
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: 4
    Type Number    sf(0)   Gaussians
     S      30      5.16       5
     C    3837      2.51       5
     N     971      2.21       5
     O    1084      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 1 residue(s): 0.00s

  Monomer Library directory:
    "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib"
  Total number of atoms: 5922
  Number of models: 1
  Model: ""
    Number of chains: 2
    Chain: "A"
      Number of atoms: 5866
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 752, 5866
          Classifications: {'peptide': 752}
          Link IDs: {'PCIS': 2, 'PTRANS': 35, 'TRANS': 714}
          Chain breaks: 1
    Chain: "A"
      Number of atoms: 56
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 4, 56
          Unusual residues: {'NAG': 4}
          Classifications: {'undetermined': 4}
          Link IDs: {None: 3}
          Unresolved non-hydrogen bonds: 4
          Unresolved non-hydrogen angles: 8
          Unresolved non-hydrogen dihedrals: 12
          Unresolved non-hydrogen chiralities: 4
  Time building chain proxies: 1.04, per 1000 atoms: 0.18
  Number of scatterers: 5922
  At special positions: 0
  Unit cell: (68.89, 87.15, 156.04, 90, 90, 90)
  Space group: P 1 (No. 1)
  Number of sites at special positions: 0
  Number of scattering types: 4
    Type Number    sf(0)
     S      30     16.00
     O    1084      8.00
     N     971      7.00
     C    3837      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=6, symmetry=0
    Simple disulfide: pdb=" SG  CYS A  29 " - pdb=" SG  CYS A  35 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A  33 " - pdb=" SG  CYS A  43 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 339 " - pdb=" SG  CYS A 364 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 470 " - pdb=" SG  CYS A 522 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 471 " - pdb=" SG  CYS A 532 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 618 " - pdb=" SG  CYS A 693 " 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 A1001 " - " ASN A 199 "
      " NAG A1002 " - " ASN A 314 "
      " NAG A1003 " - " ASN A 294 "
      " NAG A1004 " - " ASN A  68 "
  Time building additional restraints: 0.44
  Conformation dependent library (CDL) restraints added in 218.6 milliseconds
  

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1422

  Finding SS restraints...
    Secondary structure from input PDB file:
      18 helices and 6 sheets defined
      37.4% alpha, 7.0% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.15
  Creating SS restraints...
    Processing helix  chain 'A' and resid 169 through 174
    Processing helix  chain 'A' and resid 242 through 247
    Processing helix  chain 'A' and resid 337 through 342
    Processing helix  chain 'A' and resid 381 through 386
      removed outlier: 4.136A  pdb=" N   PHE A 385 " --> pdb=" O   GLU A 382 " (cutoff:3.500A)
      removed outlier: 3.769A  pdb=" N   GLN A 386 " --> pdb=" O   GLY A 383 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 452 through 456
    Processing helix  chain 'A' and resid 466 through 471
      removed outlier: 3.569A  pdb=" N   CYS A 471 " --> pdb=" O   TYR A 468 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 538 through 565
    Processing helix  chain 'A' and resid 571 through 601
      removed outlier: 3.765A  pdb=" N   ILE A 577 " --> pdb=" O   SER A 573 " (cutoff:3.500A)
      removed outlier: 3.522A  pdb=" N   GLY A 578 " --> pdb=" O   LYS A 574 " (cutoff:3.500A)
      removed outlier: 3.633A  pdb=" N   LEU A 579 " --> pdb=" O   LEU A 575 " (cutoff:3.500A)
      removed outlier: 3.507A  pdb=" N   PHE A 586 " --> pdb=" O   VAL A 582 " (cutoff:3.500A)
      removed outlier: 3.674A  pdb=" N   MET A 587 " --> pdb=" O   SER A 583 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 604 through 615
      removed outlier: 3.846A  pdb=" N   PHE A 608 " --> pdb=" O   ARG A 604 " (cutoff:3.500A)
      removed outlier: 4.516A  pdb=" N   ILE A 610 " --> pdb=" O   ALA A 606 " (cutoff:3.500A)
      removed outlier: 4.729A  pdb=" N   TRP A 611 " --> pdb=" O   GLU A 607 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 615 through 653
      removed outlier: 4.173A  pdb=" N   LYS A 619 " --> pdb=" O   GLY A 615 " (cutoff:3.500A)
      removed outlier: 4.088A  pdb=" N   MET A 651 " --> pdb=" O   ALA A 647 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 658 through 683
      Proline residue:  A 680  - end of helix
      removed outlier: 3.768A  pdb=" N   HIS A 683 " --> pdb=" O   PHE A 679 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 703 through 732
      removed outlier: 3.606A  pdb=" N   THR A 709 " --> pdb=" O   GLY A 705 " (cutoff:3.500A)
      removed outlier: 3.785A  pdb=" N   LEU A 719 " --> pdb=" O   SER A 715 " (cutoff:3.500A)
      removed outlier: 3.887A  pdb=" N   LEU A 720 " --> pdb=" O   LEU A 716 " (cutoff:3.500A)
      removed outlier: 4.023A  pdb=" N   TYR A 725 " --> pdb=" O   MET A 721 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 733 through 738
      removed outlier: 4.092A  pdb=" N   LEU A 737 " --> pdb=" O   LYS A 734 " (cutoff:3.500A)
      removed outlier: 3.915A  pdb=" N   SER A 738 " --> pdb=" O   GLU A 735 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 740 through 759
      removed outlier: 4.156A  pdb=" N   SER A 744 " --> pdb=" O   ASN A 740 " (cutoff:3.500A)
      removed outlier: 3.623A  pdb=" N   MET A 745 " --> pdb=" O   SER A 741 " (cutoff:3.500A)
      removed outlier: 3.734A  pdb=" N   PHE A 754 " --> pdb=" O   ALA A 750 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 760 through 768
    Processing helix  chain 'A' and resid 778 through 789
      removed outlier: 4.171A  pdb=" N   MET A 782 " --> pdb=" O   SER A 778 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 791 through 805
      removed outlier: 3.878A  pdb=" N   CYS A 795 " --> pdb=" O   PRO A 791 " (cutoff:3.500A)
      Proline residue:  A 798  - end of helix
    Processing helix  chain 'A' and resid 805 through 822
      removed outlier: 4.049A  pdb=" N   LYS A 809 " --> pdb=" O   ASN A 805 " (cutoff:3.500A)
      removed outlier: 3.793A  pdb=" N   GLU A 810 " --> pdb=" O   PRO A 806 " (cutoff:3.500A)
    Processing sheet with id=AA1, first strand: chain 'A' and resid 34 through 35
      removed outlier: 6.888A  pdb=" N   LEU A 134 " --> pdb=" O   TRP A 159 " (cutoff:3.500A)
      removed outlier: 6.874A  pdb=" N   LEU A 182 " --> pdb=" O   HIS A 207 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72
    Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192
      removed outlier: 3.665A  pdb=" N   ILE A 192 " --> pdb=" O   SER A 215 " (cutoff:3.500A)
  No H-bonds generated for sheet with id=AA3
    Processing sheet with id=AA4, first strand: chain 'A' and resid 262 through 263
    Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 304
      removed outlier: 6.609A  pdb=" N   ILE A 370 " --> pdb=" O   ASP A 395 " (cutoff:3.500A)
      removed outlier: 6.488A  pdb=" N   LEU A 462 " --> pdb=" O   THR A 523 " (cutoff:3.500A)
    Processing sheet with id=AA6, first strand: chain 'A' and resid 379 through 380

