Starting phenix.real_space_refine
on Wed Jun  4 23:53:55 2025 by dcliebschner
===============================================================================

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

  Found model, /net/cci-nas-00/data/ceres_data/8hnd_34911/06_2025/8hnd_34911.cif
  Found real_map, /net/cci-nas-00/data/ceres_data/8hnd_34911/06_2025/8hnd_34911.map

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

  Adding command-line PHIL:
  -------------------------
    refinement.macro_cycles=10
    scattering_table=electron
    resolution=3.19
    write_initial_geo_file=False

Final processed PHIL parameters:
-------------------------------------------------------------------------------
  data_manager {
    real_map_files = "/net/cci-nas-00/data/ceres_data/8hnd_34911/06_2025/8hnd_34911.map"
    default_real_map = "/net/cci-nas-00/data/ceres_data/8hnd_34911/06_2025/8hnd_34911.map"
    model {
      file = "/net/cci-nas-00/data/ceres_data/8hnd_34911/06_2025/8hnd_34911.cif"
    }
    default_model = "/net/cci-nas-00/data/ceres_data/8hnd_34911/06_2025/8hnd_34911.cif"
  }
  resolution = 3.19
  write_initial_geo_file = False
  refinement {
    macro_cycles = 10
  }
  qi {
    qm_restraints {
      package {
        program = *test
      }
    }
  }


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

Validating inputs
Origin is already at (0, 0, 0), no shifts will be applied
-------------------------------------------------------------------------------
Processing inputs
*****************
Set random seed
  Set to: 0
Set model cs if undefined
Decide on map wrapping
  Map wrapping is set to: False
Normalize map: mean=0, sd=1
  Input map: mean=   0.002 sd=   0.122
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: 4
    Type Number    sf(0)   Gaussians
     S      36      5.16       5
     C    2879      2.51       5
     N     685      2.21       5
     O     770      1.98       5
    sf(0) = scattering factor at diffraction angle 0.
Process input model

  Symmetric amino acids flipped. Time to flip 35 residue(s): 0.01s

  Monomer Library directory:
    "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib"
  Total number of atoms: 4370
  Number of models: 1
  Model: ""
    Number of chains: 3
    Chain: "A"
      Number of atoms: 4304
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 560, 4304
          Classifications: {'peptide': 560}
          Incomplete info: {'truncation_to_alanine': 20}
          Link IDs: {'PTRANS': 19, 'TRANS': 540}
          Chain breaks: 3
          Unresolved non-hydrogen bonds: 56
          Unresolved non-hydrogen angles: 68
          Unresolved non-hydrogen dihedrals: 44
          Unresolved non-hydrogen chiralities: 5
          Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 3, 'ARG:plan': 1}
          Unresolved non-hydrogen planarities: 26
    Chain: "B"
      Number of atoms: 28
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 28
          Unusual residues: {'NAG': 2}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 2
          Unresolved non-hydrogen angles: 4
          Unresolved non-hydrogen dihedrals: 6
          Unresolved non-hydrogen chiralities: 2
    Chain: "A"
      Number of atoms: 38
      Number of conformers: 1
      Conformer: ""
        Number of residues, atoms: 2, 38
          Unusual residues: {'FY5': 1, 'NAG': 1}
          Classifications: {'undetermined': 2}
          Link IDs: {None: 1}
          Unresolved non-hydrogen bonds: 1
          Unresolved non-hydrogen angles: 2
          Unresolved non-hydrogen dihedrals: 3
          Unresolved non-hydrogen chiralities: 1
  Time building chain proxies: 3.33, per 1000 atoms: 0.76
  Number of scatterers: 4370
  At special positions: 0
  Unit cell: (56.852, 68.036, 103.452, 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      36     16.00
     O     770      8.00
     N     685      7.00
     C    2879      6.00
    sf(0) = scattering factor at diffraction angle 0.

  Number of disulfides: simple=7, symmetry=0
    Simple disulfide: pdb=" SG  CYS A 142 " - pdb=" SG  CYS A 463 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 430 " - pdb=" SG  CYS A 530 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 459 " - pdb=" SG  CYS A 506 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 465 " - pdb=" SG  CYS A 485 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 474 " - pdb=" SG  CYS A 524 " distance=2.02
    Simple disulfide: pdb=" SG  CYS A 489 " - pdb=" SG  CYS A 504 " distance=2.03
    Simple disulfide: pdb=" SG  CYS A 599 " - pdb=" SG  CYS A 613 " 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
    BETA1-4
      " NAG B   1 " - " NAG B   2 "
    NAG-ASN
      " NAG A 802 " - " ASN A 516 "
      " NAG B   1 " - " ASN A 503 "
  Time building additional restraints: 1.53
  Conformation dependent library (CDL) restraints added in 546.2 milliseconds
  

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
  Adding C-beta torsion restraints...
  Number of C-beta restraints generated:  1018