    217 hydrogen bonds defined for protein.
    621 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: 0.78

  Time building geometry restraints manager: 0.55 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: 1825
        1.34 -     1.46: 985
        1.46 -     1.58: 3211
        1.58 -     1.70: 0
        1.70 -     1.82: 40
  Bond restraints: 6061
  Sorted by residual:
  bond pdb=" CA  SER A 290 "
       pdb=" CB  SER A 290 "
    ideal  model  delta    sigma   weight residual
    1.534  1.475  0.059 1.71e-02 3.42e+03 1.19e+01
  bond pdb=" N   ILE A  69 "
       pdb=" CA  ILE A  69 "
    ideal  model  delta    sigma   weight residual
    1.459  1.497 -0.038 1.25e-02 6.40e+03 9.08e+00
  bond pdb=" N   HIS A 171 "
       pdb=" CA  HIS A 171 "
    ideal  model  delta    sigma   weight residual
    1.461  1.489 -0.028 9.20e-03 1.18e+04 9.04e+00
  bond pdb=" N   ASP A 297 "
       pdb=" CA  ASP A 297 "
    ideal  model  delta    sigma   weight residual
    1.457  1.494 -0.036 1.29e-02 6.01e+03 7.88e+00
  bond pdb=" N   ASN A 199 "
       pdb=" CA  ASN A 199 "
    ideal  model  delta    sigma   weight residual
    1.454  1.491 -0.036 1.31e-02 5.83e+03 7.69e+00
  ... (remaining 6056 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     1.97: 8044
        1.97 -     3.94: 159
        3.94 -     5.91: 28
        5.91 -     7.88: 5
        7.88 -     9.85: 3
  Bond angle restraints: 8239
  Sorted by residual:
  angle pdb=" C   ASN A  67 "
        pdb=" N   ASN A  68 "
        pdb=" CA  ASN A  68 "
      ideal   model   delta    sigma   weight residual
     122.79  115.15    7.64 1.63e+00 3.76e-01 2.20e+01
  angle pdb=" N   ASN A 289 "
        pdb=" CA  ASN A 289 "
        pdb=" C   ASN A 289 "
      ideal   model   delta    sigma   weight residual
     111.28  106.60    4.68 1.09e+00 8.42e-01 1.85e+01
  angle pdb=" CA  SER A 296 "
        pdb=" C   SER A 296 "
        pdb=" O   SER A 296 "
      ideal   model   delta    sigma   weight residual
     121.55  117.69    3.86 1.06e+00 8.90e-01 1.32e+01
  angle pdb=" CA  ASP A 297 "
        pdb=" CB  ASP A 297 "
        pdb=" CG  ASP A 297 "
      ideal   model   delta    sigma   weight residual
     112.60  115.93   -3.33 1.00e+00 1.00e+00 1.11e+01
  angle pdb=" N   THR A  49 "
        pdb=" CA  THR A  49 "
        pdb=" C   THR A  49 "
      ideal   model   delta    sigma   weight residual
     113.17  108.99    4.18 1.26e+00 6.30e-01 1.10e+01
  ... (remaining 8234 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    15.34: 3187
       15.34 -    30.69: 356
       30.69 -    46.03: 93
       46.03 -    61.37: 33
       61.37 -    76.72: 5
  Dihedral angle restraints: 3674
    sinusoidal: 1490
      harmonic: 2184
  Sorted by residual:
  dihedral pdb=" CB  CYS A  29 "
           pdb=" SG  CYS A  29 "
           pdb=" SG  CYS A  35 "
           pdb=" CB  CYS A  35 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   45.38   47.62     1      1.00e+01 1.00e-02 3.13e+01
  dihedral pdb=" CB  CYS A 618 "
           pdb=" SG  CYS A 618 "
           pdb=" SG  CYS A 693 "
           pdb=" CB  CYS A 693 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -132.53   46.53     1      1.00e+01 1.00e-02 3.00e+01
  dihedral pdb=" CB  CYS A 339 "
           pdb=" SG  CYS A 339 "
           pdb=" SG  CYS A 364 "
           pdb=" CB  CYS A 364 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -115.43   29.43     1      1.00e+01 1.00e-02 1.24e+01
  ... (remaining 3671 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.040: 672
       0.040 -    0.079: 220
       0.079 -    0.119: 72
       0.119 -    0.159: 7
       0.159 -    0.199: 6
  Chirality restraints: 977
  Sorted by residual:
  chirality pdb=" CA  HIS A 293 "
            pdb=" N   HIS A 293 "
            pdb=" C   HIS A 293 "
            pdb=" CB  HIS A 293 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    2.71   -0.20 2.00e-01 2.50e+01 9.87e-01
  chirality pdb=" CA  ILE A 610 "
            pdb=" N   ILE A 610 "
            pdb=" C   ILE A 610 "
            pdb=" CB  ILE A 610 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.43    2.63   -0.20 2.00e-01 2.50e+01 9.57e-01
  chirality pdb=" C1  NAG A1004 "
            pdb=" ND2 ASN A  68 "
            pdb=" C2  NAG A1004 "
            pdb=" O5  NAG A1004 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.21   -0.19 2.00e-01 2.50e+01 9.25e-01
  ... (remaining 974 not shown)