  Finding SS restraints...
    Secondary structure from input PDB file:
      24 helices and 2 sheets defined
      67.9% alpha, 3.2% beta
      0 base pairs and 0 stacking pairs defined.
    Time for finding SS restraints: 0.44
  Creating SS restraints...
    Processing helix  chain 'A' and resid 27 through 50
      removed outlier: 4.176A  pdb=" N   LEU A  31 " --> pdb=" O   LEU A  27 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 51 through 60
      removed outlier: 3.641A  pdb=" N   ARG A  57 " --> pdb=" O   ILE A  53 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 62 through 86
      removed outlier: 4.090A  pdb=" N   PHE A  73 " --> pdb=" O   ILE A  69 " (cutoff:3.500A)
      removed outlier: 4.773A  pdb=" N   GLU A  74 " --> pdb=" O   ASP A  70 " (cutoff:3.500A)
      removed outlier: 3.524A  pdb=" N   VAL A  82 " --> pdb=" O   LEU A  78 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 92 through 113
    Processing helix  chain 'A' and resid 114 through 116
      No H-bonds generated for 'chain 'A' and resid 114 through 116'
    Processing helix  chain 'A' and resid 165 through 169
    Processing helix  chain 'A' and resid 170 through 186
      removed outlier: 3.817A  pdb=" N   VAL A 174 " --> pdb=" O   MET A 170 " (cutoff:3.500A)
      removed outlier: 3.538A  pdb=" N   THR A 186 " --> pdb=" O   GLY A 182 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 187 through 199
    Processing helix  chain 'A' and resid 204 through 217
    Processing helix  chain 'A' and resid 218 through 231
    Processing helix  chain 'A' and resid 258 through 274
    Processing helix  chain 'A' and resid 275 through 277
      No H-bonds generated for 'chain 'A' and resid 275 through 277'
    Processing helix  chain 'A' and resid 325 through 335
    Processing helix  chain 'A' and resid 335 through 367
      removed outlier: 4.766A  pdb=" N   PHE A 360 " --> pdb=" O   PHE A 356 " (cutoff:3.500A)
      removed outlier: 5.440A  pdb=" N   LYS A 361 " --> pdb=" O   THR A 357 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 370 through 381
      removed outlier: 3.622A  pdb=" N   ALA A 374 " --> pdb=" O   PRO A 370 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 381 through 400
      removed outlier: 3.728A  pdb=" N   ILE A 385 " --> pdb=" O   ILE A 381 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 403 through 423
      removed outlier: 3.538A  pdb=" N   LYS A 409 " --> pdb=" O   VAL A 405 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 424 through 428
    Processing helix  chain 'A' and resid 509 through 513
      removed outlier: 3.742A  pdb=" N   LEU A 512 " --> pdb=" O   VAL A 509 " (cutoff:3.500A)
      removed outlier: 3.719A  pdb=" N   GLN A 513 " --> pdb=" O   THR A 510 " (cutoff:3.500A)
      No H-bonds generated for 'chain 'A' and resid 509 through 513'
    Processing helix  chain 'A' and resid 527 through 550
      removed outlier: 3.948A  pdb=" N   TYR A 535 " --> pdb=" O   THR A 531 " (cutoff:3.500A)
      removed outlier: 3.748A  pdb=" N   PHE A 536 " --> pdb=" O   ARG A 532 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 551 through 562
      removed outlier: 3.507A  pdb=" N   HIS A 555 " --> pdb=" O   GLY A 551 " (cutoff:3.500A)
      removed outlier: 3.979A  pdb=" N   VAL A 556 " --> pdb=" O   GLY A 552 " (cutoff:3.500A)
    Processing helix  chain 'A' and resid 564 through 566
      No H-bonds generated for 'chain 'A' and resid 564 through 566'
    Processing helix  chain 'A' and resid 567 through 598
      Proline residue:  A 588  - end of helix
    Processing helix  chain 'A' and resid 617 through 651
    Processing sheet with id=AA1, first strand: chain 'A' and resid 473 through 475
      removed outlier: 3.870A  pdb=" N   SER A 491 " --> pdb=" O   TYR A 502 " (cutoff:3.500A)
    Processing sheet with id=AA2, first strand: chain 'A' and resid 599 through 604
      removed outlier: 6.984A  pdb=" N   CYS A 599 " --> pdb=" O   TYR A 616 " (cutoff:3.500A)
      removed outlier: 6.832A  pdb=" N   TYR A 616 " --> pdb=" O   CYS A 599 " (cutoff:3.500A)
      removed outlier: 6.911A  pdb=" N   LYS A 601 " --> pdb=" O   ARG A 614 " (cutoff:3.500A)
      removed outlier: 4.004A  pdb=" N   SER A 612 " --> pdb=" O   SER A 603 " (cutoff:3.500A)

    276 hydrogen bonds defined for protein.
    813 hydrogen bond angles defined for protein.
    Restraints generated for nucleic acids:
      0 hydrogen bonds
      0 hydrogen bond angles
      0 basepair planarities
      0 basepair parallelities
      0 stacking parallelities
  Total time for adding SS restraints: 1.19

  Time building geometry restraints manager: 1.55 seconds

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

  Histogram of bond lengths:
        1.20 -     1.32: 669
        1.32 -     1.44: 1283
        1.44 -     1.57: 2474
        1.57 -     1.69: 1
        1.69 -     1.81: 52
  Bond restraints: 4479
  Sorted by residual:
  bond pdb=" CA  LEU A  27 "
       pdb=" C   LEU A  27 "
    ideal  model  delta    sigma   weight residual
    1.530  1.473  0.057 1.11e-02 8.12e+03 2.60e+01
  bond pdb=" C   SER A 630 "
       pdb=" O   SER A 630 "
    ideal  model  delta    sigma   weight residual
    1.237  1.196  0.040 1.19e-02 7.06e+03 1.14e+01
  bond pdb=" O22 FY5 A 801 "
       pdb=" S21 FY5 A 801 "
    ideal  model  delta    sigma   weight residual
    1.461  1.527 -0.066 2.00e-02 2.50e+03 1.09e+01
  bond pdb=" O20 FY5 A 801 "
       pdb=" S21 FY5 A 801 "
    ideal  model  delta    sigma   weight residual
    1.673  1.613  0.060 2.00e-02 2.50e+03 8.98e+00
  bond pdb=" O23 FY5 A 801 "
       pdb=" S21 FY5 A 801 "
    ideal  model  delta    sigma   weight residual
    1.458  1.399  0.059 2.00e-02 2.50e+03 8.70e+00
  ... (remaining 4474 not shown)

  Histogram of bond angle deviations from ideal:
        0.00 -     2.18: 5686
        2.18 -     4.36: 307
        4.36 -     6.54: 44
        6.54 -     8.72: 20
        8.72 -    10.90: 16
  Bond angle restraints: 6073
  Sorted by residual:
  angle pdb=" N   LYS A  28 "
        pdb=" CA  LYS A  28 "
        pdb=" C   LYS A  28 "
      ideal   model   delta    sigma   weight residual
     113.41  103.39   10.02 1.22e+00 6.72e-01 6.74e+01
  angle pdb=" N   GLN A 369 "
        pdb=" CA  GLN A 369 "
        pdb=" C   GLN A 369 "
      ideal   model   delta    sigma   weight residual
     109.64  118.36   -8.72 1.27e+00 6.20e-01 4.72e+01
  angle pdb=" N   GLU A 523 "
        pdb=" CA  GLU A 523 "
        pdb=" C   GLU A 523 "
      ideal   model   delta    sigma   weight residual
     110.59  100.77    9.82 1.45e+00 4.76e-01 4.58e+01
  angle pdb=" C   PHE A 278 "
        pdb=" CA  PHE A 278 "
        pdb=" CB  PHE A 278 "
      ideal   model   delta    sigma   weight residual
     111.51  101.08   10.43 1.58e+00 4.01e-01 4.36e+01
  angle pdb=" N   GLU A  60 "
        pdb=" CA  GLU A  60 "
        pdb=" C   GLU A  60 "
      ideal   model   delta    sigma   weight residual
     111.52  120.47   -8.95 1.40e+00 5.10e-01 4.09e+01
  ... (remaining 6068 not shown)