  Planarity restraints: 1040
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1003 "   -0.336 2.00e-02 2.50e+03   2.91e-01 1.06e+03
        pdb=" C7  NAG A1003 "    0.080 2.00e-02 2.50e+03
        pdb=" C8  NAG A1003 "   -0.115 2.00e-02 2.50e+03
        pdb=" N2  NAG A1003 "    0.519 2.00e-02 2.50e+03
        pdb=" O7  NAG A1003 "   -0.148 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A1002 "    0.132 2.00e-02 2.50e+03   1.09e-01 1.49e+02
        pdb=" C7  NAG A1002 "   -0.030 2.00e-02 2.50e+03
        pdb=" C8  NAG A1002 "    0.096 2.00e-02 2.50e+03
        pdb=" N2  NAG A1002 "   -0.178 2.00e-02 2.50e+03
        pdb=" O7  NAG A1002 "   -0.021 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" CA  PHE A 608 "    0.009 2.00e-02 2.50e+03   1.74e-02 3.02e+00
        pdb=" C   PHE A 608 "   -0.030 2.00e-02 2.50e+03
        pdb=" O   PHE A 608 "    0.011 2.00e-02 2.50e+03
        pdb=" N   GLY A 609 "    0.010 2.00e-02 2.50e+03
  ... (remaining 1037 not shown)

  Histogram of nonbonded interaction distances:
        2.09 -     2.65: 84
        2.65 -     3.21: 5514
        3.21 -     3.78: 9143
        3.78 -     4.34: 12431
        4.34 -     4.90: 20121
  Nonbonded interactions: 47293
  Sorted by model distance:
  nonbonded pdb=" OH  TYR A 725 "
            pdb=" O   ILE A 746 "
     model   vdw
     2.089 3.040
  nonbonded pdb=" O   PHE A 445 "
            pdb=" OH  TYR A 466 "
     model   vdw
     2.291 3.040
  nonbonded pdb=" O   ALA A 764 "
            pdb=" OG  SER A 767 "
     model   vdw
     2.292 3.040
  nonbonded pdb=" NH1 ARG A 643 "
            pdb=" OE1 GLN A 742 "
     model   vdw
     2.313 3.120
  nonbonded pdb=" O   ASP A 649 "
            pdb=" N   GLY A 654 "
     model   vdw
     2.328 3.120
  ... (remaining 47288 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 group one per residue
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:             6.490
  Set stop_for_unknowns flag:              0.000
  Assert model is a single copy model:     0.000
  Assert all atoms have isotropic ADPs:    0.020
  Construct map_model_manager:             0.000
  Extract box with map and model:          0.090
  Check model and map are aligned:         0.010
  Set scattering table:                    0.020
  Process input model:                     5.700
  Find NCS groups from input model:        0.030
  Set up NCS constraints:                  0.010
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:1.460
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   13.830
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8038
moved from start:          0.0000

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.059   6071  Z= 0.245
  Angle     :  0.679  12.055   8263  Z= 0.377
  Chirality :  0.044   0.199    977
  Planarity :  0.010   0.291   1036
  Dihedral  : 14.533  76.715   2234
  Min Nonbonded Distance : 2.089

Molprobity Statistics.
  All-atom Clashscore : 6.14
  Ramachandran Plot:
    Outliers :  0.40 %
    Allowed  :  3.88 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  0.91 %
    Allowed  : 18.15 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.06 (0.32), residues: 748
  helix:  1.39 (0.35), residues: 240
  sheet: -1.32 (0.61), residues: 87
  loop : -0.40 (0.32), residues: 421

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 346 
 TYR   0.004   0.001   TYR A 687 
 PHE   0.012   0.001   PHE A 473 
 TRP   0.008   0.001   TRP A 751 
 HIS   0.003   0.001   HIS A 748 

Details of bonding type rmsd
  covalent geometry    : bond        0.00383 ( 6061)
  covalent geometry    : angle       0.64975 ( 8239)
  SS BOND              : bond        0.00127 (    6)
  SS BOND              : angle       0.46103 (   12)
  hydrogen bonds       : bond        0.26424 (  217)
  hydrogen bonds       : angle       7.23328 (  621)
  link_NAG-ASN         : bond        0.01224 (    4)
  link_NAG-ASN         : angle       5.22591 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  42 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 6
    poor density    : 36
  time to evaluate  : 0.217 
Fit side-chains
   revert: symmetry clash
REVERT: A  587 MET cc_start: 0.8735 (tpp) cc_final: 0.8481 (tpt)
  outliers start: 6
  outliers final: 4
  residues processed: 42
  average time/residue: 0.0461
  time to fit residues: 3.1528
Evaluate side-chains
  37 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 4
    poor density    : 33
  time to evaluate  : 0.218 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   68 ASN
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  473 PHE
Chi-restraints excluded: chain A residue  610 ILE
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 53 optimal weight:    0.0050
   chunk 5 optimal weight:   10.0000
   chunk 33 optimal weight:    1.9990
   chunk 65 optimal weight:    0.9980
   chunk 62 optimal weight:    0.8980
   chunk 51 optimal weight:    0.9980
   chunk 38 optimal weight:    3.9990
   chunk 61 optimal weight:    0.6980
   chunk 45 optimal weight:    0.0050
   chunk 74 optimal weight:    0.4980
   overall best weight:    0.4208

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

Flipped N/Q/H residues before XYZ refinement:
A 289 ASN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3422 r_free = 0.3422 target = 0.070516 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 38)----------------|
| r_work = 0.2997 r_free = 0.2997 target = 0.053932 restraints weight = 23076.981|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 31)----------------|
| r_work = 0.3056 r_free = 0.3056 target = 0.055999 restraints weight = 11221.212|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3094 r_free = 0.3094 target = 0.057405 restraints weight = 7300.109|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 25)----------------|
| r_work = 0.3109 r_free = 0.3109 target = 0.057975 restraints weight = 5564.892|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 33)----------------|
| r_work = 0.3132 r_free = 0.3132 target = 0.058826 restraints weight = 4845.187|
|-----------------------------------------------------------------------------|
r_work (final): 0.3129
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8177
moved from start:          0.1301