  Histogram of dihedral angle deviations from ideal:
        0.00 -    20.85: 2488
       20.85 -    41.69: 154
       41.69 -    62.54: 24
       62.54 -    83.38: 1
       83.38 -   104.23: 9
  Dihedral angle restraints: 2676
    sinusoidal: 1073
      harmonic: 1603
  Sorted by residual:
  dihedral pdb=" CB  CYS A 430 "
           pdb=" SG  CYS A 430 "
           pdb=" SG  CYS A 530 "
           pdb=" CB  CYS A 530 "
      ideal   model   delta sinusoidal    sigma   weight residual
     -86.00 -159.05   73.05     1      1.00e+01 1.00e-02 6.80e+01
  dihedral pdb=" CB  CYS A 474 "
           pdb=" SG  CYS A 474 "
           pdb=" SG  CYS A 524 "
           pdb=" CB  CYS A 524 "
      ideal   model   delta sinusoidal    sigma   weight residual
      93.00   39.59   53.41     1      1.00e+01 1.00e-02 3.88e+01
  dihedral pdb=" C   CYS A 506 "
           pdb=" N   CYS A 506 "
           pdb=" CA  CYS A 506 "
           pdb=" CB  CYS A 506 "
      ideal   model   delta  harmonic     sigma   weight residual
    -122.60 -108.76  -13.84     0      2.50e+00 1.60e-01 3.07e+01
  ... (remaining 2673 not shown)

  Histogram of chiral volume deviations from ideal:
       0.000 -    0.126: 668
       0.126 -    0.252: 26
       0.252 -    0.378: 7
       0.378 -    0.504: 1
       0.504 -    0.630: 3
  Chirality restraints: 705
  Sorted by residual:
  chirality pdb=" C1  NAG B   2 "
            pdb=" O4  NAG B   1 "
            pdb=" C2  NAG B   2 "
            pdb=" O5  NAG B   2 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -2.27   -0.13 2.00e-02 2.50e+03 3.98e+01
  chirality pdb=" C1  NAG A 802 "
            pdb=" ND2 ASN A 516 "
            pdb=" C2  NAG A 802 "
            pdb=" O5  NAG A 802 "
    both_signs  ideal   model   delta    sigma   weight residual
      False     -2.40   -3.03    0.63 2.00e-01 2.50e+01 9.93e+00
  chirality pdb=" CA  GLU A  60 "
            pdb=" N   GLU A  60 "
            pdb=" C   GLU A  60 "
            pdb=" CB  GLU A  60 "
    both_signs  ideal   model   delta    sigma   weight residual
      False      2.51    1.99    0.52 2.00e-01 2.50e+01 6.75e+00
  ... (remaining 702 not shown)

  Planarity restraints: 737
  Sorted by residual:
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   1 "   -0.356 2.00e-02 2.50e+03   3.06e-01 1.17e+03
        pdb=" C7  NAG B   1 "    0.086 2.00e-02 2.50e+03
        pdb=" C8  NAG B   1 "   -0.130 2.00e-02 2.50e+03
        pdb=" N2  NAG B   1 "    0.544 2.00e-02 2.50e+03
        pdb=" O7  NAG B   1 "   -0.145 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG A 802 "    0.300 2.00e-02 2.50e+03   2.54e-01 8.06e+02
        pdb=" C7  NAG A 802 "   -0.077 2.00e-02 2.50e+03
        pdb=" C8  NAG A 802 "    0.184 2.00e-02 2.50e+03
        pdb=" N2  NAG A 802 "   -0.438 2.00e-02 2.50e+03
        pdb=" O7  NAG A 802 "    0.030 2.00e-02 2.50e+03
                                 delta    sigma   weight rms_deltas residual
  plane pdb=" C2  NAG B   2 "    0.291 2.00e-02 2.50e+03   2.45e-01 7.53e+02
        pdb=" C7  NAG B   2 "   -0.075 2.00e-02 2.50e+03
        pdb=" C8  NAG B   2 "    0.183 2.00e-02 2.50e+03
        pdb=" N2  NAG B   2 "   -0.420 2.00e-02 2.50e+03
        pdb=" O7  NAG B   2 "    0.022 2.00e-02 2.50e+03
  ... (remaining 734 not shown)

  Histogram of nonbonded interaction distances:
        2.23 -     2.76: 1062
        2.76 -     3.30: 4596
        3.30 -     3.83: 7270
        3.83 -     4.37: 8863
        4.37 -     4.90: 14390
  Nonbonded interactions: 36181
  Sorted by model distance:
  nonbonded pdb=" O   ILE A 595 "
            pdb=" OG1 THR A 598 "
     model   vdw
     2.231 3.040
  nonbonded pdb=" NE2 GLN A 541 "
            pdb=" O23 FY5 A 801 "
     model   vdw
     2.370 3.120
  nonbonded pdb=" O   THR A 609 "
            pdb=" C   ARG A 610 "
     model   vdw
     2.380 3.270
  nonbonded pdb=" N   GLU A 523 "
            pdb=" O   GLU A 523 "
     model   vdw
     2.421 2.496
  nonbonded pdb=" OD1 ASN A 432 "
            pdb=" OG1 THR A 619 "
     model   vdw
     2.423 3.040
  ... (remaining 36176 not shown)

  NOTE: a complete listing of the restraints can be obtained by requesting
        output of .geo file.
Find NCS groups from input model
Time spend for trying shortcut: 0.00
========== 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:             0.580
  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:          0.160
  Check model and map are aligned:         0.030
  Set scattering table:                    0.060
  Process input model:                     15.510
  Find NCS groups from input model:        0.040
  Set up NCS constraints:                  0.020
  Set refine NCS operators:                0.000
  Adjust number of macro_cycles:           0.000
  Reset NCS operators:                     0.000
  Extract rigid body selections:           0.000
  Check and reset occupancies:             0.000
  Load rotamer database and sin/cos tables:2.980
  Set ADP refinement strategy:             0.000
  Make a string to write initial .geo file:0.000
  Internal consistency checks:             0.000
  Total:   19.390
-------------------------------------------------------------------------------
Set refinement monitor
**********************
-------------------------------------------------------------------------------
Setup refinement engine
***********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6971
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      :  0.008   0.075   4489  Z= 0.523
  Angle     :  1.265  18.319   6096  Z= 0.810
  Chirality :  0.074   0.630    705
  Planarity :  0.018   0.306    735
  Dihedral  : 14.366 104.227   1637
  Min Nonbonded Distance : 2.231

Molprobity Statistics.
  All-atom Clashscore : 14.77
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  4.53 %
    Favored  : 95.47 %
  Rotamer:
    Outliers :  0.65 %
    Allowed  :  5.17 %
    Favored  : 94.18 %
  Cbeta Deviations :  0.79 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -2.74 (0.30), residues: 552
  helix: -0.97 (0.25), residues: 351
  sheet:  None (None), residues: 0
  loop : -3.32 (0.32), residues: 201