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.038   6071  Z= 0.108
  Angle     :  0.540   7.333   8263  Z= 0.266
  Chirality :  0.042   0.185    977
  Planarity :  0.003   0.028   1036
  Dihedral  :  5.263  59.825    876
  Min Nonbonded Distance : 2.481

Molprobity Statistics.
  All-atom Clashscore : 4.54
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.41 %
    Favored  : 97.59 %
  Rotamer:
    Outliers :  3.03 %
    Allowed  : 14.37 %
    Favored  : 82.60 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.76 (0.32), residues: 748
  helix:  2.38 (0.34), residues: 234
  sheet: -1.33 (0.60), residues: 89
  loop : -0.11 (0.31), residues: 425

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 818 
 TYR   0.007   0.001   TYR A 725 
 PHE   0.015   0.001   PHE A 765 
 TRP   0.009   0.001   TRP A 751 
 HIS   0.003   0.001   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00229 ( 6061)
  covalent geometry    : angle       0.53152 ( 8239)
  SS BOND              : bond        0.00082 (    6)
  SS BOND              : angle       0.44238 (   12)
  hydrogen bonds       : bond        0.04728 (  217)
  hydrogen bonds       : angle       4.35250 (  621)
  link_NAG-ASN         : bond        0.00575 (    4)
  link_NAG-ASN         : angle       2.54264 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 46
  time to evaluate  : 0.162 
Fit side-chains
   revert: symmetry clash
REVERT: A   64 ILE cc_start: 0.8804 (OUTLIER) cc_final: 0.8599 (pt)
REVERT: A  716 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9150 (pp)
  outliers start: 20
  outliers final: 10
  residues processed: 60
  average time/residue: 0.0327
  time to fit residues: 3.1502
Evaluate side-chains
  54 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 12
    poor density    : 42
  time to evaluate  : 0.222 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   64 ILE
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  636 LEU
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  752 LEU
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 17 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9980
   chunk 56 optimal weight:    2.9990
   chunk 52 optimal weight:    2.9990
   chunk 72 optimal weight:    0.8980
   chunk 12 optimal weight:    3.9990
   chunk 6 optimal weight:    5.9990
   chunk 49 optimal weight:    0.0970
   chunk 37 optimal weight:    4.9990
   chunk 25 optimal weight:    3.9990
   chunk 55 optimal weight:    2.9990
   overall best weight:    1.3982

-------------------------------------------------------------------------------
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 = 0.3369 r_free = 0.3369 target = 0.068181 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2926 r_free = 0.2926 target = 0.051494 restraints weight = 22976.737|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.2982 r_free = 0.2982 target = 0.053414 restraints weight = 11616.248|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 39)----------------|
| r_work = 0.3020 r_free = 0.3020 target = 0.054742 restraints weight = 7684.581|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 32)----------------|
| r_work = 0.3039 r_free = 0.3039 target = 0.055464 restraints weight = 5927.410|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3057 r_free = 0.3057 target = 0.056105 restraints weight = 5077.871|
|-----------------------------------------------------------------------------|
r_work (final): 0.3053
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8258
moved from start:          0.1690

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.044   6071  Z= 0.200
  Angle     :  0.600  10.364   8263  Z= 0.292
  Chirality :  0.044   0.177    977
  Planarity :  0.003   0.023   1036
  Dihedral  :  5.201  58.768    872
  Min Nonbonded Distance : 2.498

Molprobity Statistics.
  All-atom Clashscore : 5.30
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.28 %
    Favored  : 95.72 %
  Rotamer:
    Outliers :  4.24 %
    Allowed  : 13.77 %
    Favored  : 82.00 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.67 (0.32), residues: 748
  helix:  2.30 (0.33), residues: 235
  sheet: -1.47 (0.58), residues: 91
  loop : -0.13 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 392 
 TYR   0.011   0.001   TYR A 687 
 PHE   0.012   0.001   PHE A 547 
 TRP   0.010   0.001   TRP A 546 
 HIS   0.002   0.001   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00456 ( 6061)
  covalent geometry    : angle       0.59342 ( 8239)
  SS BOND              : bond        0.00177 (    6)
  SS BOND              : angle       1.21566 (   12)
  hydrogen bonds       : bond        0.04765 (  217)
  hydrogen bonds       : angle       4.34397 (  621)
  link_NAG-ASN         : bond        0.00437 (    4)
  link_NAG-ASN         : angle       2.20020 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  66 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 28
    poor density    : 38
  time to evaluate  : 0.232 
Fit side-chains
   revert: symmetry clash
  outliers start: 28
  outliers final: 19
  residues processed: 58
  average time/residue: 0.0386
  time to fit residues: 3.6677
Evaluate side-chains
  52 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 33
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  119 THR
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  757 CYS
Chi-restraints excluded: chain A residue  795 CYS
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 67 optimal weight:    1.9990
   chunk 71 optimal weight:    0.5980
   chunk 70 optimal weight:    2.9990
   chunk 5 optimal weight:    5.9990
   chunk 8 optimal weight:    0.7980
   chunk 14 optimal weight:    0.7980
   chunk 24 optimal weight:    2.9990
   chunk 53 optimal weight:    3.9990
   chunk 74 optimal weight:    3.9990
   chunk 73 optimal weight:    0.8980
   chunk 4 optimal weight:    6.9990
   overall best weight:    1.0182

-------------------------------------------------------------------------------
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 = 0.3416 r_free = 0.3416 target = 0.070071 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.2979 r_free = 0.2979 target = 0.053533 restraints weight = 22884.273|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 35)----------------|
| r_work = 0.3033 r_free = 0.3033 target = 0.055410 restraints weight = 12367.787|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 38)----------------|
| r_work = 0.3068 r_free = 0.3068 target = 0.056678 restraints weight = 8458.338|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 36)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.057437 restraints weight = 6653.869|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.057966 restraints weight = 5742.131|
|-----------------------------------------------------------------------------|
r_work (final): 0.3101
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8391
moved from start:          0.1924