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.008   0.001   TRP A 259 
 HIS   0.006   0.002   HIS A 451 
 PHE   0.012   0.001   PHE A 117 
 TYR   0.019   0.001   TYR A 590 
 ARG   0.004   0.000   ARG A 253 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.05316 (    2)
  link_NAG-ASN         : angle      10.62400 (    6)
  link_BETA1-4         : bond        0.00335 (    1)
  link_BETA1-4         : angle       0.87468 (    3)
  hydrogen bonds       : bond        0.18574 (  276)
  hydrogen bonds       : angle       8.18257 (  813)
  SS BOND              : bond        0.00396 (    7)
  SS BOND              : angle       1.29125 (   14)
  covalent geometry    : bond        0.00758 ( 4479)
  covalent geometry    : angle       1.22102 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  101 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 3
    poor density    : 98
  time to evaluate  : 0.501 
Fit side-chains
   revert: symmetry clash
REVERT: A   38 PHE cc_start: 0.6996 (m-80) cc_final: 0.6754 (m-80)
REVERT: A   48 MET cc_start: 0.7698 (tpt) cc_final: 0.7447 (tpt)
REVERT: A   86 TYR cc_start: 0.6727 (t80) cc_final: 0.6460 (t80)
REVERT: A  568 LYS cc_start: 0.7704 (tttt) cc_final: 0.6777 (tptt)
REVERT: A  640 TYR cc_start: 0.8561 (OUTLIER) cc_final: 0.7549 (t80)
  outliers start: 3
  outliers final: 0
  residues processed: 100
  average time/residue: 0.1607
  time to fit residues: 20.7453
Evaluate side-chains
  76 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 1
    poor density    : 75
  time to evaluate  : 0.435 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=5.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 47 optimal weight:    4.9990
   chunk 42 optimal weight:    2.9990
   chunk 23 optimal weight:    0.9990
   chunk 14 optimal weight:    0.6980
   chunk 28 optimal weight:    0.9980
   chunk 22 optimal weight:    0.6980
   chunk 43 optimal weight:    0.9980
   chunk 16 optimal weight:    0.8980
   chunk 26 optimal weight:    0.8980
   chunk 32 optimal weight:    1.9990
   chunk 50 optimal weight:    0.8980
   overall best weight:    0.8180

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

Flipped N/Q/H residues before XYZ refinement:
A 178 ASN
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 477 ASN
A 606 ASN

Total number of N/Q/H flips: 3

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3948 r_free = 0.3948 target = 0.178316 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 29)----------------|
| r_work = 0.3542 r_free = 0.3542 target = 0.136968 restraints weight = 4744.595|
|-----------------------------------------------------------------------------|
r_work (start): 0.3459 rms_B_bonded: 2.82
r_work: 0.3304 rms_B_bonded: 3.38 restraints_weight: 0.5000
r_work (final): 0.3304
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6588
moved from start:          0.1974

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.051   4489  Z= 0.180
  Angle     :  0.739  14.250   6096  Z= 0.350
  Chirality :  0.043   0.251    705
  Planarity :  0.005   0.033    735
  Dihedral  :  8.620  74.336    706
  Min Nonbonded Distance : 2.427

Molprobity Statistics.
  All-atom Clashscore : 10.42
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.36 %
    Favored  : 97.64 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 12.07 %
    Favored  : 84.70 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole: -0.45 (0.34), residues: 552
  helix:  0.73 (0.26), residues: 359
  sheet:  None (None), residues: 0
  loop : -2.31 (0.39), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 259 
 HIS   0.003   0.001   HIS A  92 
 PHE   0.023   0.002   PHE A 341 
 TYR   0.019   0.002   TYR A 338 
 ARG   0.004   0.001   ARG A  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00228 (    2)
  link_NAG-ASN         : angle       3.67463 (    6)
  link_BETA1-4         : bond        0.01283 (    1)
  link_BETA1-4         : angle       1.20506 (    3)
  hydrogen bonds       : bond        0.04986 (  276)
  hydrogen bonds       : angle       5.15320 (  813)
  SS BOND              : bond        0.00258 (    7)
  SS BOND              : angle       1.29437 (   14)
  covalent geometry    : bond        0.00418 ( 4479)
  covalent geometry    : angle       0.72870 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  96 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 81
  time to evaluate  : 0.441 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   48 MET cc_start: 0.7594 (tpt) cc_final: 0.7380 (tpt)
REVERT: A  623 ARG cc_start: 0.7233 (ttt90) cc_final: 0.6027 (ttp-170)
REVERT: A  640 TYR cc_start: 0.8112 (OUTLIER) cc_final: 0.7338 (t80)
REVERT: A  649 LYS cc_start: 0.7720 (tptt) cc_final: 0.6555 (mmtt)
  outliers start: 15
  outliers final: 7
  residues processed: 90
  average time/residue: 0.1463
  time to fit residues: 17.2459
Evaluate side-chains
  79 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 8
    poor density    : 71
  time to evaluate  : 0.486 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  106 ILE
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=4.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 46 optimal weight:    0.7980
   chunk 10 optimal weight:   20.0000
   chunk 25 optimal weight:    0.7980
   chunk 1 optimal weight:    0.9990
   chunk 19 optimal weight:    0.1980
   chunk 24 optimal weight:    0.8980
   chunk 9 optimal weight:    0.9990
   chunk 39 optimal weight:    0.8980
   chunk 8 optimal weight:    0.5980
   chunk 41 optimal weight:    3.9990
   chunk 50 optimal weight:    1.9990
   overall best weight:    0.6580

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

No N/Q/H corrections needed this macrocycle
-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3947 r_free = 0.3947 target = 0.176289 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 46)----------------|
| r_work = 0.3510 r_free = 0.3510 target = 0.132220 restraints weight = 4794.195|
|-----------------------------------------------------------------------------|
r_work (start): 0.3458 rms_B_bonded: 3.11
r_work: 0.3310 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3310
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6439
moved from start:          0.2486

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4489  Z= 0.143
  Angle     :  0.620   8.478   6096  Z= 0.302
  Chirality :  0.040   0.172    705
  Planarity :  0.004   0.036    735
  Dihedral  :  7.055  73.638    706
  Min Nonbonded Distance : 2.547

Molprobity Statistics.
  All-atom Clashscore : 8.70
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 14.87 %
    Favored  : 81.90 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.29 (0.35), residues: 552
  helix:  1.24 (0.27), residues: 359
  sheet:  None (None), residues: 0
  loop : -1.88 (0.40), residues: 193

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 259 
 HIS   0.004   0.001   HIS A 520 
 PHE   0.018   0.001   PHE A 175 
 TYR   0.020   0.001   TYR A 590 
 ARG   0.003   0.000   ARG A 526 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    2)
  link_NAG-ASN         : angle       3.03293 (    6)
  link_BETA1-4         : bond        0.00373 (    1)
  link_BETA1-4         : angle       1.25075 (    3)
  hydrogen bonds       : bond        0.04446 (  276)
  hydrogen bonds       : angle       4.77840 (  813)
  SS BOND              : bond        0.00528 (    7)
  SS BOND              : angle       1.23146 (   14)
  covalent geometry    : bond        0.00327 ( 4479)
  covalent geometry    : angle       0.61082 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  623 ARG cc_start: 0.7215 (ttt90) cc_final: 0.5870 (ttt-90)
REVERT: A  640 TYR cc_start: 0.8013 (OUTLIER) cc_final: 0.7228 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 87
  average time/residue: 0.1447
  time to fit residues: 16.5023
Evaluate side-chains
  81 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 70
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  215 ILE
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  560 VAL
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=4.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 10 optimal weight:   20.0000
   chunk 28 optimal weight:    0.9980
   chunk 16 optimal weight:    0.9990
   chunk 29 optimal weight:    0.5980
   chunk 34 optimal weight:    0.8980
   chunk 44 optimal weight:    0.4980
   chunk 22 optimal weight:    0.8980
   chunk 38 optimal weight:    2.9990
   chunk 50 optimal weight:    0.9980
   chunk 36 optimal weight:    2.9990
   chunk 6 optimal weight:    0.8980
   overall best weight:    0.7580

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**
A 541 GLN

Total number of N/Q/H flips: 1

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3943 r_free = 0.3943 target = 0.176034 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 50)----------------|
| r_work = 0.3502 r_free = 0.3502 target = 0.131610 restraints weight = 4833.620|
|-----------------------------------------------------------------------------|
r_work (start): 0.3394 rms_B_bonded: 3.11
r_work: 0.3245 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3245
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6379
moved from start:          0.2731

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.038   4489  Z= 0.143
  Angle     :  0.604  13.100   6096  Z= 0.290
  Chirality :  0.039   0.155    705
  Planarity :  0.004   0.038    735
  Dihedral  :  6.844  72.410    706
  Min Nonbonded Distance : 2.452

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 17.03 %
    Favored  : 79.74 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.59 (0.35), residues: 552
  helix:  1.43 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.64 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 259 
 HIS   0.002   0.001   HIS A 115 
 PHE   0.016   0.001   PHE A 175 
 TYR   0.020   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00231 (    2)
  link_NAG-ASN         : angle       2.43931 (    6)
  link_BETA1-4         : bond        0.00439 (    1)
  link_BETA1-4         : angle       0.75816 (    3)
  hydrogen bonds       : bond        0.04207 (  276)
  hydrogen bonds       : angle       4.66899 (  813)
  SS BOND              : bond        0.00248 (    7)
  SS BOND              : angle       1.24423 (   14)
  covalent geometry    : bond        0.00334 ( 4479)
  covalent geometry    : angle       0.59740 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 77
  time to evaluate  : 0.481 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A   81 ILE cc_start: 0.6617 (mt) cc_final: 0.6408 (mp)
REVERT: A  118 MET cc_start: 0.8366 (mtp) cc_final: 0.7846 (mtp)
REVERT: A  517 TYR cc_start: 0.5628 (m-80) cc_final: 0.4991 (m-10)
REVERT: A  623 ARG cc_start: 0.7116 (ttt90) cc_final: 0.5902 (ttp-170)
REVERT: A  640 TYR cc_start: 0.7904 (OUTLIER) cc_final: 0.7210 (t80)
  outliers start: 15
  outliers final: 10
  residues processed: 86
  average time/residue: 0.1345
  time to fit residues: 15.5562
Evaluate side-chains
  86 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 11
    poor density    : 75
  time to evaluate  : 0.480 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=3.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 39 optimal weight:    3.9990
   chunk 49 optimal weight:    2.9990
   chunk 51 optimal weight:    0.0970
   chunk 37 optimal weight:    1.9990
   chunk 35 optimal weight:    2.9990
   chunk 40 optimal weight:    4.9990
   chunk 0 optimal weight:    6.9990
   chunk 16 optimal weight:    4.9990
   chunk 44 optimal weight:    1.9990
   chunk 10 optimal weight:    7.9990
   chunk 6 optimal weight:    0.0770
   overall best weight:    1.4342

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3904 r_free = 0.3904 target = 0.172214 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 43)----------------|
| r_work = 0.3446 r_free = 0.3446 target = 0.127043 restraints weight = 4942.649|
|-----------------------------------------------------------------------------|
r_work (start): 0.3320 rms_B_bonded: 3.15
r_work: 0.3168 rms_B_bonded: 3.62 restraints_weight: 0.5000
r_work (final): 0.3168
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6409
moved from start:          0.2868

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.005   0.049   4489  Z= 0.202
  Angle     :  0.642  13.935   6096  Z= 0.309
  Chirality :  0.041   0.158    705
  Planarity :  0.004   0.041    735
  Dihedral  :  6.978  72.252    706
  Min Nonbonded Distance : 2.436

Molprobity Statistics.
  All-atom Clashscore : 8.36
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.44 %
    Favored  : 96.56 %
  Rotamer:
    Outliers :  4.74 %
    Allowed  : 16.81 %
    Favored  : 78.45 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.60 (0.35), residues: 552
  helix:  1.42 (0.27), residues: 358
  sheet:  None (None), residues: 0
  loop : -1.61 (0.42), residues: 194

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.006   0.001   TRP A 602 
 HIS   0.006   0.002   HIS A 575 
 PHE   0.020   0.002   PHE A 175 
 TYR   0.022   0.002   TYR A 590 
 ARG   0.003   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00197 (    2)
  link_NAG-ASN         : angle       2.27700 (    6)
  link_BETA1-4         : bond        0.00454 (    1)
  link_BETA1-4         : angle       0.69257 (    3)
  hydrogen bonds       : bond        0.04597 (  276)
  hydrogen bonds       : angle       4.75684 (  813)
  SS BOND              : bond        0.00364 (    7)
  SS BOND              : angle       1.27690 (   14)
  covalent geometry    : bond        0.00487 ( 4479)
  covalent geometry    : angle       0.63578 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  95 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 22
    poor density    : 73
  time to evaluate  : 0.503 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  170 MET cc_start: 0.7661 (mmt) cc_final: 0.7456 (tpp)
REVERT: A  517 TYR cc_start: 0.5659 (m-80) cc_final: 0.5084 (m-10)
REVERT: A  623 ARG cc_start: 0.7130 (ttt90) cc_final: 0.5895 (ttp-170)
REVERT: A  640 TYR cc_start: 0.7938 (OUTLIER) cc_final: 0.7227 (t80)
  outliers start: 22
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1480
  time to fit residues: 17.5205
Evaluate side-chains
  83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 67
  time to evaluate  : 0.497 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  186 THR
Chi-restraints excluded: chain A residue  196 ILE
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  377 LEU
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=3.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 34 optimal weight:    0.3980
   chunk 9 optimal weight:    2.9990
   chunk 38 optimal weight:    0.9990
   chunk 53 optimal weight:    2.9990
   chunk 7 optimal weight:    0.8980
   chunk 31 optimal weight:    2.9990
   chunk 17 optimal weight:    0.9990
   chunk 37 optimal weight:    0.8980
   chunk 15 optimal weight:    6.9990
   chunk 55 optimal weight:    0.6980
   chunk 26 optimal weight:    0.5980
   overall best weight:    0.6980