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.036   6071  Z= 0.148
  Angle     :  0.547   8.718   8263  Z= 0.265
  Chirality :  0.042   0.177    977
  Planarity :  0.003   0.022   1036
  Dihedral  :  5.151  59.493    872
  Min Nonbonded Distance : 2.539

Molprobity Statistics.
  All-atom Clashscore : 5.21
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.94 %
    Favored  : 97.06 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 13.31 %
    Favored  : 82.75 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.75 (0.32), residues: 748
  helix:  2.36 (0.34), residues: 235
  sheet: -1.42 (0.59), residues: 87
  loop : -0.09 (0.32), residues: 426

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 392 
 TYR   0.009   0.001   TYR A 687 
 PHE   0.012   0.001   PHE A 765 
 TRP   0.006   0.001   TRP A 812 
 HIS   0.002   0.001   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00336 ( 6061)
  covalent geometry    : angle       0.54034 ( 8239)
  SS BOND              : bond        0.00149 (    6)
  SS BOND              : angle       0.65156 (   12)
  hydrogen bonds       : bond        0.04102 (  217)
  hydrogen bonds       : angle       4.18162 (  621)
  link_NAG-ASN         : bond        0.00495 (    4)
  link_NAG-ASN         : angle       2.24691 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  67 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 41
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 CYS cc_start: 0.9032 (m) cc_final: 0.8819 (m)
REVERT: A  721 MET cc_start: 0.9067 (ppp) cc_final: 0.8736 (ppp)
  outliers start: 26
  outliers final: 17
  residues processed: 58
  average time/residue: 0.0425
  time to fit residues: 3.9071
Evaluate side-chains
  54 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 37
  time to evaluate  : 0.219 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  573 SER
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  757 CYS
Chi-restraints excluded: chain A residue  795 CYS
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 42 optimal weight:    0.9980
   chunk 2 optimal weight:    8.9990
   chunk 63 optimal weight:    4.9990
   chunk 68 optimal weight:    2.9990
   chunk 69 optimal weight:    3.9990
   chunk 54 optimal weight:    0.0980
   chunk 64 optimal weight:    0.9990
   chunk 66 optimal weight:    0.9980
   chunk 37 optimal weight:    3.9990
   chunk 9 optimal weight:    0.9990
   chunk 70 optimal weight:    2.9990
   overall best weight:    0.8184

-------------------------------------------------------------------------------
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 = 0.3420 r_free = 0.3420 target = 0.070345 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.2980 r_free = 0.2980 target = 0.053639 restraints weight = 23286.924|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 34)----------------|
| r_work = 0.3035 r_free = 0.3035 target = 0.055568 restraints weight = 12350.279|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 43)----------------|
| r_work = 0.3071 r_free = 0.3071 target = 0.056876 restraints weight = 8368.704|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3090 r_free = 0.3090 target = 0.057603 restraints weight = 6538.339|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 35)----------------|
| r_work = 0.3110 r_free = 0.3110 target = 0.058322 restraints weight = 5642.549|
|-----------------------------------------------------------------------------|
r_work (final): 0.3109
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8367
moved from start:          0.2077

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.035   6071  Z= 0.128
  Angle     :  0.535   7.886   8263  Z= 0.257
  Chirality :  0.042   0.178    977
  Planarity :  0.003   0.021   1036
  Dihedral  :  4.475  58.551    870
  Min Nonbonded Distance : 2.557

Molprobity Statistics.
  All-atom Clashscore : 5.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.61 %
    Favored  : 96.39 %
  Rotamer:
    Outliers :  3.33 %
    Allowed  : 14.37 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.84 (0.32), residues: 748
  helix:  2.43 (0.34), residues: 235
  sheet: -1.45 (0.57), residues: 91
  loop :  0.01 (0.32), residues: 422

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 392 
 TYR   0.007   0.001   TYR A 725 
 PHE   0.013   0.001   PHE A 765 
 TRP   0.008   0.001   TRP A 812 
 HIS   0.003   0.001   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6061)
  covalent geometry    : angle       0.52920 ( 8239)
  SS BOND              : bond        0.00133 (    6)
  SS BOND              : angle       0.48551 (   12)
  hydrogen bonds       : bond        0.03889 (  217)
  hydrogen bonds       : angle       4.08930 (  621)
  link_NAG-ASN         : bond        0.00501 (    4)
  link_NAG-ASN         : angle       2.19379 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  64 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 42
  time to evaluate  : 0.140 
Fit side-chains
   revert: symmetry clash
REVERT: A  678 CYS cc_start: 0.9023 (m) cc_final: 0.8817 (m)
REVERT: A  716 LEU cc_start: 0.9321 (OUTLIER) cc_final: 0.9069 (pp)
REVERT: A  782 MET cc_start: 0.8518 (ptp) cc_final: 0.8301 (ptp)
  outliers start: 22
  outliers final: 18
  residues processed: 55
  average time/residue: 0.0459
  time to fit residues: 4.0307
Evaluate side-chains
  55 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 36
  time to evaluate  : 0.158 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  795 CYS
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 44 optimal weight:    0.4980
   chunk 28 optimal weight:    2.9990
   chunk 33 optimal weight:    3.9990
   chunk 54 optimal weight:    0.9980
   chunk 46 optimal weight:    0.6980
   chunk 65 optimal weight:    0.3980
   chunk 69 optimal weight:    0.6980
   chunk 21 optimal weight:    0.8980
   chunk 25 optimal weight:    0.8980
   chunk 20 optimal weight:    2.9990
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.6380

-------------------------------------------------------------------------------
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 = 0.3427 r_free = 0.3427 target = 0.070642 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 36)----------------|
| r_work = 0.2999 r_free = 0.2999 target = 0.054261 restraints weight = 22912.976|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3053 r_free = 0.3053 target = 0.056158 restraints weight = 12256.432|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3088 r_free = 0.3088 target = 0.057438 restraints weight = 8341.599|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 30)----------------|
| r_work = 0.3108 r_free = 0.3108 target = 0.058197 restraints weight = 6528.828|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 31)----------------|
| r_work = 0.3120 r_free = 0.3120 target = 0.058663 restraints weight = 5613.986|
|-----------------------------------------------------------------------------|
r_work (final): 0.3119
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8334
moved from start:          0.2200

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.034   6071  Z= 0.109
  Angle     :  0.525   7.914   8263  Z= 0.252
  Chirality :  0.042   0.181    977
  Planarity :  0.003   0.022   1036
  Dihedral  :  4.337  57.512    870
  Min Nonbonded Distance : 2.571

Molprobity Statistics.
  All-atom Clashscore : 5.38
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.93 %
    Allowed  : 13.92 %
    Favored  : 82.15 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.33), residues: 748
  helix:  2.44 (0.34), residues: 236
  sheet: -1.48 (0.56), residues: 93
  loop :  0.12 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 392 
 TYR   0.007   0.001   TYR A 725 
 PHE   0.014   0.001   PHE A 765 
 TRP   0.008   0.001   TRP A 812 
 HIS   0.003   0.000   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00246 ( 6061)
  covalent geometry    : angle       0.51906 ( 8239)
  SS BOND              : bond        0.00152 (    6)
  SS BOND              : angle       0.40973 (   12)
  hydrogen bonds       : bond        0.03713 (  217)
  hydrogen bonds       : angle       4.04132 (  621)
  link_NAG-ASN         : bond        0.00523 (    4)
  link_NAG-ASN         : angle       2.18044 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  69 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 26
    poor density    : 43
  time to evaluate  : 0.173 
Fit side-chains
   revert: symmetry clash
REVERT: A  721 MET cc_start: 0.9001 (ppp) cc_final: 0.8719 (ppp)
  outliers start: 26
  outliers final: 17
  residues processed: 61
  average time/residue: 0.0440
  time to fit residues: 4.1368
Evaluate side-chains
  56 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 17
    poor density    : 39
  time to evaluate  : 0.229 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  795 CYS
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 33 optimal weight:    3.9990
   chunk 7 optimal weight:    6.9990
   chunk 59 optimal weight:    0.7980
   chunk 20 optimal weight:    0.7980
   chunk 29 optimal weight:    2.9990
   chunk 56 optimal weight:    2.9990
   chunk 23 optimal weight:    0.0470
   chunk 41 optimal weight:    2.9990
   chunk 8 optimal weight:    1.9990
   chunk 57 optimal weight:    0.7980
   chunk 43 optimal weight:    0.5980
   overall best weight:    0.6078

-------------------------------------------------------------------------------
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 = 0.3433 r_free = 0.3433 target = 0.070870 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 35)----------------|
| r_work = 0.3003 r_free = 0.3003 target = 0.054408 restraints weight = 22934.413|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 37)----------------|
| r_work = 0.3058 r_free = 0.3058 target = 0.056333 restraints weight = 12268.337|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 30)----------------|
| r_work = 0.3093 r_free = 0.3093 target = 0.057614 restraints weight = 8325.800|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 28)----------------|
| r_work = 0.3111 r_free = 0.3111 target = 0.058349 restraints weight = 6505.495|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 26)----------------|
| r_work = 0.3129 r_free = 0.3129 target = 0.059022 restraints weight = 5595.094|
|-----------------------------------------------------------------------------|
r_work (final): 0.3132
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8359
moved from start:          0.2336

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.037   6071  Z= 0.111
  Angle     :  0.546   8.627   8263  Z= 0.258
  Chirality :  0.042   0.181    977
  Planarity :  0.003   0.021   1036
  Dihedral  :  4.304  56.991    870
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  3.48 %
    Allowed  : 14.22 %
    Favored  : 82.30 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.92 (0.33), residues: 748
  helix:  2.39 (0.34), residues: 236
  sheet: -1.47 (0.56), residues: 93
  loop :  0.16 (0.32), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 643 
 TYR   0.007   0.001   TYR A 725 
 PHE   0.018   0.001   PHE A 765 
 TRP   0.008   0.001   TRP A 812 
 HIS   0.003   0.000   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00251 ( 6061)
  covalent geometry    : angle       0.54038 ( 8239)
  SS BOND              : bond        0.00101 (    6)
  SS BOND              : angle       0.41646 (   12)
  hydrogen bonds       : bond        0.03696 (  217)
  hydrogen bonds       : angle       4.01069 (  621)
  link_NAG-ASN         : bond        0.00516 (    4)
  link_NAG-ASN         : angle       2.15697 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  61 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 23
    poor density    : 38
  time to evaluate  : 0.206 
Fit side-chains
   revert: symmetry clash
REVERT: A  716 LEU cc_start: 0.9252 (OUTLIER) cc_final: 0.8998 (pp)
REVERT: A  721 MET cc_start: 0.9023 (ppp) cc_final: 0.8737 (ppp)
  outliers start: 23
  outliers final: 18
  residues processed: 54
  average time/residue: 0.0361
  time to fit residues: 3.1877
Evaluate side-chains
  56 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 19
    poor density    : 37
  time to evaluate  : 0.178 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  295 LEU
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  716 LEU
Chi-restraints excluded: chain A residue  752 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  795 CYS
Chi-restraints excluded: chain A residue  799 VAL
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 49 optimal weight:    2.9990
   chunk 55 optimal weight:    0.9990
   chunk 69 optimal weight:    3.9990
   chunk 4 optimal weight:    3.9990
   chunk 2 optimal weight:    3.9990
   chunk 17 optimal weight:    3.9990
   chunk 63 optimal weight:    3.9990
   chunk 20 optimal weight:    1.9990
   chunk 57 optimal weight:    0.6980
   chunk 45 optimal weight:    7.9990
   chunk 13 optimal weight:    1.9990
   overall best weight:    1.7388

-------------------------------------------------------------------------------
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 = 0.3387 r_free = 0.3387 target = 0.068826 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 32)----------------|
| r_work = 0.2935 r_free = 0.2935 target = 0.052048 restraints weight = 23169.855|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 45)----------------|
| r_work = 0.2989 r_free = 0.2989 target = 0.053874 restraints weight = 12552.450|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 31)----------------|
| r_work = 0.3025 r_free = 0.3025 target = 0.055128 restraints weight = 8617.220|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3042 r_free = 0.3042 target = 0.055784 restraints weight = 6791.717|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 37)----------------|
| r_work = 0.3060 r_free = 0.3060 target = 0.056415 restraints weight = 5915.649|
|-----------------------------------------------------------------------------|
r_work (final): 0.3061
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8424
moved from start:          0.2446