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

Flipped N/Q/H residues before XYZ refinement:
** A 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY**

Total number of N/Q/H flips: 0

-------------------------------------------------------------------------------
ADP refinement
**************
|-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------|
| r_work = 0.3936 r_free = 0.3936 target = 0.175379 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 27)----------------|
| r_work = 0.3497 r_free = 0.3497 target = 0.131094 restraints weight = 4798.960|
|-----------------------------------------------------------------------------|
r_work (start): 0.3467 rms_B_bonded: 3.09
r_work: 0.3314 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3314
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6407
moved from start:          0.3046

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.055   4489  Z= 0.137
  Angle     :  0.581  11.563   6096  Z= 0.283
  Chirality :  0.039   0.127    705
  Planarity :  0.004   0.039    735
  Dihedral  :  6.924  71.106    706
  Min Nonbonded Distance : 2.491

Molprobity Statistics.
  All-atom Clashscore : 8.13
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 18.75 %
    Favored  : 77.37 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  0.89 (0.35), residues: 552
  helix:  1.73 (0.27), residues: 352
  sheet:  None (None), residues: 0
  loop : -1.56 (0.42), residues: 200

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 259 
 HIS   0.005   0.001   HIS A 575 
 PHE   0.017   0.001   PHE A 175 
 TYR   0.021   0.001   TYR A 338 
 ARG   0.002   0.000   ARG A 253 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00244 (    2)
  link_NAG-ASN         : angle       2.06748 (    6)
  link_BETA1-4         : bond        0.00395 (    1)
  link_BETA1-4         : angle       0.76622 (    3)
  hydrogen bonds       : bond        0.04157 (  276)
  hydrogen bonds       : angle       4.61075 (  813)
  SS BOND              : bond        0.00197 (    7)
  SS BOND              : angle       1.00162 (   14)
  covalent geometry    : bond        0.00322 ( 4479)
  covalent geometry    : angle       0.57641 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  92 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 74
  time to evaluate  : 0.426 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 TYR cc_start: 0.5663 (m-80) cc_final: 0.5115 (m-10)
REVERT: A  623 ARG cc_start: 0.7132 (ttt90) cc_final: 0.5949 (ttp-170)
REVERT: A  640 TYR cc_start: 0.7926 (OUTLIER) cc_final: 0.7220 (t80)
  outliers start: 18
  outliers final: 13
  residues processed: 87
  average time/residue: 0.1312
  time to fit residues: 15.2339
Evaluate side-chains
  83 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 69
  time to evaluate  : 0.429 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  392 LEU
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=2.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 4 optimal weight:    4.9990
   chunk 17 optimal weight:    1.9990
   chunk 30 optimal weight:    0.0170
   chunk 10 optimal weight:   20.0000
   chunk 28 optimal weight:    0.8980
   chunk 35 optimal weight:    0.6980
   chunk 38 optimal weight:    0.6980
   chunk 47 optimal weight:    0.0570
   chunk 13 optimal weight:    0.8980
   chunk 48 optimal weight:    1.9990
   chunk 51 optimal weight:    0.6980
   overall best weight:    0.4336

-------------------------------------------------------------------------------
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 = 0.3958 r_free = 0.3958 target = 0.177462 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 39)----------------|
| r_work = 0.3519 r_free = 0.3519 target = 0.132995 restraints weight = 4766.734|
|-----------------------------------------------------------------------------|
r_work (start): 0.3436 rms_B_bonded: 3.15
r_work: 0.3281 rms_B_bonded: 3.70 restraints_weight: 0.5000
r_work (final): 0.3281
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6405
moved from start:          0.3311

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.070   4489  Z= 0.120
  Angle     :  0.554   9.084   6096  Z= 0.275
  Chirality :  0.039   0.138    705
  Planarity :  0.004   0.038    735
  Dihedral  :  6.912  69.607    706
  Min Nonbonded Distance : 2.544

Molprobity Statistics.
  All-atom Clashscore : 7.67
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 19.61 %
    Favored  : 77.16 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.09 (0.36), residues: 552
  helix:  1.84 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -1.41 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 259 
 HIS   0.004   0.001   HIS A 575 
 PHE   0.016   0.001   PHE A 175 
 TYR   0.019   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00233 (    2)
  link_NAG-ASN         : angle       1.87500 (    6)
  link_BETA1-4         : bond        0.00449 (    1)
  link_BETA1-4         : angle       0.83971 (    3)
  hydrogen bonds       : bond        0.03953 (  276)
  hydrogen bonds       : angle       4.52078 (  813)
  SS BOND              : bond        0.00240 (    7)
  SS BOND              : angle       0.98570 (   14)
  covalent geometry    : bond        0.00278 ( 4479)
  covalent geometry    : angle       0.54914 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  90 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 75
  time to evaluate  : 0.466 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 TYR cc_start: 0.5413 (m-80) cc_final: 0.4896 (m-10)
REVERT: A  557 MET cc_start: 0.7661 (ttm) cc_final: 0.7375 (mtp)
REVERT: A  623 ARG cc_start: 0.7209 (ttt90) cc_final: 0.5973 (ttt180)
REVERT: A  640 TYR cc_start: 0.7929 (OUTLIER) cc_final: 0.7232 (t80)
  outliers start: 15
  outliers final: 12
  residues processed: 86
  average time/residue: 0.1241
  time to fit residues: 14.5449
Evaluate side-chains
  85 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 13
    poor density    : 72
  time to evaluate  : 0.452 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   99 ILE
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=2.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 29 optimal weight:    0.6980
   chunk 6 optimal weight:    2.9990
   chunk 7 optimal weight:    0.9990
   chunk 5 optimal weight:    0.9990
   chunk 4 optimal weight:    2.9990
   chunk 14 optimal weight:    0.9980
   chunk 27 optimal weight:    1.9990
   chunk 44 optimal weight:    1.9990
   chunk 3 optimal weight:    0.9990
   chunk 16 optimal weight:    0.8980
   chunk 34 optimal weight:    1.9990
   overall best weight:    0.9184

-------------------------------------------------------------------------------
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 = 0.3934 r_free = 0.3934 target = 0.174718 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 37)----------------|
| r_work = 0.3489 r_free = 0.3489 target = 0.130241 restraints weight = 4723.820|
|-----------------------------------------------------------------------------|
r_work (start): 0.3378 rms_B_bonded: 3.11
r_work: 0.3226 rms_B_bonded: 3.63 restraints_weight: 0.5000
r_work (final): 0.3226
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6365
moved from start:          0.3375