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.045   6071  Z= 0.236
  Angle     :  0.632   8.338   8263  Z= 0.305
  Chirality :  0.045   0.174    977
  Planarity :  0.003   0.023   1036
  Dihedral  :  4.773  58.133    870
  Min Nonbonded Distance : 2.566

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  5.35 %
    Favored  : 94.65 %
  Rotamer:
    Outliers :  3.18 %
    Allowed  : 15.73 %
    Favored  : 81.09 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.80 (0.33), residues: 748
  helix:  2.20 (0.34), residues: 239
  sheet: -1.67 (0.55), residues: 93
  loop :  0.16 (0.33), residues: 416

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.002   0.000   ARG A 392 
 TYR   0.007   0.001   TYR A 725 
 PHE   0.019   0.002   PHE A 765 
 TRP   0.008   0.001   TRP A 546 
 HIS   0.002   0.001   HIS A 320 

Details of bonding type rmsd
  covalent geometry    : bond        0.00538 ( 6061)
  covalent geometry    : angle       0.62629 ( 8239)
  SS BOND              : bond        0.00175 (    6)
  SS BOND              : angle       0.60548 (   12)
  hydrogen bonds       : bond        0.04392 (  217)
  hydrogen bonds       : angle       4.33223 (  621)
  link_NAG-ASN         : bond        0.00529 (    4)
  link_NAG-ASN         : angle       2.31506 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  55 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 21
    poor density    : 34
  time to evaluate  : 0.234 
Fit side-chains
REVERT: A  474 TRP cc_start: 0.6777 (OUTLIER) cc_final: 0.6303 (p-90)
  outliers start: 21
  outliers final: 15
  residues processed: 49
  average time/residue: 0.0408
  time to fit residues: 3.3040
Evaluate side-chains
  50 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 34
  time to evaluate  : 0.205 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  561 LEU
Chi-restraints excluded: chain A residue  582 VAL
Chi-restraints excluded: chain A residue  593 ILE
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  671 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  795 CYS
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 64 optimal weight:    1.9990
   chunk 38 optimal weight:    0.0770
   chunk 72 optimal weight:    0.6980
   chunk 61 optimal weight:    0.3980
   chunk 73 optimal weight:    1.9990
   chunk 12 optimal weight:    0.0970
   chunk 27 optimal weight:    1.9990
   chunk 48 optimal weight:    0.7980
   chunk 5 optimal weight:    2.9990
   chunk 31 optimal weight:    1.9990
   chunk 18 optimal weight:    1.9990
   overall best weight:    0.4136

-------------------------------------------------------------------------------
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 = 0.3435 r_free = 0.3435 target = 0.070857 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 33)----------------|
| r_work = 0.3011 r_free = 0.3011 target = 0.054549 restraints weight = 22774.488|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 28)----------------|
| r_work = 0.3064 r_free = 0.3064 target = 0.056446 restraints weight = 12061.307|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 24)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.057752 restraints weight = 8187.586|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3119 r_free = 0.3119 target = 0.058476 restraints weight = 6361.856|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 30)----------------|
| r_work = 0.3140 r_free = 0.3140 target = 0.059215 restraints weight = 5473.722|
|-----------------------------------------------------------------------------|
r_work (final): 0.3146
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8357
moved from start:          0.2526

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.002   0.033   6071  Z= 0.099
  Angle     :  0.548   9.244   8263  Z= 0.258
  Chirality :  0.042   0.182    977
  Planarity :  0.003   0.020   1036
  Dihedral  :  4.360  56.298    870
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 5.72
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.67 %
    Favored  : 97.33 %
  Rotamer:
    Outliers :  2.12 %
    Allowed  : 16.19 %
    Favored  : 81.69 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.89 (0.33), residues: 748
  helix:  2.25 (0.34), residues: 236
  sheet: -1.57 (0.56), residues: 93
  loop :  0.23 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 643 
 TYR   0.009   0.001   TYR A 725 
 PHE   0.019   0.001   PHE A 765 
 TRP   0.009   0.001   TRP A 812 
 HIS   0.003   0.000   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00219 ( 6061)
  covalent geometry    : angle       0.54263 ( 8239)
  SS BOND              : bond        0.00100 (    6)
  SS BOND              : angle       0.40465 (   12)
  hydrogen bonds       : bond        0.03715 (  217)
  hydrogen bonds       : angle       4.04352 (  621)
  link_NAG-ASN         : bond        0.00549 (    4)
  link_NAG-ASN         : angle       2.16475 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  50 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 36
  time to evaluate  : 0.215 
Fit side-chains
REVERT: A  474 TRP cc_start: 0.6616 (OUTLIER) cc_final: 0.6126 (p-90)
REVERT: A  630 GLU cc_start: 0.9294 (mm-30) cc_final: 0.9042 (mm-30)
REVERT: A  721 MET cc_start: 0.8999 (ppp) cc_final: 0.8690 (ppp)
  outliers start: 14
  outliers final: 12
  residues processed: 45
  average time/residue: 0.0371
  time to fit residues: 2.7794
Evaluate side-chains
  49 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.150 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  795 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 31 optimal weight:    0.9980
   chunk 63 optimal weight:    2.9990
   chunk 19 optimal weight:    0.9980
   chunk 20 optimal weight:    0.5980
   chunk 74 optimal weight:    3.9990
   chunk 29 optimal weight:    0.7980
   chunk 15 optimal weight:    2.9990
   chunk 13 optimal weight:    0.4980
   chunk 27 optimal weight:    1.9990
   chunk 39 optimal weight:    4.9990
   chunk 69 optimal weight:    1.9990
   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 = 0.3427 r_free = 0.3427 target = 0.070588 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.2994 r_free = 0.2994 target = 0.054004 restraints weight = 22918.536|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 36)----------------|
| r_work = 0.3048 r_free = 0.3048 target = 0.055914 restraints weight = 12285.776|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 35)----------------|
| r_work = 0.3084 r_free = 0.3084 target = 0.057191 restraints weight = 8372.378|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 26)----------------|
| r_work = 0.3101 r_free = 0.3101 target = 0.057883 restraints weight = 6557.794|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 24)----------------|
| r_work = 0.3122 r_free = 0.3122 target = 0.058619 restraints weight = 5670.338|
|-----------------------------------------------------------------------------|
r_work (final): 0.3130
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8375
moved from start:          0.2561