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.069   4489  Z= 0.152
  Angle     :  0.566   6.949   6096  Z= 0.287
  Chirality :  0.040   0.140    705
  Planarity :  0.004   0.038    735
  Dihedral  :  6.988  69.365    706
  Min Nonbonded Distance : 2.550

Molprobity Statistics.
  All-atom Clashscore : 7.90
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.26 %
    Favored  : 96.74 %
  Rotamer:
    Outliers :  4.31 %
    Allowed  : 19.40 %
    Favored  : 76.29 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.17 (0.36), residues: 552
  helix:  1.91 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -1.40 (0.43), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 602 
 HIS   0.003   0.001   HIS A 575 
 PHE   0.017   0.001   PHE A 175 
 TYR   0.022   0.001   TYR A 338 
 ARG   0.002   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00227 (    2)
  link_NAG-ASN         : angle       1.81020 (    6)
  link_BETA1-4         : bond        0.00374 (    1)
  link_BETA1-4         : angle       0.87676 (    3)
  hydrogen bonds       : bond        0.04147 (  276)
  hydrogen bonds       : angle       4.58975 (  813)
  SS BOND              : bond        0.00212 (    7)
  SS BOND              : angle       0.89811 (   14)
  covalent geometry    : bond        0.00370 ( 4479)
  covalent geometry    : angle       0.56238 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  94 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 20
    poor density    : 74
  time to evaluate  : 0.428 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 TYR cc_start: 0.5635 (m-80) cc_final: 0.5115 (m-10)
REVERT: A  557 MET cc_start: 0.7656 (ttm) cc_final: 0.7390 (mtp)
REVERT: A  623 ARG cc_start: 0.7152 (ttt90) cc_final: 0.5912 (ttt180)
REVERT: A  640 TYR cc_start: 0.7902 (OUTLIER) cc_final: 0.7194 (t80)
  outliers start: 20
  outliers final: 17
  residues processed: 88
  average time/residue: 0.1203
  time to fit residues: 14.3648
Evaluate side-chains
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 73
  time to evaluate  : 0.433 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   86 TYR
Chi-restraints excluded: chain A residue  141 THR
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  473 VAL
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  572 LEU
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=1.50
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 43 optimal weight:    3.9990
   chunk 32 optimal weight:    2.9990
   chunk 16 optimal weight:    3.9990
   chunk 7 optimal weight:    4.9990
   chunk 4 optimal weight:    3.9990
   chunk 30 optimal weight:    0.0970
   chunk 20 optimal weight:    1.9990
   chunk 52 optimal weight:    0.9980
   chunk 44 optimal weight:    0.5980
   chunk 25 optimal weight:    2.9990
   chunk 45 optimal weight:    0.9990
   overall best weight:    0.9382

-------------------------------------------------------------------------------
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 = 0.3933 r_free = 0.3933 target = 0.174729 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 45)----------------|
| r_work = 0.3483 r_free = 0.3483 target = 0.129738 restraints weight = 4797.771|
|-----------------------------------------------------------------------------|
r_work (start): 0.3327 rms_B_bonded: 3.12
r_work: 0.3172 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3172
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6270
moved from start:          0.3406

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.071   4489  Z= 0.154
  Angle     :  0.566   6.904   6096  Z= 0.289
  Chirality :  0.040   0.141    705
  Planarity :  0.004   0.038    735
  Dihedral  :  7.011  68.784    706
  Min Nonbonded Distance : 2.575

Molprobity Statistics.
  All-atom Clashscore : 6.76
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  3.08 %
    Favored  : 96.92 %
  Rotamer:
    Outliers :  3.88 %
    Allowed  : 20.04 %
    Favored  : 76.08 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.30 (0.36), residues: 552
  helix:  1.96 (0.27), residues: 354
  sheet:  None (None), residues: 0
  loop : -1.22 (0.44), residues: 198

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 602 
 HIS   0.003   0.001   HIS A 575 
 PHE   0.018   0.001   PHE A 175 
 TYR   0.020   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A 614 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00179 (    2)
  link_NAG-ASN         : angle       1.75128 (    6)
  link_BETA1-4         : bond        0.00370 (    1)
  link_BETA1-4         : angle       0.91620 (    3)
  hydrogen bonds       : bond        0.04163 (  276)
  hydrogen bonds       : angle       4.60400 (  813)
  SS BOND              : bond        0.00220 (    7)
  SS BOND              : angle       0.98026 (   14)
  covalent geometry    : bond        0.00374 ( 4479)
  covalent geometry    : angle       0.56241 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  93 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 18
    poor density    : 75
  time to evaluate  : 0.469 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 TYR cc_start: 0.5577 (m-80) cc_final: 0.5062 (m-10)
REVERT: A  623 ARG cc_start: 0.7067 (ttt90) cc_final: 0.5840 (ttt180)
REVERT: A  640 TYR cc_start: 0.7780 (OUTLIER) cc_final: 0.7075 (t80)
  outliers start: 18
  outliers final: 15
  residues processed: 88
  average time/residue: 0.1243
  time to fit residues: 14.8313
Evaluate side-chains
  91 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 16
    poor density    : 75
  time to evaluate  : 0.462 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   29 MET
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   86 TYR
Chi-restraints excluded: chain A residue  218 ILE
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 12 optimal weight:    0.9980
   chunk 47 optimal weight:    0.0020
   chunk 35 optimal weight:   10.0000
   chunk 21 optimal weight:    1.9990
   chunk 29 optimal weight:    0.9980
   chunk 34 optimal weight:    0.5980
   chunk 23 optimal weight:    0.4980
   chunk 10 optimal weight:   20.0000
   chunk 30 optimal weight:    0.8980
   chunk 2 optimal weight:    0.7980
   chunk 53 optimal weight:    2.9990
   overall best weight:    0.5588

-------------------------------------------------------------------------------
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 = 0.3954 r_free = 0.3954 target = 0.176820 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 40)----------------|
| r_work = 0.3507 r_free = 0.3507 target = 0.131972 restraints weight = 4714.626|
|-----------------------------------------------------------------------------|
r_work (start): 0.3334 rms_B_bonded: 3.12
r_work: 0.3184 rms_B_bonded: 3.64 restraints_weight: 0.5000
r_work (final): 0.3184
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6254
moved from start:          0.3550

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.003   0.068   4489  Z= 0.127
  Angle     :  0.550   7.187   6096  Z= 0.285
  Chirality :  0.039   0.153    705
  Planarity :  0.004   0.037    735
  Dihedral  :  6.980  67.973    706
  Min Nonbonded Distance : 2.546

Molprobity Statistics.
  All-atom Clashscore : 7.79
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.23 %
    Allowed  : 20.91 %
    Favored  : 75.86 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.34 (0.37), residues: 552
  helix:  1.87 (0.27), residues: 360
  sheet:  None (None), residues: 0
  loop : -1.06 (0.45), residues: 192

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.005   0.001   TRP A 259 
 HIS   0.003   0.001   HIS A 575 
 PHE   0.016   0.001   PHE A 175 
 TYR   0.021   0.001   TYR A 338 
 ARG   0.002   0.000   ARG A 633 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00210 (    2)
  link_NAG-ASN         : angle       1.62759 (    6)
  link_BETA1-4         : bond        0.00343 (    1)
  link_BETA1-4         : angle       0.94013 (    3)
  hydrogen bonds       : bond        0.04022 (  276)
  hydrogen bonds       : angle       4.53987 (  813)
  SS BOND              : bond        0.00189 (    7)
  SS BOND              : angle       0.88226 (   14)
  covalent geometry    : bond        0.00299 ( 4479)
  covalent geometry    : angle       0.54682 ( 6073)

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

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

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Re-set Ramachandran plot restraints
***********************************
  favored: oldfield
  allowed: oldfield
  outlier: oldfield

  1104 Ramachandran restraints generated.
    552 Oldfield, 0 Emsley, 552 emsley8k and 0 Phi/Psi/2.
-------------------------------------------------------------------------------
Optimize residue side-chains
****************************
Evaluate side-chains
  89 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 15
    poor density    : 74
  time to evaluate  : 0.431 
Fit side-chains
   revert: symmetry clash
   revert: symmetry clash
REVERT: A  517 TYR cc_start: 0.5570 (m-80) cc_final: 0.5079 (m-10)
REVERT: A  623 ARG cc_start: 0.7120 (ttt90) cc_final: 0.5867 (ttt180)
REVERT: A  640 TYR cc_start: 0.7769 (OUTLIER) cc_final: 0.7071 (t80)
  outliers start: 15
  outliers final: 13
  residues processed: 85
  average time/residue: 0.1494
  time to fit residues: 17.3869
Evaluate side-chains
  84 residues out of total 484 (non-[ALA,GLY,PRO]) need to be fit.
    rotamer outliers: 14
    poor density    : 70
  time to evaluate  : 0.494 
-------------------------------------------------------------------------------
Set rotamer restraints
**********************
Chi-restraints excluded: chain A residue   27 LEU
Chi-restraints excluded: chain A residue   31 LEU
Chi-restraints excluded: chain A residue   56 GLU
Chi-restraints excluded: chain A residue   66 VAL
Chi-restraints excluded: chain A residue   86 TYR
Chi-restraints excluded: chain A residue  430 CYS
Chi-restraints excluded: chain A residue  465 CYS
Chi-restraints excluded: chain A residue  523 GLU
Chi-restraints excluded: chain A residue  524 CYS
Chi-restraints excluded: chain A residue  530 CYS
Chi-restraints excluded: chain A residue  582 LEU
Chi-restraints excluded: chain A residue  603 SER
Chi-restraints excluded: chain A residue  624 VAL
Chi-restraints excluded: chain A residue  640 TYR
Rotamers are restrained with sigma=1.00
-------------------------------------------------------------------------------
XYZ refinement
**************
Weight determination summary:
   number of chunks: 56
   random chunks:
   chunk 41 optimal weight:    6.9990
   chunk 4 optimal weight:    3.9990
   chunk 28 optimal weight:    2.9990
   chunk 51 optimal weight:    0.8980
   chunk 24 optimal weight:    0.9990
   chunk 13 optimal weight:    0.9980
   chunk 11 optimal weight:    9.9990
   chunk 20 optimal weight:    1.9990
   chunk 21 optimal weight:    0.9990
   chunk 55 optimal weight:    0.3980
   chunk 7 optimal weight:    1.9990
   overall best weight:    0.8584

-------------------------------------------------------------------------------
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 = 0.3940 r_free = 0.3940 target = 0.175417 restraints weight = None  |
|-----------------------------------------------------------------------------|
|-group b-factor refinement (macro cycle = 1; iterations = 44)----------------|
| r_work = 0.3495 r_free = 0.3495 target = 0.130798 restraints weight = 4774.891|
|-----------------------------------------------------------------------------|
r_work (start): 0.3341 rms_B_bonded: 3.12
r_work: 0.3186 rms_B_bonded: 3.66 restraints_weight: 0.5000
r_work (final): 0.3186
-------------------------------------------------------------------------------
Occupancy refinement
********************
-------------------------------------------------------------------------------
Overall statistics
******************
model-to-map fit, CC_mask: 0.6285
moved from start:          0.3572

Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2
Deviations from Ideal Values - rmsd, rmsZ for bonds and angles.
  Bond      :  0.004   0.066   4489  Z= 0.147
  Angle     :  0.559   6.926   6096  Z= 0.289
  Chirality :  0.040   0.148    705
  Planarity :  0.004   0.038    735
  Dihedral  :  6.976  67.489    706
  Min Nonbonded Distance : 2.583

Molprobity Statistics.
  All-atom Clashscore : 6.87
  Ramachandran Plot:
    Outliers :  0.00 %
    Allowed  :  2.72 %
    Favored  : 97.28 %
  Rotamer:
    Outliers :  3.66 %
    Allowed  : 20.69 %
    Favored  : 75.65 %
  Cbeta Deviations :  0.00 %
  Peptide Plane:
    Cis-proline     : 0.00 %
    Cis-general     : 0.00 %
    Twisted Proline : 0.00 %
    Twisted General : 0.00 %

Rama-Z (Ramachandran plot Z-score):
Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2.
Scores for whole/helix/sheet/loop are scaled independently;
therefore, the values are not related in a simple manner.
  whole:  1.32 (0.36), residues: 552
  helix:  1.93 (0.27), residues: 355
  sheet:  None (None), residues: 0
  loop : -1.14 (0.44), residues: 197

Max deviation from planes:
   Type  MaxDev  MeanDev LineInFile
 TRP   0.004   0.001   TRP A 602 
 HIS   0.003   0.001   HIS A 115 
 PHE   0.018   0.001   PHE A 102 
 TYR   0.020   0.001   TYR A 590 
 ARG   0.002   0.000   ARG A  93 

Details of bonding type rmsd
  link_NAG-ASN         : bond        0.00182 (    2)
  link_NAG-ASN         : angle       1.57963 (    6)
  link_BETA1-4         : bond        0.00357 (    1)
  link_BETA1-4         : angle       1.01756 (    3)
  hydrogen bonds       : bond        0.04101 (  276)
  hydrogen bonds       : angle       4.57719 (  813)
  SS BOND              : bond        0.00204 (    7)
  SS BOND              : angle       0.89021 (   14)
  covalent geometry    : bond        0.00355 ( 4479)
  covalent geometry    : angle       0.55570 ( 6073)
Origin is already at (0, 0, 0), no shifts will be applied

===============================================================================
Job complete
usr+sys time: 2216.42 seconds
wall clock time: 38 minutes 53.25 seconds (2333.25 seconds total)