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6071  Z= 0.126
  Angle     :  0.592   9.767   8263  Z= 0.275
  Chirality :  0.042   0.182    977
  Planarity :  0.003   0.021   1036
  Dihedral  :  4.359  56.220    870
  Min Nonbonded Distance : 2.574

Molprobity Statistics.
  All-atom Clashscore : 6.22
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.07 %
    Favored  : 96.93 %
  Rotamer:
    Outliers :  1.97 %
    Allowed  : 17.10 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.88 (0.33), residues: 748
  helix:  2.23 (0.34), residues: 236
  sheet: -1.55 (0.56), residues: 93
  loop :  0.23 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 392 
 TYR   0.007   0.001   TYR A 725 
 PHE   0.018   0.001   PHE A 765 
 TRP   0.009   0.001   TRP A 812 
 HIS   0.003   0.000   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00290 ( 6061)
  covalent geometry    : angle       0.58673 ( 8239)
  SS BOND              : bond        0.00103 (    6)
  SS BOND              : angle       0.45338 (   12)
  hydrogen bonds       : bond        0.03799 (  217)
  hydrogen bonds       : angle       4.08469 (  621)
  link_NAG-ASN         : bond        0.00509 (    4)
  link_NAG-ASN         : angle       2.16019 (   12)

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

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

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1496 Ramachandran restraints generated.
    748 Oldfield, 0 Emsley, 748 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  49 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.222 
Fit side-chains
REVERT: A  474 TRP cc_start: 0.6620 (OUTLIER) cc_final: 0.6117 (p-90)
REVERT: A  721 MET cc_start: 0.9016 (ppp) cc_final: 0.8705 (ppp)
  outliers start: 13
  outliers final: 12
  residues processed: 45
  average time/residue: 0.0411
  time to fit residues: 3.0010
Evaluate side-chains
  49 residues out of total 661 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 36
  time to evaluate  : 0.141 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   79 ASN
Chi-restraints excluded: chain A residue  205 VAL
Chi-restraints excluded: chain A residue  474 TRP
Chi-restraints excluded: chain A residue  546 TRP
Chi-restraints excluded: chain A residue  557 LEU
Chi-restraints excluded: chain A residue  610 ILE
Chi-restraints excluded: chain A residue  641 VAL
Chi-restraints excluded: chain A residue  645 LEU
Chi-restraints excluded: chain A residue  667 LEU
Chi-restraints excluded: chain A residue  732 LEU
Chi-restraints excluded: chain A residue  753 ILE
Chi-restraints excluded: chain A residue  754 PHE
Chi-restraints excluded: chain A residue  795 CYS
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 75
   random chunks:
   chunk 8 optimal weight:    1.9990
   chunk 36 optimal weight:    2.9990
   chunk 28 optimal weight:    0.9990
   chunk 14 optimal weight:    0.0000
   chunk 4 optimal weight:    8.9990
   chunk 24 optimal weight:    2.9990
   chunk 44 optimal weight:    4.9990
   chunk 73 optimal weight:    0.4980
   chunk 68 optimal weight:    1.9990
   chunk 22 optimal weight:    0.9980
   chunk 32 optimal weight:    2.9990
   overall best weight:    0.8988

-------------------------------------------------------------------------------
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 = 0.3419 r_free = 0.3419 target = 0.070270 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.2990 r_free = 0.2990 target = 0.053810 restraints weight = 23024.798|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 2; iterations = 26)----------------|
| r_work = 0.3043 r_free = 0.3043 target = 0.055690 restraints weight = 12316.621|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 3; iterations = 27)----------------|
| r_work = 0.3077 r_free = 0.3077 target = 0.056939 restraints weight = 8398.959|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 4; iterations = 29)----------------|
| r_work = 0.3097 r_free = 0.3097 target = 0.057728 restraints weight = 6582.946|
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 5; iterations = 38)----------------|
| r_work = 0.3115 r_free = 0.3115 target = 0.058338 restraints weight = 5657.809|
|-----------------------------------------------------------------------------|
r_work (final): 0.3112
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.8350
moved from start:          0.2618

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.034   6071  Z= 0.139
  Angle     :  0.597   9.403   8263  Z= 0.282
  Chirality :  0.043   0.180    977
  Planarity :  0.003   0.021   1036
  Dihedral  :  4.387  56.165    870
  Min Nonbonded Distance : 2.572

Molprobity Statistics.
  All-atom Clashscore : 6.05
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.81 %
    Favored  : 97.19 %
  Rotamer:
    Outliers :  2.42 %
    Allowed  : 16.64 %
    Favored  : 80.94 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 5.41 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z values with (uncertainties):
Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores below are scaled independently, so they are not related in a simple way.
  whole:  0.85 (0.33), residues: 748
  helix:  2.15 (0.34), residues: 236
  sheet: -1.57 (0.56), residues: 93
  loop :  0.25 (0.33), residues: 419

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 ARG   0.001   0.000   ARG A 643 
 TYR   0.007   0.001   TYR A 725 
 PHE   0.017   0.001   PHE A 765 
 TRP   0.010   0.001   TRP A 812 
 HIS   0.002   0.000   HIS A 256 

Details of bonding type rmsd
  covalent geometry    : bond        0.00319 ( 6061)
  covalent geometry    : angle       0.59202 ( 8239)
  SS BOND              : bond        0.00105 (    6)
  SS BOND              : angle       0.46861 (   12)
  hydrogen bonds       : bond        0.03919 (  217)
  hydrogen bonds       : angle       4.15107 (  621)
  link_NAG-ASN         : bond        0.00504 (    4)
  link_NAG-ASN         : angle       2.17191 (   12)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 1021.66 seconds
wall clock time: 18 minutes 17.40 seconds (1097.40 seconds total)